Index
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form
A
- A - Enum constant in enum class picard.analysis.artifacts.Transition.Base
- A - Enum constant in enum class picard.illumina.parser.IntensityChannel
- aa - Enum constant in enum class picard.fingerprint.DiploidHaplotype
- Aa - Enum constant in enum class picard.fingerprint.DiploidHaplotype
- AA - Enum constant in enum class picard.arrays.illumina.IlluminaGenotype
- AA - Enum constant in enum class picard.arrays.illumina.InfiniumVcfFields.GENOTYPE_VALUES
- AA - Enum constant in enum class picard.fingerprint.DiploidGenotype
- AA - Enum constant in enum class picard.fingerprint.DiploidHaplotype
- AA_CALL - Static variable in class picard.arrays.illumina.InfiniumGTCFile
- AB - Enum constant in enum class picard.arrays.illumina.IlluminaGenotype
- AB - Enum constant in enum class picard.arrays.illumina.InfiniumVcfFields.GENOTYPE_VALUES
- AB_CALL - Static variable in class picard.arrays.illumina.InfiniumGTCFile
- AB_FILTER - Static variable in class picard.vcf.filter.AlleleBalanceFilter
-
The filter string used for sites that fail the allele balance filter.
- AbstractAlignmentMerger - Class in picard.sam
-
Abstract class that coordinates the general task of taking in a set of alignment information, possibly in SAM format, possibly in other formats, and merging that with the set of all reads for which alignment was attempted, stored in an unmapped SAM file.
- AbstractAlignmentMerger(File, File, File, boolean, boolean, boolean, SAMProgramRecord, List<String>, List<String>, Integer, Integer, List<SamPairUtil.PairOrientation>, SAMFileHeader.SortOrder, PrimaryAlignmentSelectionStrategy, boolean, boolean) - Constructor for class picard.sam.AbstractAlignmentMerger
-
constructor with a default setting for unmappingReadsStrategy.
- AbstractAlignmentMerger(File, File, File, boolean, boolean, boolean, SAMProgramRecord, List<String>, List<String>, Integer, Integer, List<SamPairUtil.PairOrientation>, SAMFileHeader.SortOrder, PrimaryAlignmentSelectionStrategy, boolean, boolean, AbstractAlignmentMerger.UnmappingReadStrategy) - Constructor for class picard.sam.AbstractAlignmentMerger
-
Constructor
- AbstractAlignmentMerger.UnmappingReadStrategy - Enum Class in picard.sam
- AbstractIlluminaPositionFileReader - Class in picard.illumina.parser.readers
-
The position files of Illumina are nearly the same form: Pos files consist of text based tabbed x-y coordinate float pairs, locs files are binary x-y float pairs, clocs are compressed binary x-y float pairs.
- AbstractIlluminaPositionFileReader(File) - Constructor for class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
- AbstractIlluminaPositionFileReader(File, int, int) - Constructor for class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
-
Use this ctor if lane and tile are not discernible from file name.
- AbstractIlluminaPositionFileReader.PositionInfo - Class in picard.illumina.parser.readers
- AbstractInputParser - Class in picard.util
-
Class for parsing text files where each line consists of fields separated by whitespace.
- AbstractInputParser() - Constructor for class picard.util.AbstractInputParser
- AbstractMarkDuplicatesCommandLineProgram - Class in picard.sam.markduplicates.util
-
Abstract class that holds parameters and methods common to classes that perform duplicate detection and/or marking within SAM/BAM/CRAM files.
- AbstractMarkDuplicatesCommandLineProgram() - Constructor for class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator - Class in picard.sam.markduplicates.util
-
Little class used to package up a header and an iterable/iterator.
- AbstractOpticalDuplicateFinderCommandLineProgram - Class in picard.sam.markduplicates.util
-
Abstract class that holds parameters and methods common to classes that optical duplicate detection.
- AbstractOpticalDuplicateFinderCommandLineProgram() - Constructor for class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
- AbstractWgsMetricsCollector<T extends htsjdk.samtools.util.AbstractRecordAndOffset> - Class in picard.analysis
-
Class for collecting data on reference coverage, base qualities and excluded bases from one AbstractLocusInfo object for CollectWgsMetrics.
- AC - Enum constant in enum class picard.fingerprint.DiploidGenotype
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectAlignmentSummaryMetrics
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectBaseDistributionByCycle
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectGcBiasMetrics
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectInsertSizeMetrics
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectQualityYieldMetrics
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectRnaSeqMetrics
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.MeanQualityByCycle
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.QualityScoreDistribution
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.analysis.SinglePassSamProgram
-
Should be implemented by subclasses to accept SAMRecords one at a time.
- acceptRead(SAMRecord, ReferenceSequence) - Method in class picard.sam.markduplicates.CollectDuplicateMetrics
- acceptRecord(ARGTYPE) - Method in interface picard.metrics.PerUnitMetricCollector
-
Add a SAMRecord (with ReferenceSequence and Read Group info) to the metric(s) being calculated)
- acceptRecord(SAMRecord) - Method in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
- acceptRecord(SAMRecord) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
-
Adds information about an individual SAMRecord to the statistics.
- acceptRecord(SAMRecord, ReferenceSequence) - Method in class picard.analysis.AlignmentSummaryMetricsCollector
- acceptRecord(SAMRecord, ReferenceSequence) - Method in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsCollector
- acceptRecord(SAMRecord, ReferenceSequence) - Method in class picard.analysis.directed.InsertSizeMetricsCollector
- acceptRecord(SAMRecord, ReferenceSequence) - Method in class picard.metrics.MultiLevelCollector
-
Construct a argument of ARGTYPE using the given SAMRecord and ReferenceSequence then pass this value to all collectors that should include this record
- acceptRecord(InsertSizeCollectorArgs) - Method in class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
- acceptRecord(GcBiasCollectorArgs) - Method in class picard.analysis.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
- acceptRecord(SAMRecordAndReference) - Method in class picard.analysis.AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector
- acceptRecord(SAMRecordAndReference) - Method in class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
- accumulate(VariantContext) - Method in class picard.vcf.CallingMetricAccumulator
-
Incorporates the provided variant's data into the metric analysis.
- accumulate(VariantContext) - Method in class picard.vcf.GvcfMetricAccumulator
- accumulate(VariantContext) - Method in interface picard.vcf.processor.VariantProcessor.Accumulator
- AccumulateQualityYieldMetrics - Class in picard.util
-
Combines multiple Picard QualityYieldMetrics files into a single file.
- AccumulateQualityYieldMetrics() - Constructor for class picard.util.AccumulateQualityYieldMetrics
- AccumulateVariantCallingMetrics - Class in picard.vcf
-
Combines multiple Variant Calling Metrics files into a single file.
- AccumulateVariantCallingMetrics() - Constructor for class picard.vcf.AccumulateVariantCallingMetrics
- ACCUMULATION_LEVEL - Variable in class picard.analysis.GcBiasDetailMetrics
- ACCUMULATION_LEVEL - Variable in class picard.analysis.GcBiasSummaryMetrics
- accumulators() - Method in interface picard.vcf.processor.VariantAccumulatorExecutor
-
Returns the
VariantProcessor.Accumulator
s associated with this executor. - accumulators() - Method in class picard.vcf.processor.VariantAccumulatorExecutor.MultiThreadedChunkBased
- ACCURACY - Variable in class picard.sam.DownsampleSam
- ACGT_CODES - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
- ACTION - Variable in class picard.util.IntervalListTools
- ADAPTER_SEQUENCE - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
- ADAPTER_TRUNCATION_LENGTH - Variable in class picard.illumina.MarkIlluminaAdapters
- AdapterMarker - Class in picard.util
-
Store one or more AdapterPairs to use to mark adapter sequence of SAMRecords.
- AdapterMarker(int, AdapterPair...) - Constructor for class picard.util.AdapterMarker
- AdapterMarker(AdapterPair...) - Constructor for class picard.util.AdapterMarker
-
Truncates adapters to DEFAULT_ADAPTER_LENGTH
- AdapterPair - Interface in picard.util
- ADAPTERS - Variable in class picard.illumina.MarkIlluminaAdapters
- ADAPTERS_TO_CHECK - Variable in class picard.illumina.IlluminaBasecallsToFastq
- ADAPTERS_TO_CHECK - Variable in class picard.illumina.IlluminaBasecallsToSam
- adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord) - Method in class picard.util.AdapterMarker
- adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, int, double) - Method in class picard.util.AdapterMarker
-
Overrides defaults for minMatchBases and maxErrorRate
- adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, int, double, AdapterPair...) - Static method in class picard.util.ClippingUtility
-
Invokes adapterTrimIlluminaRead with explicit parameters for a pair of reads.
- adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, AdapterPair) - Static method in class picard.util.ClippingUtility
-
Deprecated.Use the varargs version. This no longer returns a warning string..
- adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, AdapterPair...) - Static method in class picard.util.ClippingUtility
-
Invokes adapterTrimIlluminaPairedReads with default less stringent parameters for a pair of reads.
- adapterTrimIlluminaPairedReads(SAMRecord, SAMRecord, AdapterPair, int, double) - Static method in class picard.util.ClippingUtility
-
Deprecated.Use the varargs version. This no longer returns a warning string..
- adapterTrimIlluminaSingleRead(SAMRecord) - Method in class picard.util.AdapterMarker
- adapterTrimIlluminaSingleRead(SAMRecord, int, double) - Method in class picard.util.AdapterMarker
-
Overrides defaults for minMatchBases and maxErrorRate
- adapterTrimIlluminaSingleRead(SAMRecord, int, double, AdapterPair...) - Static method in class picard.util.ClippingUtility
-
Invokes adapterTrimIlluminRead with explicit matching thresholds for a single read.
- adapterTrimIlluminaSingleRead(SAMRecord, AdapterPair) - Static method in class picard.util.ClippingUtility
-
Deprecated.Use the varargs version. This no longer returns a warning string..
- adapterTrimIlluminaSingleRead(SAMRecord, AdapterPair...) - Static method in class picard.util.ClippingUtility
-
Invokes adapterTrimIlluminRead with default parameters for a single read.
- adapterTrimIlluminaSingleRead(SAMRecord, AdapterPair, int, double) - Static method in class picard.util.ClippingUtility
-
Deprecated.Use the varargs version. This no longer returns a warning string..
- AdapterUtility - Class in picard.analysis
-
A utility class for matching reads to adapters.
- AdapterUtility(List<String>) - Constructor for class picard.analysis.AdapterUtility
- add(HaplotypeProbabilities) - Method in class picard.fingerprint.Fingerprint
- add(PedFile.PedTrio) - Method in class picard.pedigree.PedFile
-
Adds a trio to the PedFile keyed by the individual id.
- add(ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
-
Adds the end to this set, if not already added based on physical location
- add(ReadEndsForMateCigar, SamRecordTrackingBuffer, DuplicationMetrics) - Method in class picard.sam.markduplicates.util.MarkQueue
-
Add a record to the mark queue.
- ADD_MATE_CIGAR - Variable in class picard.sam.FixMateInformation
- ADD_MATE_CIGAR - Variable in class picard.sam.MergeBamAlignment
- ADD_PG_TAG_TO_READS - Variable in class picard.sam.util.PGTagArgumentCollection
- addAllLevelsToFile(MetricsFile<METRIC_TYPE, Histogram_KEY>) - Method in class picard.metrics.MultiLevelCollector
-
Add all metrics to the given file in the following MetricAccumulationLevel order ALL_READS, SAMPLE, LIBRARY, READ_GROUP.
- addBase(int) - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
-
Adds a single point of depth at the desired offset into the coverage array.
- addBase(int, int) - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
-
Adds some depth at the desired offset into the coverage array.
- addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in interface picard.sam.SamErrorMetric.BaseCalculator
-
The function by which new loci are "shown" to the calculator
- addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.BaseErrorAggregation
- addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.BaseErrorCalculator
-
the function by which new loci are "shown" to the calculator
- addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.IndelErrorCalculator
- addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.OverlappingReadsErrorCalculator
-
The function by which new loci are "shown" to the calculator
- addBase(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.SimpleErrorCalculator
-
The function by which new loci are "shown" to the calculator
- addBaseQHistogram(MetricsFile<WgsMetrics, Integer>) - Method in class picard.analysis.AbstractWgsMetricsCollector
- AddCommentsToBam - Class in picard.sam
-
A tool to add comments to a BAM file header.
- AddCommentsToBam() - Constructor for class picard.sam.AddCommentsToBam
- addCoverageCounts(int, int, int[]) - Method in class picard.annotation.Gene.Transcript
- addData(ClusterData, BarcodeData) - Method in class picard.illumina.parser.BaseIlluminaDataProvider
- addData(ClusterData, PfData) - Method in class picard.illumina.parser.BaseIlluminaDataProvider
- addData(ClusterData, PositionalData) - Method in class picard.illumina.parser.BaseIlluminaDataProvider
- addDuplicateReadToMetrics(SAMRecord) - Method in class picard.sam.DuplicationMetrics
-
Adds duplicated read to the metrics
- addDuplicateReadToMetrics(SAMRecord) - Method in class picard.sam.FlowBasedDuplicationMetrics
- addEdge(Node, Node) - Method in class picard.util.GraphUtils.Graph
- addExon(int, int) - Method in class picard.annotation.Gene.Transcript
- addHaplotype(HaplotypeBlock) - Method in class picard.fingerprint.HaplotypeMap
-
Adds a HaplotypeBlock to the map and updates all the relevant caches/indices.
- addInfo(AbstractLocusInfo<EdgingRecordAndOffset>, ReferenceSequence, boolean) - Method in class picard.analysis.FastWgsMetricsCollector
- addInfo(AbstractLocusInfo<SamLocusIterator.RecordAndOffset>, ReferenceSequence, boolean) - Method in class picard.analysis.CollectWgsMetrics.WgsMetricsCollector
- addInfo(AbstractLocusInfo<T>, ReferenceSequence, boolean) - Method in class picard.analysis.AbstractWgsMetricsCollector
-
Accumulates the data from AbstractLocusInfo in inner structures
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.BarcodeFileFaker
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.BciFileFaker
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.BclFileFaker
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.BclIndexFaker
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.ClocsFileFaker
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.FileFaker
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.FilterFileFaker
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.LocsFileFaker
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.MultiTileBclFileFaker
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.MultiTileLocsFileFaker
- addLeadingZeros() - Method in class picard.illumina.parser.fakers.PosFileFaker
- addLocationInformation(String, PhysicalLocation) - Method in class picard.sam.util.ReadNameParser
- addMetricsByLibrary(String, DuplicationMetrics) - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
- addMetricsToFile(MetricsFile<BEAN, HKEY>) - Method in interface picard.metrics.PerUnitMetricCollector
-
Any metrics collected will be added to the metric file provided.
- addMetricsToFile(MetricsFile<METRIC_TYPE, Integer>) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
- addMetricsToFile(MetricsFile<AlignmentSummaryMetrics, Integer>) - Method in class picard.analysis.AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector
- addMetricsToFile(MetricsFile<AlignmentSummaryMetrics, Integer>) - Method in class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
- addMetricsToFile(MetricsFile<CollectQualityYieldMetrics.QualityYieldMetrics, Integer>) - Method in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsCollector
- addMetricsToFile(MetricsFile<InsertSizeMetrics, Integer>) - Method in class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
- addMetricsToFile(MetricsFile<RnaSeqMetrics, Integer>) - Method in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
- addMetricsToFile(MetricsFile<GcBiasMetrics, Integer>) - Method in class picard.analysis.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
- addMissingTruthAndMissingCallStates(double, long, GenotypeConcordanceCounts) - Static method in class picard.vcf.GenotypeConcordance
-
Method to add missing sites that are KNOWN to be HOM_REF in the case of the NIST truth data set.
- addNode(Node) - Method in class picard.util.GraphUtils.Graph
- AddOATag - Class in picard.sam
- AddOATag() - Constructor for class picard.sam.AddOATag
- AddOrReplaceReadGroups - Class in picard.sam
-
Assigns all the reads in a file to a single new read-group.
- AddOrReplaceReadGroups() - Constructor for class picard.sam.AddOrReplaceReadGroups
- addReadData(ClusterData, int, BaseData) - Method in class picard.illumina.parser.BaseIlluminaDataProvider
- addReadData(ClusterData, int, CbclData) - Method in class picard.illumina.parser.BaseIlluminaDataProvider
- addReadData(ClusterData, int, QualityData) - Method in class picard.illumina.parser.BaseIlluminaDataProvider
- addReadToLibraryMetrics(SAMRecord) - Method in class picard.sam.DuplicationMetrics
-
Adds a read to the metrics
- addReadToLibraryMetrics(SAMRecord) - Method in class picard.sam.FlowBasedDuplicationMetrics
- addReadToLibraryMetrics(SAMRecord, SAMFileHeader, LibraryIdGenerator, boolean) - Static method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- addRecordToHistogramGenerator(SAMRecord) - Method in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsFlow
- ADDRESS_A_ID_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- ADDRESS_B_ID_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- addResults(MatchResults) - Method in class picard.fingerprint.FingerprintResults
- addRow(GenotypeConcordanceStates.CallState, GenotypeConcordanceStates.ContingencyState[]...) - Method in class picard.vcf.GenotypeConcordanceScheme
-
Adds a row to the scheme
- addSingletonToCount(LibraryIdGenerator) - Static method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- addSnp(Snp) - Method in class picard.fingerprint.HaplotypeBlock
-
Adds a SNP to the haplotype.
- addToLogLikelihoods(Snp, List<Allele>, double[]) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
-
Adds a base observation with the observed quality to the evidence for this haplotype based on the fact that the SNP is part of the haplotype.
- addToMetricsFile(MetricsFile<WgsMetrics, Integer>, boolean, CountingFilter, CountingFilter, CountingFilter, CountingPairedFilter) - Method in class picard.analysis.AbstractWgsMetricsCollector
-
Adds collected metrics and depth histogram to file
- addToMetricsFile(MetricsFile<WgsMetrics, Integer>, boolean, CountingFilter, CountingFilter, CountingFilter, CountingPairedFilter) - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
- addToMetricsFile(MetricsFile<WgsMetrics, Integer>, boolean, CountingFilter, CountingFilter, CountingFilter, CountingPairedFilter) - Method in interface picard.analysis.WgsMetricsProcessor
-
Adds result metric's data to input file
- addToMetricsFile(MetricsFile<WgsMetrics, Integer>, boolean, CountingFilter, CountingFilter, CountingFilter, CountingPairedFilter) - Method in class picard.analysis.WgsMetricsProcessorImpl
- addToProbs(Snp, byte, byte) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
-
Adds a base observation with the observed quality to the evidence for this haplotype based on the fact that the SNP is part of the haplotype.
- addToProbs(Snp, byte, byte) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
-
Adds a base observation with the observed quality to the evidence for this haplotype based on the fact that the SNP is part of the haplotype.
- addTranscript(String, int, int, int, int, int) - Method in class picard.annotation.Gene
- addUmiObservation(String, String) - Method in class picard.sam.markduplicates.UmiMetrics
-
Add an observation of a UMI to the metrics
- addUmiObservationN() - Method in class picard.sam.markduplicates.UmiMetrics
-
Add an observation of a UMI containing at least one N to the metrics
- advance() - Method in class picard.util.AbstractInputParser
- advanceFile() - Method in class picard.util.BasicInputParser
- afterExecute(Runnable, Throwable) - Method in class picard.util.ThreadPoolExecutorWithExceptions
- AG - Enum constant in enum class picard.fingerprint.DiploidGenotype
- Aligned - Enum constant in enum class picard.sam.ViewSam.AlignmentStatus
- ALIGNED_BAM - Variable in class picard.sam.MergeBamAlignment
- ALIGNED_READS - Variable in class picard.analysis.GcBiasSummaryMetrics
-
The total number of aligned reads used to compute the gc bias metrics.
- ALIGNED_READS_ONLY - Variable in class picard.analysis.CollectBaseDistributionByCycle
- ALIGNED_READS_ONLY - Variable in class picard.analysis.MeanQualityByCycle
- ALIGNED_READS_ONLY - Variable in class picard.analysis.QualityScoreDistribution
- ALIGNED_READS_ONLY - Variable in class picard.sam.MergeBamAlignment
- ALIGNER_PROPER_PAIR_FLAGS - Variable in class picard.sam.MergeBamAlignment
- ALIGNMENT_STATUS - Variable in class picard.sam.ViewSam
- AlignmentSummaryMetrics - Class in picard.analysis
-
High level metrics about the alignment of reads within a SAM file, produced by the CollectAlignmentSummaryMetrics program and usually stored in a file with the extension ".alignment_summary_metrics".
- AlignmentSummaryMetrics() - Constructor for class picard.analysis.AlignmentSummaryMetrics
- AlignmentSummaryMetrics.Category - Enum Class in picard.analysis
- AlignmentSummaryMetricsCollector - Class in picard.analysis
- AlignmentSummaryMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, boolean, List<String>, int, Set<SamPairUtil.PairOrientation>, boolean) - Constructor for class picard.analysis.AlignmentSummaryMetricsCollector
- AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector - Class in picard.analysis
- AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector - Class in picard.analysis
-
Class that counts reads that match various conditions
- All - Enum constant in enum class picard.sam.markduplicates.MarkDuplicates.DuplicateTaggingPolicy
- All - Enum constant in enum class picard.sam.ViewSam.AlignmentStatus
- All - Enum constant in enum class picard.sam.ViewSam.PfStatus
- ALL - Enum constant in enum class picard.sam.markduplicates.CheckDuplicateMarking.Mode
- ALL_GTS_FILTERED - Static variable in class picard.vcf.filter.FilterApplyingVariantIterator
-
Filter string that is used to filter a Variant when all variant genotypes are filtered out.
- ALL_READS - Enum constant in enum class picard.analysis.MetricAccumulationLevel
- allAlleles - Variable in class picard.vcf.GenotypeConcordance.Alleles
- ALLELE_A - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- ALLELE_A_PROBE_SEQ_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- ALLELE_B - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- ALLELE_B_PROBE_SEQ_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- ALLELE_FRACTION - Variable in class picard.analysis.CollectWgsMetrics
- ALLELE_FRACTION - Variable in class picard.analysis.directed.CollectTargetedMetrics
- ALLELE_FRACTION - Variable in class picard.analysis.TheoreticalSensitivityMetrics
-
The allele fraction which theoretical sensitivity is calculated for.
- AlleleBalanceFilter - Class in picard.vcf.filter
-
Filters out a record if the allele balance for heterozygotes is out of a defined range across all samples.
- AlleleBalanceFilter(double) - Constructor for class picard.vcf.filter.AlleleBalanceFilter
- Alleles(OrderedSet<String>, String, String, String, String) - Constructor for class picard.vcf.GenotypeConcordance.Alleles
- allelesToStringList(List<Allele>) - Static method in class picard.util.LiftoverUtils
-
This is a utility method that will convert a list of alleles into a list of base strings.
- AlleleSubsettingUtils - Class in picard.util
-
Utilities class containing methods for restricting
VariantContext
andGenotypesContext
objects to a reduced set of alleles, as well as for choosing the best set of alleles to keep and for cleaning up annotations and genotypes after subsetting. - AlleleSubsettingUtils() - Constructor for class picard.util.AlleleSubsettingUtils
- ALLOW_AND_IGNORE_EMPTY_LINES - Variable in class picard.sam.FastqToSam
- ALLOW_CONTIG_LENGTH_DISCORDANCE - Variable in class picard.sam.ReorderSam
- ALLOW_DUPLICATE_READS - Variable in class picard.fingerprint.CrosscheckFingerprints
- ALLOW_EMPTY_FASTQ - Variable in class picard.sam.FastqToSam
- ALLOW_INCOMPLETE_DICT_CONCORDANCE - Variable in class picard.sam.ReorderSam
- ALLOW_MISSING_FIELDS_IN_HEADER - Variable in class picard.vcf.LiftoverVcf
- ALLOW_MISSING_UMIS - Variable in class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
- ALLOW_MULTIPLE_DOWNSAMPLING_DESPITE_WARNINGS - Variable in class picard.sam.PositionBasedDownsampleSam
- allVisitedAlignmentsEqual() - Method in class picard.sam.SamComparisonMetric
- ALSO_IGNORE_DUPLICATES - Variable in class picard.analysis.CollectGcBiasMetrics
- ALT_BASE - Variable in class picard.analysis.artifacts.ErrorSummaryMetrics
-
The alternative base (or it's complement).
- ALT_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The (upper-case) alternative base that is called as a result of DNA damage.
- ALT_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
The (upper-case) alternative base that is called as a result of DNA damage.
- ALT_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The (upper-case) alternative base that is called as a result of DNA damage.
- ALT_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
The (upper-case) alternative base that is called as a result of DNA damage.
- ALT_COUNT - Variable in class picard.analysis.artifacts.ErrorSummaryMetrics
-
The number of alt bases observed.
- ALT_NAMES - Variable in class picard.sam.CreateSequenceDictionary
- ALT_NONOXO_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The count of observed A basecalls at C reference positions and T basecalls at G reference bases that are correlated to instrument read number in a way that rules out oxidation as the cause
- ALT_OXO_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The count of observed A basecalls at C reference positions and T basecalls at G reference bases that are correlated to instrument read number in a way that is consistent with oxidative damage.
- ALTERNATIVE_SINGLE_END - Enum constant in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- altValues() - Static method in enum class picard.analysis.artifacts.Transition
-
Like values(), but ignores the ref:ref "transitions".
- AMPLICON_INTERVALS - Variable in class picard.analysis.directed.CollectTargetedPcrMetrics
- AMPLICON_TERRITORY - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The number of unique bases covered by the intervals of all amplicons in the amplicon set
- ANALYSIS_VERSION - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The version number of the analysis run
- ANALYSIS_VERSION_NUMBER - Variable in class picard.arrays.GtcToVcf
- ANALYSIS_VERSION_NUMBER - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- AnnotationException - Exception in picard.annotation
-
Exception thrown when loading gene annotations.
- AnnotationException(String) - Constructor for exception picard.annotation.AnnotationException
- AnnotationException(String, Throwable) - Constructor for exception picard.annotation.AnnotationException
- APPLY_EAMSS_FILTER - Variable in class picard.illumina.IlluminaBasecallsToFastq
- APPLY_EAMSS_FILTER - Variable in class picard.illumina.IlluminaBasecallsToSam
- ARE_EQUAL - Variable in class picard.sam.SamComparisonMetric
-
Whether or not to consider the two input files equal.
- areComparableForDuplicates(ReadEndsForMarkDuplicates, ReadEndsForMarkDuplicates, boolean, boolean) - Method in class picard.sam.markduplicates.MarkDuplicates
- areEqual() - Method in class picard.sam.util.SamComparison
- areHistogramsEmpty() - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
- ARRAY_TYPE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- ArraysControlCodesSummaryMetrics() - Constructor for class picard.arrays.CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
- ArraysControlInfo - Class in picard.arrays.illumina
-
A simple class to store names and counts for the the Control Information fields that are stored in an Illumina GTC file.
- ArraysControlInfo(String, String, int, int) - Constructor for class picard.arrays.illumina.ArraysControlInfo
- ArraysVariantCallingDetailMetrics() - Constructor for class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
- ArraysVariantCallingSummaryMetrics() - Constructor for class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
- ARTIFACT_NAME - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
A "nickname" of this artifact, if it is a known error mode.
- ARTIFACT_NAME - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
A "nickname" of this artifact, if it is a known error mode.
- asList() - Method in class picard.vcf.GenotypeConcordance.Alleles
- assertMinimumQualities() - Method in class picard.illumina.parser.readers.BclQualityEvaluationStrategy
-
Reviews the qualities observed thus far and throws an exception if any are below the minimum quality threshold.
- assertPairedMates(SAMRecord, SAMRecord) - Static method in class picard.sam.SamToFastq
- assertProperFileStructure(File) - Method in class picard.illumina.parser.readers.BclReader
- assertSorted(SAMFileHeader.SortOrder) - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
-
Establishes that records returned by this iterator are expected to be in the specified sort order.
- assignLocusFunctionForRange(int, LocusFunction[]) - Method in class picard.annotation.Gene.Transcript
-
Write into locusFunctions the function of each position from start to start + locusFunctions.length relative to this transcript.
- ASSUME_SORT_ORDER - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- ASSUME_SORT_ORDER_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- ASSUME_SORTED - Variable in class picard.analysis.CollectMultipleMetrics
- ASSUME_SORTED - Variable in class picard.analysis.CollectRrbsMetrics
- ASSUME_SORTED - Variable in class picard.analysis.SinglePassSamProgram
- ASSUME_SORTED - Variable in class picard.sam.FixMateInformation
- ASSUME_SORTED - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
-
Deprecated.
- ASSUME_SORTED - Variable in class picard.sam.MergeSamFiles
- ASSUME_SORTED_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- asVcf(ReferenceSequenceFile) - Method in class picard.fingerprint.HaplotypeMap
- AsyncIterator<T> - Class in picard.util
-
Wrapper around a CloseableIterator that reads in a separate thread, for cases in which that might be efficient.
- AsyncIterator(CloseableIterator<T>, int, String) - Constructor for class picard.util.AsyncIterator
- AT - Enum constant in enum class picard.fingerprint.DiploidGenotype
- AT_DROPOUT - Variable in class picard.analysis.directed.PanelMetricsBase
-
A measure of how undercovered <= 50% GC regions are relative to the mean.
- AT_DROPOUT - Variable in class picard.analysis.GcBiasSummaryMetrics
-
Illumina-style AT dropout metric.
- AtoA - Enum constant in enum class picard.analysis.artifacts.Transition
- AtoC - Enum constant in enum class picard.analysis.artifacts.Transition
- AtoG - Enum constant in enum class picard.analysis.artifacts.Transition
- AtomicIterator<T> - Interface in picard.util
-
Describes
- atomicIteratorOf(Iterable<E>) - Static method in class picard.util.Iterators
- atomicIteratorOf(Iterator<E>) - Static method in class picard.util.Iterators
- AtoT - Enum constant in enum class picard.analysis.artifacts.Transition
- ATTEMPTED_ALLELES - Static variable in class picard.vcf.LiftoverVcf
-
Attribute used to store the position of the failed variant on the target contig prior to finding out that alleles do not match.
- ATTEMPTED_LOCUS - Static variable in class picard.vcf.LiftoverVcf
-
Attribute used to store the position of the failed variant on the target contig prior to finding out that alleles do not match.
- ATTRIBUTE_TO_CLEAR - Variable in class picard.sam.RevertSam
- ATTRIBUTE_TO_REVERSE - Variable in class picard.sam.RevertSam
- ATTRIBUTE_TO_REVERSE_COMPLEMENT - Variable in class picard.sam.RevertSam
- ATTRIBUTES_TO_REMOVE - Variable in class picard.sam.MergeBamAlignment
- ATTRIBUTES_TO_RETAIN - Variable in class picard.sam.MergeBamAlignment
- ATTRIBUTES_TO_REVERSE - Variable in class picard.sam.MergeBamAlignment
- ATTRIBUTES_TO_REVERSE_COMPLEMENT - Variable in class picard.sam.MergeBamAlignment
- AUTOCALL_CALL_RATE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The overall autocall call rate
- AUTOCALL_DATE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The date this sample was autocalled
- AUTOCALL_DATE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- AUTOCALL_GENDER - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The sex, as determined by Autocall
- AUTOCALL_GENDER - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- AUTOCALL_PF - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
Whether the sample passes QC based on call rate threshold
- AUTOCALL_VERSION - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The version of autocall used for calling this sample
- AUTOCALL_VERSION - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- AVG_POS_3PRIME_SOFTCLIP_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The average length of the soft-clipped bases at the 3' end of reads.
- awaitCompletion() - Method in interface picard.vcf.processor.VariantAccumulatorExecutor
-
Blocks until the work is complete.
- awaitCompletion() - Method in class picard.vcf.processor.VariantAccumulatorExecutor.MultiThreadedChunkBased
- awaitThreadPoolTermination(String, ThreadPoolExecutorWithExceptions, Duration) - Static method in class picard.util.ThreadPoolExecutorUtil
- awaitTileProcessingCompletion() - Method in class picard.illumina.SortedBasecallsConverter
B
- B - Enum constant in enum class picard.illumina.parser.ReadType
- BAD_ASSAYS_FILE - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- BAD_CYCLES - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of instrument cycles in which 80% or more of base calls were no-calls.
- BAF - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- BafRegressMetrics - Class in picard.arrays
- BafRegressMetrics() - Constructor for class picard.arrays.BafRegressMetrics
- BAIT_BIAS_DETAILS_EXT - Static variable in class picard.analysis.artifacts.SequencingArtifactMetrics
- BAIT_BIAS_IN - Variable in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
- BAIT_BIAS_SUMMARY_EXT - Static variable in class picard.analysis.artifacts.SequencingArtifactMetrics
- BAIT_DESIGN_EFFICIENCY - Variable in class picard.analysis.directed.HsMetrics
-
The ratio of TARGET_TERRITORY/BAIT_TERRITORY.
- BAIT_INTERVALS - Variable in class picard.analysis.directed.CollectHsMetrics
- BAIT_OFFSET - Variable in class picard.util.BaitDesigner
- BAIT_SET - Variable in class picard.analysis.directed.HsMetrics
-
The name of the bait set used in the hybrid selection.
- BAIT_SET_NAME - Variable in class picard.analysis.directed.CollectHsMetrics
- BAIT_SIZE - Variable in class picard.util.BaitDesigner
- BAIT_TERRITORY - Variable in class picard.analysis.directed.HsMetrics
-
The number of bases which are localized to one or more baits.
- BaitBiasDetailMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
- BaitBiasSummaryMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
- BaitDesigner - Class in picard.util
-
Designs baits for hybrid selection!
- BaitDesigner() - Constructor for class picard.util.BaitDesigner
- BaitDesigner.DesignStrategy - Enum Class in picard.util
-
Set of possible design strategies for bait design.
- BALANCING_WITHOUT_INTERVAL_SUBDIVISION - Enum constant in enum class picard.util.IntervalList.IntervalListScatterMode
-
A scatter approach that differs from
IntervalListScatterMode.INTERVAL_SUBDIVISION
in a few ways. - BALANCING_WITHOUT_INTERVAL_SUBDIVISION_WITH_OVERFLOW - Enum constant in enum class picard.util.IntervalList.IntervalListScatterMode
-
A scatter approach that differs from
IntervalListScatterMode.BALANCING_WITHOUT_INTERVAL_SUBDIVISION
. - bAlleleFreq - Variable in class picard.arrays.illumina.InfiniumGTCRecord
- bam - Enum constant in enum class picard.sam.RevertSam.FileType
- BamIndexStats - Class in picard.sam
-
Command line program to print statistics from BAM index (.bai) file Statistics include count of aligned and unaligned reads for each reference sequence and a count of all records with no start coordinate.
- BamIndexStats() - Constructor for class picard.sam.BamIndexStats
- BamToBfqWriter - Class in picard.fastq
-
Deprecated.
- BamToBfqWriter(File, File, String, Integer, Integer, boolean, String, boolean, boolean, Integer) - Constructor for class picard.fastq.BamToBfqWriter
-
Deprecated.
- BamToBfqWriter(File, String, boolean, String, boolean) - Constructor for class picard.fastq.BamToBfqWriter
-
Deprecated.
- barcode - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
- Barcode - Enum constant in enum class picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
- Barcode - Static variable in enum class picard.illumina.parser.ReadType
- BARCODE - Variable in class picard.illumina.BarcodeMetric
-
The barcode (from the set of expected barcodes) for which the following metrics apply.
- BARCODE - Variable in class picard.illumina.ExtractIlluminaBarcodes
- BARCODE_BQ - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- BARCODE_COLUMN - Static variable in class picard.illumina.ExtractBarcodesProgram
-
Column header for the first barcode sequence (preferred).
- BARCODE_DELIMITER - Static variable in class picard.util.IlluminaUtil
- BARCODE_FILE - Variable in class picard.illumina.ExtractIlluminaBarcodes
- BARCODE_NAME - Variable in class picard.illumina.BarcodeMetric
-
The barcode name.
- BARCODE_NAME_COLUMN - Static variable in class picard.illumina.ExtractBarcodesProgram
-
Column header for the barcode name.
- BARCODE_PARAMS - Variable in class picard.illumina.IlluminaBasecallsToSam
- BARCODE_POPULATION_STRATEGY - Variable in class picard.illumina.IlluminaBasecallsToSam
- BARCODE_PREFIXES - Static variable in class picard.illumina.ExtractBarcodesProgram
- BARCODE_SEQUENCE_COLUMN - Static variable in class picard.illumina.ExtractBarcodesProgram
- BARCODE_TAG - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- BARCODE_TAG - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
- BARCODE_TAG - Variable in class picard.sam.markduplicates.MarkDuplicates
- BARCODE_WITHOUT_DELIMITER - Variable in class picard.illumina.BarcodeMetric
- barcodeBytes - Variable in class picard.illumina.BarcodeMetric
- barcodeBytes - Variable in class picard.util.BarcodeEditDistanceQuery
-
list of barcodes (e.g.
- BarcodeEditDistanceQuery - Class in picard.util
-
A class for finding the distance between multiple (matched) barcodes and multiple barcode reads.
- BarcodeEditDistanceQuery(byte[][], byte[][], byte[][], int, int) - Constructor for class picard.util.BarcodeEditDistanceQuery
- barcodeExtractor - Variable in class picard.illumina.BasecallsConverter
- BarcodeExtractor - Class in picard.illumina
-
BarcodeExtractor is used to match barcodes and collect barcode match metrics.
- BarcodeExtractor(Map<String, BarcodeMetric>, BarcodeMetric, ReadStructure, int, int, int, int, DistanceMetric) - Constructor for class picard.illumina.BarcodeExtractor
- BarcodeExtractor.BarcodeMatch - Class in picard.illumina
-
Utility class to hang onto data about the best match for a given barcode
- BarcodeFileFaker - Class in picard.illumina.parser.fakers
-
Created by jcarey on 3/13/14.
- BarcodeFileFaker() - Constructor for class picard.illumina.parser.fakers.BarcodeFileFaker
- BarcodeFileReader - Class in picard.illumina.parser.readers
-
Reads a single barcode file line by line and returns the barcode if there was a match or NULL otherwise.
- BarcodeFileReader(File) - Constructor for class picard.illumina.parser.readers.BarcodeFileReader
- BarcodeMatch() - Constructor for class picard.illumina.BarcodeExtractor.BarcodeMatch
- BarcodeMetric - Class in picard.illumina
-
Metrics produced by the ExtractIlluminaBarcodes program that is used to parse data in the basecalls directory and determine to which barcode each read should be assigned.
- BarcodeMetric() - Constructor for class picard.illumina.BarcodeMetric
-
This ctor is necessary for when reading metrics from file
- BarcodeMetric(String, String, String, String[]) - Constructor for class picard.illumina.BarcodeMetric
- barcodeRecordWriterMap - Variable in class picard.illumina.BasecallsConverter
- Barcodes - Enum constant in enum class picard.illumina.parser.IlluminaDataType
- BARCODES_DIR - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
- BARCODES_DIR - Variable in class picard.illumina.IlluminaBasecallsToFastq
- BARCODES_DIR - Variable in class picard.illumina.IlluminaBasecallsToSam
- barcodeSeqsToString(byte[][]) - Static method in class picard.util.IlluminaUtil
-
Concatenates all the barcode sequences with BARCODE_DELIMITER
- barcodeSeqsToString(String[]) - Static method in class picard.util.IlluminaUtil
-
Concatenates all the barcode sequences with BARCODE_DELIMITER
- barcodeSeqsToString(List<String>) - Static method in class picard.util.IlluminaUtil
-
Concatenates all the barcode sequences with BARCODE_DELIMITER
- barcodeToMetrics - Variable in class picard.illumina.ExtractBarcodesProgram
- base - Variable in enum class picard.analysis.artifacts.Transition.Base
- base - Variable in class picard.illumina.parser.ParameterizedFileUtil
-
If you think of the file system as a tree, this is the deepest directory(node) on the tree that still contains all of the files for this given type (e.g.
- BaseBclReader - Class in picard.illumina.parser.readers
- BaseBclReader.CycleData - Class in picard.illumina.parser.readers
- BaseBclReader.TileData - Class in picard.illumina.parser.readers
- BaseCalculator - Interface in picard.sam.SamErrorMetric
-
An interface that can take a collection of bases (provided as
SamLocusIterator.RecordAndOffset
andSamLocusAndReferenceIterator.SAMLocusAndReference
) and generates aErrorMetric
from them. - BaseCallingProgramGroup - Class in picard.cmdline.programgroups
-
Tools that process sequencing machine data, e.g.
- BaseCallingProgramGroup() - Constructor for class picard.cmdline.programgroups.BaseCallingProgramGroup
- BaseCalls - Enum constant in enum class picard.illumina.parser.IlluminaDataType
- BASECALLS_DIR - Variable in class picard.illumina.CheckIlluminaDirectory
- BASECALLS_DIR - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
- BASECALLS_DIR - Variable in class picard.illumina.ExtractBarcodesProgram
- BASECALLS_DIR - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
- BasecallsConverter<CLUSTER_OUTPUT_RECORD> - Class in picard.illumina
-
BasecallsConverter utilizes an underlying IlluminaDataProvider to convert parsed and decoded sequencing data from standard Illumina formats to specific output records (FASTA records/SAM records).
- BasecallsConverter(File, File, int[], ReadStructure, Map<String, ? extends Writer<CLUSTER_OUTPUT_RECORD>>, boolean, Integer, Integer, BclQualityEvaluationStrategy, boolean, boolean, boolean, AsyncWriterPool, BarcodeExtractor) - Constructor for class picard.illumina.BasecallsConverter
-
Constructs a new BasecallsConverter object.
- BasecallsConverter.ClusterDataConverter<OUTPUT_RECORD> - Interface in picard.illumina
-
Interface that defines a converter that takes ClusterData and returns OUTPUT_RECORD type objects.
- BasecallsConverter.ConvertedClusterDataWriter<OUTPUT_RECORD> - Interface in picard.illumina
-
Interface that defines a writer that will write out OUTPUT_RECORD type objects.
- BasecallsConverterBuilder<CLUSTER_OUTPUT_RECORD> - Class in picard.illumina
-
BasecallsConverterBuilder creates and configures BasecallsConverter objects.
- BasecallsConverterBuilder(File, int[], ReadStructure, Map<String, ? extends Writer<CLUSTER_OUTPUT_RECORD>>) - Constructor for class picard.illumina.BasecallsConverterBuilder
-
Constructs a new builder used for creating BasecallsConverter objects.
- baseCycleStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Get the one-based cycle number of the base, taking the direction of the read into account
- BaseDistributionByCycleMetrics - Class in picard.analysis
- BaseDistributionByCycleMetrics() - Constructor for class picard.analysis.BaseDistributionByCycleMetrics
- BaseErrorAggregation<CALCULATOR extends BaseCalculator> - Class in picard.sam.SamErrorMetric
-
An interface and implementations for classes that apply a
RecordAndOffsetStratifier
to put bases into various "bins" and then compute anErrorMetric
on these bases using aBaseErrorCalculator
. - BaseErrorAggregation(Supplier<CALCULATOR>, ReadBaseStratification.RecordAndOffsetStratifier) - Constructor for class picard.sam.SamErrorMetric.BaseErrorAggregation
- BaseErrorCalculator - Class in picard.sam.SamErrorMetric
- BaseErrorCalculator() - Constructor for class picard.sam.SamErrorMetric.BaseErrorCalculator
- BaseErrorMetric - Class in picard.sam.SamErrorMetric
-
An error metric for the errors in bases.
- BaseErrorMetric() - Constructor for class picard.sam.SamErrorMetric.BaseErrorMetric
- BaseErrorMetric(String, long, long) - Constructor for class picard.sam.SamErrorMetric.BaseErrorMetric
- BaseIlluminaDataProvider - Class in picard.illumina.parser
-
Parse various formats and versions of Illumina Basecall files, and use them the to populate ClusterData objects.
- BaseIlluminaDataProvider(int, OutputMapping) - Constructor for class picard.illumina.parser.BaseIlluminaDataProvider
- baseIndexMap - Static variable in enum class picard.analysis.artifacts.Transition
- baseQualityStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies into the base-quality of the base under consideration
- bases - Variable in class picard.illumina.parser.BclData
- BasicInputParser - Class in picard.util
-
TextFileParser which reads a single text file.
- BasicInputParser(boolean, int, File...) - Constructor for class picard.util.BasicInputParser
-
Constructor.
- BasicInputParser(boolean, int, InputStream...) - Constructor for class picard.util.BasicInputParser
- BasicInputParser(boolean, File...) - Constructor for class picard.util.BasicInputParser
-
Constructor.
- BasicInputParser(boolean, InputStream...) - Constructor for class picard.util.BasicInputParser
-
Constructor.
- BB - Enum constant in enum class picard.arrays.illumina.IlluminaGenotype
- BB - Enum constant in enum class picard.arrays.illumina.InfiniumVcfFields.GENOTYPE_VALUES
- BB_CALL - Static variable in class picard.arrays.illumina.InfiniumGTCFile
- bci - Variable in class picard.illumina.parser.MultiTileFileUtil
- BciFileFaker - Class in picard.illumina.parser.fakers
-
Created by jcarey on 3/14/14.
- BciFileFaker() - Constructor for class picard.illumina.parser.fakers.BciFileFaker
- Bcl - Enum constant in enum class picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
- BclData - Class in picard.illumina.parser
-
A class that implements the IlluminaData interfaces provided by this parser One BclData object is returned to IlluminaDataProvider per cluster and each first level array in bases and qualities represents a single read in that cluster
- BclData(int[]) - Constructor for class picard.illumina.parser.BclData
- BclFileFaker - Class in picard.illumina.parser.fakers
- BclFileFaker() - Constructor for class picard.illumina.parser.fakers.BclFileFaker
- BclIndexFaker - Class in picard.illumina.parser.fakers
- BclIndexFaker() - Constructor for class picard.illumina.parser.fakers.BclIndexFaker
- BclIndexReader - Class in picard.illumina.parser.readers
-
Annoyingly, there are two different files with extension .bci in NextSeq output.
- BclIndexReader(File) - Constructor for class picard.illumina.parser.readers.BclIndexReader
- bclQualityEvaluationStrategy - Variable in class picard.illumina.ExtractBarcodesProgram
- bclQualityEvaluationStrategy - Variable in class picard.illumina.parser.MultiTileBclParser
- BclQualityEvaluationStrategy - Class in picard.illumina.parser.readers
-
Describes a mechanism for revising and evaluating qualities read from a BCL file.
- BclQualityEvaluationStrategy(int) - Constructor for class picard.illumina.parser.readers.BclQualityEvaluationStrategy
- BclReader - Class in picard.illumina.parser.readers
-
BCL Files are base call and quality score binary files containing a (base,quality) pair for successive clusters.
- BclReader(File, BclQualityEvaluationStrategy, boolean) - Constructor for class picard.illumina.parser.readers.BclReader
- BclReader(List<File>, int[], BclQualityEvaluationStrategy, boolean) - Constructor for class picard.illumina.parser.readers.BclReader
- BEAD_SET_ID_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- BEADSET_ID - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- BedToIntervalList - Class in picard.util
- BedToIntervalList() - Constructor for class picard.util.BedToIntervalList
- beforeExecute(Thread, Runnable) - Method in class picard.util.ThreadPoolExecutorWithExceptions
- BestEndMapqPrimaryAlignmentStrategy - Class in picard.sam
-
For an aligner that aligns each end independently, select the alignment for each end with the best MAPQ, and make that the primary.
- BestEndMapqPrimaryAlignmentStrategy() - Constructor for class picard.sam.BestEndMapqPrimaryAlignmentStrategy
- BestMapqPrimaryAlignmentSelectionStrategy - Class in picard.sam
-
This strategy was designed for TopHat output, but could be of general utility.
- BestMapqPrimaryAlignmentSelectionStrategy() - Constructor for class picard.sam.BestMapqPrimaryAlignmentSelectionStrategy
- binnedHomopolymerStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies a base onto the make up (repeating base and following reference base) and length-scale of the homopolymer from whence it came.
- binnedReadCycleStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies into quintiles of read cycle.
- BinnedReadCycleStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.BinnedReadCycleStratifier
- biSiteHeterogeneityRate - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
the rate of heterogeneity within doubleton sets.
- biSiteHomogeneityRate - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
the rate of homogeneity within doubleton sets.
- BLOCK_SIZE - Variable in class picard.sam.markduplicates.MarkDuplicatesWithMateCigar
- BOT - Enum constant in enum class picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
- BpmToNormalizationManifestCsv - Class in picard.arrays.illumina
-
A simple program to convert an Illumina bpm (bead pool manifest file) into a normalization manifest (bpm.csv) file The normalization manifest (bpm.csv) is a simple text file generated by Illumina tools - it has a specific format and is used by ZCall .
- BpmToNormalizationManifestCsv() - Constructor for class picard.arrays.illumina.BpmToNormalizationManifestCsv
- BREAK_BANDS_AT_MULTIPLES_OF - Variable in class picard.util.IntervalListTools
- BUFFER_SIZE - Variable in class picard.util.FifoBuffer
- bufferSize() - Method in class picard.illumina.parser.fakers.BarcodeFileFaker
- bufferSize() - Method in class picard.illumina.parser.fakers.BciFileFaker
- bufferSize() - Method in class picard.illumina.parser.fakers.BclFileFaker
- bufferSize() - Method in class picard.illumina.parser.fakers.BclIndexFaker
- bufferSize() - Method in class picard.illumina.parser.fakers.ClocsFileFaker
- bufferSize() - Method in class picard.illumina.parser.fakers.FileFaker
- bufferSize() - Method in class picard.illumina.parser.fakers.FilterFileFaker
- bufferSize() - Method in class picard.illumina.parser.fakers.LocsFileFaker
- bufferSize() - Method in class picard.illumina.parser.fakers.MultiTileBclFileFaker
- bufferSize() - Method in class picard.illumina.parser.fakers.MultiTileLocsFileFaker
- bufferSize() - Method in class picard.illumina.parser.fakers.PosFileFaker
- build() - Method in class picard.illumina.BasecallsConverterBuilder
-
Builds a basecalls converter
- build() - Method in interface picard.vcf.processor.VariantProcessor.AccumulatorGenerator
- build() - Method in class picard.vcf.processor.VariantProcessor.Builder
- BUILD_37 - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
- Build37ExtendedIlluminaManifest - Class in picard.arrays.illumina
-
A class to represent an 'Extended' Illumina Manifest file.
- Build37ExtendedIlluminaManifest(File) - Constructor for class picard.arrays.illumina.Build37ExtendedIlluminaManifest
- Build37ExtendedIlluminaManifestRecord - Class in picard.arrays.illumina
-
A class to represent a record (line) from an Extended Illumina Manifest [Assay] entry
- Build37ExtendedIlluminaManifestRecord.Flag - Enum Class in picard.arrays.illumina
- Build37ExtendedIlluminaManifestRecordCreator - Class in picard.arrays.illumina
- BuildBamIndex - Class in picard.sam
-
Command line program to generate a BAM index (.bai) file from a BAM (.bam) file
- BuildBamIndex() - Constructor for class picard.sam.BuildBamIndex
- buildMetricsMap(List<? extends MetricBase>) - Method in class picard.analysis.CompareMetrics
- buildReadEnds(SAMFileHeader, long, SAMRecord, boolean) - Method in class picard.sam.markduplicates.MarkDuplicates
-
Builds a read ends object that represents a single read.
- buildReadEnds(SAMFileHeader, long, SAMRecord, boolean) - Method in class picard.sam.markduplicates.MarkDuplicatesForFlowHelper
-
Builds a read ends object that represents a single read - for flow based read
- buildReadEnds(SAMFileHeader, long, SAMRecord, boolean) - Method in interface picard.sam.markduplicates.MarkDuplicatesHelper
- byHundredMegabaseChunks(List<File>) - Static method in class picard.vcf.processor.VariantIteratorProducer
-
Produces a chunking with segments of size 100 megabases (or less if a contig boundary is reached).
- byHundredMegabaseChunksWithOnTheFlyFilteringByInterval(List<File>, IntervalList) - Static method in class picard.vcf.processor.VariantIteratorProducer
-
Produces a chunking with segments of size 100 megabases (or less if a contig boundary is reached), that also performs on-the-fly filtering of
VariantContext
- byHundredMegabasePathChunks(List<PicardHtsPath>) - Static method in class picard.vcf.processor.VariantIteratorProducer
-
Produces a chunking with segments of size 100 megabases (or less if a contig boundary is reached).
- byHundredMegabasePathChunksWithOnTheFlyFilteringByInterval(List<PicardHtsPath>, IntervalList) - Static method in class picard.vcf.processor.VariantIteratorProducer
-
Produces a chunking with segments of size 100 megabases (or less if a contig boundary is reached), that also performs on-the-fly filtering of
VariantContext
- ByIntervalListVariantContextIterator - Class in picard.vcf
-
Takes a VCFFileReader and an IntervalList and provides a single iterator over all variants in all the intervals.
- ByIntervalListVariantContextIterator(VCFFileReader, IntervalList) - Constructor for class picard.vcf.ByIntervalListVariantContextIterator
- byteArrayToCharArray(byte[]) - Static method in class picard.arrays.illumina.InfiniumDataFile
- byteArrayToFloat(byte[]) - Static method in class picard.arrays.illumina.InfiniumDataFile
-
Utility method to convert a byte array to a float value.
- byteArrayToInt(byte[]) - Static method in class picard.arrays.illumina.InfiniumDataFile
-
Utility method to convert an unsigned short to an int.
- byteArrayToString(byte[][], String) - Static method in class picard.util.IlluminaUtil
-
Concatenates all the barcode sequences with BARCODE_DELIMITER
- byWholeContigSubdividingWithWidth(long) - Static method in class picard.vcf.processor.VcfFileSegmentGenerator
-
Deprecated.
- byWholeContigSubdividingWithWidth(long) - Static method in class picard.vcf.processor.VcfPathSegmentGenerator
C
- C - Enum constant in enum class picard.analysis.artifacts.Transition.Base
- C - Enum constant in enum class picard.illumina.parser.IntensityChannel
- C_QUALITY_THRESHOLD - Variable in class picard.analysis.CollectRrbsMetrics
- C_REF_ALT_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The number of alt (A/T) basecalls observed at sites where the genome reference == C.
- C_REF_OXO_ERROR_RATE - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The rate at which C>A and G>T substitutions are observed at C reference sites above the expected rate if there were no bias between sites with a C reference base vs.
- C_REF_OXO_Q - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
C_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score.
- C_REF_REF_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The number of ref basecalls observed at sites where the genome reference == C.
- CALCULATE_BY - Variable in class picard.fingerprint.CalculateFingerprintMetrics
- CALCULATE_TUMOR_AWARE_RESULTS - Variable in class picard.fingerprint.CrosscheckFingerprints
- calculateAllGcs(byte[], int, int) - Static method in class picard.analysis.GcBiasUtils
- calculateDerivedFields() - Method in class picard.analysis.artifacts.ErrorSummaryMetrics
- calculateDerivedFields() - Method in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
- calculateDerivedFields() - Method in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsFlow
- calculateDerivedFields() - Method in class picard.analysis.MergeableMetricBase
-
Placeholder method that will calculate the derived fields from the other ones.
- calculateDerivedFields() - Method in class picard.analysis.replicates.IndependentReplicateMetric
- calculateDerivedFields() - Method in class picard.analysis.WgsMetrics
- calculateDerivedFields() - Method in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
- calculateDerivedFields() - Method in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
- calculateDerivedFields() - Method in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
- calculateDerivedFields() - Method in class picard.sam.DuplicationMetrics
-
Fills in the ESTIMATED_LIBRARY_SIZE based on the paired read data examined where possible and the PERCENT_DUPLICATION.
- calculateDerivedFields() - Method in class picard.sam.FlowBasedDuplicationMetrics
- calculateDerivedFields() - Method in class picard.sam.markduplicates.UmiMetrics
- calculateDerivedFields() - Method in class picard.sam.SamErrorMetric.BaseErrorMetric
- calculateDerivedFields() - Method in class picard.sam.SamErrorMetric.IndelErrorMetric
- calculateDerivedFields() - Method in class picard.sam.SamErrorMetric.OverlappingErrorMetric
- calculateDerivedFields() - Method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
- calculateDerivedFields() - Method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
- calculateDerivedFields() - Method in class picard.vcf.MendelianViolations.MendelianViolationMetrics
- calculateDerivedMetrics() - Method in class picard.sam.DuplicationMetrics
-
Deprecated.
- calculateDerivedStatistics() - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
Calculate the error rate given the raw counts.
- calculateDerivedStatistics() - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
Calculate the error rate given the raw counts.
- CalculateFingerprintMetrics - Class in picard.fingerprint
-
Calculates various metrics on a sample fingerprint, indicating whether the fingerprint satisfies the assumptions we have.
- CalculateFingerprintMetrics() - Constructor for class picard.fingerprint.CalculateFingerprintMetrics
- calculateFromDerivedFields() - Method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
- calculateFromDerivedFields(long) - Method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
- calculateGc(byte[], int, int, GcBiasUtils.CalculateGcState) - Static method in class picard.analysis.GcBiasUtils
- calculateGenotypeConcordance(GenotypeConcordanceScheme, boolean) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Genotype Concordance is the number of times the truth and call states match exactly / all truth and call combinations made If the GA4GH scheme is being used, any MISSING sites in truth OR call will not be included in the discordance calculations.
- calculateMatchResults(Fingerprint, Fingerprint) - Static method in class picard.fingerprint.FingerprintChecker
-
Compares two fingerprints and calculates a MatchResults object which contains detailed information about the match (or mismatch) between fingerprints including the LOD score for whether or not the two are likely from the same sample.
- calculateMatchResults(Fingerprint, Fingerprint, double, double) - Static method in class picard.fingerprint.FingerprintChecker
- calculateMatchResults(Fingerprint, Fingerprint, double, double, boolean, boolean) - Static method in class picard.fingerprint.FingerprintChecker
-
Compares two fingerprints and calculates a MatchResults object which contains detailed information about the match (or mismatch) between fingerprints including the LOD score for whether or not the two are likely from the same sample.
- calculateNonRefGenotypeConcordance(GenotypeConcordanceScheme, boolean) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Non Ref Genotype Concordance is the number of times the truth and call states match exactly for *vars only* / all truth and call *var* combinations made If the GA4GH scheme is being used, any MISSING sites in truth OR call will not be included in the discordance calculations.
- CalculateReadGroupChecksum - Class in picard.sam
- CalculateReadGroupChecksum() - Constructor for class picard.sam.CalculateReadGroupChecksum
- calculateRefWindowsByGc(int, File, int) - Static method in class picard.analysis.GcBiasUtils
- calculateRoiHistogram() - Method in class picard.sam.DuplicationMetrics
-
Calculates a histogram using the estimateRoi method to estimate the effective yield doing x sequencing for x=1..10.
- calculateSensitivities(int, Histogram<Integer>, Histogram<Integer>, List<Double>) - Static method in class picard.analysis.TheoreticalSensitivity
-
This is a utility function to calculate the metrics specific to running theoretical sensitivity over several different allele fractions.
- calculateWordCount(byte[]) - Method in class picard.util.AbstractInputParser
-
Calculates the number of delimiter-separated "words" in a line and sets the value of
wordCount
- call() - Method in enum class picard.analysis.artifacts.Transition
-
Gets the call for the transition.
- CALL_RATE - Variable in class picard.arrays.BafRegressMetrics
-
The call rate of the sample (number of non-missing genotypes)
- CALL_RATE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The overall call rate
- CALL_RATE_PF_THRESHOLD - Static variable in class picard.arrays.CollectArraysVariantCallingMetrics
- CALL_SAMPLE - Variable in class picard.vcf.GenotypeConcordance
- CALL_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
-
The name of the 'call' sample
- CALL_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
-
The name of the 'call' sample
- CALL_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The name of the 'call' sample
- CALL_STATE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
-
The state of the 'call' sample (i.e.
- CALL_VCF - Variable in class picard.vcf.GenotypeConcordance
- callAllele1 - Variable in class picard.vcf.GenotypeConcordance.Alleles
- callAllele2 - Variable in class picard.vcf.GenotypeConcordance.Alleles
- callAlleles() - Method in class picard.vcf.GenotypeConcordance.Alleles
- CallingMetricAccumulator - Class in picard.vcf
-
Collects variants and generates metrics about them.
- CallingMetricAccumulator(DbSnpBitSetUtil.DbSnpBitSets) - Constructor for class picard.vcf.CallingMetricAccumulator
- CallingMetricAccumulator.Result - Class in picard.vcf
- callState - Variable in class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
- callVersion - Variable in class picard.arrays.illumina.InfiniumEGTFile
- CAN_SKIP - Enum constant in enum class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
- canMerge(MergeableMetricBase) - Method in class picard.analysis.MergeableMetricBase
-
Checks if this instance can be merged with another Other must have all the fields that this instance has, and the fields that are annotated as MergeByAssertEquals must contain the same value
- CANNOT_SKIP_FOUND_NO_MC - Enum constant in enum class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
- CANNOT_SKIP_FOUND_OQ - Enum constant in enum class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
- canSkip() - Method in enum class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
- canSkipSAMFile(File, int, boolean, File) - Static method in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
-
Checks if we can skip the SAM/BAM/CRAM file when reverting origin base qualities and adding mate cigars.
- capFromAbove(double[], double) - Static method in class picard.util.MathUtil
-
Returns the array capped (from above) by the value of top
- capFromBelow(double[], double) - Static method in class picard.util.MathUtil
-
Returns the array capped (from below) by the value of floor
- CappedHaplotypeProbabilities - Class in picard.fingerprint
- CappedHaplotypeProbabilities(HaplotypeProbabilities, double) - Constructor for class picard.fingerprint.CappedHaplotypeProbabilities
- CASAVA_1_8 - Enum constant in enum class picard.illumina.IlluminaBasecallsToFastq.ReadNameFormat
- Casava18ReadNameEncoder - Class in picard.fastq
-
A read name encoder conforming to the standard described by Illumina Casava 1.8.
- Casava18ReadNameEncoder(String, String, String) - Constructor for class picard.fastq.Casava18ReadNameEncoder
- CATEGORY - Variable in class picard.analysis.AlignmentSummaryMetrics
-
One of either UNPAIRED (for a fragment run), FIRST_OF_PAIR when metrics are for only the first read in a paired run, SECOND_OF_PAIR when the metrics are for only the second read in a paired run or PAIR when the metrics are aggregated for both first and second reads in a pair.
- CATEGORY - Variable in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
-
One of either WHOLE_GENOME or NON_ZERO_REGIONS
- CATEGORY - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
-
Grouping categories for controls.
- Cbcl - Enum constant in enum class picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
- CbclData - Class in picard.illumina.parser
-
This class provides that data structure for cbcls.
- CbclData(int[], int) - Constructor for class picard.illumina.parser.CbclData
- CbclReader - Class in picard.illumina.parser.readers
-
------------------------------------- CBCL Header ----------------------------------- Bytes 0 - 1 Version number, current version is 1 unsigned 16 bits little endian integer Bytes 2 - 5 Header size unsigned 32 bits little endian integer Byte 6 Number of bits per basecall unsigned Byte 7 Number of bits per q-score unsigned
- CbclReader(List<File>, Map<Integer, File>, int[], int, List<AbstractIlluminaPositionFileReader.PositionInfo>, int[]) - Constructor for class picard.illumina.parser.readers.CbclReader
- CC - Enum constant in enum class picard.fingerprint.DiploidGenotype
- CDS_END - Enum constant in enum class picard.annotation.RefFlatReader.RefFlatColumns
- CDS_START - Enum constant in enum class picard.annotation.RefFlatReader.RefFlatColumns
- CenteredConstrained - Enum constant in enum class picard.util.BaitDesigner.DesignStrategy
-
Implementation that "constrains" baits to be within the target region when possible.
- CG - Enum constant in enum class picard.fingerprint.DiploidGenotype
- CHAIN - Variable in class picard.fingerprint.LiftOverHaplotypeMap
- CHAIN - Variable in class picard.util.LiftOverIntervalList
- CHAIN - Variable in class picard.vcf.LiftoverVcf
- CHART_OUTPUT - Variable in class picard.analysis.CollectBaseDistributionByCycle
- CHART_OUTPUT - Variable in class picard.analysis.CollectGcBiasMetrics
- CHART_OUTPUT - Variable in class picard.analysis.CollectRnaSeqMetrics
- CHART_OUTPUT - Variable in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
- CHART_OUTPUT - Variable in class picard.analysis.MeanQualityByCycle
- CHART_OUTPUT - Variable in class picard.analysis.QualityScoreDistribution
- CHECK_FIRST_N_RECORDS - Variable in class picard.vcf.FixVcfHeader
- CheckDuplicateMarking - Class in picard.sam.markduplicates
- CheckDuplicateMarking() - Constructor for class picard.sam.markduplicates.CheckDuplicateMarking
- CheckDuplicateMarking.Mode - Enum Class in picard.sam.markduplicates
- CheckFingerprint - Class in picard.fingerprint
-
Checks the sample identity of the sequence/genotype data in the provided file (SAM/BAM or VCF) against a set of known genotypes in the supplied genotype file (in VCF format).
- CheckFingerprint() - Constructor for class picard.fingerprint.CheckFingerprint
- checkFingerprints(List<Path>, List<Path>, String, boolean) - Method in class picard.fingerprint.FingerprintChecker
-
Top level method to take a set of one or more SAM files and one or more Genotype files and compare each read group in each SAM file to each set of fingerprint genotypes.
- checkFingerprintsFromPaths(List<Path>, List<Path>, String, String) - Method in class picard.fingerprint.FingerprintChecker
-
Top level method to take a set of one or more observed genotype (VCF) files and one or more expected genotype (VCF) files and compare one or more sample in the observed genotype file with one or more in the expected file and generate results for each set.
- CheckIlluminaDirectory - Class in picard.illumina
-
Program to check a lane of an Illumina output directory.
- CheckIlluminaDirectory() - Constructor for class picard.illumina.CheckIlluminaDirectory
- checkOutOfBounds(int) - Method in class picard.analysis.CounterManager
-
Method checks that new locus position is not out of bounds of Counter arrays and there is enough space in them to hold information on at least one more read of length
CounterManager.readLength
. - checkRInstallation(boolean) - Static method in class picard.cmdline.CommandLineProgram
-
Check if R is installed
- CheckTerminatorBlock - Class in picard.sam
-
Simple class to check the terminator block of a SAM file.
- CheckTerminatorBlock() - Constructor for class picard.sam.CheckTerminatorBlock
- checkTileCount() - Method in class picard.illumina.parser.ParameterizedFileUtil
- checkTileCount() - Method in class picard.illumina.parser.PerTileOrPerRunFileUtil
- CHI_SQUARED_PVALUE - Variable in class picard.fingerprint.FingerprintMetrics
-
The Chi-squared pvalue of the observed counts vector relative to the expected counts, (3x2 table)
- CHIMERA_KB_MIN - Variable in class picard.analysis.CollectJumpingLibraryMetrics
- ChimeraUtil - Class in picard.analysis
- ChimeraUtil() - Constructor for class picard.analysis.ChimeraUtil
- CHIMERIC - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
- CHIMERIC_PAIRS - Variable in class picard.analysis.JumpingLibraryMetrics
-
The number of pairs where either (a) the ends fall on different chromosomes or (b) the insert size is greater than the maximum of 100000 or 2 times the mode of the insert size for outward-facing pairs.
- CHIP_TYPE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The chip type name
- CHIP_WELL_BARCODE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The chip well barcode of the Illumina array being assayed
- CHIP_WELL_BARCODE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- CHROM - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The chromosome on which the SNP resides.
- CHROMOSOME - Enum constant in enum class picard.annotation.RefFlatReader.RefFlatColumns
- CHROMOSOME_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- CigarOperatorsInReadStratifier(CigarOperator) - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.CigarOperatorsInReadStratifier
- CircularByteBuffer - Class in picard.util
-
Implementation of a circular byte buffer that uses a large byte[] internally and supports basic read/write operations from/to other byte[]s passed as arguments.
- CircularByteBuffer(int) - Constructor for class picard.util.CircularByteBuffer
-
Constructs a buffer capable of holding the given number of bytes.
- CLASSIFICATION - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
-
The classification of this read: {EMPTY, POLYCLONAL, MISALIGNED, UNKNOWN} (See PFFailSummaryMetric for explanation regarding the possible classification.)
- classifyVariants(Optional<VariantContext>, String, Optional<VariantContext>, String, int, int, boolean) - Static method in class picard.vcf.GenotypeConcordance
- classifyVariants(Optional<VariantContext>, String, Optional<VariantContext>, String, Optional<GenotypeConcordanceCounts>, Optional<GenotypeConcordanceCounts>, int, int, boolean) - Static method in class picard.vcf.GenotypeConcordance
-
Attempts to determine the concordance state given the truth and all variant context and optionally increments the genotype concordance count for the given variant type (SNP or INDEL).
- CleanSam - Class in picard.sam
- CleanSam() - Constructor for class picard.sam.CleanSam
- cleanUp() - Method in class picard.util.ThreadPoolExecutorWithExceptions
-
Calls `shutdownNow, adjusts the core size to 0 and low timeout to ensure threads get killed and garbage collected.
- clear() - Method in class picard.analysis.CounterManager
-
Clears all inner Counter arrays
- clear() - Method in class picard.illumina.parser.readers.CbclReader
- CLEAR_DT - Variable in class picard.sam.markduplicates.MarkDuplicates
- CLIP_ADAPTERS - Variable in class picard.sam.MergeBamAlignment
- CLIP_OVERLAPPING_READS - Variable in class picard.analysis.directed.CollectTargetedMetrics
- CLIP_OVERLAPPING_READS - Variable in class picard.sam.MergeBamAlignment
- clipForOverlappingReads(SAMRecord, SAMRecord, boolean) - Static method in class picard.sam.AbstractAlignmentMerger
-
Checks to see whether the ends of the reads overlap and clips reads if necessary.
- CLIPPING_ACTION - Variable in class picard.sam.SamToFastq
- CLIPPING_ATTRIBUTE - Variable in class picard.sam.SamToFastq
- CLIPPING_MIN_LENGTH - Variable in class picard.sam.SamToFastq
- CLIPPING_TAG_CONTAINS_A - Static variable in class picard.sam.markduplicates.MarkDuplicatesForFlowHelper
- CLIPPING_TAG_CONTAINS_AQ - Static variable in class picard.sam.markduplicates.MarkDuplicatesForFlowHelper
- CLIPPING_TAG_CONTAINS_QZ - Static variable in class picard.sam.markduplicates.MarkDuplicatesForFlowHelper
- CLIPPING_TAG_NAME - Static variable in class picard.sam.markduplicates.MarkDuplicatesForFlowHelper
- ClippingUtility - Class in picard.util
-
Utilities to clip the adapter sequence from a SAMRecord read
- ClippingUtility() - Constructor for class picard.util.ClippingUtility
- Clocs - Enum constant in enum class picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
- ClocsFileFaker - Class in picard.illumina.parser.fakers
- ClocsFileFaker() - Constructor for class picard.illumina.parser.fakers.ClocsFileFaker
- ClocsFileReader - Class in picard.illumina.parser.readers
-
The clocs file format is one of 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively.
- ClocsFileReader(File) - Constructor for class picard.illumina.parser.readers.ClocsFileReader
- clone() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
- clone() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
- clone() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
- clone() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodesCodec
- clone() - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
- close() - Method in class picard.arrays.illumina.IlluminaAdpcFileWriter
- close() - Method in class picard.arrays.illumina.IlluminaBPMFile
- close() - Method in class picard.arrays.illumina.InfiniumEGTFile
- close() - Method in class picard.arrays.illumina.InfiniumGTCFile
- close() - Method in interface picard.illumina.BasecallsConverter.ConvertedClusterDataWriter
-
Closes the writer.
- close() - Method in class picard.illumina.parser.BaseIlluminaDataProvider
- close() - Method in class picard.illumina.parser.MultiTileParser
- close() - Method in class picard.illumina.parser.MultiTileFilterParser
- close() - Method in class picard.illumina.parser.MultiTileLocsParser
- close() - Method in class picard.illumina.parser.MultiTileBclParser
- close() - Method in class picard.illumina.parser.PerTileParser
- close() - Method in class picard.illumina.parser.readers.BarcodeFileReader
- close() - Method in class picard.illumina.parser.readers.BclReader
- close() - Method in class picard.illumina.parser.readers.CbclReader
- close() - Method in class picard.illumina.parser.readers.ClocsFileReader
- close() - Method in class picard.illumina.parser.readers.LocsFileReader
- close() - Method in class picard.illumina.parser.readers.PosFileReader
- close() - Method in class picard.sam.AbstractAlignmentMerger
- close() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
- close() - Method in class picard.util.AbstractInputParser
-
Closes this stream and releases any system resources associated with it.
- close() - Method in class picard.util.AsyncIterator
-
Stops the thread and then calls synchronouslyClose() to allow implementation to do any one time clean up.
- close() - Method in class picard.util.BasicInputParser
-
Closes the underlying stream
- close() - Method in class picard.util.CircularByteBuffer
-
Signals that the buffer is closed and no further writes will occur.
- close() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
- close() - Method in class picard.util.TabbedTextFileWithHeaderParser
-
Release all resources associated with the parser.
- close() - Method in class picard.vcf.filter.FilterApplyingVariantIterator
- close() - Method in class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
- close() - Method in class picard.vcf.processor.VariantIteratorProducer
-
Closes any latent file handles that may have been opened by calls to
VariantIteratorProducer.iterators()
. - closeWriter() - Method in class picard.sam.FixMateInformation
- closeWriters() - Method in class picard.illumina.BasecallsConverter
-
Closes all writers.
- cluster() - Method in class picard.util.GraphUtils.Graph
-
returns the cluster map of connected components
- CLUSTER - Variable in class picard.fingerprint.ClusteredCrosscheckMetric
-
The cluster identifier to which the two groups within this metric (
CrosscheckMetric.LEFT_GROUP_VALUE
andCrosscheckMetric.RIGHT_GROUP_VALUE
) belong. - CLUSTER_DENSITY - Variable in class picard.illumina.IlluminaLaneMetrics
-
The number of clusters per unit area on the this lane expressed in units of [cluster / mm^2].
- CLUSTER_FILE - Variable in class picard.arrays.GtcToVcf
- CLUSTER_FILE - Variable in class picard.arrays.illumina.BpmToNormalizationManifestCsv
- CLUSTER_FILE - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- CLUSTER_FILE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- CLUSTER_FILE_NAME - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The name of the cluster file used
- CLUSTER_ID - Enum constant in enum class picard.illumina.parser.IlluminaMetricsCode
- CLUSTER_SIZE - Variable in class picard.fingerprint.ClusteredCrosscheckMetric
-
The number of different groups that are assigned to this cluster.
- ClusterCrosscheckMetrics - Class in picard.fingerprint
-
Summary
- ClusterCrosscheckMetrics() - Constructor for class picard.fingerprint.ClusterCrosscheckMetrics
- ClusterData - Class in picard.illumina.parser
-
Store the information from Illumina files for a single cluster with one or more reads.
- ClusterData(ReadData...) - Constructor for class picard.illumina.parser.ClusterData
-
Used for testing, reads is set directly with no copying to the input array
- ClusterData(ReadType[]) - Constructor for class picard.illumina.parser.ClusterData
-
Creates a ClusterData with one read for each type provided
- ClusterDataToSamConverter - Class in picard.illumina
-
Takes ClusterData provided by an IlluminaDataProvider into one or two SAMRecords, as appropriate, and optionally marking adapter sequence.
- ClusterDataToSamConverter(String, Map<Integer, String>, ReadStructure, List<AdapterPair>, ClusterDataToSamConverter.PopulateBarcode, boolean) - Constructor for class picard.illumina.ClusterDataToSamConverter
-
Constructor
- ClusteredCrosscheckMetric - Class in picard.fingerprint
-
A metric class to hold the result of
ClusterCrosscheckMetrics
fingerprints. - ClusteredCrosscheckMetric() - Constructor for class picard.fingerprint.ClusteredCrosscheckMetric
- ClusteredCrosscheckMetric(CrosscheckMetric) - Constructor for class picard.fingerprint.ClusteredCrosscheckMetric
- clusterVersion - Variable in class picard.arrays.illumina.InfiniumEGTFile
- code() - Method in enum class picard.sam.markduplicates.MarkDuplicates.DuplicateType
- CODING - Enum constant in enum class picard.annotation.LocusFunction
- CODING_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
Number of bases in primary alignments that align to a non-UTR coding base for some gene, and not ribosomal sequence.
- codingEnd - Variable in class picard.annotation.Gene.Transcript
- codingStart - Variable in class picard.annotation.Gene.Transcript
- COLLECT_ALIGNMENT_INFORMATION - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
- CollectAlignmentRefArgCollection() - Constructor for class picard.analysis.CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
- CollectAlignmentSummaryMetrics - Class in picard.analysis
-
A command line tool to read a BAM file and produce standard alignment metrics that would be applicable to any alignment.
- CollectAlignmentSummaryMetrics - Enum constant in enum class picard.analysis.CollectMultipleMetrics.Program
- CollectAlignmentSummaryMetrics() - Constructor for class picard.analysis.CollectAlignmentSummaryMetrics
- CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection - Class in picard.analysis
- CollectArraysVariantCallingMetrics - Class in picard.arrays
-
Collects summary and per-sample metrics about variant calls in a VCF file.
- CollectArraysVariantCallingMetrics() - Constructor for class picard.arrays.CollectArraysVariantCallingMetrics
- CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics - Class in picard.arrays
- CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics - Class in picard.arrays
- CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics - Class in picard.arrays
- CollectBaseDistributionByCycle - Class in picard.analysis
- CollectBaseDistributionByCycle - Enum constant in enum class picard.analysis.CollectMultipleMetrics.Program
- CollectBaseDistributionByCycle() - Constructor for class picard.analysis.CollectBaseDistributionByCycle
- CollectDuplicateMetrics - Class in picard.sam.markduplicates
-
Collect DuplicateMark'ing metrics from an input file that was already Duplicate-Marked.
- CollectDuplicateMetrics() - Constructor for class picard.sam.markduplicates.CollectDuplicateMetrics
- collectErrorMessages(List<String>, String[]) - Method in class picard.illumina.ExtractBarcodesProgram
- CollectGcBiasMetrics - Class in picard.analysis
-
Tool to collect information about GC bias in the reads in a given BAM file.
- CollectGcBiasMetrics - Enum constant in enum class picard.analysis.CollectMultipleMetrics.Program
- CollectGcBiasMetrics() - Constructor for class picard.analysis.CollectGcBiasMetrics
- CollectHiSeqXPfFailMetrics - Class in picard.illumina.quality
-
Collect metrics regarding the reason for reads (sequenced by HiSeqX) not passing the Illumina PF Filter.
- CollectHiSeqXPfFailMetrics() - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics
- CollectHiSeqXPfFailMetrics.PFFailDetailedMetric - Class in picard.illumina.quality
-
a metric class for describing FP failing reads from an Illumina HiSeqX lane *
- CollectHiSeqXPfFailMetrics.PFFailSummaryMetric - Class in picard.illumina.quality
-
Metrics produced by the GetHiSeqXPFFailMetrics program.
- CollectHiSeqXPfFailMetrics.ReadClassifier - Class in picard.illumina.quality
- CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason - Enum Class in picard.illumina.quality
- CollectHsMetrics - Class in picard.analysis.directed
-
This tool takes a SAM/BAM file input and collects metrics that are specific for sequence datasets generated through hybrid-selection.
- CollectHsMetrics() - Constructor for class picard.analysis.directed.CollectHsMetrics
- CollectIlluminaBasecallingMetrics - Class in picard.illumina
-
A Command line tool to collect Illumina Basecalling metrics for a sequencing run Requires a Lane and an input file of Barcodes to expect.
- CollectIlluminaBasecallingMetrics() - Constructor for class picard.illumina.CollectIlluminaBasecallingMetrics
- CollectIlluminaLaneMetrics - Class in picard.illumina
-
Command-line wrapper around
CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
. - CollectIlluminaLaneMetrics() - Constructor for class picard.illumina.CollectIlluminaLaneMetrics
- CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector - Class in picard.illumina
-
Utility for collating Tile records from the Illumina TileMetrics file into lane-level and phasing-level metrics.
- CollectIndependentReplicateMetrics - Class in picard.analysis.replicates
-
A CLP that, given a BAM and a VCF with genotypes of the same sample, estimates the rate of independent replication of reads within the bam.
- CollectIndependentReplicateMetrics() - Constructor for class picard.analysis.replicates.CollectIndependentReplicateMetrics
- CollectInsertSizeMetrics - Class in picard.analysis
-
Command line program to read non-duplicate insert sizes, create a Histogram and report distribution statistics.
- CollectInsertSizeMetrics - Enum constant in enum class picard.analysis.CollectMultipleMetrics.Program
- CollectInsertSizeMetrics() - Constructor for class picard.analysis.CollectInsertSizeMetrics
- CollectionStratifier(Collection<ReadBaseStratification.RecordAndOffsetStratifier<?>>) - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.CollectionStratifier
- CollectJumpingLibraryMetrics - Class in picard.analysis
-
Command-line program to compute metrics about outward-facing pairs, inward-facing pairs, and chimeras in a jumping library.
- CollectJumpingLibraryMetrics() - Constructor for class picard.analysis.CollectJumpingLibraryMetrics
- collectLaneMetrics(File, File, String, MetricsFile<MetricBase, Comparable<?>>, MetricsFile<MetricBase, Comparable<?>>, ReadStructure, String, ValidationStringency) - Static method in class picard.illumina.CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
-
Parses the tile data from the basecall directory and writes to both the lane and phasing metrics files
- CollectMultipleMetrics - Class in picard.analysis
-
Class that is designed to instantiate and execute multiple metrics programs that extend SinglePassSamProgram while making only a single pass through the SAM file and supplying each program with the records as it goes.
- CollectMultipleMetrics() - Constructor for class picard.analysis.CollectMultipleMetrics
- CollectMultipleMetrics.Program - Enum Class in picard.analysis
- CollectMultipleMetrics.ProgramInterface - Interface in picard.analysis
- CollectOxoGMetrics - Class in picard.analysis
-
Class for trying to quantify the CpCG->CpCA error rate.
- CollectOxoGMetrics() - Constructor for class picard.analysis.CollectOxoGMetrics
- CollectOxoGMetrics.CpcgMetrics - Class in picard.analysis
-
Metrics class for outputs.
- CollectQualityYieldMetrics - Class in picard.analysis
-
Command line program to calculate quality yield metrics
- CollectQualityYieldMetrics - Enum constant in enum class picard.analysis.CollectMultipleMetrics.Program
- CollectQualityYieldMetrics() - Constructor for class picard.analysis.CollectQualityYieldMetrics
- CollectQualityYieldMetrics.QualityYieldMetrics - Class in picard.analysis
-
A set of metrics used to describe the general quality of a BAM file
- CollectQualityYieldMetrics.QualityYieldMetricsCollector - Class in picard.analysis
- CollectQualityYieldMetrics.QualityYieldMetricsFlow - Class in picard.analysis
- CollectRawWgsMetrics - Class in picard.analysis
-
Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments, same implementation as
CollectWgsMetrics
, with different defaults: lacks baseQ and mappingQ filters and has much higher coverage cap. - CollectRawWgsMetrics() - Constructor for class picard.analysis.CollectRawWgsMetrics
- CollectRawWgsMetrics.RawWgsMetrics - Class in picard.analysis
- CollectRnaSeqMetrics - Class in picard.analysis
- CollectRnaSeqMetrics() - Constructor for class picard.analysis.CollectRnaSeqMetrics
- CollectRrbsMetrics - Class in picard.analysis
-
Calculates and reports QC metrics for RRBS data based on the methylation status at individual C/G bases as well as CpG sites across all reads in the input BAM/SAM file.
- CollectRrbsMetrics() - Constructor for class picard.analysis.CollectRrbsMetrics
- CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection - Class in picard.analysis
- CollectRrbsMetricsReferenceArgumentCollection() - Constructor for class picard.analysis.CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection
- CollectSamErrorMetrics - Class in picard.sam.SamErrorMetric
-
Program to collect error metrics on bases stratified in various ways.
- CollectSamErrorMetrics() - Constructor for class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- CollectSequencingArtifactMetrics - Class in picard.analysis.artifacts
-
Quantify substitution errors caused by mismatched base pairings during various stages of sample / library prep.
- CollectSequencingArtifactMetrics - Enum constant in enum class picard.analysis.CollectMultipleMetrics.Program
- CollectSequencingArtifactMetrics() - Constructor for class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- CollectTargetedMetrics<METRIC extends MultilevelMetrics,
COLLECTOR extends TargetMetricsCollector<METRIC>> - Class in picard.analysis.directed -
Both CollectTargetedPCRMetrics and CollectHsSelection share virtually identical program structures except for the name of their targeting mechanisms (e.g.
- CollectTargetedMetrics() - Constructor for class picard.analysis.directed.CollectTargetedMetrics
- CollectTargetedPcrMetrics - Class in picard.analysis.directed
-
This tool calculates a set of PCR-related metrics from an aligned SAM or BAM file containing targeted sequencing data.
- CollectTargetedPcrMetrics() - Constructor for class picard.analysis.directed.CollectTargetedPcrMetrics
- CollectVariantCallingMetrics - Class in picard.vcf
-
Collects summary and per-sample metrics about variant calls in a VCF file.
- CollectVariantCallingMetrics() - Constructor for class picard.vcf.CollectVariantCallingMetrics
- CollectVariantCallingMetrics.VariantCallingDetailMetrics - Class in picard.vcf
-
A collection of metrics relating to snps and indels within a variant-calling file (VCF) for a given sample.
- CollectVariantCallingMetrics.VariantCallingSummaryMetrics - Class in picard.vcf
-
A collection of metrics relating to snps and indels within a variant-calling file (VCF).
- CollectWgsMetrics - Class in picard.analysis
-
Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments.
- CollectWgsMetrics() - Constructor for class picard.analysis.CollectWgsMetrics
- CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection - Class in picard.analysis
- CollectWgsMetrics.WgsMetricsCollector - Class in picard.analysis
- CollectWgsMetricsIntervalArgumentCollection() - Constructor for class picard.analysis.CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection
- CollectWgsMetricsWithNonZeroCoverage - Class in picard.analysis
- CollectWgsMetricsWithNonZeroCoverage() - Constructor for class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
- CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage - Class in picard.analysis
-
Metrics for evaluating the performance of whole genome sequencing experiments.
- CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category - Enum Class in picard.analysis
- CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector - Class in picard.analysis
- COLOR_STATUS - Static variable in class picard.cmdline.CommandLineDefaults
-
Implementation note, this is duplicate code stolen from HTSJDK's Default.java /** Decides if we want to write colors to the terminal.
- columnLabels() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
- columnLabels() - Method in class picard.util.TabbedTextFileWithHeaderParser
- columnLabelsList() - Method in class picard.util.TabbedTextFileWithHeaderParser
- CombineGenotypingArrayVcfs - Class in picard.arrays
-
A simple program to combine multiple genotyping array VCFs into one VCF The input VCFs must have the same sequence dictionary and same list of variant loci.
- CombineGenotypingArrayVcfs() - Constructor for class picard.arrays.CombineGenotypingArrayVcfs
- combiningResultsBy(VariantProcessor.ResultMerger<R>) - Method in class picard.vcf.processor.VariantProcessor.Builder
- CommandLineDefaults - Class in picard.cmdline
-
Embodies defaults for global values that affect how the Picard Command Line operates.
- CommandLineDefaults() - Constructor for class picard.cmdline.CommandLineDefaults
- CommandLineProgram - Class in picard.cmdline
-
Abstract class to facilitate writing command-line programs.
- CommandLineProgram() - Constructor for class picard.cmdline.CommandLineProgram
- CommandLineSyntaxTranslater - Class in picard.cmdline
-
Class for handling translation of Picard-style command line argument syntax to POSIX-style argument syntax; used for running tests written with Picard style syntax against the Barclay command line parser.
- CommandLineSyntaxTranslater() - Constructor for class picard.cmdline.CommandLineSyntaxTranslater
- COMMENT - Variable in class picard.sam.AddCommentsToBam
- COMMENT - Variable in class picard.sam.FastqToSam
- COMMENT - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- COMMENT - Variable in class picard.sam.MergeSamFiles
- COMMENT - Variable in class picard.util.IntervalListTools
- COMMENT - Variable in class picard.vcf.GatherVcfs
- COMMENT - Variable in class picard.vcf.MergeVcfs
- compare(int, int) - Static method in class picard.util.MathUtil
- COMPARE_MQ - Variable in class picard.sam.util.SAMComparisonArgumentCollection
- CompareGtcFiles - Class in picard.arrays.illumina
-
A simple tool to compare two Illumina GTC files.
- CompareGtcFiles() - Constructor for class picard.arrays.illumina.CompareGtcFiles
- CompareMetrics - Class in picard.analysis
-
Compare two metrics files.
- CompareMetrics() - Constructor for class picard.analysis.CompareMetrics
- CompareMetrics.MetricComparisonDifferences - Class in picard.analysis
- compareMetricsForEntry(MetricBase, MetricBase, Field[], Set<String>, String) - Method in class picard.analysis.CompareMetrics
- compareMetricValues(Object, Object, String) - Method in class picard.analysis.CompareMetrics
- CompareSAMs - Class in picard.sam
-
Rudimentary SAM comparer.
- CompareSAMs() - Constructor for class picard.sam.CompareSAMs
- compareTo(SequencingArtifactMetrics.BaitBiasDetailMetrics) - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
- compareTo(SequencingArtifactMetrics.PreAdapterDetailMetrics) - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
- compareTo(Gene) - Method in class picard.annotation.Gene
- compareTo(HaplotypeBlock) - Method in class picard.fingerprint.HaplotypeBlock
- compareTo(MatchResults) - Method in class picard.fingerprint.MatchResults
-
Provides a natural sort so that better matches (by LOD) sort earlier.
- compareTo(Snp) - Method in class picard.fingerprint.Snp
- compareTo(Pair<X, Y>) - Method in class picard.sam.util.Pair
- compareTo(PrimaryAlignmentKey) - Method in class picard.sam.util.PrimaryAlignmentKey
- compareTo(GenotypeConcordanceStates.TruthAndCallStates) - Method in class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
- CompareVariantContextToLocus(SAMSequenceDictionary, VariantContext, Locus) - Static method in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
-
Compares a VariantContext to a Locus providing information regarding possible overlap, or relative location
- complement() - Method in enum class picard.analysis.artifacts.Transition
-
Return the complementary transition.
- COMPRESS_OUTPUTS - Variable in class picard.illumina.ExtractBarcodesProgram
- COMPRESS_OUTPUTS_PER_RG - Variable in class picard.sam.SamToFastq
- COMPRESS_OUTPUTS_PER_TAG_GROUP - Variable in class picard.sam.SamToFastqWithTags
- COMPRESSION_LEVEL - Variable in class picard.cmdline.CommandLineProgram
- computeQScore(long) - Method in class picard.sam.SamErrorMetric.ErrorMetric
-
compute a qscore given the number of errors and the total number of bases.
- computeQScore(long, long) - Method in class picard.sam.SamErrorMetric.ErrorMetric
-
compute a qscore given the number of errors and the total number of bases.
- CON_ALT_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The number of REF_BASE:ALT_BASE alignments having a read number and orientation that refutes the presence of this artifact.
- CON_REF_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The number of REF_BASE:REF_BASE alignments having a read number and orientation that refutes the presence of this artifact.
- CONCAT - Enum constant in enum class picard.util.IntervalListTools.Action
- CONCAT_ALL - Enum constant in enum class picard.vcf.VcfToIntervalList.VARIANT_ID_TYPES
- consensusStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratify by tags used during duplex and single index consensus calling.
- ConsensusStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.ConsensusStratifier
- contains(Snp) - Method in class picard.fingerprint.HaplotypeBlock
-
Returns true if the SNP is contained within the haplotype block, false otherwise.
- contamination - Variable in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
- CONTAMINATION - Variable in class picard.fingerprint.ExtractFingerprint
- CONTAMINATION - Variable in class picard.fingerprint.IdentifyContaminant
- CONTEXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The sequence context to which the analysis is constrained.
- CONTEXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The sequence context to which the analysis is constrained.
- CONTEXT - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The sequence context being reported on.
- CONTEXT_SIZE - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- CONTEXT_SIZE - Variable in class picard.analysis.CollectOxoGMetrics
- CONTEXTS - Variable in class picard.analysis.CollectOxoGMetrics
- CONTEXTS_TO_PRINT - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- contig() - Method in class picard.vcf.processor.VcfFileSegment
-
Deprecated.
- contig() - Method in class picard.vcf.processor.VcfPathSegment
- CONTINGENCY_METRICS_FILE_EXTENSION - Static variable in class picard.vcf.GenotypeConcordance
- CONTINGENCY_STATE_HEADER_LINE - Static variable in class picard.vcf.GenotypeConcordance
- CONTINGENCY_STATE_TAG - Static variable in class picard.vcf.GenotypeConcordance
- CONTINGENCY_VALUES - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
-
The list of contingency table values (TP, TN, FP, FN) that are deduced from the truth/call state comparison, given the reference.
- CONTROL - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
-
Various control intensities that are present on the infinium chips.
- CONTROL_INFO - Static variable in class picard.arrays.illumina.ArraysControlInfo
- convert(File, File, File, Boolean) - Static method in class picard.sam.SamFormatConverter
-
Convert a file from one of sam/bam/cram format to another based on the extension of output.
- convertClusterToOutputRecord(ClusterData) - Method in interface picard.illumina.BasecallsConverter.ClusterDataConverter
-
Creates the OUTPUT_RECORDs from the cluster
- convertClusterToOutputRecord(ClusterData) - Method in class picard.illumina.ClusterDataToSamConverter
-
Creates the SAMRecord for each read in the cluster
- CONVERTED_SITES - Variable in class picard.analysis.RrbsCpgDetailMetrics
-
Number of times this CpG site was converted (TG for + strand, CA for - strand)
- converter - Variable in class picard.illumina.BasecallsConverter
- ConvertHaplotypeDatabaseToVcf - Class in picard.fingerprint
- ConvertHaplotypeDatabaseToVcf() - Constructor for class picard.fingerprint.ConvertHaplotypeDatabaseToVcf
- convertMetric(TargetMetrics) - Method in class picard.analysis.directed.HsMetricCollector
- convertMetric(TargetMetrics) - Method in class picard.analysis.directed.TargetedPcrMetricsCollector
- convertMetric(TargetMetrics) - Method in class picard.analysis.directed.TargetMetricsCollector
- convertPicardStyleToPosixStyle(String[]) - Static method in class picard.cmdline.CommandLineSyntaxTranslater
- ConvertSequencingArtifactToOxoG - Class in picard.analysis.artifacts
- ConvertSequencingArtifactToOxoG() - Constructor for class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
- convertSolexaQualityAscii_1_1_ToPhredBinary(byte[]) - Static method in class picard.util.IlluminaUtil
-
Converts from Solexa ASCII to Phred binary in place.
- copy() - Method in class picard.illumina.BarcodeMetric
-
Creates a copy of metric initialized with only non-accumulated and non-calculated values set
- COPY_TO_TAG - Enum constant in enum class picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
- copyFromBaseClass(T, S) - Static method in class picard.util.ReflectionUtil
- CORRECT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
-
Number of aligned reads that are mapped to the correct strand.
- correspondingInterval() - Method in class picard.vcf.processor.VcfFileSegment
-
Deprecated.
- correspondingInterval() - Method in class picard.vcf.processor.VcfPathSegment
- COUNT - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
-
The number of events of type TRUTH_STATE and CALL_STATE for the EVENT_TYPE and SAMPLEs
- COUNT_OUTPUT - Variable in class picard.util.IntervalListTools
- COUNT_UNPAIRED - Variable in class picard.analysis.CollectWgsMetrics
- counter - Variable in class picard.analysis.AbstractWgsMetricsCollector
-
The number of processed genomic bases
- CounterManager - Class in picard.analysis
-
Class for managing a list of Counters of integer, provides methods to access data from Counters with respect to an offset.
- CounterManager(int, int) - Constructor for class picard.analysis.CounterManager
-
Constructor creates new CounterManager without any Counters, counters are added to CounterManager via newCounter() method
- CounterManager.Counter - Class in picard.analysis
-
Class represents an integer array with methods to increment and get the values from it with respect to offset of outer
CounterManager
. - CountingAdapterFilter - Class in picard.filter
-
Counting filter that discards reads are unaligned or aligned with MQ==0 and whose 5' ends look like adapter Sequence
- CountingAdapterFilter() - Constructor for class picard.filter.CountingAdapterFilter
- CountingDuplicateFilter - Class in picard.filter
-
Counting filter that discards reads that have been marked as duplicates.
- CountingDuplicateFilter() - Constructor for class picard.filter.CountingDuplicateFilter
- CountingFilter - Class in picard.filter
-
A SamRecordFilter that counts the number of bases in the reads which it filters out.
- CountingFilter() - Constructor for class picard.filter.CountingFilter
- CountingMapQFilter - Class in picard.filter
-
Counting filter that discards reads below a configurable mapping quality threshold.
- CountingMapQFilter(int) - Constructor for class picard.filter.CountingMapQFilter
- CountingPairedFilter - Class in picard.filter
-
Counting filter that discards reads that are unpaired in sequencing and paired reads whose mates are not mapped.
- CountingPairedFilter() - Constructor for class picard.filter.CountingPairedFilter
- COVARIATE - Variable in class picard.sam.SamErrorMetric.ErrorMetric
-
The value of the covariate define the bases included in this metric
- Coverage(Interval, int) - Constructor for class picard.analysis.directed.TargetMetricsCollector.Coverage
-
Constructs a new coverage object for the provided mapping with the desired padding either side.
- COVERAGE_CAP - Variable in class picard.analysis.CollectWgsMetrics
- COVERAGE_CAP - Variable in class picard.analysis.directed.CollectTargetedMetrics
- coverageCap - Variable in class picard.analysis.AbstractWgsMetricsCollector
-
Positions with coverage exceeding this value are treated as if they had coverage at this value
- coverageCap - Variable in class picard.analysis.WgsMetrics
-
The maximum depth/coverage to consider.
- CpcgMetrics() - Constructor for class picard.analysis.CollectOxoGMetrics.CpcgMetrics
- CPG_BASES_CONVERTED - Variable in class picard.analysis.RrbsSummaryMetrics
-
Number of CpG sites that were converted (TG for +, CA for -)
- CPG_BASES_SEEN - Variable in class picard.analysis.RrbsSummaryMetrics
-
Number of CpG sites encountered
- cram - Enum constant in enum class picard.sam.RevertSam.FileType
- CREATE_INDEX - Variable in class picard.cmdline.CommandLineProgram
- CREATE_MD5_FILE - Variable in class picard.cmdline.CommandLineProgram
- CreateBafRegressMetricsFile - Class in picard.arrays
-
A simple program to create a standard picard metrics file from the output of bafRegress
- CreateBafRegressMetricsFile() - Constructor for class picard.arrays.CreateBafRegressMetricsFile
- createBarcodeExtractor() - Method in class picard.illumina.ExtractBarcodesProgram
- CreateExtendedIlluminaManifest - Class in picard.arrays.illumina
-
Create an Extended Illumina Manifest by performing a liftover to Build 37.
- CreateExtendedIlluminaManifest() - Constructor for class picard.arrays.illumina.CreateExtendedIlluminaManifest
- createMetrics() - Static method in class picard.sam.DuplicationMetricsFactory
-
Create non-flow duplication metrics
- createMetrics(boolean) - Static method in class picard.sam.DuplicationMetricsFactory
-
Create empty regular of flow duplication metrics
- createNewCigarsIfMapsOffEndOfReference(SAMRecord) - Static method in class picard.sam.AbstractAlignmentMerger
-
Soft-clip an alignment that hangs off the end of its reference sequence.
- createRecord(IlluminaManifestRecord) - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
- createSamFileHeader() - Method in class picard.sam.FastqToSam
-
Creates a simple header with the values provided on the command line.
- createSamFileWriter(SAMFileHeader) - Method in class picard.sam.FixMateInformation
- CreateSeqDictReferenceArgumentCollection() - Constructor for class picard.sam.CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
- CreateSequenceDictionary - Class in picard.sam
-
Create a SAM/BAM file from a fasta containing reference sequence.
- CreateSequenceDictionary() - Constructor for class picard.sam.CreateSequenceDictionary
- CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection - Class in picard.sam
- createSnpAndIndelBitSets(File, SAMSequenceDictionary) - Static method in class picard.util.DbSnpBitSetUtil
-
Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
- createSnpAndIndelBitSets(File, SAMSequenceDictionary, IntervalList) - Static method in class picard.util.DbSnpBitSetUtil
-
Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
- createSnpAndIndelBitSets(File, SAMSequenceDictionary, IntervalList, Optional<Log>) - Static method in class picard.util.DbSnpBitSetUtil
-
Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
- createSnpAndIndelBitSets(PicardHtsPath, SAMSequenceDictionary, IntervalList) - Static method in class picard.util.DbSnpBitSetUtil
-
Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
- createSnpAndIndelBitSets(PicardHtsPath, SAMSequenceDictionary, IntervalList, Optional<Log>) - Static method in class picard.util.DbSnpBitSetUtil
-
Factory method to create both a SNP bitmask and an indel bitmask in a single pass of the VCF.
- createVCSetFromFingerprint(Fingerprint, ReferenceSequenceFile, String) - Static method in class picard.fingerprint.FingerprintUtils
-
A utility function that takes a fingerprint and returns a VariantContextSet with variants representing the haplotypes in the fingerprint
- CreateVerifyIDIntensityContaminationMetricsFile - Class in picard.arrays
-
A simple program to create a standard picard metrics file from the output of VerifyIDIntensity
- CreateVerifyIDIntensityContaminationMetricsFile() - Constructor for class picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile
- CROSS_ENTROPY_LOD - Variable in class picard.fingerprint.FingerprintMetrics
-
The categorical cross entropy of the counts of genotypes relative to expected (big is bad)
- CROSSCHECK_BY - Variable in class picard.fingerprint.CrosscheckFingerprints
- CROSSCHECK_LIBRARIES - Variable in class picard.fingerprint.CrosscheckReadGroupFingerprints
-
Deprecated.
- CROSSCHECK_MODE - Variable in class picard.fingerprint.CrosscheckFingerprints
- CROSSCHECK_SAMPLES - Variable in class picard.fingerprint.CrosscheckReadGroupFingerprints
-
Deprecated.
- CrosscheckFingerprints - Class in picard.fingerprint
-
Checks that all data in the set of input files appear to come from the same individual.
- CrosscheckFingerprints() - Constructor for class picard.fingerprint.CrosscheckFingerprints
- CrosscheckMetric - Class in picard.fingerprint
-
A class to hold the result of crosschecking fingerprints.
- CrosscheckMetric() - Constructor for class picard.fingerprint.CrosscheckMetric
- CrosscheckMetric.DataType - Enum Class in picard.fingerprint
-
The data type.
- CrosscheckMetric.FingerprintResult - Enum Class in picard.fingerprint
- CrosscheckReadGroupFingerprints - Class in picard.fingerprint
-
Deprecated.6/6/2017 Use
CrosscheckFingerprints
instead. - CrosscheckReadGroupFingerprints() - Constructor for class picard.fingerprint.CrosscheckReadGroupFingerprints
-
Deprecated.
- CsvInputParser - Class in picard.util
- CsvInputParser(boolean, File...) - Constructor for class picard.util.CsvInputParser
-
Constructor
- CsvInputParser(boolean, InputStream...) - Constructor for class picard.util.CsvInputParser
-
Constructor
- CT - Enum constant in enum class picard.fingerprint.DiploidGenotype
- CtoA - Enum constant in enum class picard.analysis.artifacts.Transition
- CtoC - Enum constant in enum class picard.analysis.artifacts.Transition
- CtoG - Enum constant in enum class picard.analysis.artifacts.Transition
- CtoT - Enum constant in enum class picard.analysis.artifacts.Transition
- currentReadBaseStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies bases into the current (uppercase) base as it was read from the sequencer (i.e.
- currentTile - Variable in class picard.illumina.parser.MultiTileBclParser
-
The current tile number
- CUSTOM_AMPLICON_SET - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The name of the amplicon set used in this metrics collection run
- CUSTOM_AMPLICON_SET_NAME - Variable in class picard.analysis.directed.CollectTargetedPcrMetrics
- customCommandLineValidation() - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- customCommandLineValidation() - Method in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
- customCommandLineValidation() - Method in class picard.analysis.CollectAlignmentSummaryMetrics
- customCommandLineValidation() - Method in class picard.analysis.CollectBaseDistributionByCycle
- customCommandLineValidation() - Method in class picard.analysis.CollectGcBiasMetrics
- customCommandLineValidation() - Method in class picard.analysis.CollectInsertSizeMetrics
-
Put any custom command-line validation in an override of this method.
- customCommandLineValidation() - Method in class picard.analysis.CollectMultipleMetrics
- customCommandLineValidation() - Method in class picard.analysis.CollectOxoGMetrics
- customCommandLineValidation() - Method in class picard.analysis.CollectRnaSeqMetrics
- customCommandLineValidation() - Method in class picard.analysis.CollectRrbsMetrics
- customCommandLineValidation() - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
- customCommandLineValidation() - Method in class picard.analysis.CompareMetrics
- customCommandLineValidation() - Method in class picard.analysis.directed.CollectTargetedMetrics
- customCommandLineValidation() - Method in class picard.analysis.MeanQualityByCycle
- customCommandLineValidation() - Method in class picard.analysis.QualityScoreDistribution
- customCommandLineValidation() - Method in class picard.arrays.CollectArraysVariantCallingMetrics
- customCommandLineValidation() - Method in class picard.arrays.GtcToVcf
- customCommandLineValidation() - Method in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- customCommandLineValidation() - Method in class picard.cmdline.CommandLineProgram
-
Put any custom command-line validation in an override of this method.
- customCommandLineValidation() - Method in class picard.fingerprint.CheckFingerprint
- customCommandLineValidation() - Method in class picard.fingerprint.CrosscheckFingerprints
- customCommandLineValidation() - Method in class picard.fingerprint.CrosscheckReadGroupFingerprints
-
Deprecated.
- customCommandLineValidation() - Method in class picard.illumina.CheckIlluminaDirectory
- customCommandLineValidation() - Method in class picard.illumina.ExtractBarcodesProgram
-
Parses all barcodes from input files and validates all barcodes are the same length and unique
- customCommandLineValidation() - Method in class picard.illumina.ExtractIlluminaBarcodes
- customCommandLineValidation() - Method in class picard.illumina.IlluminaBasecallsToFastq
- customCommandLineValidation() - Method in class picard.illumina.IlluminaBasecallsToSam
-
Put any custom command-line validation in an override of this method.
- customCommandLineValidation() - Method in class picard.illumina.MarkIlluminaAdapters
- customCommandLineValidation() - Method in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
- customCommandLineValidation() - Method in class picard.sam.AddOrReplaceReadGroups
- customCommandLineValidation() - Method in class picard.sam.CreateSequenceDictionary
-
Use reference filename to create URI to go into header if URI was not passed on cmd line.
- customCommandLineValidation() - Method in class picard.sam.DownsampleSam
- customCommandLineValidation() - Method in class picard.sam.FastqToSam
- customCommandLineValidation() - Method in class picard.sam.FilterSamReads
- customCommandLineValidation() - Method in class picard.sam.markduplicates.EstimateLibraryComplexity
- customCommandLineValidation() - Method in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
- customCommandLineValidation() - Method in class picard.sam.MergeBamAlignment
-
Put any custom command-line validation in an override of this method.
- customCommandLineValidation() - Method in class picard.sam.MergeSamFiles
- customCommandLineValidation() - Method in class picard.sam.PositionBasedDownsampleSam
- customCommandLineValidation() - Method in class picard.sam.RevertSam
-
Enforce that output ordering is queryname when sanitization is turned on since it requires a queryname sort.
- customCommandLineValidation() - Method in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- customCommandLineValidation() - Method in class picard.sam.SamToFastq
-
Put any custom command-line validation in an override of this method.
- customCommandLineValidation() - Method in class picard.sam.SamToFastqWithTags
- customCommandLineValidation() - Method in class picard.sam.SplitSamByNumberOfReads
- customCommandLineValidation() - Method in class picard.sam.ValidateSamFile
- customCommandLineValidation() - Method in class picard.sam.ViewSam
- customCommandLineValidation() - Method in class picard.util.BaitDesigner
- customCommandLineValidation() - Method in class picard.util.IntervalListTools
- customCommandLineValidation() - Method in class picard.vcf.FixVcfHeader
- customCommandLineValidation() - Method in class picard.vcf.GenotypeConcordance
- customCommandLineValidation() - Method in class picard.vcf.MendelianViolations.FindMendelianViolations
-
Validates that the sex chromosomes don't overlap and parses the pseudo-autosomal regions into usable objects to ensure their parsability
- cycle - Variable in class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
- CYCLE - Variable in class picard.analysis.BaseDistributionByCycleMetrics
- CYCLE_SUBDIRECTORY_PATTERN - Static variable in class picard.illumina.parser.IlluminaFileUtil
D
- DATA_TYPE - Variable in class picard.fingerprint.CrosscheckMetric
-
The data type that was being compared.
- DATA_TYPES - Variable in class picard.illumina.CheckIlluminaDirectory
- DATA_TYPES_WITH_BARCODE - Static variable in class picard.illumina.BasecallsConverter
- DATA_TYPES_WITHOUT_BARCODE - Static variable in class picard.illumina.BasecallsConverter
- dataFile - Variable in class picard.illumina.parser.MultiTileFileUtil
- dateCreated - Variable in class picard.arrays.illumina.InfiniumEGTFile
- DB_SNP - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- DB_SNP - Variable in class picard.analysis.CollectMultipleMetrics
- DB_SNP - Variable in class picard.analysis.CollectOxoGMetrics
- DBSNP - Variable in class picard.arrays.CollectArraysVariantCallingMetrics
- DBSNP - Variable in class picard.vcf.CollectVariantCallingMetrics
- DBSNP_FILE - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- DBSNP_INS_DEL_RATIO - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The Insertion/Deletion ratio of the indel calls made at dbSNP sites
- DBSNP_TITV - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The Transition/Transversion ratio of the passing bi-allelic SNP calls made at dbSNP sites
- DbSnpBitSets() - Constructor for class picard.util.DbSnpBitSetUtil.DbSnpBitSets
- DbSnpBitSetUtil - Class in picard.util
-
Utility class to use with DbSnp files to determine is a locus is a dbSnp site.
- DbSnpBitSetUtil(File, SAMSequenceDictionary) - Constructor for class picard.util.DbSnpBitSetUtil
-
Constructor that creates a bit set with bits set to true for all variant types.
- DbSnpBitSetUtil(File, SAMSequenceDictionary, Collection<VariantType>) - Constructor for class picard.util.DbSnpBitSetUtil
-
Constructor that creates a bit set with bits set to true for the given variant types.
- DbSnpBitSetUtil(File, SAMSequenceDictionary, Collection<VariantType>, IntervalList) - Constructor for class picard.util.DbSnpBitSetUtil
-
Constructor that creates a bit set with bits set to true for the given variant types over the given regions.
- DbSnpBitSetUtil(File, SAMSequenceDictionary, Collection<VariantType>, IntervalList, Optional<Log>) - Constructor for class picard.util.DbSnpBitSetUtil
-
Constructor.
- DbSnpBitSetUtil(Path, SAMSequenceDictionary) - Constructor for class picard.util.DbSnpBitSetUtil
-
Constructor that creates a bit set with bits set to true for all variant types.
- DbSnpBitSetUtil(Path, SAMSequenceDictionary, Collection<VariantType>) - Constructor for class picard.util.DbSnpBitSetUtil
-
Constructor that creates a bit set with bits set to true for the given variant types.
- DbSnpBitSetUtil(Path, SAMSequenceDictionary, Collection<VariantType>, IntervalList) - Constructor for class picard.util.DbSnpBitSetUtil
-
Constructor that creates a bit set with bits set to true for the given variant types over the given regions.
- DbSnpBitSetUtil(Path, SAMSequenceDictionary, Collection<VariantType>, IntervalList, Optional<Log>) - Constructor for class picard.util.DbSnpBitSetUtil
-
Constructor.
- DbSnpBitSetUtil.DbSnpBitSets - Class in picard.util
-
Little tuple class to contain one bitset for SNPs and another for Indels.
- DEBUG_FREQUENCY - Variable in class picard.util.FifoBuffer
- decode() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
- decode() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodesCodec
- decode() - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
- deduceIdealSplitWeight(IntervalList, int) - Method in interface picard.util.IntervalList.IntervalListScatterer
-
A method that determines the ideal target "weight" of the output IntervalList.
- deduceIdealSplitWeight(IntervalList, int) - Method in class picard.util.IntervalList.IntervalListScattererByBaseCount
- deduceIdealSplitWeight(IntervalList, int) - Method in class picard.util.IntervalList.IntervalListScattererByIntervalCount
- deduceIdealSplitWeight(IntervalList, int) - Method in class picard.util.IntervalList.IntervalListScattererWithoutSubdivision
- deepCopy() - Method in class picard.fingerprint.CappedHaplotypeProbabilities
- deepCopy() - Method in class picard.fingerprint.HaplotypeProbabilities
- deepCopy() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
- deepCopy() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
- deepCopy() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
- deepCopy() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
- deepCopy() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
- DEFAULT_ADAPTER_LENGTH - Static variable in class picard.util.AdapterMarker
- DEFAULT_ADAPTER_SEQUENCE - Static variable in class picard.analysis.AdapterUtility
- DEFAULT_BIG_DUPLICATE_SET_SIZE - Static variable in class picard.sam.markduplicates.util.OpticalDuplicateFinder
- DEFAULT_EXPECTED_ORIENTATIONS - Static variable in class picard.analysis.ChimeraUtil
- DEFAULT_GENOTYPING_ERROR_RATE - Static variable in class picard.fingerprint.FingerprintChecker
- DEFAULT_INSERT_SIZE_LIMIT - Static variable in class picard.analysis.ChimeraUtil
- DEFAULT_MAX_DUPLICATE_SET_SIZE - Static variable in class picard.sam.markduplicates.util.OpticalDuplicateFinder
- DEFAULT_MINIMUM_BASE_QUALITY - Static variable in class picard.fingerprint.FingerprintChecker
- DEFAULT_MINIMUM_MAPPING_QUALITY - Static variable in class picard.fingerprint.FingerprintChecker
- DEFAULT_NUM_ADAPTERS_TO_KEEP - Static variable in class picard.util.AdapterMarker
- DEFAULT_OPTICAL_DUPLICATE_DISTANCE - Static variable in class picard.sam.markduplicates.util.OpticalDuplicateFinder
- DEFAULT_PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN - Static variable in class picard.util.AdapterMarker
- DEFAULT_QUEUE_SIZE - Static variable in class picard.util.AsyncIterator
- DEFAULT_READ_NAME_REGEX - Static variable in class picard.sam.util.ReadNameParser
-
The read name regular expression (regex) is used to extract three pieces of information from the read name: tile, x location, and y location.
- DEFAULT_TAGS_TO_DROP - Static variable in class picard.util.LiftoverUtils
- DEFAULT_TAGS_TO_REVERSE - Static variable in class picard.util.LiftoverUtils
-
Default list of attributes that need to be reversed or dropped from the INFO field when alleles have been swapped.
- defaultEndBiasBases - Static variable in class picard.analysis.directed.RnaSeqMetricsCollector
- DefaultSkipEmptyFiles - Static variable in class picard.illumina.parser.ParameterizedFileUtil
- DEFINITE_GENOTYPES - Variable in class picard.fingerprint.FingerprintMetrics
-
Number of haplotypes that had enough evidence to make a definite genotype call (genotype LOD > Threshold
- deletion - Enum constant in enum class picard.util.VariantType
- DELETIONS_Q - Variable in class picard.sam.SamErrorMetric.IndelErrorMetric
-
The (phred) rate of deletions.
- deletionsInReadStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratify by Deletions in the read cigars.
- DelimitedTextFileWithHeaderIterator - Class in picard.util
-
Iterate through a delimited text file in which columns are found by looking at a header line rather than by position.
- DelimitedTextFileWithHeaderIterator(BasicInputParser) - Constructor for class picard.util.DelimitedTextFileWithHeaderIterator
- DelimitedTextFileWithHeaderIterator.Row - Class in picard.util
- demultiplex - Variable in class picard.illumina.BasecallsConverter
- DENSITY_ID - Enum constant in enum class picard.illumina.parser.IlluminaMetricsCode
- DepthFilter - Class in picard.vcf.filter
-
Filters out a record if all variant samples have depth lower than the given value.
- DepthFilter(int) - Constructor for class picard.vcf.filter.DepthFilter
- DESCRIPTION - Variable in class picard.sam.FastqToSam
- descriptors - Variable in class picard.illumina.parser.ReadStructure
- DESIGN_NAME - Variable in class picard.util.BaitDesigner
- DESIGN_ON_TARGET_STRAND - Variable in class picard.util.BaitDesigner
- DESIGN_STRATEGY - Variable in class picard.util.BaitDesigner
- DETAIL_FILE_EXTENSION - Static variable in class picard.analysis.CollectRrbsMetrics
- DETAIL_OUTPUT - Variable in class picard.fingerprint.CheckFingerprint
- DETAILED_METRICS_FILE_EXTENSION - Static variable in class picard.vcf.GenotypeConcordance
- detailedMetricsExtension - Static variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
- DETAILS - Variable in class picard.metrics.GcBiasMetrics
- determineFormats(Set<IlluminaDataType>, IlluminaFileUtil) - Static method in class picard.illumina.parser.IlluminaDataProviderFactory
-
For all requestedDataTypes return a map of file format to set of provided data types that covers as many requestedDataTypes as possible and chooses the most preferred available formats possible
- determineQualityFormat(FastqReader, FastqReader, FastqQualityFormat) - Static method in class picard.sam.FastqToSam
-
Looks at fastq input(s) and attempts to determine the proper quality format Closes the reader(s) by side effect
- determineState(VariantContext, String, VariantContext, String, int, int, Boolean) - Static method in class picard.vcf.GenotypeConcordance
-
A method to determine the truth and call states for a pair of variant contexts representing truth and call.
- DEV_R - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- DEV_THETA - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- DEV_X - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- DEV_Y - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- DEVIATIONS - Variable in class picard.analysis.CollectInsertSizeMetrics
- devR - Variable in class picard.arrays.illumina.InfiniumEGTFile
- devTheta - Variable in class picard.arrays.illumina.InfiniumEGTFile
- DiagnosticsAndQCProgramGroup - Class in picard.cmdline.programgroups
-
Tools that collect sequencing quality-related and comparative metrics
- DiagnosticsAndQCProgramGroup() - Constructor for class picard.cmdline.programgroups.DiagnosticsAndQCProgramGroup
- DiploidGenotype - Enum Class in picard.fingerprint
-
A genotype produced by one of the concrete implementations of AbstractAlleleCaller.
- DiploidHaplotype - Enum Class in picard.fingerprint
-
Simple enum to represent the three possible combinations of major/major, major/minor and minor/minor haplotypes for a diploid individual.
- DISABLE_SORT - Variable in class picard.vcf.LiftoverVcf
- DISAGREES_WITH_REF_AND_MATE_ONLY_Q - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
-
The (phred) rate of bases that disagree with both the reference and their mate (which agree with each other)
- DISAGREES_WITH_REFERENCE_ONLY_Q - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
-
The (phred) rate of bases that disagree with the reference, but agree with their mate
- DISCORDANT - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
- DISCRIMINATORY_POWER - Variable in class picard.fingerprint.FingerprintMetrics
-
The difference in fingerprinting LOD between LOD_SELF_CHECK and the LOD score found when fingerprinting it against a random permutation of the probablity vectors (PLs) in each of the haplotypes.
- DiskBasedReadEndsForMarkDuplicatesMap - Class in picard.sam.markduplicates.util
-
Disk-based implementation of ReadEndsForMarkDuplicatesMap.
- DiskBasedReadEndsForMarkDuplicatesMap(int, ReadEndsForMarkDuplicatesCodec) - Constructor for class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
- distance(BarcodeEditDistanceQuery) - Method in enum class picard.illumina.DistanceMetric
- DISTANCE_MODE - Variable in class picard.illumina.ExtractBarcodesProgram
- distance0(SingleBarcodeDistanceMetric) - Method in enum class picard.illumina.DistanceMetric
- DistanceMetric - Enum Class in picard.illumina
- divide(double[], double[]) - Static method in class picard.util.MathUtil
-
Calculates the ratio of two arrays of the same length.
- divide(double, double) - Static method in class picard.util.MathUtil
-
Divide two Doubles but return 0.0 if the denominator is 0
- DO_NOT_ALLOW_CALLS_ON_ZEROED_OUT_ASSAYS - Variable in class picard.arrays.GtcToVcf
- DO_NOT_CHANGE - Enum constant in enum class picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
- DO_NOT_CHANGE_INVALID - Enum constant in enum class picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
- DOC_CAT_BASE_CALLING - Static variable in class picard.util.help.HelpConstants
-
Definition of the group names / descriptions for documentation/help purposes.
- DOC_CAT_BASE_CALLING_SUMMARY - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_DIAGNOSTICS_AND_QC - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_DIAGNOSTICS_AND_QC_SUMMARY - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_GENOTYPING_ARRAYS_MANIPULATION - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_GENOTYPING_ARRAYS_MANIPULATION_SUMMARY - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_INTERVALS_MANIPULATION - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_INTERVALS_MANIPULATION_SUMMARY - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_METRICS - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_METRICS_SUMMARY - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_OTHER - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_OTHER_SUMMARY - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_READ_DATA_MANIPULATION - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_READ_DATA_MANIPULATION_SUMMARY - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_REFERENCE - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_REFERENCE_SUMMARY - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_TEST - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_TEST_SUMMARY - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_VARIANT_EVALUATION - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_VARIANT_EVALUATION_SUMMARY - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_VARIANT_FILTERING - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_VARIANT_FILTERING_SUMMARY - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_VARIANT_MANIPULATION - Static variable in class picard.util.help.HelpConstants
- DOC_CAT_VARIANT_MANIPULATION_SUMMARY - Static variable in class picard.util.help.HelpConstants
- DOC_SUPERCAT_EXCLUDE - Static variable in class picard.util.help.HelpConstants
- DOC_SUPERCAT_TOOLS - Static variable in class picard.util.help.HelpConstants
-
List of "supercategory" values used for doc purposes.
- DOC_SUPERCAT_UTILITIES - Static variable in class picard.util.help.HelpConstants
- DONT_MERGE_ABUTTING - Variable in class picard.util.IntervalListTools
- DontTag - Enum constant in enum class picard.sam.markduplicates.MarkDuplicates.DuplicateTaggingPolicy
- doPaired(FastqReader, FastqReader, SAMFileWriter) - Method in class picard.sam.FastqToSam
-
More complicated method that takes two fastq files and builds pairing information in the SAM.
- doUnpaired(FastqReader, SAMFileWriter) - Method in class picard.sam.FastqToSam
-
Creates a simple SAM file from a single fastq file.
- DownsampleSam - Class in picard.sam
-
Summary
- DownsampleSam() - Constructor for class picard.sam.DownsampleSam
- doWork() - Method in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
- doWork() - Method in class picard.analysis.CollectJumpingLibraryMetrics
-
Calculates the detailed statistics about the jumping library and then generates the results.
- doWork() - Method in class picard.analysis.CollectMultipleMetrics
- doWork() - Method in class picard.analysis.CollectOxoGMetrics
- doWork() - Method in class picard.analysis.CollectRrbsMetrics
- doWork() - Method in class picard.analysis.CollectWgsMetrics
- doWork() - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
- doWork() - Method in class picard.analysis.CompareMetrics
- doWork() - Method in class picard.analysis.directed.CollectTargetedMetrics
-
Asserts that files are readable and writable and then fires off an HsMetricsCalculator instance to do the real work.
- doWork() - Method in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- doWork() - Method in class picard.analysis.SinglePassSamProgram
-
Final implementation of doWork() that checks and loads the input and optionally reference sequence files and the runs the sublcass through the setup() acceptRead() and finish() steps.
- doWork() - Method in class picard.annotation.SortGff
- doWork() - Method in class picard.arrays.CollectArraysVariantCallingMetrics
- doWork() - Method in class picard.arrays.CombineGenotypingArrayVcfs
- doWork() - Method in class picard.arrays.CreateBafRegressMetricsFile
- doWork() - Method in class picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile
- doWork() - Method in class picard.arrays.GtcToVcf
- doWork() - Method in class picard.arrays.illumina.BpmToNormalizationManifestCsv
- doWork() - Method in class picard.arrays.illumina.CompareGtcFiles
- doWork() - Method in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- doWork() - Method in class picard.arrays.MergePedIntoVcf
- doWork() - Method in class picard.arrays.VcfToAdpc
- doWork() - Method in class picard.cmdline.CommandLineProgram
-
Do the work after command line has been parsed.
- doWork() - Method in class picard.fingerprint.CalculateFingerprintMetrics
- doWork() - Method in class picard.fingerprint.CheckFingerprint
- doWork() - Method in class picard.fingerprint.ClusterCrosscheckMetrics
- doWork() - Method in class picard.fingerprint.ConvertHaplotypeDatabaseToVcf
- doWork() - Method in class picard.fingerprint.CrosscheckFingerprints
- doWork() - Method in class picard.fingerprint.CrosscheckReadGroupFingerprints
-
Deprecated.
- doWork() - Method in class picard.fingerprint.ExtractFingerprint
- doWork() - Method in class picard.fingerprint.IdentifyContaminant
- doWork() - Method in class picard.fingerprint.LiftOverHaplotypeMap
- doWork() - Method in class picard.illumina.CheckIlluminaDirectory
- doWork() - Method in class picard.illumina.CollectIlluminaBasecallingMetrics
- doWork() - Method in class picard.illumina.CollectIlluminaLaneMetrics
- doWork() - Method in class picard.illumina.ExtractIlluminaBarcodes
- doWork() - Method in class picard.illumina.IlluminaBasecallsToFastq
- doWork() - Method in class picard.illumina.IlluminaBasecallsToSam
- doWork() - Method in class picard.illumina.MarkIlluminaAdapters
- doWork() - Method in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
- doWork() - Method in class picard.reference.ExtractSequences
- doWork() - Method in class picard.reference.NonNFastaSize
- doWork() - Method in class picard.reference.NormalizeFasta
- doWork() - Method in class picard.sam.AddCommentsToBam
- doWork() - Method in class picard.sam.AddOATag
- doWork() - Method in class picard.sam.AddOrReplaceReadGroups
- doWork() - Method in class picard.sam.BamIndexStats
-
Main method for the program.
- doWork() - Method in class picard.sam.BuildBamIndex
-
Main method for the program.
- doWork() - Method in class picard.sam.CalculateReadGroupChecksum
- doWork() - Method in class picard.sam.CheckTerminatorBlock
- doWork() - Method in class picard.sam.CleanSam
-
Do the work after command line has been parsed.
- doWork() - Method in class picard.sam.CompareSAMs
-
Do the work after command line has been parsed.
- doWork() - Method in class picard.sam.CreateSequenceDictionary
-
Do the work after command line has been parsed.
- doWork() - Method in class picard.sam.DownsampleSam
- doWork() - Method in class picard.sam.FastqToSam
- doWork() - Method in class picard.sam.FilterSamReads
- doWork() - Method in class picard.sam.FixMateInformation
- doWork() - Method in class picard.sam.GatherBamFiles
- doWork() - Method in class picard.sam.markduplicates.CheckDuplicateMarking
- doWork() - Method in class picard.sam.markduplicates.EstimateLibraryComplexity
-
Method that does most of the work.
- doWork() - Method in class picard.sam.markduplicates.MarkDuplicates
-
Main work method.
- doWork() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigar
-
Main work method.
- doWork() - Method in class picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar
-
Main work method.
- doWork() - Method in class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
- doWork() - Method in class picard.sam.MergeBamAlignment
- doWork() - Method in class picard.sam.MergeSamFiles
-
Combines multiple SAM/BAM/CRAM files into one.
- doWork() - Method in class picard.sam.PositionBasedDownsampleSam
- doWork() - Method in class picard.sam.ReorderSam
- doWork() - Method in class picard.sam.ReplaceSamHeader
-
Do the work after command line has been parsed.
- doWork() - Method in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
- doWork() - Method in class picard.sam.RevertSam
- doWork() - Method in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- doWork() - Method in class picard.sam.SamFormatConverter
- doWork() - Method in class picard.sam.SamToFastq
- doWork() - Method in class picard.sam.SetNmMdAndUqTags
- doWork() - Method in class picard.sam.SortSam
- doWork() - Method in class picard.sam.SplitSamByLibrary
- doWork() - Method in class picard.sam.SplitSamByNumberOfReads
- doWork() - Method in class picard.sam.ValidateSamFile
-
Do the work after command line has been parsed.
- doWork() - Method in class picard.sam.ViewSam
- doWork() - Method in class picard.util.AccumulateQualityYieldMetrics
- doWork() - Method in class picard.util.BaitDesigner
- doWork() - Method in class picard.util.BedToIntervalList
- doWork() - Method in class picard.util.FifoBuffer
- doWork() - Method in class picard.util.IntervalListToBed
- doWork() - Method in class picard.util.IntervalListTools
- doWork() - Method in class picard.util.LiftOverIntervalList
-
Do the work after command line has been parsed.
- doWork() - Method in class picard.util.ScatterIntervalsByNs
- doWork() - Method in class picard.vcf.AccumulateVariantCallingMetrics
- doWork() - Method in class picard.vcf.CollectVariantCallingMetrics
- doWork() - Method in class picard.vcf.filter.FilterVcf
- doWork() - Method in class picard.vcf.FixVcfHeader
- doWork() - Method in class picard.vcf.GatherVcfs
- doWork() - Method in class picard.vcf.GenotypeConcordance
- doWork() - Method in class picard.vcf.LiftoverVcf
- doWork() - Method in class picard.vcf.MakeSitesOnlyVcf
- doWork() - Method in class picard.vcf.MakeVcfSampleNameMap
- doWork() - Method in class picard.vcf.MendelianViolations.FindMendelianViolations
- doWork() - Method in class picard.vcf.MergeVcfs
- doWork() - Method in class picard.vcf.RenameSampleInVcf
- doWork() - Method in class picard.vcf.SortVcf
- doWork() - Method in class picard.vcf.SplitVcfs
- doWork() - Method in class picard.vcf.UpdateVcfSequenceDictionary
- doWork() - Method in class picard.vcf.VcfFormatConverter
- doWork() - Method in class picard.vcf.VcfToIntervalList
- draw() - Method in class picard.analysis.TheoreticalSensitivity.RouletteWheel
- DROP_MISSING_CONTIGS - Variable in class picard.util.BedToIntervalList
- DUAL_INDEXED - Enum constant in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- DUPE - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
The record passes validation but is a duplicate (another assay at the same locus with the same alleles)
- DUPE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- DUPLEX_CONSENSUS - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
-
Consensus read which has two or more observations in both directions.
- DUPLEX_SINGLETON - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
-
Read which has two observations, one from each direction.
- DUPLEX_UMI - Variable in class picard.sam.markduplicates.MarkDuplicates
- DUPLICATE_MARKINGS_DIFFER - Variable in class picard.sam.SamComparisonMetric
-
The number of primary records for which duplicate markings are different.
- DUPLICATE_SCORING_STRATEGY - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- DUPLICATE_SET_INDEX_TAG - Static variable in class picard.sam.markduplicates.MarkDuplicates
-
The attribute in the SAM/BAM file used to store which read was selected as representative out of a duplicate set
- DUPLICATE_SET_SIZE_TAG - Static variable in class picard.sam.markduplicates.MarkDuplicates
-
The attribute in the SAM/BAM file used to store the size of a duplicate set
- DUPLICATE_SETS_IGNORING_UMI - Variable in class picard.sam.markduplicates.UmiMetrics
-
Number of duplicate sets found before taking UMIs into account
- DUPLICATE_SETS_WITH_UMI - Variable in class picard.sam.markduplicates.UmiMetrics
-
Number of duplicate sets found after taking UMIs into account
- DUPLICATE_TYPE_LIBRARY - Static variable in class picard.sam.markduplicates.MarkDuplicates
-
The duplicate type tag value for duplicate type: library.
- DUPLICATE_TYPE_SEQUENCING - Static variable in class picard.sam.markduplicates.MarkDuplicates
-
The duplicate type tag value for duplicate type: sequencing (optical & pad-hopping, or "co-localized").
- DUPLICATE_TYPE_TAG - Static variable in class picard.sam.markduplicates.MarkDuplicates
-
The optional attribute in SAM/BAM/CRAM files used to store the duplicate type.
- duplicateIndexes - Variable in class picard.sam.markduplicates.MarkDuplicates
- duplicateSetSize - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
- DuplicationMetrics - Class in picard.sam
-
Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords.
- DuplicationMetrics() - Constructor for class picard.sam.DuplicationMetrics
- DuplicationMetricsFactory - Class in picard.sam
-
Factory class that creates either regular or flow-based duplication metrics.
- DuplicationMetricsFactory() - Constructor for class picard.sam.DuplicationMetricsFactory
- dynamic - Enum constant in enum class picard.sam.RevertSam.FileType
E
- EarliestFragmentPrimaryAlignmentSelectionStrategy - Class in picard.sam
-
When it is necessary to pick a primary alignment from a group of alignments for a read, pick the one that maps the earliest base in the read.
- EarliestFragmentPrimaryAlignmentSelectionStrategy() - Constructor for class picard.sam.EarliestFragmentPrimaryAlignmentSelectionStrategy
- EmpiricalPhasingMetricsOutReader - Class in picard.illumina.parser.readers
- EmpiricalPhasingMetricsOutReader(File) - Constructor for class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader
- EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics - Class in picard.illumina.parser.readers
- EMPTY - Enum constant in enum class picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
- EMPTY - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.ContingencyState
- EMPTY - Static variable in class picard.vcf.GenotypeConcordanceScheme
- EMPTY_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
-
The empty (no contingency info) count across all variants
- EmptyOutputArgumentCollection - Class in picard.cmdline.argumentcollections
- EmptyOutputArgumentCollection() - Constructor for class picard.cmdline.argumentcollections.EmptyOutputArgumentCollection
- encode(ReadEndsForMarkDuplicates) - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
- encode(ReadEndsForMarkDuplicates) - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodesCodec
- encode(RepresentativeReadIndexer) - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
- encodeDictionary(BufferedWriter, Iterator<SAMSequenceRecord>) - Static method in class picard.util.SequenceDictionaryUtils
-
Encodes a sequence dictionary
- encodeMappingInformation(SAMRecord) - Static method in class picard.sam.AbstractAlignmentMerger
-
Encodes mapping information from a record into a string according to the format sepcified in the Sam-Spec under the SA tag.
- end - Variable in class picard.annotation.Gene.Transcript.Exon
- end - Variable in class picard.illumina.parser.Range
- end() - Method in class picard.annotation.Gene.Transcript
- END_BIAS_BASES - Variable in class picard.analysis.CollectRnaSeqMetrics
- ENFORCE_SAME_SAMPLES - Variable in class picard.vcf.FixVcfHeader
- equals(Object) - Method in class picard.annotation.Gene
- equals(Object) - Method in class picard.annotation.Gene.Transcript
- equals(Object) - Method in class picard.fingerprint.FingerprintIdDetails
- equals(Object) - Method in class picard.fingerprint.HaplotypeBlock
- equals(Object) - Method in class picard.fingerprint.Snp
- equals(Object) - Method in class picard.illumina.parser.Range
- equals(Object) - Method in class picard.illumina.parser.ReadDescriptor
- equals(Object) - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
- equals(Object) - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
- equals(Object) - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
- equals(Object) - Method in class picard.illumina.parser.ReadStructure
- equals(Object) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
- equals(Object) - Method in class picard.sam.util.Pair
-
Calculate whether this pair object is equal to another object.
- equals(Object) - Method in class picard.sam.util.PrimaryAlignmentKey
- equals(Object) - Method in class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
- ERROR_BAR_WIDTH - Variable in class picard.analysis.GcBiasDetailMetrics
-
The radius of error bars in this bin based on the number of observations made.
- ERROR_BASES - Variable in class picard.sam.SamErrorMetric.BaseErrorMetric
-
The number of bases that disagree with the reference
- ERROR_METRICS - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- ERROR_RATE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The bait bias error rate, calculated as max(1e-10, FWD_ERROR_RATE - REV_ERROR_RATE).
- ERROR_RATE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The estimated error rate due to this artifact.
- ERROR_SUMMARY_EXT - Static variable in class picard.analysis.artifacts.SequencingArtifactMetrics
- ERROR_VALUE - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- ErrorMetric - Class in picard.sam.SamErrorMetric
-
Created by farjoun on 6/26/18.
- ErrorMetric() - Constructor for class picard.sam.SamErrorMetric.ErrorMetric
- ErrorMetric(String, long) - Constructor for class picard.sam.SamErrorMetric.ErrorMetric
- ErrorSummaryMetrics - Class in picard.analysis.artifacts
-
Summary metrics produced by
CollectSequencingArtifactMetrics
as a roll up of the context-specific error rates, to provide global error rates per type of base substitution. - ErrorSummaryMetrics() - Constructor for class picard.analysis.artifacts.ErrorSummaryMetrics
- escapePeriods(String) - Static method in class picard.illumina.parser.ParameterizedFileUtil
-
Escape the period character.
- ESTIMATE - Variable in class picard.arrays.BafRegressMetrics
-
The estimate of contamination from the model (on the 0.0-1.0 scale)
- ESTIMATED_LIBRARY_SIZE - Variable in class picard.sam.DuplicationMetrics
-
The estimated number of unique molecules in the library based on PE duplication.
- EstimateLibraryComplexity - Class in picard.sam.markduplicates
-
Attempts to estimate library complexity from sequence alone.
- EstimateLibraryComplexity() - Constructor for class picard.sam.markduplicates.EstimateLibraryComplexity
- estimateLibrarySize(long, long) - Static method in class picard.sam.DuplicationMetrics
-
Estimates the size of a library based on the number of paired end molecules observed and the number of unique pairs observed.
- estimateRoi(long, double, long, long) - Static method in class picard.sam.DuplicationMetrics
-
Estimates the ROI (return on investment) that one would see if a library was sequenced to x higher coverage than the observed coverage.
- exception - Variable in class picard.util.ThreadPoolExecutorWithExceptions
- excludeAligned - Enum constant in enum class picard.sam.FilterSamReads.Filter
- excludeReadList - Enum constant in enum class picard.sam.FilterSamReads.Filter
- excludeTagValues - Enum constant in enum class picard.sam.FilterSamReads.Filter
- excludingNonOverlaps(VcfFileSegmentGenerator, OverlapDetector<T>) - Static method in class picard.vcf.processor.VcfFileSegmentGenerator
-
Deprecated.Returns a decorated
VcfFileSegmentGenerator
that filters outVcfFileSegment
s that have no overlap with the providedOverlapDetector
. - excludingNonOverlaps(VcfPathSegmentGenerator, OverlapDetector<T>) - Static method in class picard.vcf.processor.VcfPathSegmentGenerator
-
Returns a decorated
VcfPathSegmentGenerator
that filters outVcfPathSegment
s that have no overlap with the providedOverlapDetector
. - executeFromClasspath(String, String...) - Static method in class picard.util.RExecutor
-
Executes the given R script that is stored in a file on the classpath.
- executeFromFile(File, String...) - Static method in class picard.util.RExecutor
-
Executes the given R script that is stored in a file by a call to Rscript.
- EXIT_CODE_WHEN_CONTIG_NOT_IN_REFERENCE - Static variable in class picard.vcf.LiftoverVcf
- EXIT_CODE_WHEN_EXPECTED_SAMPLE_NOT_FOUND - Variable in class picard.fingerprint.CheckFingerprint
- EXIT_CODE_WHEN_MISMATCH - Variable in class picard.fingerprint.CrosscheckFingerprints
- EXIT_CODE_WHEN_NO_VALID_CHECKS - Variable in class picard.fingerprint.CheckFingerprint
- EXIT_CODE_WHEN_NO_VALID_CHECKS - Variable in class picard.fingerprint.CrosscheckFingerprints
- Exon(int, int) - Constructor for class picard.annotation.Gene.Transcript.Exon
- EXON_COUNT - Enum constant in enum class picard.annotation.RefFlatReader.RefFlatColumns
- EXON_ENDS - Enum constant in enum class picard.annotation.RefFlatReader.RefFlatColumns
- EXON_STARTS - Enum constant in enum class picard.annotation.RefFlatReader.RefFlatColumns
- exons - Variable in class picard.annotation.Gene.Transcript
- EXP_CLUSTERS_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- EXPECT_ALL_GROUPS_TO_MATCH - Variable in class picard.fingerprint.CrosscheckFingerprints
- EXPECT_ALL_READ_GROUPS_TO_MATCH - Variable in class picard.fingerprint.CrosscheckReadGroupFingerprints
-
Deprecated.
- EXPECTED_GENDER - Variable in class picard.arrays.GtcToVcf
- EXPECTED_GENDER - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- EXPECTED_GENOTYPE - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The expected genotype of the sample at the SNP locus.
- EXPECTED_HET - Variable in class picard.fingerprint.FingerprintMetrics
-
Expected number of heterozygous calls
- EXPECTED_HOM_ALLELE1 - Variable in class picard.fingerprint.FingerprintMetrics
-
Expected number of major allele homozygous calls
- EXPECTED_HOM_ALLELE2 - Variable in class picard.fingerprint.FingerprintMetrics
-
Expected number of major allele homozygous calls
- EXPECTED_INSERT_SIZE_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- EXPECTED_MATCH - Enum constant in enum class picard.fingerprint.CrosscheckMetric.FingerprintResult
- EXPECTED_MISMATCH - Enum constant in enum class picard.fingerprint.CrosscheckMetric.FingerprintResult
- EXPECTED_ORIENTATIONS - Variable in class picard.sam.MergeBamAlignment
- EXPECTED_PAIR_ORIENTATIONS - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
- EXPECTED_SAMPLE_ALIAS - Variable in class picard.fingerprint.CheckFingerprint
- EXPECTED_VERSION - Static variable in class picard.illumina.parser.readers.FilterFileReader
-
Expected Version
- EXTENDED_ILLUMINA_MANIFEST - Variable in class picard.arrays.GtcToVcf
- EXTENDED_ILLUMINA_MANIFEST_FILE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- EXTENDED_ILLUMINA_MANIFEST_VERSION - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- EXTENDED_MANIFEST_VERSION - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The version of the Extended Illumina Manifest used for calling this sample
- extendedIterator() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifest
- extension - Variable in class picard.illumina.parser.ParameterizedFileUtil
-
The file extension for this class, file extension does not have the standard meaning in this instance.
- EXTENSION - Static variable in class picard.arrays.illumina.InfiniumEGTFile
- EXTRA_ARGUMENT - Variable in class picard.analysis.CollectMultipleMetrics
- EXTRACT_CONTAMINATED - Variable in class picard.fingerprint.IdentifyContaminant
- EXTRACT_CONTAMINATION - Variable in class picard.fingerprint.ExtractFingerprint
- ExtractBarcodesProgram - Class in picard.illumina
- ExtractBarcodesProgram() - Constructor for class picard.illumina.ExtractBarcodesProgram
- ExtractFingerprint - Class in picard.fingerprint
-
Program to create a fingerprint for the contaminating sample when the level of contamination is both known and uniform in the genome.
- ExtractFingerprint() - Constructor for class picard.fingerprint.ExtractFingerprint
- ExtractIlluminaBarcodes - Class in picard.illumina
-
Determine the barcode for each read in an Illumina lane.
- ExtractIlluminaBarcodes() - Constructor for class picard.illumina.ExtractIlluminaBarcodes
- ExtractIlluminaBarcodes.PerTileBarcodeExtractor - Class in picard.illumina
-
Extracts barcodes and accumulates metrics for an entire tile.
- ExtractSequences - Class in picard.reference
-
Simple command line program that allows sub-sequences represented by an interval list to be extracted from a reference sequence file.
- ExtractSequences() - Constructor for class picard.reference.ExtractSequences
F
- F - Static variable in class picard.sam.markduplicates.util.ReadEnds
- F1F2 - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
- F1R2 - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
- F2R1 - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
- FAIL_REF - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- FAKE_FILES - Variable in class picard.illumina.CheckIlluminaDirectory
- fakeBciFile(File, List<Integer>) - Method in class picard.illumina.parser.fakers.BciFileFaker
- fakeBciFile(File, TileIndex) - Method in class picard.illumina.parser.fakers.BclIndexFaker
- fakeFile(File, int, int, String) - Method in class picard.illumina.parser.fakers.FileFaker
- fakeFile(File, Integer) - Method in class picard.illumina.parser.fakers.FileFaker
- fakeFile(File, List<Integer>, int, String) - Method in class picard.illumina.parser.fakers.FileFaker
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.BarcodeFileFaker
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.BciFileFaker
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.BclFileFaker
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.BclIndexFaker
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.ClocsFileFaker
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.FileFaker
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.FilterFileFaker
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.LocsFileFaker
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.MultiTileBclFileFaker
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.MultiTileLocsFileFaker
- fakeFile(ByteBuffer) - Method in class picard.illumina.parser.fakers.PosFileFaker
- fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.MultiTileBclFileUtil
- fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.MultiTileFileUtil
- fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.ParameterizedFileUtil
-
Given the expected tiles/expected cycles for this file type create a set of fake files such that the verification criteria are met.
- fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.PerTileFileUtil
- fakeFiles(List<Integer>, int[], IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
- fakeMultiTileBclFile(File, TileIndex) - Method in class picard.illumina.parser.fakers.MultiTileBclFileFaker
- faker - Variable in class picard.illumina.parser.ParameterizedFileUtil
- FAMILY_ID - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The family ID assigned to the trio for which these metrics are calculated.
- FASTQ - Variable in class picard.sam.FastqToSam
- FASTQ - Variable in class picard.sam.SamToFastq
- FASTQ2 - Variable in class picard.sam.FastqToSam
- FastqToSam - Class in picard.sam
-
Converts a FASTQ file to an unaligned BAM or SAM file.
- FastqToSam() - Constructor for class picard.sam.FastqToSam
- FastWgsMetricsCollector - Class in picard.analysis
-
Class represents fast algorithm for collecting data from
AbstractLocusInfo
with a list of alignedEdgingRecordAndOffset
objects. - FastWgsMetricsCollector(CollectWgsMetrics, int, IntervalList) - Constructor for class picard.analysis.FastWgsMetricsCollector
-
Creates a collector and initializes the inner data structures
- FATHER - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The ID of the father within the trio.
- Female - Enum constant in enum class picard.pedigree.Sex
- FEMALE_CHROMS - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
- FF - Static variable in class picard.sam.markduplicates.util.ReadEnds
- FifoBuffer - Class in picard.util
-
Summary
- FifoBuffer() - Constructor for class picard.util.FifoBuffer
-
Constructor that defaults to QUIET since Fifos don't do anything beyond buffering having their start/end information logged is often undesirable.
- FifoBuffer(InputStream, PrintStream) - Constructor for class picard.util.FifoBuffer
-
Constructor that defaults to QUIET since Fifos don't do anything beyond buffering having their start/end information logged is often undesirable.
- FILE - Enum constant in enum class picard.fingerprint.CrosscheckMetric.DataType
- FILE_EXTENSION - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- FILE_EXTENSION - Variable in class picard.analysis.CollectMultipleMetrics
- FILE_EXTENSION - Static variable in class picard.arrays.CreateBafRegressMetricsFile
- FILE_EXTENSION - Static variable in class picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile
- FILE_EXTENSION - Variable in class picard.illumina.CollectIlluminaLaneMetrics
- FILE_NAME_PATTERN - Static variable in class picard.illumina.parser.BaseIlluminaDataProvider
- FileFaker - Class in picard.illumina.parser.fakers
- FileFaker() - Constructor for class picard.illumina.parser.fakers.FileFaker
- filesAvailable() - Method in class picard.illumina.parser.MultiTileBclFileUtil
- filesAvailable() - Method in class picard.illumina.parser.MultiTileFileUtil
- filesAvailable() - Method in class picard.illumina.parser.ParameterizedFileUtil
-
Determine whether or not files are available
- filesAvailable() - Method in class picard.illumina.parser.PerTileFileUtil
- filesAvailable() - Method in class picard.illumina.parser.PerTileOrPerRunFileUtil
- filesAvailable() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
- fileToTile(String) - Static method in class picard.illumina.parser.BaseIlluminaDataProvider
- fileToTile(String) - Method in class picard.illumina.parser.ParameterizedFileUtil
-
Returns only lane and tile information as PerTileFt's do not have End information.
- FILL_POOLS - Variable in class picard.util.BaitDesigner
- filter(VariantContext) - Method in class picard.vcf.filter.AlleleBalanceFilter
- filter(VariantContext) - Method in class picard.vcf.filter.FisherStrandFilter
- filter(VariantContext) - Method in class picard.vcf.filter.QdFilter
- filter(VariantContext) - Method in interface picard.vcf.filter.VariantFilter
-
Check to see if the VariantContext should have a filter applied to it.
- filter(VariantContext, Genotype) - Method in class picard.vcf.filter.DepthFilter
- filter(VariantContext, Genotype) - Method in interface picard.vcf.filter.GenotypeFilter
-
Test whether or not the genotype should be filtered out.
- filter(VariantContext, Genotype) - Method in class picard.vcf.filter.GenotypeQualityFilter
- Filter - Enum constant in enum class picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
- FILTER - Variable in class picard.sam.FilterSamReads
- FILTER_CANNOT_LIFTOVER_REV_COMP - Static variable in class picard.vcf.LiftoverVcf
-
Filter name to use when a target cannot be lifted over.
- FILTER_INDEL_STRADDLES_TWO_INTERVALS - Static variable in class picard.vcf.LiftoverVcf
-
Filter name to use when an indel cannot be lifted over since it straddles two intervals in a chain which means that it is unclear what are the right alleles to be used.
- FILTER_MISMATCHING_REF_ALLELE - Static variable in class picard.vcf.LiftoverVcf
-
Filter name to use when a target is lifted over, but the reference allele doesn't match the new reference.
- FILTER_NAME - Static variable in class picard.vcf.filter.QdFilter
- FILTER_NO_TARGET - Static variable in class picard.vcf.LiftoverVcf
-
Filter name to use when a target cannot be lifted over.
- FILTER_UNPAIRED_READS - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- FilterApplyingVariantIterator - Class in picard.vcf.filter
-
Iterator that dynamically applies filter strings to VariantContext records supplied by an underlying iterator.
- FilterApplyingVariantIterator(Iterator<VariantContext>, Collection<VariantFilter>, Collection<GenotypeFilter>) - Constructor for class picard.vcf.filter.FilterApplyingVariantIterator
-
Constructs an iterator from an underlying iterator and the provided (possibly empty) collections of variant and genotype filters.
- FILTERED_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of indels that are filtered
- FILTERED_SNPS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of SNPs that are filtered
- FilterFileFaker - Class in picard.illumina.parser.fakers
-
Created by jcarey on 3/13/14.
- FilterFileFaker() - Constructor for class picard.illumina.parser.fakers.FilterFileFaker
- FilterFileReader - Class in picard.illumina.parser.readers
-
Illumina uses an algorithm described in "Theory of RTA" that determines whether or not a cluster passes filter("PF") or not.
- FilterFileReader(File) - Constructor for class picard.illumina.parser.readers.FilterFileReader
- filterOut(SAMRecord) - Method in class picard.filter.CountingFilter
- filterOut(SAMRecord, SAMRecord) - Method in class picard.filter.CountingFilter
- FilterSamReads - Class in picard.sam
-
Summary
- FilterSamReads() - Constructor for class picard.sam.FilterSamReads
- FilterSamReads.Filter - Enum Class in picard.sam
- filterSuspectSites() - Method in class picard.fingerprint.Fingerprint
-
Attempts to filter out haplotypes that may have suspect genotyping by removing haplotypes that reach a minimum confidence score yet have a significant fraction of observations from a third or fourth allele.
- FilterVcf - Class in picard.vcf.filter
-
Applies a set of hard filters to Variants and to Genotypes within a VCF.
- FilterVcf() - Constructor for class picard.vcf.filter.FilterVcf
-
Constructor to default to having index creation on.
- finalizeAndWriteMetrics(LibraryIdGenerator, MetricsFile<DuplicationMetrics, Double>, File) - Static method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
-
Writes the metrics given by the libraryIdGenerator to the outputFile.
- finalizeMetrics(Map<String, BarcodeMetric>, BarcodeMetric) - Static method in class picard.illumina.ExtractBarcodesProgram
- findAdapterPairAndIndexForSingleRead(byte[], int) - Method in class picard.util.AdapterMarker
-
Return the adapter to be trimmed from a read represented as an array of bytes[]
- findAdapterPairAndIndexForSingleRead(byte[], int, double, int) - Method in class picard.util.AdapterMarker
-
Return the adapter to be trimmed from a read represented as an array of bytes[]
- findAdapterPairAndIndexForSingleRead(byte[], int, double, int, AdapterPair...) - Static method in class picard.util.ClippingUtility
-
Return the adapter to be trimmed from a read represented as an array of bytes[]
- findByKey(int) - Static method in enum class picard.illumina.parser.readers.TileMetricsOutReader.TileMetricsVersion
- findIndexOfClipSequence(byte[], byte[], int, double) - Static method in class picard.util.ClippingUtility
-
Finds the first index of the adapterSequence sequence in the read sequence requiring at least minMatch bases of pairwise alignment with a maximum number of errors dictated by maxErrorRate.
- FindMendelianViolations - Class in picard.vcf.MendelianViolations
-
Summary
- FindMendelianViolations() - Constructor for class picard.vcf.MendelianViolations.FindMendelianViolations
- findOpticalDuplicates(List<? extends PhysicalLocation>, PhysicalLocation) - Method in class picard.sam.markduplicates.util.OpticalDuplicateFinder
-
Finds which reads within the list of duplicates that are likely to be optical/co-localized duplicates of one another.
- findPreferredFormat(IlluminaDataType, IlluminaFileUtil) - Static method in class picard.illumina.parser.IlluminaDataProviderFactory
-
Given a data type find the most preferred file format even if files are not available
- findTile(int) - Method in class picard.illumina.parser.TileIndex
- findTileMetricsFiles(File, int) - Static method in class picard.illumina.parser.TileMetricsUtil
-
Finds all of the tile metrics files for a given run directory and cycle count.
- findUnmatchedTypes(Set<IlluminaDataType>, Map<IlluminaFileUtil.SupportedIlluminaFormat, Set<IlluminaDataType>>) - Static method in class picard.illumina.parser.IlluminaDataProviderFactory
-
Given a set of formats to data types they provide, find any requested data types that do not have a format associated with them and return them
- Fingerprint - Class in picard.fingerprint
-
class to represent a genetic fingerprint as a set of HaplotypeProbabilities objects that give the relative probabilities of each of the possible haplotypes at a locus.
- Fingerprint(String, Path, String) - Constructor for class picard.fingerprint.Fingerprint
- FINGERPRINT_DETAIL_FILE_SUFFIX - Static variable in class picard.fingerprint.CheckFingerprint
- FINGERPRINT_GENDER - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- FINGERPRINT_GENOTYPES_VCF_FILE - Variable in class picard.arrays.GtcToVcf
- FINGERPRINT_SUMMARY_FILE_SUFFIX - Static variable in class picard.fingerprint.CheckFingerprint
- FingerprintChecker - Class in picard.fingerprint
-
Major class that coordinates the activities involved in comparing genetic fingerprint data whether the source is from a genotyping platform or derived from sequence data.
- FingerprintChecker(File) - Constructor for class picard.fingerprint.FingerprintChecker
-
Creates a fingerprint checker that will work with the set of haplotypes stored in the supplied file.
- FingerprintChecker(HaplotypeMap) - Constructor for class picard.fingerprint.FingerprintChecker
-
Creates a fingerprint checker that will work with the set of haplotyped provided.
- fingerprintFiles(Collection<Path>, int, int, TimeUnit) - Method in class picard.fingerprint.FingerprintChecker
-
Deprecated.
- fingerprintFiles(Collection<Path>, Map<Path, Path>, Boolean, int, int, TimeUnit) - Method in class picard.fingerprint.FingerprintChecker
- FingerprintIdDetails - Class in picard.fingerprint
-
class to hold the details of a element of fingerprinting PU tag
- FingerprintIdDetails() - Constructor for class picard.fingerprint.FingerprintIdDetails
- FingerprintIdDetails(SAMReadGroupRecord, String) - Constructor for class picard.fingerprint.FingerprintIdDetails
- FingerprintIdDetails(String, String) - Constructor for class picard.fingerprint.FingerprintIdDetails
- FingerprintingDetailMetrics - Class in picard.analysis
-
Detailed metrics about an individual SNP/Haplotype comparison within a fingerprint comparison.
- FingerprintingDetailMetrics() - Constructor for class picard.analysis.FingerprintingDetailMetrics
- FingerprintingSummaryMetrics - Class in picard.analysis
-
Summary fingerprinting metrics and statistics about the comparison of the sequence data from a single read group (lane or index within a lane) vs.
- FingerprintingSummaryMetrics() - Constructor for class picard.analysis.FingerprintingSummaryMetrics
- FingerprintMetrics - Class in picard.fingerprint
-
Class for holding metrics on a single fingerprint.
- FingerprintMetrics() - Constructor for class picard.fingerprint.FingerprintMetrics
- FingerprintResults - Class in picard.fingerprint
-
Class that is used to represent the results of comparing a read group within a SAM file, or a sample within a VCF against one or more set of fingerprint genotypes.
- FingerprintResults(Path, String, String) - Constructor for class picard.fingerprint.FingerprintResults
- fingerprintSamFile(Path, IntervalList) - Method in class picard.fingerprint.FingerprintChecker
-
Deprecated.
- fingerprintSamFile(Path, Path, boolean, Function<HaplotypeBlock, HaplotypeProbabilities>) - Method in class picard.fingerprint.FingerprintChecker
- fingerprintSamFile(Path, Function<HaplotypeBlock, HaplotypeProbabilities>) - Method in class picard.fingerprint.FingerprintChecker
-
Deprecated.
- FingerprintUtils - Class in picard.fingerprint
-
A set of utilities used in the fingerprinting environment
- FingerprintUtils() - Constructor for class picard.fingerprint.FingerprintUtils
- FingerprintUtils.VariantContextSet - Class in picard.fingerprint
-
A class that holds VariantContexts sorted by genomic position
- fingerprintVcf(Path) - Method in class picard.fingerprint.FingerprintChecker
-
Deprecated.
- fingerprintVcf(Path, Path, boolean) - Method in class picard.fingerprint.FingerprintChecker
- finish() - Method in class picard.analysis.AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector
- finish() - Method in class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
- finish() - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- finish() - Method in class picard.analysis.CollectAlignmentSummaryMetrics
- finish() - Method in class picard.analysis.CollectBaseDistributionByCycle
- finish() - Method in class picard.analysis.CollectGcBiasMetrics
- finish() - Method in class picard.analysis.CollectInsertSizeMetrics
- finish() - Method in class picard.analysis.CollectQualityYieldMetrics
- finish() - Method in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsCollector
- finish() - Method in class picard.analysis.CollectRnaSeqMetrics
- finish() - Method in class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
- finish() - Method in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
- finish() - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
- finish() - Method in class picard.analysis.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
- finish() - Method in class picard.analysis.MeanQualityByCycle
- finish() - Method in class picard.analysis.QualityScoreDistribution
- finish() - Method in class picard.analysis.SinglePassSamProgram
-
Should be implemented by subclasses to do one-time finalization work.
- finish() - Method in class picard.metrics.MultiLevelCollector
-
Call finish on all PerUnitMetricCollectors
- finish() - Method in interface picard.metrics.PerUnitMetricCollector
-
When all records have been collected, compute any final values needed to finish constructing metrics/Histogram
- finish() - Method in class picard.sam.markduplicates.CollectDuplicateMetrics
- FIRST - Enum constant in enum class picard.illumina.parser.TileTemplateRead
- FIRST - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ReadOrdinality
- FIRST_OF_PAIR - Enum constant in enum class picard.analysis.AlignmentSummaryMetrics.Category
- FIRST_READ_TRANSCRIPTION_STRAND - Enum constant in enum class picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
- FIRST_TILE - Variable in class picard.illumina.IlluminaBasecallsToFastq
- FIRST_TILE - Variable in class picard.illumina.IlluminaBasecallsToSam
- firstTile(Integer) - Method in class picard.illumina.BasecallsConverterBuilder
-
Configures the first tile that the converter will begin processing at.
- FisherStrandFilter - Class in picard.vcf.filter
-
Filters records based on the phred scaled p-value from the Fisher Strand test stored in the FS attribute.
- FisherStrandFilter(double) - Constructor for class picard.vcf.filter.FisherStrandFilter
- FIVE_PRIME_ADAPTER - Variable in class picard.illumina.IlluminaBasecallsToFastq
- FIVE_PRIME_ADAPTER - Variable in class picard.illumina.IlluminaBasecallsToSam
- FIVE_PRIME_ADAPTER - Variable in class picard.illumina.MarkIlluminaAdapters
- FIVE_PRIME_SEQUENCE - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
- FixedOffset - Enum constant in enum class picard.util.BaitDesigner.DesignStrategy
-
Design that places baits at fixed offsets over targets, allowing them to hang off the ends as dictated by the target size and offset.
- fixGenotypes(GenotypesContext, List<Allele>, List<Allele>) - Static method in class picard.util.LiftoverUtils
- FixMateInformation - Class in picard.sam
-
Summary
- FixMateInformation() - Constructor for class picard.sam.FixMateInformation
- fixNmMdAndUq(SAMRecord, ReferenceSequenceFileWalker, boolean) - Static method in class picard.sam.AbstractAlignmentMerger
-
Calculates and sets the NM, MD, and and UQ tags from the record and the reference
- fixUq(SAMRecord, ReferenceSequenceFileWalker, boolean) - Static method in class picard.sam.AbstractAlignmentMerger
-
Calculates and sets UQ tag from the record and the reference
- FixVcfHeader - Class in picard.vcf
-
Tool for replacing or fixing up a VCF header.
- FixVcfHeader() - Constructor for class picard.vcf.FixVcfHeader
- FLAG_DUPLICATES - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- flip() - Method in class picard.fingerprint.Snp
-
Returns a new SNP object with the alleles swapped and MAF corrected.
- floatToByteArray(float) - Static method in class picard.arrays.illumina.InfiniumDataFile
-
Utility method to convert a float to a byte array
- FLOW_EFFECTIVE_QUALITY_THRESHOLD - Variable in class picard.sam.markduplicates.MarkDuplicatesForFlowArgumentCollection
- FLOW_MODE - Variable in class picard.analysis.CollectQualityYieldMetrics
- FLOW_MODE - Variable in class picard.sam.markduplicates.MarkDuplicatesForFlowArgumentCollection
- FLOW_Q_IS_KNOWN_END - Variable in class picard.sam.markduplicates.MarkDuplicatesForFlowArgumentCollection
- FLOW_QUALITY_SUM_STRATEGY - Variable in class picard.sam.markduplicates.MarkDuplicatesForFlowArgumentCollection
- FLOW_SKIP_FIRST_N_FLOWS - Variable in class picard.sam.markduplicates.MarkDuplicatesForFlowArgumentCollection
- flowBasedArguments - Variable in class picard.sam.markduplicates.MarkDuplicates
- FlowBasedDuplicationMetrics - Class in picard.sam
- FlowBasedDuplicationMetrics() - Constructor for class picard.sam.FlowBasedDuplicationMetrics
- FLOWCELL_BARCODE - Variable in class picard.illumina.IlluminaBasecallsToFastq
- flowCellTileStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies base into their read's tile which is parsed from the read-name.
- FlowCellTileStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellTileStratifier
- flowCellXStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies base into their read's tile which is parsed from the read-name.
- FlowCellXStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellXStratifier
- flowCellYStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies base into their read's tile which is parsed from the read-name.
- FlowCellYStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellYStratifier
- FLUIDIGM - Enum constant in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- FN - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.ContingencyState
- FN_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
-
The FN (false negative) count across all variants
- FN_ONLY - Static variable in class picard.vcf.GenotypeConcordanceScheme
- FOLD_80_BASE_PENALTY - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to the mean coverage level in those targets.
- FOLD_80_BASE_PENALTY - Variable in class picard.analysis.WgsMetrics
-
The fold over-coverage necessary to raise 80% of bases to the mean coverage level.
- FOLD_90_BASE_PENALTY - Variable in class picard.analysis.WgsMetrics
-
The fold over-coverage necessary to raise 90% of bases to the mean coverage level.
- FOLD_95_BASE_PENALTY - Variable in class picard.analysis.WgsMetrics
-
The fold over-coverage necessary to raise 95% of bases to the mean coverage level.
- FOLD_ENRICHMENT - Variable in class picard.analysis.directed.HsMetrics
-
The fold by which the baited region has been amplified above genomic background.
- FOLD_ENRICHMENT - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The fold by which the amplicon region has been amplified above genomic background.
- FOLD_ENRICHMENT - Variable in class picard.analysis.directed.TargetMetrics
-
The fold by which the probed region has been amplified above genomic background, (ON_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES))/(PROBE_TERRITORY/GENOME_SIZE)
- foldInto(CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics, Collection<CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics>) - Static method in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
- foldInto(T, Collection<T>) - Static method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
- FORCE_GC - Variable in class picard.illumina.IlluminaBasecallsToFastq
- formatFloatForVcf(float) - Static method in class picard.arrays.GtcToVcf
- formatToDataTypes - Variable in class picard.illumina.parser.IlluminaDataProviderFactory
-
A Map of file formats to the dataTypes they will provide for this run.
- forVcf(File) - Method in class picard.vcf.processor.VcfFileSegmentGenerator
-
Deprecated.
- forVcf(PicardHtsPath) - Method in class picard.vcf.processor.VcfPathSegmentGenerator
- FOUND_NO_EVIDENCE - Enum constant in enum class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
- FP - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.ContingencyState
- FP_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
-
The FP (false positive) count across all variants
- FP_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
- FP_GENDER - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The sex, as reported for the fingerprinted sample
- FP_ONLY - Static variable in class picard.vcf.GenotypeConcordanceScheme
- FP_TN - Static variable in class picard.vcf.GenotypeConcordanceScheme
- FP_TN_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
- FR - Static variable in class picard.sam.markduplicates.util.ReadEnds
- FRACTION - Variable in class picard.sam.PositionBasedDownsampleSam
- FRAGMENTS - Variable in class picard.analysis.JumpingLibraryMetrics
-
The number of fragments in the SAM file
- fragSort - Variable in class picard.sam.markduplicates.MarkDuplicates
- FREE - Enum constant in enum class picard.illumina.DistanceMetric
- freeDistance() - Method in class picard.util.SingleBarcodeDistanceMetric
-
+++lifted from Commons Lang Text +++
- fromBases(byte[]) - Static method in enum class picard.fingerprint.DiploidGenotype
-
Converts a pair of bases into a DiploidGenotype regardless of base order or case
- fromBases(byte, byte) - Static method in enum class picard.fingerprint.DiploidGenotype
-
Converts a pair of bases into a DiploidGenotype regardless of base order or case
- fromCode(int) - Static method in enum class picard.pedigree.Sex
-
Decodes the Sex from a numeric code.
- fromFile(File, boolean) - Static method in class picard.pedigree.PedFile
-
Attempts to read a pedigree file into memory.
- fromPath(Path) - Static method in class picard.nio.PicardHtsPath
-
Construct a
PicardHtsPath
from aPath
- fromPaths(Collection<String>) - Static method in class picard.nio.PicardHtsPath
-
Create a
List<PicardHtsPath>
from path representations. - fromSexMap(Map<String, Sex>) - Static method in class picard.pedigree.PedFile
-
Function that accepts a map from sample-name to its sex and creates a PEDFile documenting the sexes.
- fromString(String) - Static method in enum class picard.pedigree.Sex
-
Decodes the Sex from a String.
- fullString() - Method in class picard.arrays.illumina.ArraysControlInfo
- FWD_CXT_ALT_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The number of REF_BASE:ALT_BASE alignments at sites with the given reference context.
- FWD_CXT_REF_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The number of REF_BASE:REF_BASE alignments at sites with the given reference context.
- FWD_ERROR_RATE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The substitution rate of REF_BASE:ALT_BASE, calculated as max(1e-10, FWD_CXT_ALT_BASES / (FWD_CXT_ALT_BASES + FWD_CXT_REF_BASES)).
G
- G - Enum constant in enum class picard.analysis.artifacts.Transition.Base
- G - Enum constant in enum class picard.illumina.parser.IntensityChannel
- G_REF_ALT_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The number of alt (A/T) basecalls observed at sites where the genome reference == G.
- G_REF_OXO_ERROR_RATE - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The rate at which C>A and G>T substitutions are observed at G reference sites above the expected rate if there were no bias between sites with a C reference base vs.
- G_REF_OXO_Q - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
G_REF_OXO_ERROR_RATE expressed as a phred-scaled quality score.
- G_REF_REF_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The number of ref basecalls observed at sites where the genome reference == G.
- GA4GHScheme - Class in picard.vcf
-
The scheme is defined in the constructor.
- GA4GHScheme() - Constructor for class picard.vcf.GA4GHScheme
- GA4GHSchemeWithMissingAsHomRef - Class in picard.vcf
-
The default scheme is derived from the GA4GH Benchmarking Work Group's proposed evaluation scheme.
- GA4GHSchemeWithMissingAsHomRef() - Constructor for class picard.vcf.GA4GHSchemeWithMissingAsHomRef
- GatherBamFiles - Class in picard.sam
-
Concatenate efficiently BAM files that resulted from a scattered parallel analysis.
- GatherBamFiles() - Constructor for class picard.sam.GatherBamFiles
- GatherVcfs - Class in picard.vcf
-
Simple little class that combines multiple VCFs that have exactly the same set of samples and nonoverlapping sets of loci.
- GatherVcfs() - Constructor for class picard.vcf.GatherVcfs
- GC - Variable in class picard.analysis.GcBiasDetailMetrics
-
The G+C content of the reference sequence represented by this bin.
- GC_DROPOUT - Variable in class picard.analysis.directed.PanelMetricsBase
-
A measure of how undercovered >= 50% GC regions are relative to the mean.
- GC_DROPOUT - Variable in class picard.analysis.GcBiasSummaryMetrics
-
Illumina-style GC dropout metric.
- GC_NC_0_19 - Variable in class picard.analysis.GcBiasSummaryMetrics
-
Normalized coverage over quintile of GC content ranging from 0 - 19.
- GC_NC_20_39 - Variable in class picard.analysis.GcBiasSummaryMetrics
-
Normalized coverage over each quintile of GC content ranging from 20 - 39.
- GC_NC_40_59 - Variable in class picard.analysis.GcBiasSummaryMetrics
-
Normalized coverage over each quintile of GC content ranging from 40 - 59.
- GC_NC_60_79 - Variable in class picard.analysis.GcBiasSummaryMetrics
-
Normalized coverage over each quintile of GC content ranging from 60 - 79.
- GC_NC_80_100 - Variable in class picard.analysis.GcBiasSummaryMetrics
-
Normalized coverage over each quintile of GC content ranging from 80 - 100.
- GC_SCORE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- GcBiasDetailMetrics - Class in picard.analysis
-
Class that holds detailed metrics about reads that fall within windows of a certain GC bin on the reference genome.
- GcBiasDetailMetrics() - Constructor for class picard.analysis.GcBiasDetailMetrics
- GcBiasMetrics - Class in picard.metrics
- GcBiasMetrics() - Constructor for class picard.metrics.GcBiasMetrics
- GcBiasMetricsCollector - Class in picard.analysis
-
Calculates GC Bias Metrics on multiple levels Created by kbergin on 3/23/15.
- GcBiasMetricsCollector(Set<MetricAccumulationLevel>, int[], List<SAMReadGroupRecord>, int, boolean) - Constructor for class picard.analysis.GcBiasMetricsCollector
- GcBiasMetricsCollector(Set<MetricAccumulationLevel>, int[], List<SAMReadGroupRecord>, int, boolean, boolean) - Constructor for class picard.analysis.GcBiasMetricsCollector
- GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector - Class in picard.analysis
- GcBiasSummaryMetrics - Class in picard.analysis
-
High level metrics that capture how biased the coverage in a certain lane is.
- GcBiasSummaryMetrics() - Constructor for class picard.analysis.GcBiasSummaryMetrics
- GcBiasUtils - Class in picard.analysis
-
Utilities to calculate GC Bias Created by kbergin on 9/23/15.
- GcBiasUtils() - Constructor for class picard.analysis.GcBiasUtils
- gcContentStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
A stratifier that uses GC (of the read) to stratify.
- GCContentStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.GCContentStratifier
- GCS - Enum constant in enum class picard.nio.PathProvider
- gencallVersion - Variable in class picard.arrays.illumina.InfiniumEGTFile
- GENDER_CONCORDANCE_PF - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
Whether or not the three sexs agree
- GENDER_GTC - Variable in class picard.arrays.GtcToVcf
- Gene - Class in picard.annotation
-
Holds annotation of a gene for storage in an OverlapDetector.
- Gene(String, int, int, boolean, String) - Constructor for class picard.annotation.Gene
- GENE_NAME - Enum constant in enum class picard.annotation.RefFlatReader.RefFlatColumns
- Gene.Transcript - Class in picard.annotation
-
A single transcript of a gene.
- Gene.Transcript.Exon - Class in picard.annotation
-
1-based, inclusive representation of an exon.
- GeneAnnotationReader - Class in picard.annotation
-
Load gene annotations into an OverlapDetector of Gene objects.
- GeneAnnotationReader() - Constructor for class picard.annotation.GeneAnnotationReader
- generateAdditionalWriters(List<SAMReadGroupRecord>, FastqWriterFactory) - Method in class picard.sam.SamToFastq
- generateAdditionalWriters(List<SAMReadGroupRecord>, FastqWriterFactory) - Method in class picard.sam.SamToFastqWithTags
- generateDuplicateIndexes(boolean, boolean) - Method in class picard.sam.markduplicates.MarkDuplicates
-
Goes through the accumulated ReadEndsForMarkDuplicates objects and determines which of them are to be marked as duplicates.
- generateDuplicateIndexes(boolean, boolean) - Method in class picard.sam.markduplicates.MarkDuplicatesForFlowHelper
-
This method is identical in function to generateDuplicateIndexes except that it accomodates for the possible significance of the end side of the reads (w/ or w/o uncertainty).
- generateDuplicateIndexes(boolean, boolean) - Method in interface picard.sam.markduplicates.MarkDuplicatesHelper
- generateNoMatchBarcode(ReadStructure) - Static method in class picard.illumina.BarcodeExtractor
- generateReadName(ClusterData, Integer) - Method in class picard.fastq.Casava18ReadNameEncoder
- generateReadName(ClusterData, Integer) - Method in class picard.fastq.IlluminaReadNameEncoder
- generateReadName(ClusterData, Integer) - Method in interface picard.fastq.ReadNameEncoder
-
Generates a read name string for the provided cluster.
- generateShortName(ClusterData) - Method in class picard.fastq.Casava18ReadNameEncoder
- generateShortName(ClusterData) - Method in class picard.fastq.IlluminaReadNameEncoder
- generateShortName(ClusterData) - Method in interface picard.fastq.ReadNameEncoder
-
Generates a short read name that includes a minimal amount of information, this is used primarily for read sorting.
- generateWgsMetrics(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, double, int, Histogram<Integer>, int) - Method in class picard.analysis.CollectRawWgsMetrics
- generateWgsMetrics(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, double, int, Histogram<Integer>, int) - Method in class picard.analysis.CollectWgsMetrics
- generateWgsMetrics(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, double, int, Histogram<Integer>, int) - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
- generatingAccumulatorsBy(VariantProcessor.AccumulatorGenerator<A, R>) - Static method in class picard.vcf.processor.VariantProcessor.Builder
- GENOME_ASSEMBLY - Variable in class picard.sam.CreateSequenceDictionary
- GENOME_BUILD_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- GENOME_SIZE - Variable in class picard.analysis.directed.PanelMetricsBase
-
The number of bases in the reference genome used for alignment.
- GENOME_TERRITORY - Variable in class picard.analysis.WgsMetrics
-
The number of non-N bases in the genome reference over which coverage will be evaluated.
- genotype - Variable in class picard.arrays.illumina.InfiniumGTCRecord
- GENOTYPE_CONCORDANCE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The genotype concordance for all possible states.
- GENOTYPE_LOD_THRESHOLD - Variable in class picard.fingerprint.CalculateFingerprintMetrics
- GENOTYPE_LOD_THRESHOLD - Variable in class picard.fingerprint.CheckFingerprint
- GenotypeConcordance - Class in picard.vcf
-
Summary
- GenotypeConcordance() - Constructor for class picard.vcf.GenotypeConcordance
- GenotypeConcordance.Alleles - Class in picard.vcf
-
A simple structure to return the results of getAlleles.
- GenotypeConcordanceContingencyMetrics - Class in picard.vcf
-
Class that holds metrics about the Genotype Concordance contingency tables.
- GenotypeConcordanceContingencyMetrics() - Constructor for class picard.vcf.GenotypeConcordanceContingencyMetrics
-
Empty constructor - needed for unit tests
- GenotypeConcordanceContingencyMetrics(VariantContext.Type, GenotypeConcordanceCounts, String, String, boolean) - Constructor for class picard.vcf.GenotypeConcordanceContingencyMetrics
- GenotypeConcordanceCounts - Class in picard.vcf
-
A class to store the counts for various truth and call state classifications relative to a reference.
- GenotypeConcordanceCounts() - Constructor for class picard.vcf.GenotypeConcordanceCounts
- GenotypeConcordanceDetailMetrics - Class in picard.vcf
-
Class that holds detail metrics about Genotype Concordance
- GenotypeConcordanceDetailMetrics() - Constructor for class picard.vcf.GenotypeConcordanceDetailMetrics
- GenotypeConcordanceScheme - Class in picard.vcf
-
This defines for each valid TruthState and CallState tuple, the set of contingency table entries that to which the tuple should contribute.
- GenotypeConcordanceScheme() - Constructor for class picard.vcf.GenotypeConcordanceScheme
- GenotypeConcordanceSchemeFactory - Class in picard.vcf
-
Created by kbergin on 6/19/15.
- GenotypeConcordanceSchemeFactory() - Constructor for class picard.vcf.GenotypeConcordanceSchemeFactory
- GenotypeConcordanceStateCodes - Enum Class in picard.vcf
-
Created by kbergin on 7/30/15.
- GenotypeConcordanceStates - Class in picard.vcf
-
A class to store the various classifications for: 1.
- GenotypeConcordanceStates() - Constructor for class picard.vcf.GenotypeConcordanceStates
- GenotypeConcordanceStates.CallState - Enum Class in picard.vcf
-
These states represent the relationship between the call genotype and the truth genotype relative to a reference sequence.
- GenotypeConcordanceStates.ContingencyState - Enum Class in picard.vcf
-
A specific state for a 2x2 contingency table.
- GenotypeConcordanceStates.TruthAndCallStates - Class in picard.vcf
-
A minute class to store the truth and call state respectively.
- GenotypeConcordanceStates.TruthState - Enum Class in picard.vcf
-
These states represent the relationship between a truth genotype and the reference sequence.
- GenotypeConcordanceSummaryMetrics - Class in picard.vcf
-
Class that holds summary metrics about Genotype Concordance
- GenotypeConcordanceSummaryMetrics() - Constructor for class picard.vcf.GenotypeConcordanceSummaryMetrics
-
Empty constructor - needed for unit tests
- GenotypeConcordanceSummaryMetrics(VariantContext.Type, GenotypeConcordanceCounts, String, String, boolean) - Constructor for class picard.vcf.GenotypeConcordanceSummaryMetrics
- GenotypeFilter - Interface in picard.vcf.filter
-
An interface for classes that perform Genotype filtration.
- GenotypeQualityFilter - Class in picard.vcf.filter
-
Genotype filter that filters out genotypes below a given quality threshold.
- GenotypeQualityFilter(int) - Constructor for class picard.vcf.filter.GenotypeQualityFilter
- GENOTYPES - Variable in class picard.fingerprint.CheckFingerprint
- genotypeScore - Variable in class picard.arrays.illumina.InfiniumGTCRecord
- GENOTYPING_ERROR_RATE - Variable in class picard.fingerprint.CrosscheckFingerprints
- GenotypingArraysProgramGroup - Class in picard.cmdline.programgroups
-
Miscellaneous tools, e.g.
- GenotypingArraysProgramGroup() - Constructor for class picard.cmdline.programgroups.GenotypingArraysProgramGroup
- get(int) - Method in class picard.analysis.CounterManager.Counter
- get(int) - Method in class picard.illumina.parser.readers.BclIndexReader
- get(int) - Method in class picard.illumina.parser.ReadStructure.Substructure
- get3PrimeAdapter() - Method in interface picard.util.AdapterPair
- get3PrimeAdapter() - Method in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- get3PrimeAdapterBytes() - Method in interface picard.util.AdapterPair
- get3PrimeAdapterBytes() - Method in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- get3PrimeAdapterBytesInReadOrder() - Method in interface picard.util.AdapterPair
- get3PrimeAdapterBytesInReadOrder() - Method in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- get3PrimeAdapterInReadOrder() - Method in interface picard.util.AdapterPair
- get3PrimeAdapterInReadOrder() - Method in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- get3PrimeSoftClippedBases(Cigar, boolean) - Static method in class picard.analysis.AlignmentSummaryMetricsCollector
-
returns the length of the soft clip on the 3' end If there are no-non-clipping operators, method will return 0 as it is unclear which clips should be considered on the "3'" end.
- get5PrimeAdapter() - Method in interface picard.util.AdapterPair
- get5PrimeAdapter() - Method in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- get5PrimeAdapterBytes() - Method in interface picard.util.AdapterPair
- get5PrimeAdapterBytes() - Method in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- get5PrimeAdapterBytesInReadOrder() - Method in interface picard.util.AdapterPair
- get5PrimeAdapterBytesInReadOrder() - Method in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- get5PrimeAdapterInReadOrder() - Method in interface picard.util.AdapterPair
- get5PrimeAdapterInReadOrder() - Method in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- getAaCalls() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getAbCalls() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getActualTiles(List<IlluminaFileUtil.SupportedIlluminaFormat>) - Method in class picard.illumina.parser.IlluminaFileUtil
-
Get the available tiles for the given formats, if the formats have tile lists that differ then throw an exception, if any of the format
- getAddressA() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getAddressAId() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getAddressB() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getAddressBId() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getAlignedReadHistogram() - Method in class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
- getAllele1() - Method in enum class picard.fingerprint.DiploidGenotype
- getAllele1() - Method in class picard.fingerprint.Snp
- getAllele2() - Method in enum class picard.fingerprint.DiploidGenotype
- getAllele2() - Method in class picard.fingerprint.Snp
- getAlleleA() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- getAlleleAProbeSeq() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getAlleleAProbeSeq() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getAlleleB() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- getAlleleBProbeSeq() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getAlleleBProbeSeq() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getAlleles() - Method in class picard.fingerprint.Snp
- getAlleleString() - Method in class picard.fingerprint.Snp
- getAllNormalizationIds() - Method in class picard.arrays.illumina.IlluminaBPMFile
- getAllPossibleHeaderNames() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifest
- getAllPossibleHeaderNames() - Method in class picard.arrays.illumina.IlluminaManifest
- getAllReadsCollector() - Method in class picard.metrics.MultiLevelCollector
-
Get the PerUnitMetricCollector that collects reads for all levels
- getAllSnps() - Method in class picard.fingerprint.HaplotypeMap
-
Returns an unmodifiable collection of all SNPs in all Haplotype blocks.
- getAllTiles() - Method in class picard.illumina.parser.readers.CbclReader
- getAssayFormat() - Method in class picard.arrays.illumina.IlluminaManifest
- getAssayHeaderNames() - Method in class picard.arrays.illumina.IlluminaManifest
- getAssayHeaderNameToIndex() - Method in class picard.arrays.illumina.IlluminaManifest
- getAssayType() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getAttributesToReverse() - Method in class picard.sam.AbstractAlignmentMerger
-
Gets the set of attributes to be reversed on reads marked as negative strand.
- getAttributesToReverseComplement() - Method in class picard.sam.AbstractAlignmentMerger
-
Gets the set of attributes to be reverse complemented on reads marked as negative strand.
- getAutoCallDate() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getAutoCallVersion() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getAvailableTiles() - Method in class picard.illumina.parser.IlluminaDataProviderFactory
-
Return the list of tiles available for this flowcell and lane.
- getB37Chr() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- getB37Pos() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- getbAlleleFreqs() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getBarcode() - Method in class picard.illumina.BarcodeExtractor.BarcodeMatch
- getBarcodeValue(SAMRecord) - Method in class picard.sam.markduplicates.EstimateLibraryComplexity
- getBaseCalls() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getBaseQualityHistogram() - Method in class picard.analysis.directed.TargetMetricsCollector
- getBases() - Method in class picard.illumina.parser.BclData
- getBases() - Method in class picard.illumina.parser.ReadData
- getBasesExcludedBy(CountingFilter) - Method in class picard.analysis.CollectWgsMetrics
-
If INTERVALS is specified, this will count bases beyond the interval list when the read overlaps the intervals and extends beyond the edge.
- getBbCalls() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getBciFile() - Method in class picard.illumina.parser.readers.BclIndexReader
- getBeadSetId() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getByteBufferIterator(int, int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
- getByteIterator(int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
- getBytesAvailableToRead() - Method in class picard.util.CircularByteBuffer
-
Returns the number of bytes that are in the buffer at the time of the method invocation.
- getCallRate() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getCapacity() - Method in class picard.util.CircularByteBuffer
-
Returns the total capacity of the buffer (empty+filled).
- getCategory() - Method in class picard.arrays.illumina.ArraysControlInfo
- getChainedPgIds(SAMFileHeader) - Method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
-
We have to re-chain the program groups based on this algorithm.
- getChr() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getChrom() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getChrom() - Method in class picard.fingerprint.Snp
- getChromosomes() - Method in class picard.arrays.illumina.InfiniumNormalizationManifest
- getClusterCount() - Method in class picard.illumina.parser.Tile
-
Returns the number of on this tile.
- getClusterDensity() - Method in class picard.illumina.parser.Tile
-
Returns the cluster density of this tile, in units of [cluster/mm^2].
- getClusterFile() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getCode() - Method in enum class picard.vcf.GenotypeConcordanceStates.CallState
- getCode() - Method in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- getCollector(int, IntervalList) - Method in class picard.analysis.CollectWgsMetrics
-
Creates
AbstractWgsMetricsCollector
implementation according toCollectWgsMetrics.USE_FAST_ALGORITHM
value. - getCollector(int, IntervalList) - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
- getColumnNames() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
- getColumnNames() - Method in class picard.util.TabbedTextFileWithHeaderParser
- getCommandLine() - Method in class picard.cmdline.CommandLineProgram
- getCommandLineParser() - Method in class picard.cmdline.CommandLineProgram
- getCommandLineParserForArgs(String[]) - Method in class picard.cmdline.CommandLineProgram
- getCompressedBlockSize() - Method in class picard.illumina.parser.readers.BaseBclReader.TileData
- getConcordanceStateArray(GenotypeConcordanceStates.TruthAndCallStates) - Method in class picard.vcf.GenotypeConcordanceScheme
-
Get the concordance state array associate with the given truth state and call state tuple.
- getConcordanceStateArray(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceScheme
-
Get the concordance state array associate with the given truth state and call state tuple.
- getContingencyStateCounts(GenotypeConcordanceScheme) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns the total number of times each contingency state is encountered, summed across all truth/call state pairs.
- getContingencyStateSet(GenotypeConcordanceStates.ContingencyState[]) - Method in class picard.vcf.GenotypeConcordanceScheme
-
Get the contingency state array as a set
- getContingencyStateString(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceScheme
-
Get the contingency state array as a parse-able string
- getControl() - Method in class picard.arrays.illumina.ArraysControlInfo
- getControlConfig() - Method in class picard.arrays.illumina.IlluminaBPMFile
- getCount(GenotypeConcordanceStates.TruthAndCallStates) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns the count defined by the truth state set and call state set.
- getCount(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns the count defined by the truth state set and call state set.
- getCounterSize() - Method in class picard.vcf.GenotypeConcordanceCounts
- getCoverageByTarget() - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
-
Returns the accumulated coverage per target.
- getCurrentLine() - Method in class picard.util.BasicInputParser
-
Provides access to the current (just parsed) line in pre-parsed format.
- getCurrentLine() - Method in class picard.util.DelimitedTextFileWithHeaderIterator.Row
- getCurrentLine() - Method in class picard.util.TabbedTextFileWithHeaderParser.Row
- getCurrentLineNumber() - Method in class picard.util.BasicInputParser
-
NOTE: Because AbstractInputParser pre-fetches the next line, this method actually returns the next line, not the most recent line returned by next().
- getCurrentLineNumber() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
- getCurrentLineNumber() - Method in class picard.util.TabbedTextFileWithHeaderParser
- getCustomerStrand() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getCycleData() - Method in class picard.illumina.parser.readers.CbclReader
- getCycleFromDir(File) - Static method in class picard.illumina.parser.PerTilePerCycleFileUtil
- getCycleIndexRanges() - Method in class picard.illumina.parser.OutputMapping
- getCycleIndexRanges() - Method in class picard.illumina.parser.ReadStructure.Substructure
- getCycles() - Method in class picard.illumina.parser.ReadStructure.Substructure
- getDataTypesFromReadStructure(ReadStructure, boolean, File) - Static method in class picard.illumina.BasecallsConverter
-
Given a read structure return the data types that need to be parsed for this run
- getDateFromVcfOtherHeaderLine(VCFHeader, String, SimpleDateFormat) - Static method in class picard.arrays.illumina.InfiniumVcfFields
- getDateManufactured() - Method in class picard.arrays.illumina.IlluminaManifest
- getDefaultHeaders() - Method in class picard.cmdline.CommandLineProgram
- getDefaultSampleID() - Method in class picard.fingerprint.FingerprintChecker
- getDensity() - Method in class picard.illumina.parser.readers.TileMetricsOutReader
- getDepthHistogram() - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
- getDepthHistogram() - Method in class picard.analysis.directed.TargetMetricsCollector
- getDepths() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
-
Gets the coverage depths as an array of ints.
- getDescription() - Method in class picard.cmdline.programgroups.BaseCallingProgramGroup
- getDescription() - Method in class picard.cmdline.programgroups.DiagnosticsAndQCProgramGroup
- getDescription() - Method in class picard.cmdline.programgroups.GenotypingArraysProgramGroup
- getDescription() - Method in class picard.cmdline.programgroups.IntervalsManipulationProgramGroup
- getDescription() - Method in class picard.cmdline.programgroups.OtherProgramGroup
- getDescription() - Method in class picard.cmdline.programgroups.ReadDataManipulationProgramGroup
- getDescription() - Method in class picard.cmdline.programgroups.ReferenceProgramGroup
- getDescription() - Method in class picard.cmdline.programgroups.Testing
- getDescription() - Method in class picard.cmdline.programgroups.VariantEvaluationProgramGroup
- getDescription() - Method in class picard.cmdline.programgroups.VariantFilteringProgramGroup
- getDescription() - Method in class picard.cmdline.programgroups.VariantManipulationProgramGroup
- getDescriptorFileName() - Method in class picard.arrays.illumina.IlluminaManifest
- getDescriptorLengths() - Method in class picard.illumina.parser.ReadStructure.Substructure
- getDetectedCycles() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
- getDictionaryForMergedBam() - Method in class picard.sam.AbstractAlignmentMerger
- getDictionaryForMergedBam() - Method in class picard.sam.SamAlignmentMerger
- getDiploidHaplotype(Snp, DiploidGenotype) - Method in class picard.fingerprint.HaplotypeBlock
-
Gets the diploid haplotype for this haplotype block given the provided SNP and SNP genotype.
- getDuplicateCountHist() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
- getDuplicateMarkingsDiffer() - Method in class picard.sam.util.SamComparison
- getDuplicateSetIterator(AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator, SAMRecordDuplicateComparator) - Method in class picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar
- getDuplicateSetIterator(AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator, SAMRecordDuplicateComparator) - Method in class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
- getDx() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getException() - Method in class picard.illumina.ExtractIlluminaBarcodes.PerTileBarcodeExtractor
- getExpClusters() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getExpClusters() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getExpectedTiles() - Method in class picard.illumina.parser.IlluminaFileUtil
-
Return the list of tiles we would expect for this lane based on the metrics found in InterOp/TileMetricsOut.bin
- getExtendedManifestVersion() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifest
- getExtension() - Static method in class picard.illumina.IlluminaLaneMetrics
-
This property is not exposed in a field to avoid complications with MetricBase's dependency on reflection.
- getExtension() - Static method in class picard.illumina.IlluminaPhasingMetrics
-
This property is not exposed in a field to avoid complications with MetricBase's dependency on reflection.
- getExtension() - Static method in class picard.vcf.MendelianViolations.MendelianViolationMetrics
- getFamilyId() - Method in class picard.pedigree.PedFile.PedTrio
- getFaqLink() - Static method in class picard.cmdline.CommandLineProgram
- getField(String) - Method in class picard.util.DelimitedTextFileWithHeaderIterator.Row
- getField(String) - Method in class picard.util.TabbedTextFileWithHeaderParser.Row
- getFields() - Method in class picard.util.DelimitedTextFileWithHeaderIterator.Row
- getFields() - Method in class picard.util.TabbedTextFileWithHeaderParser.Row
- getFile() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
- getFile() - Method in class picard.illumina.parser.TileIndex
- getFileExtension() - Static method in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
- getFileExtension() - Static method in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
- getFileExtension() - Static method in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
- getFileExtension() - Static method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
- getFileExtension() - Static method in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
- getFileName() - Method in class picard.util.AbstractInputParser
- getFileName() - Method in class picard.util.BasicInputParser
-
Gets the name of the file being parsed
- getFiles() - Method in class picard.illumina.parser.PerTileFileUtil
- getFiles() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
- getFiles(int[]) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
-
Returns a cycleIlluminaFileMap with all available tiles but limited to the cycles passed in.
- getFiles(List<Integer>) - Method in class picard.illumina.parser.PerTileFileUtil
- getFiles(List<Integer>) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
- getFiles(List<Integer>, int[]) - Method in class picard.illumina.parser.MultiTileBclFileUtil
- getFiles(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
-
Returns a cycleIlluminaFileMap that contains only the tiles and cycles specified (and fewer if the original CycleIlluminaFileMap, created on util instantiation, doesn't contain any of these tiles/cycles).
- getFilesForCycle(int) - Method in class picard.illumina.parser.readers.CbclReader
- getFilteredBases() - Method in class picard.filter.CountingFilter
-
Gets the number of bases that have been filtered out thus far.
- getFilteredRecords() - Method in class picard.filter.CountingFilter
-
Gets the number of records that have been filtered out thus far.
- getFingerprintFile() - Method in class picard.fingerprint.MatchResults
- getFingerprintIdDetailsStringFunction(CrosscheckMetric.DataType) - Static method in class picard.fingerprint.Fingerprint
- getFingerprintMetrics(Fingerprint) - Method in class picard.fingerprint.CalculateFingerprintMetrics
- getFingerprintPanels() - Method in class picard.fingerprint.Snp
- getFirstSnp() - Method in class picard.fingerprint.HaplotypeBlock
-
Gets the arbitrarily first SNP in the haplotype.
- getFlag() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- getFloatIterator(int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
- getFlowSumOfBaseQualities(SAMRecord, int) - Static method in class picard.sam.markduplicates.MarkDuplicatesForFlowHelper
-
A quality summing scoring strategy used for flow based reads.
- getForceSort() - Method in class picard.sam.SamAlignmentMerger
- getFracA() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getFracC() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getFracG() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getFracT() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getFractionUnexpectedAlleleObs() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
- getGender() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getGene() - Method in class picard.annotation.Gene.Transcript
- getGenesForPickTranscripts() - Method in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
-
Derived class may override this method in order to return a different set of genes for picking transcripts for computing coverage, or to cache the value returned by geneOverlapDetector.getAll(), because it can be expensive to compute repeatedly.
- getGenomeBuild() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getGenomeBuild() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getGenotype(String, InfiniumGTCRecord, IlluminaManifestRecord, Allele, Allele) - Method in class picard.arrays.GtcToVcf
- getGenotypeBytes() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getGenotypeScores() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getGreen() - Method in class picard.arrays.illumina.ArraysControlInfo
- getHaplotype() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns the haplotype for which the probabilities apply.
- getHaplotype(String) - Method in class picard.fingerprint.HaplotypeMap
-
Queries a HaplotypeBlock by Snp name.
- getHaplotype(String, int) - Method in class picard.fingerprint.HaplotypeMap
-
Queries a HaplotypeBlock by Snp chromosome and position.
- getHaplotype(Snp) - Method in class picard.fingerprint.HaplotypeMap
-
Queries a HaplotypeBlock by Snp object.
- getHaplotypeFrequencies() - Method in class picard.fingerprint.HaplotypeBlock
-
Gets the set of haplotype frequencies.
- getHaplotypeFrequency(int) - Method in class picard.fingerprint.HaplotypeBlock
-
Gets the frequency of the i'th diploid haplotype where haplotypes are ordered accorinding to DiploidHaplotype.
- getHaplotypes() - Method in class picard.fingerprint.HaplotypeMap
-
Returns an unmodifiable collection of all the haplotype blocks in the map.
- getHeader() - Method in class picard.fingerprint.FingerprintChecker
- getHeader() - Method in class picard.fingerprint.HaplotypeMap
- getHeader() - Method in class picard.sam.AbstractAlignmentMerger
- getHeaderContents() - Method in class picard.arrays.illumina.IlluminaManifest
- getHeaderSize() - Method in class picard.illumina.parser.readers.CbclReader
- getHelpDoc() - Method in enum class picard.analysis.CollectMultipleMetrics.Program
- getHelpDoc() - Method in enum class picard.illumina.DistanceMetric
- getHelpDoc() - Method in enum class picard.sam.FilterSamReads.Filter
- getHelpDoc() - Method in enum class picard.sam.markduplicates.CheckDuplicateMarking.Mode
- getHelpDoc() - Method in enum class picard.sam.RevertSam.FileType
- getHelpDoc() - Method in enum class picard.util.IntervalList.IntervalListScatterMode
- getHelpDoc() - Method in enum class picard.util.IntervalListTools.Action
- getHet(int, int) - Static method in enum class picard.vcf.GenotypeConcordanceStates.CallState
- getHeterogyzousGenotype() - Method in class picard.fingerprint.Snp
- getHetPercent() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getHgGenomeBuild() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getHighQualityDepthHistogram() - Method in class picard.analysis.AbstractWgsMetricsCollector
- getHistogram(long[], String, String) - Method in class picard.analysis.AbstractWgsMetricsCollector
- getHom(int) - Static method in enum class picard.vcf.GenotypeConcordanceStates.CallState
- getHom(int) - Static method in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- getHomozygousAllele1Genotype() - Method in class picard.fingerprint.Snp
- getHomozygousAllele2Genotype() - Method in class picard.fingerprint.Snp
- getIdentifier() - Method in class picard.arrays.illumina.InfiniumDataFile
- getIlmnId() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getIlmnId() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getIlmnStrand() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getIlmnStrand() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getImagingDate() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getImagingUser() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getIndelCounter() - Method in class picard.vcf.GenotypeConcordance
- getIndelElement(SamLocusIterator.RecordAndOffset) - Static method in class picard.sam.SamErrorMetric.ReadBaseStratification
- getIndex() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getIndex() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getIndices() - Method in class picard.illumina.parser.ReadStructure.Substructure
- getIndividualId() - Method in class picard.pedigree.PedFile.PedTrio
- getInfo() - Method in class picard.fingerprint.Fingerprint
- getInputFile() - Method in class picard.fingerprint.FingerprintResults
- getInputStream() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
- getInputStream() - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
- getIntegerField(String) - Method in class picard.util.DelimitedTextFileWithHeaderIterator.Row
- getIntegerField(String) - Method in class picard.util.TabbedTextFileWithHeaderParser.Row
- getIntegerFromVcfOtherHeaderLine(VCFHeader, String) - Static method in class picard.arrays.illumina.InfiniumVcfFields
- getIntegerIterator(int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
- getIntensityOnly() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getIntervalFile() - Method in class picard.analysis.CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection
- getIntervalFile() - Method in interface picard.cmdline.argumentcollections.IntervalArgumentCollection
- getIntervalList() - Method in class picard.fingerprint.HaplotypeMap
-
Returns an IntervalList with an entry for every SNP in every Haplotype in the map.
- getIntervalsToExamine() - Method in class picard.analysis.CollectWgsMetrics
-
Gets the intervals over which we will calculate metrics.
- getLane() - Method in class picard.illumina.parser.ClusterData
- getLane() - Method in class picard.illumina.parser.IlluminaFileUtil
-
Return the lane we're inspecting
- getLane() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
- getLaneFactories() - Method in class picard.illumina.BasecallsConverter
-
Gets the data provider factory used to create the underlying data provider.
- getLaneNumber() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
- getLaneNumber() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
- getLaneNumber() - Method in class picard.illumina.parser.Tile
-
Returns the number of this tile's parent lane.
- getLaneTileCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
- getLastThreeFields(String, char, int[]) - Static method in class picard.sam.util.ReadNameParser
-
Given a string, splits the string by the delimiter, and returns the the last three fields parsed as integers.
- getLeft() - Method in class picard.sam.util.Pair
- getLibraryId() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
- getLibraryId() - Method in class picard.sam.markduplicates.util.ReadEnds
- getLibraryId() - Method in interface picard.sam.util.PhysicalLocation
- getLibraryId() - Method in class picard.sam.util.PhysicalLocationInt
- getLibraryId(SAMRecord) - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
-
Get the library ID for the given SAM record.
- getLibraryIdGenerator() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
- getLibraryIdsMap() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
- getLibraryName(SAMFileHeader, SAMRecord) - Static method in class picard.sam.markduplicates.util.LibraryIdGenerator
-
Gets the library name from the header for the record.
- getLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns the likelihoods, in order, of the AA, Aa and aa haplotypes given the evidence
- getLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
- getLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
- getLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
-
Converts the loglikelihoods into linear-space with normalizing.
- getLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
- getLikelihoods0() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
- getLine() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- getLine() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getLocations(ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.MarkQueue
-
Returns the nonDuplicateReadEndsSet of read ends that should be considered for tracking optical duplicates.
- getLocationSet() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
- getLociCount() - Method in class picard.arrays.illumina.IlluminaManifest
- getLociToGenotype(Collection<Fingerprint>) - Method in class picard.fingerprint.FingerprintChecker
-
Takes a set of fingerprints and returns an IntervalList containing all the loci that can be productively examined in sequencing data to compare to one or more of the fingerprints.
- getLocusEntries() - Method in class picard.arrays.illumina.IlluminaBPMFile
- getLocusIterator(SamReader) - Method in class picard.analysis.CollectWgsMetrics
-
Creates
AbstractLocusIterator
implementation according toCollectWgsMetrics.USE_FAST_ALGORITHM
value. - getLocusMaxReads() - Method in class picard.fingerprint.FingerprintChecker
- getLocusResults() - Method in class picard.fingerprint.MatchResults
- getLOD() - Method in class picard.fingerprint.MatchResults
- getLodMostProbableGenotype() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns the LOD score between the most probable haplotype and the second most probable.
- getLodMostProbableGenotype() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
-
Overridden to calculate the LOD from the loglikelihoods instead of the probabilities because it will allow for more accurate calculation before overflowing.
- getLodNT() - Method in class picard.fingerprint.MatchResults
- getLodTN() - Method in class picard.fingerprint.MatchResults
- getLog_of_base() - Method in class picard.util.MathUtil.LogMath
- getLogFromProbability(double[]) - Static method in class picard.util.MathUtil
-
Takes a complete set of mutually exclusive Likelihoods and converts them to logLikelihoods.
- getLogLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilities
- getLogLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
- getLogLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
-
Since this class uses log-rawLikelihoods natively, we override and return the native variable
- getLogRDev() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getLogRRatios() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getLogValue(double) - Method in class picard.util.MathUtil.LogMath
-
Returns the log-representation of the provided decimal value.
- getLogValue(double[]) - Method in class picard.util.MathUtil.LogMath
-
Returns the log-representation of the provided decimal array.
- getLongIterator(int, File) - Static method in class picard.illumina.parser.readers.MMapBackedIteratorFactory
- getMaf() - Method in class picard.fingerprint.HaplotypeBlock
-
Returns the minor allele frequency of this haplotype.
- getMaf() - Method in class picard.fingerprint.Snp
- getMajorGenomeBuild() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getManifestFile() - Method in class picard.arrays.illumina.IlluminaManifest
- getManifestFileHeaderNames() - Method in class picard.arrays.illumina.IlluminaManifest
- getManifestFileParser() - Method in class picard.arrays.illumina.IlluminaManifest
- getManifestName() - Method in class picard.arrays.illumina.IlluminaBPMFile
- getManifestName() - Method in class picard.arrays.illumina.InfiniumEGTFile
- getMapInfo() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getMappingsDiffer() - Method in class picard.sam.util.SamComparison
- getMappingsMatch() - Method in class picard.sam.util.SamComparison
- getMaskedBaseCount(byte[], int, int) - Static method in class picard.util.BaitDesigner
-
Returns the total of soft or hard masked bases in the interval of bases.
- getMatchedBarcode() - Method in class picard.illumina.parser.ClusterData
- getMatchResults() - Method in class picard.fingerprint.FingerprintResults
- getMaternalId() - Method in class picard.pedigree.PedFile.PedTrio
- getMaxPairErrorRate() - Method in class picard.util.AdapterMarker
- getMaxSingleEndErrorRate() - Method in class picard.util.AdapterMarker
- getMedianPhasingMap() - Method in class picard.illumina.LanePhasingMetricsCollector
- getMedianPrePhasingMap() - Method in class picard.illumina.LanePhasingMetricsCollector
- getMessage(int) - Method in enum class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
- getMetric() - Method in interface picard.sam.SamErrorMetric.BaseCalculator
-
Returns the metric generated by the observed loci
- getMetric() - Method in class picard.sam.SamErrorMetric.IndelErrorCalculator
-
Returns the metric generated by the observed loci
- getMetric() - Method in class picard.sam.SamErrorMetric.OverlappingReadsErrorCalculator
-
Returns the metric generated by the observed loci
- getMetric() - Method in class picard.sam.SamErrorMetric.SimpleErrorCalculator
-
Returns the metric generated by the observed loci
- getMetricCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
- getMetricCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
- getMetrics() - Method in class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
- getMetrics() - Method in class picard.illumina.BarcodeExtractor
- getMetrics() - Method in class picard.illumina.ExtractIlluminaBarcodes.PerTileBarcodeExtractor
- getMetrics() - Method in class picard.sam.SamErrorMetric.BaseErrorAggregation
- getMetrics(CountingFilter, CountingFilter, CountingFilter, CountingPairedFilter) - Method in class picard.analysis.AbstractWgsMetricsCollector
-
Creates CollectWgsMetrics.WgsMetrics - the object holding the result of CollectWgsMetrics
- getMetricsByLibrary(String) - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
- getMetricsByLibraryMap() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
- getMetricsCode() - Method in enum class picard.illumina.parser.IlluminaMetricsCode
- getMetricsFile() - Method in class picard.cmdline.CommandLineProgram
-
Gets a MetricsFile with default headers already written into it.
- getMetricValue() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
- getMinimumBaseQuality() - Method in class picard.illumina.BarcodeExtractor
- getMinPairMatchBases() - Method in class picard.util.AdapterMarker
- getMinSingleEndMatchBases() - Method in class picard.util.AdapterMarker
- getMismatches() - Method in class picard.illumina.BarcodeExtractor.BarcodeMatch
- getMismatchesToSecondBest() - Method in class picard.illumina.BarcodeExtractor.BarcodeMatch
- getMissingLeft() - Method in class picard.sam.util.SamComparison
- getMissingRight() - Method in class picard.sam.util.SamComparison
- getMostLikelyGenotype(Snp) - Method in class picard.fingerprint.HaplotypeProbabilities
-
Gets the genotype for this Snp given the most likely haplotype.
- getMostLikelyHaplotype() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Gets the most likely haplotype given the probabilities.
- getName() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getName() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getName() - Method in class picard.cmdline.programgroups.BaseCallingProgramGroup
- getName() - Method in class picard.cmdline.programgroups.DiagnosticsAndQCProgramGroup
- getName() - Method in class picard.cmdline.programgroups.GenotypingArraysProgramGroup
- getName() - Method in class picard.cmdline.programgroups.IntervalsManipulationProgramGroup
- getName() - Method in class picard.cmdline.programgroups.OtherProgramGroup
- getName() - Method in class picard.cmdline.programgroups.ReadDataManipulationProgramGroup
- getName() - Method in class picard.cmdline.programgroups.ReferenceProgramGroup
- getName() - Method in class picard.cmdline.programgroups.Testing
- getName() - Method in class picard.cmdline.programgroups.VariantEvaluationProgramGroup
- getName() - Method in class picard.cmdline.programgroups.VariantFilteringProgramGroup
- getName() - Method in class picard.cmdline.programgroups.VariantManipulationProgramGroup
- getName() - Method in class picard.fingerprint.Snp
- getName() - Method in interface picard.util.AdapterPair
- getName() - Method in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- getNearProbeDistance() - Method in class picard.analysis.directed.TargetMetricsCollector
-
Gets the distance that is allowed between a read and the nearest probe for it to be considered "near probe" and "selected.
- getNextReadPair(PeekableIterator<SAMRecord>) - Static method in class picard.util.QuerySortedReadPairIteratorUtil
-
Get the next read pair (where both have the same read name).
- getNodes() - Method in class picard.util.GraphUtils.Graph
- getNoMatchMetric() - Method in class picard.illumina.BarcodeExtractor
- getNoMatchMetric() - Method in class picard.illumina.ExtractIlluminaBarcodes.PerTileBarcodeExtractor
- getNonLogValue(double) - Method in class picard.util.MathUtil.LogMath
-
Returns the decimal representation of the provided log values.
- getNonOpticalDuplicateCountHist() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
- getNormalizationId() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getNormalizedXIntensities() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getNormalizedYIntensities() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getNumAdaptersToKeep() - Method in class picard.util.AdapterMarker
- getNumAlignedBases(SAMRecord) - Method in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
- getNumAssays() - Method in class picard.arrays.illumina.IlluminaManifest
- getNumBasesPassingMinimumBaseQuality(SAMRecord, AlignmentBlock, int) - Static method in class picard.analysis.directed.TargetMetricsCollector
-
Get the the number of bases in the given alignment block and record that have base quality greater or equal to the minimum
- getNumberOfClusters(File) - Static method in class picard.illumina.parser.readers.BclReader
- getNumberOfOpticalDuplicateClusters() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
- getNumberOfSnps() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getNumCalls() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getNumClustersInTile() - Method in class picard.illumina.parser.TileIndex.TileIndexRecord
- getNumDescriptors() - Method in class picard.illumina.parser.ReadStructure
- getNumDuplicates() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
- getNumDuplicates() - Method in class picard.sam.markduplicates.util.MarkQueue
-
Returns the number of duplicates detected
- getNumIntensityOnly() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getNumNoCalls() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getNumReads() - Method in class picard.illumina.parser.ClusterData
- getNumRecordsWithNoMateCigar() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
-
Useful for statistics after the iterator has been exhausted and closed.
- getNumTiles() - Method in class picard.illumina.parser.readers.BclIndexReader
- getNumTiles() - Method in class picard.illumina.parser.TileIndex
- getObsAllele1() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns the number of observations of alleles supporting the first/major haplotype allele.
- getObsAllele1() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
-
Returns the number of bases/reads that support the first allele.
- getObsAllele1() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
- getObsAllele2() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns the number of observations of alleles supporting the second/minor haplotype allele.
- getObsAllele2() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
-
Returns the number of bases/reads that support the second allele.
- getObsAllele2() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
- getOffset() - Method in class picard.arrays.illumina.InfiniumFileTOC
- getOffsetX() - Method in class picard.arrays.illumina.InfiniumTransformation
- getOffsetY() - Method in class picard.arrays.illumina.InfiniumTransformation
- getOpticalDupesByLibraryId() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
- getOpticalDuplicateCountHist() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
- getOpticalDuplicatesByLibraryIdMap() - Method in class picard.sam.markduplicates.util.LibraryIdGenerator
- getOptionalDoubleFromVcfOtherHeaderLine(VCFHeader, String) - Static method in class picard.arrays.illumina.InfiniumVcfFields
- getOptionalIntegerFromVcfOtherHeaderLine(VCFHeader, String) - Static method in class picard.arrays.illumina.InfiniumVcfFields
- getOptionalValueFromVcfOtherHeaderLine(VCFHeader, String) - Static method in class picard.arrays.illumina.InfiniumVcfFields
- getOrientationByte(boolean, boolean) - Static method in class picard.sam.markduplicates.util.ReadEnds
-
Returns a single byte that encodes the orientation of the two reads in a pair.
- getOutputArgumentCollection() - Method in class picard.analysis.SinglePassSamProgram
- getOutputArgumentCollection() - Method in class picard.sam.markduplicates.CollectDuplicateMetrics
- getOutputCycles() - Method in class picard.illumina.parser.OutputMapping
- getOutputDescriptors() - Method in class picard.illumina.parser.OutputMapping
- getOutputFile() - Method in class picard.cmdline.argumentcollections.EmptyOutputArgumentCollection
- getOutputFile() - Method in interface picard.cmdline.argumentcollections.OutputArgumentCollection
- getOutputFile() - Method in class picard.cmdline.argumentcollections.RequiredOutputArgumentCollection
- getOutputFileName(File) - Static method in class picard.sam.CalculateReadGroupChecksum
-
Creates a file name (not including the path) for an RG MD5 file based on the name of the input file.
- getOutputIndexForCycle(int) - Method in class picard.illumina.parser.OutputMapping
-
Return an index that where: index.arrayIndex - represents either the read number the cycle will be output too, or (in some cases) an array index into a two dimensional array of byte[][] where the top level array corresponds to read number index.elementIndex - represents the element a cycle will appear in inside it's give read, or the element in an array as described above
- getOutputReadLengths() - Method in class picard.illumina.parser.OutputMapping
- getOutputReadStructure() - Method in class picard.illumina.parser.IlluminaDataProviderFactory
-
Sometimes (in the case of skipped reads) the logical read structure of the output cluster data is different from the input readStructure
- getOutputReadStructure() - Method in class picard.illumina.parser.OutputMapping
- getOutputStream() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
- getOutputStream() - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
- getP05Green() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getP05Red() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getP10GC() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getP50GC() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getP50Green() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getP50Red() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getP95Green() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getP95Red() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getPackageList() - Static method in class picard.cmdline.PicardCommandLine
-
The packages we wish to include in our command line
- getPaternalId() - Method in class picard.pedigree.PedFile.PedTrio
- getPerTilePerCycleFiles() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
-
For the given tiles, populate a CycleIlluminaFileMap that contains all these tiles and will iterate through all the files for these tiles in expectedBase Side Effect: Assigns numCycles
- getPGRecord(SAMFileHeader) - Method in class picard.cmdline.CommandLineProgram
- getPhasingCode(int, IlluminaMetricsCode) - Static method in enum class picard.illumina.parser.IlluminaMetricsCode
-
Phasing codes are between 200 and 299 (inclusive).
- getPhasingMap() - Method in class picard.illumina.parser.Tile
- getPhasingMetricsForTiles(long, Collection<Tile>, boolean) - Static method in class picard.illumina.IlluminaPhasingMetrics
-
Calculate the median phasing & prephasing values for a lane's tiles and create the appropriate IlluminaPhasingMetrics for them
- getPhasingValue() - Method in class picard.illumina.parser.TilePhasingValue
- getPhenotype() - Method in class picard.pedigree.PedFile.PedTrio
- getPlatformUnit() - Method in class picard.fingerprint.FingerprintIdDetails
- getPloidy() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getPloidy() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getPloidy() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getPloidyType() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getPmtGreen() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getPmtRed() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getPoorQualityFrequencies() - Method in class picard.illumina.parser.readers.BclQualityEvaluationStrategy
-
Returns a view of number of qualities that failed, where the key is the quality score and the value is the number of observations.
- getPopulationLikelihood() - Method in class picard.fingerprint.MatchResults
- getPos() - Method in class picard.fingerprint.Snp
- getPosition() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getPositionInfo() - Method in class picard.illumina.parser.CbclData
- getPositions() - Method in class picard.arrays.illumina.InfiniumNormalizationManifest
- getPosteriorLikelihoods() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns the probabilities, in order, of the AA, Aa and aa haplotypes.
- getPosteriorProbabilities() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns the probabilities, in order, of the AA, Aa and aa haplotypes.
- getPosteriorProbabilities() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
-
getter for posteriorProbs
- getPosteriorProbabilities0() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
-
Returns the posterior probability of the haplotypes given the evidence (uses the internal prior)
- getPrePhasingMap() - Method in class picard.illumina.parser.Tile
- getPrePhasingValue() - Method in class picard.illumina.parser.TilePhasingValue
- getPrintableId() - Method in class picard.fingerprint.Fingerprint
- getPriorProbablities() - Method in class picard.fingerprint.HaplotypeProbabilities
- getProbabilityFromLog(double[]) - Static method in class picard.util.MathUtil
-
Takes a complete set of mutually exclusive logLikelihoods and converts them to probabilities with no rescaling.
- getProbeIntervals() - Method in class picard.analysis.directed.CollectHsMetrics
- getProbeIntervals() - Method in class picard.analysis.directed.CollectTargetedMetrics
- getProbeIntervals() - Method in class picard.analysis.directed.CollectTargetedPcrMetrics
- getProbeSetName() - Method in class picard.analysis.directed.CollectHsMetrics
- getProbeSetName() - Method in class picard.analysis.directed.CollectTargetedMetrics
- getProbeSetName() - Method in class picard.analysis.directed.CollectTargetedPcrMetrics
- getProgramProperty(Class) - Static method in class picard.cmdline.PicardCommandLine
- getProgramRecord() - Method in class picard.sam.AbstractAlignmentMerger
- getQualities() - Method in class picard.illumina.parser.BclData
- getQualities() - Method in class picard.illumina.parser.ReadData
- getQuerynameSortedAlignedRecords() - Method in class picard.sam.AbstractAlignmentMerger
- getQuerynameSortedAlignedRecords() - Method in class picard.sam.SamAlignmentMerger
-
Reads the aligned SAM records into a SortingCollection and returns an iterator over that collection
- getRawControlXIntensities() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getRawControlXIntensity(int) - Method in class picard.arrays.illumina.InfiniumGTCFile
- getRawControlYIntensities() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getRawControlYIntensity(int) - Method in class picard.arrays.illumina.InfiniumGTCFile
- getRawXIntensities() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getRawYIntensities() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getRead(int) - Method in class picard.illumina.parser.ClusterData
- getReadBarcodeValue(SAMRecord, String) - Static method in class picard.sam.markduplicates.EstimateLibraryComplexity
- getReadDuplicateScore(SAMRecord, ReadEndsForMarkDuplicates) - Method in class picard.sam.markduplicates.MarkDuplicates
-
Calculates score for the duplicate read
- getReadDuplicateScore(SAMRecord, ReadEndsForMarkDuplicates) - Method in class picard.sam.markduplicates.MarkDuplicatesForFlowHelper
-
update score for pairedEnds
- getReadDuplicateScore(SAMRecord, ReadEndsForMarkDuplicates) - Method in interface picard.sam.markduplicates.MarkDuplicatesHelper
- getReadEndCoordinate(SAMRecord, boolean, boolean, MarkDuplicatesForFlowArgumentCollection) - Static method in class picard.sam.markduplicates.MarkDuplicatesForFlowHelper
- getReadEnds() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
-
Gets the set of read ends
- getReadEndSetForOpticalDuplicates() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
-
Gets the read ends for optical duplicate tracking
- getReadGroup() - Method in class picard.fingerprint.FingerprintResults
- getReadGroup() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
- getReadGroup() - Method in class picard.sam.markduplicates.util.ReadEnds
- getReadGroup() - Method in interface picard.sam.util.PhysicalLocation
- getReadGroup() - Method in class picard.sam.util.PhysicalLocationInt
- getReadGroupLibraryName(SAMReadGroupRecord) - Static method in class picard.sam.markduplicates.util.LibraryIdGenerator
- getReadHistogram() - Method in class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
- getReadType() - Method in class picard.illumina.parser.ReadData
- getRecord() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
- getRecord(int) - Method in class picard.arrays.illumina.InfiniumGTCFile
- getRecordReadName() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
- getRed() - Method in class picard.arrays.illumina.ArraysControlInfo
- getRefAllele() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- getReferenceFasta() - Method in class picard.fingerprint.FingerprintChecker
- getReferenceFile() - Method in class picard.analysis.CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
- getReferenceFile() - Method in class picard.analysis.CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection
- getReferenceFile() - Method in class picard.cmdline.argumentcollections.OptionalReferenceArgumentCollection
- getReferenceFile() - Method in interface picard.cmdline.argumentcollections.ReferenceArgumentCollection
- getReferenceFile() - Method in class picard.cmdline.argumentcollections.RequiredReferenceArgumentCollection
- getReferenceFile() - Method in class picard.sam.CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
- getReferenceFile() - Method in class picard.util.ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
- getReferenceSequence() - Method in class picard.metrics.SAMRecordAndReference
- getReferenceStrand() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- getRefStrand() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getRefStrand() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getRepresentativeSnp() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns a representative SNP for this haplotype.
- getRepresentativeSnp() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
-
Returns the SNP who's genotype was used to construct the likelihoods.
- getRepresentativeSnp() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
-
Simple returns the SNP from the haplotype that has the lowest genome coordinate.
- getRepresentativeSnp() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
- getReserved1() - Method in class picard.arrays.illumina.InfiniumTransformation
- getReserved2() - Method in class picard.arrays.illumina.InfiniumTransformation
- getReserved3() - Method in class picard.arrays.illumina.InfiniumTransformation
- getReserved4() - Method in class picard.arrays.illumina.InfiniumTransformation
- getReserved5() - Method in class picard.arrays.illumina.InfiniumTransformation
- getReserved6() - Method in class picard.arrays.illumina.InfiniumTransformation
- getRight() - Method in class picard.sam.util.Pair
- getRIlmn() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getRsId() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- getRunFile(File, Pattern) - Method in class picard.illumina.parser.ParameterizedFileUtil
- getSamFileHeader() - Method in class picard.analysis.CollectWgsMetrics
-
This method should only be called after
CollectWgsMetrics.getSamReader()
is called. - getSample() - Method in class picard.fingerprint.Fingerprint
- getSample() - Method in class picard.fingerprint.FingerprintIdDetails
- getSample() - Method in class picard.fingerprint.MatchResults
- getSampleAlias() - Method in class picard.fingerprint.FingerprintResults
- getSampleLikelihood() - Method in class picard.fingerprint.MatchResults
- getSampleName() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getSamplePlate() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getSampleWell() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getSamReader() - Method in class picard.analysis.CollectWgsMetrics
-
Gets the SamReader from which records will be examined.
- getSamReader() - Method in class picard.analysis.CollectWgsMetricsWithNonZeroCoverage
- getSamRecord() - Method in class picard.metrics.SAMRecordAndReference
- getSamRecordIndex() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
-
A number of convenience functions
- getScaleX() - Method in class picard.arrays.illumina.InfiniumTransformation
- getScaleY() - Method in class picard.arrays.illumina.InfiniumTransformation
- getScannerName() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getScannerVersion() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getScheme(boolean) - Method in class picard.vcf.GenotypeConcordanceSchemeFactory
- getSensitivity(GenotypeConcordanceScheme, GenotypeConcordanceStates.TruthState[]) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns the sensitivity defined by the scheme across the subset of truth states.
- getSentrixBarcode() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getSequentialFileList(Path) - Static method in class picard.sam.FastqToSam
-
Get a list of FASTQs that are sequentially numbered based on the first (base) fastq.
- getSex() - Method in class picard.pedigree.PedFile.PedTrio
- getSexConcordance(String, String, String) - Static method in class picard.arrays.CollectArraysVariantCallingMetrics
- getShear() - Method in class picard.arrays.illumina.InfiniumTransformation
- getSingleBarcodeDistanceQuery(int, int) - Method in class picard.util.BarcodeEditDistanceQuery
- getSingletonSample(VariantContext) - Static method in class picard.vcf.CallingMetricAccumulator
- getSizeOf() - Static method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
- getSizeOf() - Static method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
- getSnp() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getSnp() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getSnp(String) - Method in class picard.fingerprint.HaplotypeBlock
-
Gets a SNP by name if it belongs to this haplotype.
- getSnp(String, int) - Method in class picard.fingerprint.HaplotypeMap
-
Queries a Snp by chromosome and position.
- getSnpAlleleA() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- getSnpAlleleB() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- getSnpCounter() - Method in class picard.vcf.GenotypeConcordance
- getSnpGenotype(Snp, DiploidHaplotype) - Method in class picard.fingerprint.HaplotypeBlock
-
Gets the expected genotype of the provided SNP given the provided haplotype of this haplotype block.
- getSnpManifest() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getSnpRefAllele() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- getSnps() - Method in class picard.fingerprint.HaplotypeBlock
-
Returns an unmodifiable, unordered, collection of all SNPs in this haplotype block.
- getSolexaQualityCharFromFourQualities(String[], int, FormatUtil) - Static method in class picard.util.IlluminaUtil
-
Get a Solexa ASCII quality value from an array of strings that are integer qualities in this order: [cycle-1-A, cycle-1-C, cycle-1-G, cycle-1-T, cycle-2-A, ...].
- getSource() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getSource() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getSource() - Method in class picard.fingerprint.Fingerprint
- getSourceSeq() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getSourceSeq() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getSourceStrand() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getSourceStrand() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getSourceVersion() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getSourceVersion() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getSpecies() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getSpecies() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getSpecificity(GenotypeConcordanceScheme, GenotypeConcordanceStates.TruthState[]) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns the specificity defined by the scheme across the subset of truth states.
- getStandardUsagePreamble() - Method in class picard.cmdline.CommandLineProgram
- getStandardUsagePreamble(Class<?>) - Static method in class picard.cmdline.CommandLineProgram
-
A typical command line program will call this to get the beginning of the usage message, and then typically append a description of the program, like this: public String USAGE = getStandardUsagePreamble(getClass()) + "Frobnicate the freebozle."
- getSuffix() - Method in interface picard.sam.SamErrorMetric.BaseCalculator
-
The suffix that pertains to the implementation of aggregation
- getSuffix() - Method in class picard.sam.SamErrorMetric.BaseErrorAggregation
- getSuffix() - Method in class picard.sam.SamErrorMetric.IndelErrorCalculator
-
The suffix that pertains to the implementation of aggregation
- getSuffix() - Method in class picard.sam.SamErrorMetric.OverlappingReadsErrorCalculator
-
The suffix that pertains to the implementation of aggregation
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.BinnedReadCycleStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.CigarOperatorsInReadStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.CollectionStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.ConsensusStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellTileStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellXStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellYStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.GCContentStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.IndelLengthStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.IndelsInReadStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymerStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.MismatchesInReadStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.NsInReadStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.PairStratifier
- getSuffix() - Method in interface picard.sam.SamErrorMetric.ReadBaseStratification.RecordAndOffsetStratifier
- getSuffix() - Method in class picard.sam.SamErrorMetric.SimpleErrorCalculator
-
The suffix that pertains to the implementation of aggregation
- getSum() - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns the sum of all pairs of tuples defined by the truth state set and call state set.
- getSum(Set<GenotypeConcordanceStates.TruthState>, Set<GenotypeConcordanceStates.CallState>) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns the sum of all pairs of tuples defined by the truth state set and call state set.
- getSuperCategoryMap() - Static method in class picard.util.help.HelpConstants
- getSuperCategoryProperty(String) - Static method in class picard.util.help.HelpConstants
-
Given a group name, return a supercategory string for use by the online doc system to determine which supercateogry the group is in.
- getTheta() - Method in class picard.arrays.illumina.InfiniumTransformation
- getThetaIlmn() - Method in class picard.arrays.illumina.InfiniumGTCFile
- getThresholdForSelectingAdaptersToKeep() - Method in class picard.util.AdapterMarker
- getTile() - Method in class picard.illumina.parser.CbclData
- getTile() - Method in class picard.illumina.parser.ClusterData
- getTile() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
- getTile() - Method in interface picard.sam.util.PhysicalLocation
- getTile() - Method in class picard.sam.util.PhysicalLocationInt
- getTiledFiles(File, Pattern) - Static method in class picard.illumina.BasecallsConverter
-
Applies an lane and tile based regex to return all files matching that regex for each tile.
- getTiledFiles(File, Pattern) - Method in class picard.illumina.parser.ParameterizedFileUtil
-
Return all files that match pattern of the given file type in the given base directory
- getTileFromReadName(String) - Static method in class picard.util.IlluminaUtil
-
Parse the tile # from the read name.
- getTileInfo() - Method in class picard.illumina.parser.readers.BaseBclReader.CycleData
- getTileNum() - Method in class picard.illumina.parser.readers.BaseBclReader.TileData
- getTileNumber() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
- getTileNumber() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
- getTileNumber() - Method in class picard.illumina.parser.Tile
-
Returns the number/name of this tile.
- getTileOfNextCluster() - Method in class picard.illumina.parser.MultiTileParser
- getTileOfNextCluster() - Method in class picard.illumina.parser.MultiTileBclParser
-
Returns the tile of the next cluster that will be returned by PerTilePerCycleParser and therefore should be called before next() if you want to know the tile for the data returned by next()
- getTileOfNextCluster() - Method in class picard.illumina.parser.PerTileParser
-
Return the tile of the NEXT ILLUMINA_DATA object to be returned by the method next.
- getTiles() - Method in class picard.illumina.parser.MultiTileBclFileUtil
- getTiles() - Method in class picard.illumina.parser.MultiTileFileUtil
- getTiles() - Method in class picard.illumina.parser.ParameterizedFileUtil
-
Return a list of all tiles available for this file format and run
- getTiles() - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
-
Discover all files of this type in expectedBase that match pattern and construct a list of tiles available based on these files.
- getTiles() - Method in class picard.illumina.parser.TileIndex
- getTileTemplateRead() - Method in class picard.illumina.parser.TilePhasingValue
- getToMarkQueueMinimumDistance() - Method in class picard.sam.markduplicates.util.MarkQueue
-
Returns the minimum genomic distance such that we can be assured that all duplicates have been considered.
- getTopGenomicSeq() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getTopGenomicSeq() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- getTotal() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
- getTotalCycles() - Method in class picard.illumina.parser.ReadStructure.Substructure
- getTotalInserts() - Method in class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
- getTotalObs() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns the total number of observations of any allele.
- getTotalObs() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
-
Gets the total number of observations presented at this locus.
- getTotalObs() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
- getTotalOutputCycles() - Method in class picard.illumina.parser.OutputMapping
- getTranscriptCoordinate(int) - Method in class picard.annotation.Gene.Transcript
-
Given a coordinate on the genome (same chromosome) give the corresponding coordinate in the transcript.
- getUnfilteredBaseQHistogram() - Method in class picard.analysis.AbstractWgsMetricsCollector
- getUnfilteredDepthHistogram() - Method in class picard.analysis.AbstractWgsMetricsCollector
- getUniqueNormalizationIds() - Method in class picard.arrays.illumina.IlluminaBPMFile
- getUnmappedBoth() - Method in class picard.sam.util.SamComparison
- getUnmappedLeft() - Method in class picard.sam.util.SamComparison
- getUnmappedRight() - Method in class picard.sam.util.SamComparison
- getUnsupportedBuilds() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
- getUtil(IlluminaFileUtil.SupportedIlluminaFormat) - Method in class picard.illumina.parser.IlluminaFileUtil
-
Given a file type, get the Parameterized File Util object associated with it
- getValidationStringency() - Method in class picard.fingerprint.FingerprintChecker
- getValueFromVcfOtherHeaderLine(VCFHeader, String) - Static method in class picard.arrays.illumina.InfiniumVcfFields
- getVar(int, int) - Static method in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- getVariantTypeFromOrdinal(int) - Static method in enum class picard.util.VariantType
-
Gets the enum for a given ordinal
- getVersion() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- getVersion() - Method in class picard.arrays.illumina.InfiniumTransformation
- getVersion() - Method in class picard.cmdline.CommandLineProgram
- getVersion() - Method in class picard.illumina.parser.readers.TileMetricsOutReader
- getWordCount() - Method in class picard.util.AbstractInputParser
- getX() - Method in class picard.illumina.parser.ClusterData
- getX() - Method in interface picard.sam.util.PhysicalLocation
- getX() - Method in class picard.sam.util.PhysicalLocationInt
- getXCoordinate() - Method in class picard.illumina.parser.CbclData
- getY() - Method in class picard.illumina.parser.ClusterData
- getY() - Method in interface picard.sam.util.PhysicalLocation
- getY() - Method in class picard.sam.util.PhysicalLocationInt
- getYCoordinate() - Method in class picard.illumina.parser.CbclData
- getZeroBasedTileNumber() - Method in class picard.illumina.parser.TileIndex.TileIndexRecord
- GG - Enum constant in enum class picard.fingerprint.DiploidGenotype
- Graph() - Constructor for class picard.util.GraphUtils.Graph
- GraphUtils - Class in picard.util
-
Created by farjoun on 11/2/16.
- GraphUtils() - Constructor for class picard.util.GraphUtils
- GraphUtils.Graph<Node extends Comparable<Node>> - Class in picard.util
- GREEN - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
-
The green intensity value for the control.
- GroupAlignmentSummaryMetricsPerUnitMetricCollector(String, String, String) - Constructor for class picard.analysis.AlignmentSummaryMetricsCollector.GroupAlignmentSummaryMetricsPerUnitMetricCollector
- GT - Enum constant in enum class picard.fingerprint.DiploidGenotype
- GT_FILTERED - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- GT_FILTERED - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- GT_FILTERED_CODE - Enum constant in enum class picard.vcf.GenotypeConcordanceStateCodes
- GTA - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- GTC_CALL_RATE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The call rate as determined by Autocall/IAAP (and stored in the GTC File)
- GTC_CALL_RATE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- GTC_CALL_RATE_DETAIL - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- GtcToVcf - Class in picard.arrays
-
Class to convert an Illumina GTC file into a VCF file.
- GtcToVcf() - Constructor for class picard.arrays.GtcToVcf
- GtoA - Enum constant in enum class picard.analysis.artifacts.Transition
- GtoC - Enum constant in enum class picard.analysis.artifacts.Transition
- GtoG - Enum constant in enum class picard.analysis.artifacts.Transition
- GtoT - Enum constant in enum class picard.analysis.artifacts.Transition
- GTZ - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- GVCF_INPUT - Variable in class picard.vcf.CollectVariantCallingMetrics
- GvcfMetricAccumulator - Class in picard.vcf
-
An accumulator for collecting metrics about a single-sample GVCF.
- GvcfMetricAccumulator(DbSnpBitSetUtil.DbSnpBitSets) - Constructor for class picard.vcf.GvcfMetricAccumulator
H
- HAMMING - Enum constant in enum class picard.illumina.DistanceMetric
- hammingDistance() - Method in class picard.util.SingleBarcodeDistanceMetric
- handleAdditionalRecords(SAMRecord, Map<SAMReadGroupRecord, List<FastqWriter>>, SAMRecord, SAMRecord) - Method in class picard.sam.SamToFastq
- handleAdditionalRecords(SAMRecord, Map<SAMReadGroupRecord, List<FastqWriter>>, SAMRecord, SAMRecord) - Method in class picard.sam.SamToFastqWithTags
- handleChunk(List<ReadEndsForMarkDuplicates>) - Method in class picard.sam.markduplicates.MarkDuplicates
- HAPLOTYPE_MAP - Variable in class picard.fingerprint.CalculateFingerprintMetrics
- HAPLOTYPE_MAP - Variable in class picard.fingerprint.CheckFingerprint
- HAPLOTYPE_MAP - Variable in class picard.fingerprint.CrosscheckFingerprints
- HAPLOTYPE_MAP - Variable in class picard.fingerprint.ExtractFingerprint
- HAPLOTYPE_MAP - Variable in class picard.fingerprint.IdentifyContaminant
- HaplotypeBlock - Class in picard.fingerprint
-
Represents information about a group of SNPs that form a haplotype in perfect LD with one another.
- HaplotypeBlock(double) - Constructor for class picard.fingerprint.HaplotypeBlock
-
Constructs a haplotype block with the provided minor allele frequency.
- HaplotypeMap - Class in picard.fingerprint
-
A collection of metadata about Haplotype Blocks including multiple in memory "indices" of the data to make it easy to query the correct HaplotypeBlock or Snp by snp names, positions etc.
- HaplotypeMap(SAMFileHeader) - Constructor for class picard.fingerprint.HaplotypeMap
-
Constructs an empty HaplotypeMap using the provided SAMFileHeader's sequence dictionary.
- HaplotypeMap(File) - Constructor for class picard.fingerprint.HaplotypeMap
- HaplotypeMap(Collection<HaplotypeBlock>) - Constructor for class picard.fingerprint.HaplotypeMap
-
since this constructor doesn't initialize the HaplotypeMap "properly", it should be used carefully!
- HaplotypeProbabilities - Class in picard.fingerprint
-
Abstract class for storing and calculating various likelihoods and probabilities for haplotype alleles given evidence.
- HaplotypeProbabilities(HaplotypeBlock) - Constructor for class picard.fingerprint.HaplotypeProbabilities
- HaplotypeProbabilities.Genotype - Enum Class in picard.fingerprint
-
Log10(P(evidence| haplotype)) for the 3 different possible haplotypes {aa, ab, bb}
- HaplotypeProbabilitiesFromContaminatorSequence - Class in picard.fingerprint
-
Represents the probability of the underlying haplotype of the contaminating sample given the data.
- HaplotypeProbabilitiesFromContaminatorSequence(HaplotypeBlock, double) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
- HaplotypeProbabilitiesFromContaminatorSequence(HaplotypeProbabilitiesFromContaminatorSequence) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
- HaplotypeProbabilitiesFromGenotype - Class in picard.fingerprint
-
Represents a set of HaplotypeProbabilities that were derived from a single SNP genotype at a point in time.
- HaplotypeProbabilitiesFromGenotype(HaplotypeProbabilitiesFromGenotype) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
- HaplotypeProbabilitiesFromGenotype(Snp, HaplotypeBlock, double, double, double) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
- HaplotypeProbabilitiesFromGenotypeLikelihoods - Class in picard.fingerprint
-
Represents the likelihood of the HaplotypeBlock given the GenotypeLikelihoods (GL field from a VCF, which is actually a log10-likelihood) for each of the SNPs in that block.
- HaplotypeProbabilitiesFromGenotypeLikelihoods(HaplotypeBlock) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
- HaplotypeProbabilitiesFromGenotypeLikelihoods(HaplotypeProbabilitiesFromGenotypeLikelihoods) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
- HaplotypeProbabilitiesFromSequence - Class in picard.fingerprint
-
Represents the probability of the underlying haplotype given the data.
- HaplotypeProbabilitiesFromSequence(HaplotypeBlock) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromSequence
- HaplotypeProbabilitiesFromSequence(HaplotypeProbabilitiesFromSequence) - Constructor for class picard.fingerprint.HaplotypeProbabilitiesFromSequence
- HaplotypeProbabilityOfNormalGivenTumor - Class in picard.fingerprint
-
A wrapper class for any HaplotypeProbabilities instance that will assume that the given evidence is that of a tumor sample and provide an hp for the normal sample that tumor came from.
- HaplotypeProbabilityOfNormalGivenTumor(HaplotypeProbabilities, double) - Constructor for class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
- HaplotypeProbabilityOfNormalGivenTumor(HaplotypeProbabilityOfNormalGivenTumor) - Constructor for class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
- HAPLOTYPES - Variable in class picard.fingerprint.FingerprintMetrics
-
Number of haplotypes examined
- HAPLOTYPES_CONFIDENTLY_CHECKED - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
The subset of genotyped haplotypes for which there was sufficient sequence data to confidently genotype the haplotype.
- HAPLOTYPES_CONFIDENTLY_MATCHING - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
The subset of confidently checked haplotypes that match the expected genotypes.
- HAPLOTYPES_WITH_EVIDENCE - Variable in class picard.fingerprint.FingerprintMetrics
-
Number of haplotypes that had evidence in the source file
- HAPLOTYPES_WITH_GENOTYPES - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
The number of haplotypes that had expected genotypes to compare to.
- HARD_CLIP_OVERLAPPING_READS - Variable in class picard.sam.MergeBamAlignment
- hasBothParents() - Method in class picard.pedigree.PedFile.PedTrio
-
True if this record has paternal and maternal ids, otherwise false.
- hasCbcls(File, int) - Static method in class picard.illumina.parser.IlluminaFileUtil
- hasColumn(String) - Method in class picard.util.DelimitedTextFileWithHeaderIterator
- hasColumn(String) - Method in class picard.util.TabbedTextFileWithHeaderParser
- hasCoverage() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
-
Returns true if any base in the range has coverage of > 0
- hasError() - Method in class picard.util.ThreadPoolExecutorWithExceptions
- hasEvidence() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns true if evidence has been added, false if the probabilities are just the priors.
- hasEvidence() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
- hasEvidence() - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
- hasEvidence() - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
- hashCode() - Method in class picard.annotation.Gene.Transcript
- hashCode() - Method in class picard.fingerprint.FingerprintIdDetails
- hashCode() - Method in class picard.fingerprint.HaplotypeBlock
- hashCode() - Method in class picard.fingerprint.Snp
- hashCode() - Method in class picard.illumina.parser.Range
- hashCode() - Method in class picard.illumina.parser.ReadDescriptor
- hashCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
- hashCode() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
- hashCode() - Method in class picard.illumina.parser.ReadStructure
- hashCode() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
- hashCode() - Method in class picard.sam.util.Pair
-
Basic hashcode function.
- hashCode() - Method in class picard.sam.util.PrimaryAlignmentKey
- hashCode() - Method in class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
- hasLocation() - Method in interface picard.sam.util.PhysicalLocation
-
Default implementation of a method to check whether real location data has been set.
- hasNext() - Method in class picard.illumina.parser.MultiTileParser
- hasNext() - Method in class picard.illumina.parser.MultiTileBclParser
- hasNext() - Method in class picard.illumina.parser.PerTileParser
- hasNext() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
-
Return true if the file has more elements to return, false otherwise
- hasNext() - Method in class picard.illumina.parser.readers.BarcodeFileReader
- hasNext() - Method in class picard.illumina.parser.readers.BclReader
- hasNext() - Method in class picard.illumina.parser.readers.CbclReader
- hasNext() - Method in class picard.illumina.parser.readers.ClocsFileReader
- hasNext() - Method in class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader
- hasNext() - Method in class picard.illumina.parser.readers.FilterFileReader
- hasNext() - Method in class picard.illumina.parser.readers.LocsFileReader
- hasNext() - Method in class picard.illumina.parser.readers.PosFileReader
- hasNext() - Method in class picard.illumina.parser.readers.TileMetricsOutReader
- hasNext() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
- hasNext() - Method in class picard.util.AsyncIterator
- hasNext() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
- hasNext() - Method in class picard.util.SequenceDictionaryUtils.SamSequenceRecordsIterator
- hasNext() - Method in class picard.vcf.ByIntervalListVariantContextIterator
- hasNext() - Method in class picard.vcf.filter.FilterApplyingVariantIterator
- hasNext() - Method in class picard.vcf.PairedVariantSubContextIterator
- hasNext() - Method in class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
- hasSampleBarcode() - Method in class picard.illumina.parser.ReadStructure
- hasWebDocumentation(Class<?>) - Static method in class picard.cmdline.CommandLineProgram
-
Determine if a class has web documentation based on its package name
- header - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
- HEADER - Variable in class picard.sam.ReplaceSamHeader
- HEADER - Variable in class picard.vcf.FixVcfHeader
- HEADER_NAMES - Static variable in class picard.arrays.illumina.IlluminaManifest
- HEADER_ONLY - Variable in class picard.sam.ViewSam
- headerLines() - Method in class picard.vcf.filter.AlleleBalanceFilter
- headerLines() - Method in class picard.vcf.filter.FisherStrandFilter
- headerLines() - Method in class picard.vcf.filter.QdFilter
- headerLines() - Method in interface picard.vcf.filter.VariantFilter
-
Return VCF header lines that define filters that may be applied by the VariantFilter.
- HelpConstants - Class in picard.util.help
- HET_ALLELE12 - Enum constant in enum class picard.fingerprint.HaplotypeProbabilities.Genotype
- HET_AS_HOM - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
num of hets, observed as homs with LOD > threshold
- HET_CHI_SQUARED_PVALUE - Variable in class picard.fingerprint.FingerprintMetrics
-
The Chi-squared pvalue for the number of HETs and HOMs relative to the expected counts (2x2 table)
- HET_CROSS_ENTROPY_LOD - Variable in class picard.fingerprint.FingerprintMetrics
-
The categorical cross entropy of the counts of HETs and HOMs relative to the expected counts (big is bad)
- HET_GENOTYPE_FOR_PHASING - Static variable in class picard.fingerprint.HaplotypeMap
- HET_HOMVAR_RATIO - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
(count of hets)/(count of homozygous non-ref) for this sample
- HET_HOMVAR_RATIO - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
-
(count of hets)/(count of homozygous non-ref) for this sample
- HET_PCT - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
100 * (count of hets) / (total calls) for this sample
- HET_PPV - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The ppv (positive predictive value) for all heterozygous variants (PPV is the TP / (TP + FP))
- HET_REF_VAR1 - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- HET_REF_VAR1 - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- HET_REF_VAR1_CODE - Enum constant in enum class picard.vcf.GenotypeConcordanceStateCodes
- HET_REF_VAR2 - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- HET_REF_VAR3 - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- HET_SENSITIVITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The sensitivity for all heterozygous variants (Sensitivity is TP / (TP + FN))
- HET_SNP_Q - Variable in class picard.analysis.directed.PanelMetricsBase
-
The Phred Scaled Q Score of the theoretical HET SNP sensitivity.
- HET_SNP_Q - Variable in class picard.analysis.WgsMetrics
-
The Phred Scaled Q Score of the theoretical HET SNP sensitivity.
- HET_SNP_SENSITIVITY - Variable in class picard.analysis.directed.PanelMetricsBase
-
The theoretical HET SNP sensitivity.
- HET_SNP_SENSITIVITY - Variable in class picard.analysis.WgsMetrics
-
The theoretical HET SNP sensitivity.
- HET_SPECIFICITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The specificity for all heterozygous variants cannot be calculated
- HET_VAR1_VAR2 - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- HET_VAR1_VAR2 - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- HET_VAR1_VAR2_CODE - Enum constant in enum class picard.vcf.GenotypeConcordanceStateCodes
- HET_VAR1_VAR3 - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- HET_VAR3_VAR4 - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- hetAltDepthDistribution(int) - Static method in class picard.analysis.TheoreticalSensitivity
- hetSNPSensitivity(double[], double[], int, double) - Static method in class picard.analysis.TheoreticalSensitivity
- hetSNPSensitivity(double[], double[], int, double, boolean) - Static method in class picard.analysis.TheoreticalSensitivity
- HG_TO_NCBI - Static variable in class picard.arrays.illumina.IlluminaManifest
- HG17 - Static variable in class picard.arrays.illumina.IlluminaManifest
- HG18 - Static variable in class picard.arrays.illumina.IlluminaManifest
- HG19 - Static variable in class picard.arrays.illumina.IlluminaManifest
- highQualityDepthHistogram - Variable in class picard.analysis.WgsMetrics
-
Count of sites with a given depth of coverage.
- highQualityDepthHistogramArray - Variable in class picard.analysis.AbstractWgsMetricsCollector
-
Count of sites with a given depth of coverage.
- Histogram_FILE - Variable in class picard.analysis.CollectInsertSizeMetrics
- HISTOGRAM_FILE - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
- Histogram_R_SCRIPT - Static variable in class picard.analysis.CollectInsertSizeMetrics
- HISTOGRAM_WIDTH - Variable in class picard.analysis.CollectInsertSizeMetrics
- histogramGenerator - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsFlow
- HOM_ALLELE1 - Enum constant in enum class picard.fingerprint.HaplotypeProbabilities.Genotype
- HOM_ALLELE2 - Enum constant in enum class picard.fingerprint.HaplotypeProbabilities.Genotype
- HOM_AS_HET - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
num of homs, observed as hets with LOD > threshold
- HOM_AS_OTHER_HOM - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
num of homs, observed as other homs with LOD > threshold
- HOM_CHI_SQUARED_PVALUE - Variable in class picard.fingerprint.FingerprintMetrics
-
The Chi-squared pvalue for
FingerprintMetrics.NUM_HOM_ALLELE1
andFingerprintMetrics.NUM_HOM_ALLELE2
relative to the expected counts (2x2 table) - HOM_CROSS_ENTROPY_LOD - Variable in class picard.fingerprint.FingerprintMetrics
-
The categorical cross entropy of
FingerprintMetrics.NUM_HOM_ALLELE1
andFingerprintMetrics.NUM_HOM_ALLELE2
relative to the expected counts (big is bad) - HOM_REF - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- HOM_REF - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- HOM_REF_CODE - Enum constant in enum class picard.vcf.GenotypeConcordanceStateCodes
- HOM_VAR1 - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- HOM_VAR1 - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- HOM_VAR1_CODE - Enum constant in enum class picard.vcf.GenotypeConcordanceStateCodes
- HOM_VAR2 - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- HOM_VAR3 - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- homoPolymerLengthStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies a base onto the length of the homopolymer preceding it (in the read direction).
- homopolymerStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies a base onto the make up (repeating base and following reference base) and length of the homopolymer from whence it came.
- HOMVAR_PPV - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The ppv (positive predictive value) for all homozygous variants (PPV is the TP / (TP + FP))
- HOMVAR_SENSITIVITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The sensitivity for all homozygous variants (Sensitivity is TP / (TP + FN))
- HOMVAR_SPECIFICITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The specificity for all homozygous variants cannot be calculated.
- HS_LIBRARY_SIZE - Variable in class picard.analysis.directed.HsMetrics
-
The estimated number of unique molecules in the selected part of the library.
- HS_PENALTY_100X - Variable in class picard.analysis.directed.HsMetrics
-
The "hybrid selection penalty" incurred to get 80% of target bases to 100X.
- HS_PENALTY_10X - Variable in class picard.analysis.directed.HsMetrics
-
The "hybrid selection penalty" incurred to get 80% of target bases to 10X.
- HS_PENALTY_20X - Variable in class picard.analysis.directed.HsMetrics
-
The "hybrid selection penalty" incurred to get 80% of target bases to 20X.
- HS_PENALTY_30X - Variable in class picard.analysis.directed.HsMetrics
-
The "hybrid selection penalty" incurred to get 80% of target bases to 30X.
- HS_PENALTY_40X - Variable in class picard.analysis.directed.HsMetrics
-
The "hybrid selection penalty" incurred to get 80% of target bases to 40X.
- HS_PENALTY_50X - Variable in class picard.analysis.directed.HsMetrics
-
The "hybrid selection penalty" incurred to get 80% of target bases to 50X.
- HsMetricCollector - Class in picard.analysis.directed
-
Calculates HS metrics for a given SAM or BAM file.
- HsMetricCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, boolean, boolean, int, int) - Constructor for class picard.analysis.directed.HsMetricCollector
- HsMetricCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, int, int) - Constructor for class picard.analysis.directed.HsMetricCollector
- HsMetrics - Class in picard.analysis.directed
-
Metrics generated by CollectHsMetrics for the analysis of target-capture sequencing experiments.
- HsMetrics() - Constructor for class picard.analysis.directed.HsMetrics
I
- ID - Variable in class picard.arrays.VerifyIDIntensityContaminationMetrics
-
The ID of this entry
- identifyContaminant(Path, double) - Method in class picard.fingerprint.FingerprintChecker
-
Generates a per-sample Fingerprint for the contaminant in the supplied SAM file.
- IdentifyContaminant - Class in picard.fingerprint
-
Program to create a fingerprint for the contaminating sample when the level of contamination is both known and uniform in the genome.
- IdentifyContaminant() - Constructor for class picard.fingerprint.IdentifyContaminant
- IGC - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- IGNORE - Variable in class picard.sam.ValidateSamFile
- IGNORE_FILTER_STATUS - Variable in class picard.vcf.GenotypeConcordance
- IGNORE_HISTOGRAM_DIFFERENCES - Variable in class picard.analysis.CompareMetrics
- IGNORE_MISSING_MATES - Variable in class picard.sam.FixMateInformation
- IGNORE_READ_GROUPS - Variable in class picard.fingerprint.CheckFingerprint
- IGNORE_SEQUENCE - Variable in class picard.analysis.CollectMultipleMetrics
- IGNORE_SEQUENCE - Variable in class picard.analysis.CollectRnaSeqMetrics
- IGNORE_UNEXPECTED_BARCODES - Variable in class picard.illumina.IlluminaBasecallsToFastq
- IGNORE_UNEXPECTED_BARCODES - Variable in class picard.illumina.IlluminaBasecallsToSam
- IGNORE_WARNINGS - Variable in class picard.sam.ValidateSamFile
- ignoreAlignment(SAMRecord) - Method in class picard.sam.AbstractAlignmentMerger
- ignoreAlignment(SAMRecord) - Method in class picard.sam.SamAlignmentMerger
-
For now, we ignore only those alignments that have more than
SamAlignmentMerger.maxGaps
insertions or deletions. - IGNORED_READS - Variable in class picard.analysis.RnaSeqMetrics
-
Number of primary alignments that are mapped to a sequence specified on command-line as IGNORED_SEQUENCE.
- ignoreUnexpectedBarcodes - Variable in class picard.illumina.BasecallsConverter
- ILLUMINA - Enum constant in enum class picard.illumina.IlluminaBasecallsToFastq.ReadNameFormat
- ILLUMINA_ALLEGED_MINIMUM_QUALITY - Static variable in class picard.illumina.parser.readers.BclQualityEvaluationStrategy
- ILLUMINA_BEAD_POOL_MANIFEST_FILE - Variable in class picard.arrays.GtcToVcf
- ILLUMINA_BEAD_POOL_MANIFEST_FILE - Variable in class picard.arrays.illumina.CompareGtcFiles
- ILLUMINA_BUILD - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- ILLUMINA_CHR - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- ILLUMINA_FLAGGED - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Flagged by Illumina as a bad assay
- ILLUMINA_FLAGGED_BAD_CHR - Static variable in class picard.arrays.illumina.IlluminaManifestRecord
- ILLUMINA_ID_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- ILLUMINA_POS - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- ILLUMINA_STRAND - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- ILLUMINA_STRAND_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- IlluminaAdpcFileWriter - Class in picard.arrays.illumina
-
A class to encompass writing an Illumina adpc.bin file.
- IlluminaAdpcFileWriter(File) - Constructor for class picard.arrays.illumina.IlluminaAdpcFileWriter
- IlluminaAdpcFileWriter.Record - Class in picard.arrays.illumina
- IlluminaBasecallingMetrics - Class in picard.illumina
-
Metric for Illumina Basecalling that stores means and standard deviations on a per-barcode per-lane basis.
- IlluminaBasecallingMetrics() - Constructor for class picard.illumina.IlluminaBasecallingMetrics
- IlluminaBasecallsToFastq - Class in picard.illumina
- IlluminaBasecallsToFastq() - Constructor for class picard.illumina.IlluminaBasecallsToFastq
- IlluminaBasecallsToFastq.ReadNameFormat - Enum Class in picard.illumina
-
Simple switch to control the read name format to emit.
- IlluminaBasecallsToSam - Class in picard.illumina
-
IlluminaBasecallsToSam transforms a lane of Illumina data file formats (bcl, locs, clocs, qseqs, etc.) into SAM, BAM or CRAM file format.
- IlluminaBasecallsToSam() - Constructor for class picard.illumina.IlluminaBasecallsToSam
- IlluminaBPMFile - Class in picard.arrays.illumina
-
A class to parse the contents of an Illumina Bead Pool Manifest (BPM) file A BPM file contains metadata (including the alleles, mapping and normalization information) on an Illumina Genotyping Array Each type of genotyping array has a specific BPM .
- IlluminaBPMFile(File) - Constructor for class picard.arrays.illumina.IlluminaBPMFile
- IlluminaBPMLocusEntry - Class in picard.arrays.illumina
-
A simple class to represent a locus entry in an Illumina Bead Pool Manifest (BPM) file
- IlluminaBPMLocusEntry() - Constructor for class picard.arrays.illumina.IlluminaBPMLocusEntry
- IlluminaDataProviderFactory - Class in picard.illumina.parser
-
IlluminaDataProviderFactory accepts options for parsing Illumina data files for a lane and creates an IlluminaDataProvider, an iterator over the ClusterData for that lane, which utilizes these options.
- IlluminaDataProviderFactory(File, int, ReadStructure, BclQualityEvaluationStrategy, Set<IlluminaDataType>) - Constructor for class picard.illumina.parser.IlluminaDataProviderFactory
-
Create factory with the specified options, one that favors using QSeqs over all other files
- IlluminaDataProviderFactory(File, File, int, ReadStructure, BclQualityEvaluationStrategy, Set<IlluminaDataType>) - Constructor for class picard.illumina.parser.IlluminaDataProviderFactory
-
Create factory with the specified options, one that favors using QSeqs over all other files
- IlluminaDataType - Enum Class in picard.illumina.parser
-
List of data types of interest when parsing Illumina data.
- IlluminaFileUtil - Class in picard.illumina.parser
-
General utils for dealing with IlluminaFiles as well as utils for specific, support formats.
- IlluminaFileUtil(File, int) - Constructor for class picard.illumina.parser.IlluminaFileUtil
- IlluminaFileUtil(File, File, int) - Constructor for class picard.illumina.parser.IlluminaFileUtil
- IlluminaFileUtil.SupportedIlluminaFormat - Enum Class in picard.illumina.parser
- IlluminaGenotype - Enum Class in picard.arrays.illumina
- IlluminaLaneMetrics - Class in picard.illumina
-
Embodies characteristics that describe a lane.
- IlluminaLaneMetrics() - Constructor for class picard.illumina.IlluminaLaneMetrics
- IlluminaLaneMetricsCollector() - Constructor for class picard.illumina.CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
- IlluminaLaneTileCode(int, int, int) - Constructor for class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaLaneTileCode
- IlluminaManifest - Class in picard.arrays.illumina
-
A class to represent an Illumina Manifest file.
- IlluminaManifest(File) - Constructor for class picard.arrays.illumina.IlluminaManifest
- IlluminaManifest(File, int) - Constructor for class picard.arrays.illumina.IlluminaManifest
- IlluminaManifestRecord - Class in picard.arrays.illumina
-
A class to represent a record (line) from an Illumina Manifest [Assay] entry
- IlluminaManifestRecord.IlluminaStrand - Enum Class in picard.arrays.illumina
- IlluminaMetricsCode - Enum Class in picard.illumina.parser
-
Illumina's TileMetricsOut.bin file codes various metrics, both concrete (all density id's are code 100) or as a base code (e.g.
- IlluminaPhasingMetrics - Class in picard.illumina
-
Metrics for Illumina Basecalling that stores median phasing and prephasing percentages on a per-template-read, per-lane basis.
- IlluminaPhasingMetrics() - Constructor for class picard.illumina.IlluminaPhasingMetrics
- IlluminaReadNameEncoder - Class in picard.fastq
-
A read name encoder following the encoding initially produced by picard fastq writers.
- IlluminaReadNameEncoder(String) - Constructor for class picard.fastq.IlluminaReadNameEncoder
- IlluminaTileMetrics(int, int, int, float) - Constructor for class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
- IlluminaTileMetrics(ByteBuffer, TileMetricsOutReader.TileMetricsVersion) - Constructor for class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
- IlluminaUtil - Class in picard.util
-
Misc utilities for working with Illumina specific files and data
- IlluminaUtil() - Constructor for class picard.util.IlluminaUtil
- IlluminaUtil.IlluminaAdapterPair - Enum Class in picard.util
-
Describes adapters used on each pair of strands
- IMAGING_DATE - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The date that this sample was imaged
- IMAGING_DATE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- IMPROPER - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
- in - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
- in - Variable in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
- INCLUDE_BARCODE_QUALITY - Variable in class picard.illumina.IlluminaBasecallsToSam
- INCLUDE_BC_IN_RG_TAG - Variable in class picard.illumina.IlluminaBasecallsToSam
- INCLUDE_BQ_HISTOGRAM - Variable in class picard.analysis.CollectWgsMetrics
- INCLUDE_DUPLICATES - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- INCLUDE_DUPLICATES - Variable in class picard.analysis.CollectInsertSizeMetrics
- INCLUDE_FILTERED - Variable in class picard.util.IntervalListTools
- INCLUDE_FILTERED - Variable in class picard.vcf.VcfToIntervalList
- INCLUDE_FILTERED_SHORT_NAME - Static variable in class picard.vcf.VcfToIntervalList
- INCLUDE_INDELS - Variable in class picard.analysis.directed.CollectTargetedMetrics
- INCLUDE_NO_CALLS - Variable in class picard.analysis.QualityScoreDistribution
- INCLUDE_NON_PF_READS - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- INCLUDE_NON_PF_READS - Variable in class picard.analysis.CollectOxoGMetrics
- INCLUDE_NON_PF_READS - Variable in class picard.illumina.IlluminaBasecallsToFastq
- INCLUDE_NON_PF_READS - Variable in class picard.illumina.IlluminaBasecallsToSam
- INCLUDE_NON_PF_READS - Variable in class picard.sam.SamToFastq
- INCLUDE_NON_PRIMARY_ALIGNMENTS - Variable in class picard.sam.SamToFastq
- INCLUDE_SECONDARY_ALIGNMENTS - Variable in class picard.analysis.CollectQualityYieldMetrics
- INCLUDE_SECONDARY_ALIGNMENTS - Variable in class picard.sam.MergeBamAlignment
- INCLUDE_SUPPLEMENTAL_ALIGNMENTS - Variable in class picard.analysis.CollectQualityYieldMetrics
- INCLUDE_UNPAIRED - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- INCLUDE_UNPAIRED - Variable in class picard.analysis.CollectMultipleMetrics
- includeAligned - Enum constant in enum class picard.sam.FilterSamReads.Filter
- includeJavascript - Enum constant in enum class picard.sam.FilterSamReads.Filter
- includeNonPfReads - Variable in class picard.illumina.BasecallsConverter
- includePairedIntervals - Enum constant in enum class picard.sam.FilterSamReads.Filter
- includeReadList - Enum constant in enum class picard.sam.FilterSamReads.Filter
- includeSupplementalAlignments - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsCollector
- includeTagValues - Enum constant in enum class picard.sam.FilterSamReads.Filter
- INCOMPARABLE_CODE - Enum constant in enum class picard.vcf.GenotypeConcordanceStateCodes
- INCONCLUSIVE - Enum constant in enum class picard.fingerprint.CrosscheckMetric.FingerprintResult
- INCORRECT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
-
Number of aligned reads that are mapped to the incorrect strand.
- increment(int) - Method in class picard.analysis.CounterManager.Counter
-
Increments value corresponding to reference sequence index
- increment(GenotypeConcordanceStates.TruthAndCallStates) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Increments a count for the truth/call state tuple.
- increment(GenotypeConcordanceStates.TruthAndCallStates, double) - Method in class picard.vcf.GenotypeConcordanceCounts
- incrementReadCount() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
-
Increments the # of reads mapping to this target.
- INDEL_CONFLICT - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Both insertion and deletion sequence found in reference.
- INDEL_EXTENSION_ERROR - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Deprecated.- but used in existing extended manifest files.
- INDEL_NOT_FOUND - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Neither insertion nor deletion sequence found in reference.
- INDEL_OUTPUT - Variable in class picard.vcf.SplitVcfs
- INDEL_SEQ_MISMATCH - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Deprecated.- but used in existing extended manifest files.
- INDEL_SEQUENCE - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
- indelCounter - Variable in class picard.vcf.GenotypeConcordance
- IndelErrorCalculator - Class in picard.sam.SamErrorMetric
-
A calculator that estimates the error rate of the bases it observes for indels only.
- IndelErrorCalculator() - Constructor for class picard.sam.SamErrorMetric.IndelErrorCalculator
- IndelErrorMetric - Class in picard.sam.SamErrorMetric
-
Metric to be used for InDel errors
- IndelErrorMetric() - Constructor for class picard.sam.SamErrorMetric.IndelErrorMetric
- IndelErrorMetric(String, long, long, long, long, long) - Constructor for class picard.sam.SamErrorMetric.IndelErrorMetric
- indelLengthStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies into the number of bases in an insertion
- IndelLengthStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.IndelLengthStratifier
- indels - Variable in class picard.util.DbSnpBitSetUtil.DbSnpBitSets
- indelsInReadStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratify by Indels in the read cigars.
- IndelsInReadStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.IndelsInReadStratifier
- IndependentReplicateMetric - Class in picard.analysis.replicates
-
A class to store information relevant for biological rate estimation
- IndependentReplicateMetric() - Constructor for class picard.analysis.replicates.IndependentReplicateMetric
- independentReplicationRateFromBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
- independentReplicationRateFromTriDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The biological duplication rate (as a fraction of the duplicates sets) calculated from tripleton sets.
- independentReplicationRateFromUmi - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
Given the UMIs one can estimate the rate of biological duplication directly, as this would be the rate of having different UMIs in all duplicate sets.
- INDEX_VALIDATION_STRINGENCY - Variable in class picard.sam.ValidateSamFile
- INDEXED - Enum constant in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- indexOfMax(double[]) - Static method in class picard.util.MathUtil
-
Returns the index of the largest element in the array.
- indexOfMax(long[]) - Static method in class picard.util.MathUtil
-
Returns the index of the largest element in the array.
- indexOfMin(double[]) - Static method in class picard.util.MathUtil
-
Returns the index of the smallest element in the array.
- indexOfMin(int[]) - Static method in class picard.util.MathUtil
-
Returns the index of the smallest element in the array.
- IndividualAlignmentSummaryMetricsCollector(AlignmentSummaryMetrics.Category, String, String, String) - Constructor for class picard.analysis.AlignmentSummaryMetricsCollector.IndividualAlignmentSummaryMetricsCollector
- inferArtifactName() - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
Label the artifacts corresponding to known error modes.
- inferArtifactName() - Method in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
Label the artifacts corresponding to known error modes.
- INFERRED_UMI_ENTROPY - Variable in class picard.sam.markduplicates.UmiMetrics
-
Entropy (in base 4) of the inferred UMI sequences, indicating the effective number of bases in the inferred UMIs.
- INFERRED_UNIQUE_UMIS - Variable in class picard.sam.markduplicates.UmiMetrics
-
Number of different inferred UMI sequences derived
- InfiniumDataFile - Class in picard.arrays.illumina
-
A class to provide methods for accessing Illumina Infinium Data Files.
- InfiniumEGTFile - Class in picard.arrays.illumina
-
A class to parse the contents of an Illumina Infinium cluster (EGT) file A cluster file contains information about the clustering information used in mapping red / green intensity information to genotype calls
- InfiniumEGTFile(File) - Constructor for class picard.arrays.illumina.InfiniumEGTFile
- InfiniumFileTOC - Class in picard.arrays.illumina
-
A class to encapsulate the table of contents for an Illumina Infinium Data Files.
- InfiniumFileTOC() - Constructor for class picard.arrays.illumina.InfiniumFileTOC
- InfiniumGTCFile - Class in picard.arrays.illumina
-
A class to parse the contents of an Illumina Infinium genotype (GTC) file A GTC file is the output of Illumina's genotype calling software (either Autocall or Autoconvert) and contains genotype calls, confidence scores, basecalls and raw intensities for all calls made on the chip.
- InfiniumGTCFile(File, File) - Constructor for class picard.arrays.illumina.InfiniumGTCFile
-
Creates an InfiniumGTCFile object and parses the given input file.
- InfiniumGTCRecord - Class in picard.arrays.illumina
- InfiniumGTCRecord(String) - Constructor for class picard.arrays.illumina.InfiniumGTCRecord
- InfiniumNormalizationManifest - Class in picard.arrays.illumina
-
A class to parse the contents of an Illumina Infinium Normalization Manifest file An Illumina Infinium Normalization Manifest file contains a subset of the information contained in the Illumina Manifest file in addition to the normalization ID which is needed for normalizating intensities in GtcToVcf
- InfiniumNormalizationManifest(File) - Constructor for class picard.arrays.illumina.InfiniumNormalizationManifest
- InfiniumTransformation - Class in picard.arrays.illumina
- InfiniumTransformation() - Constructor for class picard.arrays.illumina.InfiniumTransformation
- InfiniumVcfFields - Class in picard.arrays.illumina
-
A class to store fields that are specific to a VCF generated from an Illumina GTC file.
- InfiniumVcfFields() - Constructor for class picard.arrays.illumina.InfiniumVcfFields
- InfiniumVcfFields.GENOTYPE_VALUES - Enum Class in picard.arrays.illumina
- INFO - Variable in class picard.fingerprint.FingerprintMetrics
-
Additional information about the fingerprint
- initialize() - Method in class picard.illumina.parser.MultiTileBclParser
- initialize() - Method in enum class picard.nio.PathProvider
- initializeAdditionalWriters() - Method in class picard.sam.SamToFastq
- initializeAdditionalWriters() - Method in class picard.sam.SamToFastqWithTags
- initiateScheme() - Method in class picard.vcf.GA4GHScheme
- initiateScheme() - Method in class picard.vcf.GA4GHSchemeWithMissingAsHomRef
- initiateScheme() - Method in class picard.vcf.GenotypeConcordanceScheme
- INPUT - Variable in class picard.analysis.CollectJumpingLibraryMetrics
- INPUT - Variable in class picard.analysis.CollectMultipleMetrics
- INPUT - Variable in class picard.analysis.CollectOxoGMetrics
- INPUT - Variable in class picard.analysis.CollectRrbsMetrics
- INPUT - Variable in class picard.analysis.CollectWgsMetrics
- INPUT - Variable in class picard.analysis.CompareMetrics
- INPUT - Variable in class picard.analysis.directed.CollectTargetedMetrics
- INPUT - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- INPUT - Variable in class picard.analysis.SinglePassSamProgram
- INPUT - Variable in class picard.annotation.SortGff
- INPUT - Variable in class picard.arrays.CollectArraysVariantCallingMetrics
- INPUT - Variable in class picard.arrays.CombineGenotypingArrayVcfs
- INPUT - Variable in class picard.arrays.CreateBafRegressMetricsFile
- INPUT - Variable in class picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile
- INPUT - Variable in class picard.arrays.GtcToVcf
- INPUT - Variable in class picard.arrays.illumina.BpmToNormalizationManifestCsv
- INPUT - Variable in class picard.arrays.illumina.CompareGtcFiles
- INPUT - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- INPUT - Variable in class picard.fingerprint.CalculateFingerprintMetrics
- INPUT - Variable in class picard.fingerprint.CheckFingerprint
- INPUT - Variable in class picard.fingerprint.ClusterCrosscheckMetrics
- INPUT - Variable in class picard.fingerprint.ConvertHaplotypeDatabaseToVcf
- INPUT - Variable in class picard.fingerprint.CrosscheckFingerprints
- INPUT - Variable in class picard.fingerprint.ExtractFingerprint
- INPUT - Variable in class picard.fingerprint.IdentifyContaminant
- INPUT - Variable in class picard.fingerprint.LiftOverHaplotypeMap
- INPUT - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
- INPUT - Variable in class picard.illumina.MarkIlluminaAdapters
- INPUT - Variable in class picard.reference.NonNFastaSize
- INPUT - Variable in class picard.reference.NormalizeFasta
- INPUT - Variable in class picard.sam.AddCommentsToBam
- INPUT - Variable in class picard.sam.AddOATag
- INPUT - Variable in class picard.sam.AddOrReplaceReadGroups
- INPUT - Variable in class picard.sam.BamIndexStats
- INPUT - Variable in class picard.sam.BuildBamIndex
- INPUT - Variable in class picard.sam.CalculateReadGroupChecksum
- INPUT - Variable in class picard.sam.CheckTerminatorBlock
- INPUT - Variable in class picard.sam.CleanSam
- INPUT - Variable in class picard.sam.DownsampleSam
- INPUT - Variable in class picard.sam.FilterSamReads
- INPUT - Variable in class picard.sam.FixMateInformation
- INPUT - Variable in class picard.sam.GatherBamFiles
- INPUT - Variable in class picard.sam.markduplicates.CheckDuplicateMarking
- INPUT - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
- INPUT - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- INPUT - Variable in class picard.sam.MergeSamFiles
- INPUT - Variable in class picard.sam.PositionBasedDownsampleSam
- INPUT - Variable in class picard.sam.ReorderSam
- INPUT - Variable in class picard.sam.ReplaceSamHeader
- INPUT - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
- INPUT - Variable in class picard.sam.RevertSam
- INPUT - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- INPUT - Variable in class picard.sam.SamFormatConverter
- INPUT - Variable in class picard.sam.SamToFastq
- INPUT - Variable in class picard.sam.SetNmMdAndUqTags
- INPUT - Variable in class picard.sam.SortSam
- INPUT - Variable in class picard.sam.SplitSamByLibrary
- INPUT - Variable in class picard.sam.SplitSamByNumberOfReads
- INPUT - Variable in class picard.sam.ValidateSamFile
- INPUT - Variable in class picard.sam.ViewSam
- INPUT - Variable in class picard.util.AccumulateQualityYieldMetrics
- INPUT - Variable in class picard.util.BedToIntervalList
- INPUT - Variable in class picard.util.IntervalListToBed
- INPUT - Variable in class picard.util.IntervalListTools
- INPUT - Variable in class picard.util.LiftOverIntervalList
- INPUT - Variable in class picard.vcf.AccumulateVariantCallingMetrics
- INPUT - Variable in class picard.vcf.CollectVariantCallingMetrics
- INPUT - Variable in class picard.vcf.filter.FilterVcf
- INPUT - Variable in class picard.vcf.FixVcfHeader
- INPUT - Variable in class picard.vcf.GatherVcfs
- INPUT - Variable in class picard.vcf.LiftoverVcf
- INPUT - Variable in class picard.vcf.MakeSitesOnlyVcf
- INPUT - Variable in class picard.vcf.MakeVcfSampleNameMap
- INPUT - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
- INPUT - Variable in class picard.vcf.MergeVcfs
- INPUT - Variable in class picard.vcf.RenameSampleInVcf
- INPUT - Variable in class picard.vcf.SortVcf
- INPUT - Variable in class picard.vcf.SplitVcfs
- INPUT - Variable in class picard.vcf.UpdateVcfSequenceDictionary
- INPUT - Variable in class picard.vcf.VcfFormatConverter
- INPUT - Variable in class picard.vcf.VcfToIntervalList
- INPUT_BASE - Variable in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
- INPUT_INDEX_MAP - Variable in class picard.fingerprint.CrosscheckFingerprints
- INPUT_PARAMS_FILE - Variable in class picard.illumina.ExtractBarcodesProgram
- INPUT_SAMPLE_FILE_MAP - Variable in class picard.fingerprint.CrosscheckFingerprints
- INPUT_SAMPLE_MAP - Variable in class picard.fingerprint.CrosscheckFingerprints
- INPUT_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- inputReadStructure - Variable in class picard.illumina.ExtractBarcodesProgram
-
The read structure of the actual Illumina Run, i.e.
- insertion - Enum constant in enum class picard.util.VariantType
- INSERTIONS_Q - Variable in class picard.sam.SamErrorMetric.IndelErrorMetric
-
The (phred) rate of insertions.
- insertionsInReadStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratify by Insertions in the read cigars.
- insertLengthStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies into the read-pairs estimated insert-length, as long as it isn't larger than 10x the length of the read
- InsertSizeMetrics - Class in picard.analysis
-
Metrics about the insert size distribution of a paired-end library, created by the CollectInsertSizeMetrics program and usually written to a file with the extension ".insert_size_metrics".
- InsertSizeMetrics() - Constructor for class picard.analysis.InsertSizeMetrics
- InsertSizeMetricsCollector - Class in picard.analysis.directed
-
Collects InsertSizeMetrics on the specified accumulationLevels using
- InsertSizeMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, double, Integer, Integer, double, boolean) - Constructor for class picard.analysis.directed.InsertSizeMetricsCollector
- InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector - Class in picard.analysis.directed
-
A Collector for individual InsertSizeMetrics for a given SAMPLE or SAMPLE/LIBRARY or SAMPLE/LIBRARY/READ_GROUP (depending on aggregation levels)
- instanceMain(String[]) - Method in class picard.cmdline.CommandLineProgram
- instanceMain(String[]) - Method in class picard.cmdline.PicardCommandLine
-
For testing
- instanceMain(String[], List<String>, String) - Method in class picard.cmdline.PicardCommandLine
-
The main method.
- instanceMainWithExit(String[]) - Method in class picard.cmdline.CommandLineProgram
- INTENSITY_ONLY_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- IntensityChannel - Enum Class in picard.illumina.parser
-
The channels in a FourChannelIntensityData object, and the channels produced by a ClusterIntensityFileReader, for cases in which it is desirable to handle these abstractly rather than having the specific names in the source code.
- INTERGENIC - Enum constant in enum class picard.annotation.LocusFunction
- INTERGENIC_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
Number of bases in primary alignments that do not align to any gene.
- INTERLEAVE - Variable in class picard.sam.SamToFastq
- INTEROP_SUBDIRECTORY_NAME - Static variable in class picard.illumina.parser.TileMetricsUtil
-
The path to the directory containing the tile metrics file relative to the basecalling directory.
- interruptAndShutdownExecutors(ThreadPoolExecutorWithExceptions...) - Method in class picard.illumina.BasecallsConverter
- INTERSECT - Enum constant in enum class picard.util.IntervalListTools.Action
- INTERSECT_INTERVALS - Variable in class picard.vcf.GenotypeConcordance
- INTERVAL_COUNT - Enum constant in enum class picard.util.IntervalList.IntervalListScatterMode
-
A scatter by interval **count** which attempts to fill each resulting interval list with the same number of intervals, disregarding the base count.
- INTERVAL_COUNT_WITH_DISTRIBUTED_REMAINDER - Enum constant in enum class picard.util.IntervalList.IntervalListScatterMode
-
A scatter by interval **count** which attempts to fill each resulting interval list with approximately equal numbers of intervals, disregarding the base count.
- INTERVAL_ITERATOR - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- INTERVAL_LIST - Variable in class picard.reference.ExtractSequences
- INTERVAL_LIST - Variable in class picard.sam.AddOATag
- INTERVAL_LIST - Variable in class picard.sam.FilterSamReads
- INTERVAL_LIST - Variable in class picard.sam.ViewSam
- INTERVAL_SUBDIVISION - Enum constant in enum class picard.util.IntervalList.IntervalListScatterMode
-
A simple scatter approach in which all output intervals have size equal to the total base count of the source list divide by the scatter count (except for possible variance in the final interval list).
- intervalArgumentCollection - Variable in class picard.analysis.CollectWgsMetrics
- IntervalArgumentCollection - Interface in picard.cmdline.argumentcollections
-
Base interface for an interval argument collection.
- IntervalListScatter - Class in picard.util.IntervalList
- IntervalListScatter(IntervalListScatterer, IntervalList, int) - Constructor for class picard.util.IntervalList.IntervalListScatter
- IntervalListScatterer - Interface in picard.util.IntervalList
-
An interface for a class that scatters IntervalLists.
- IntervalListScattererByBaseCount - Class in picard.util.IntervalList
-
a Baseclass for scatterers that scatter by uniqued base count.
- IntervalListScattererByBaseCount() - Constructor for class picard.util.IntervalList.IntervalListScattererByBaseCount
- IntervalListScattererByIntervalCount - Class in picard.util.IntervalList
-
Scatters
IntervalList
by interval count so that resultingIntervalList
's have the same number of intervals in them. - IntervalListScattererByIntervalCount() - Constructor for class picard.util.IntervalList.IntervalListScattererByIntervalCount
- IntervalListScattererByIntervalCountWithDistributedRemainder - Class in picard.util.IntervalList
-
Scatters
IntervalList
by into `interval count` shards so that resultingIntervalList
's have approximately same number of intervals in them. - IntervalListScattererByIntervalCountWithDistributedRemainder() - Constructor for class picard.util.IntervalList.IntervalListScattererByIntervalCountWithDistributedRemainder
- IntervalListScattererWithoutSubdivision - Class in picard.util.IntervalList
-
A BaseCount Scatterer that avoid breaking-up intervals.
- IntervalListScattererWithoutSubdivision() - Constructor for class picard.util.IntervalList.IntervalListScattererWithoutSubdivision
- IntervalListScattererWithoutSubdivisionWithOverflow - Class in picard.util.IntervalList
-
Like
IntervalListScattererWithoutSubdivision
but will overflow current list if the projected size of the remaining lists is bigger than the "ideal". - IntervalListScattererWithoutSubdivisionWithOverflow() - Constructor for class picard.util.IntervalList.IntervalListScattererWithoutSubdivisionWithOverflow
- IntervalListScattererWithSubdivision - Class in picard.util.IntervalList
-
An IntervalListScatterer that attempts to place the same number of (uniquified) bases in each output interval list.
- IntervalListScattererWithSubdivision() - Constructor for class picard.util.IntervalList.IntervalListScattererWithSubdivision
- IntervalListScatterMode - Enum Class in picard.util.IntervalList
-
An enum to control the creation of the various IntervalListScatter objects
- IntervalListToBed - Class in picard.util
-
Trivially simple command line program to convert an IntervalList file to a BED file.
- IntervalListToBed() - Constructor for class picard.util.IntervalListToBed
- IntervalListTools - Class in picard.util
-
Performs various
IntervalList
manipulations. - IntervalListTools() - Constructor for class picard.util.IntervalListTools
- IntervalListTools.Action - Enum Class in picard.util
- intervals - Variable in class picard.analysis.AbstractWgsMetricsCollector
- intervals - Variable in class picard.analysis.WgsMetrics
-
The intervals over which this metric was computed.
- INTERVALS - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- INTERVALS - Variable in class picard.analysis.CollectMultipleMetrics
- INTERVALS - Variable in class picard.analysis.CollectOxoGMetrics
- INTERVALS - Variable in class picard.analysis.CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection
- INTERVALS - Variable in class picard.analysis.CollectWgsMetrics
- INTERVALS - Variable in class picard.reference.NonNFastaSize
- INTERVALS - Variable in class picard.sam.MergeSamFiles
- INTERVALS - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- INTERVALS - Variable in class picard.vcf.GenotypeConcordance
- IntervalsManipulationProgramGroup - Class in picard.cmdline.programgroups
-
Tools that process genomic intervals in various formats.
- IntervalsManipulationProgramGroup() - Constructor for class picard.cmdline.programgroups.IntervalsManipulationProgramGroup
- intervalWeight(Interval) - Method in interface picard.util.IntervalList.IntervalListScatterer
-
A method that defines the "weight" of an interval list for the purpose of scattering.
- intervalWeight(Interval) - Method in class picard.util.IntervalList.IntervalListScattererByBaseCount
- intervalWeight(Interval) - Method in class picard.util.IntervalList.IntervalListScattererByIntervalCount
- INTRONIC - Enum constant in enum class picard.annotation.LocusFunction
- INTRONIC_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
Number of bases in primary alignments that align to an intronic base for some gene, and not a coding or UTR base.
- INVERT - Variable in class picard.util.IntervalListTools
- IO_SIZE - Variable in class picard.util.FifoBuffer
- IS_BISULFITE_SEQUENCE - Variable in class picard.sam.MergeBamAlignment
- IS_BISULFITE_SEQUENCE - Variable in class picard.sam.SetNmMdAndUqTags
- IS_BISULFITE_SEQUENCED - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
- IS_BISULFITE_SEQUENCED - Variable in class picard.analysis.CollectGcBiasMetrics
- IS_BISULFITE_SEQUENCED - Variable in class picard.sam.ValidateSamFile
- IS_MIXED - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- IS_MIXED - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- IS_MIXED_CODE - Enum constant in enum class picard.vcf.GenotypeConcordanceStateCodes
- IS_ZCALLED - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
Whether the sample was zcalled
- isAdapter(SAMRecord) - Method in class picard.analysis.AdapterUtility
-
Checks the first ADAPTER_MATCH_LENGTH bases of the read against known adapter sequences and returns true if the read matches an adapter sequence with MAX_ADAPTER_ERRORS mismsatches or fewer.
- isAdapterClipped(SAMRecord) - Static method in class picard.sam.markduplicates.MarkDuplicatesForFlowHelper
- isAdapterClippedWithQ(SAMRecord) - Static method in class picard.sam.markduplicates.MarkDuplicatesForFlowHelper
- isAdapterSequence(byte[]) - Method in class picard.analysis.AdapterUtility
-
Checks the first ADAPTER_MATCH_LENGTH bases of the read against known adapter sequences and returns true if the read matches an adapter sequence with MAX_ADAPTER_ERRORS mismsatches or fewer.
- isAdapterSequence(byte[], boolean) - Method in class picard.analysis.AdapterUtility
-
Checks the first ADAPTER_MATCH_LENGTH bases of the read against known adapter sequences and returns true if the read matches an adapter sequence with MAX_ADAPTER_ERRORS mismsatches or fewer.
- isAmbiguous() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- isAvailable - Variable in enum class picard.nio.PathProvider
- isBlank(byte[]) - Method in class picard.util.AbstractInputParser
-
Determines whether a given line is a comment
- isBlockGzipped(File) - Static method in class picard.illumina.parser.readers.BclReader
- isChimeric(SAMRecord, int, Set<SamPairUtil.PairOrientation>) - Static method in class picard.analysis.ChimeraUtil
-
Checks whether the given read is part of a chimeric pair.
- isChimeric(SAMRecord, SAMRecord, int, Set<SamPairUtil.PairOrientation>) - Static method in class picard.analysis.ChimeraUtil
-
Checks whether the given read is part of a chimeric pair.
- isClipOverlappingReads() - Method in class picard.sam.AbstractAlignmentMerger
- isClosed() - Method in class picard.util.CircularByteBuffer
-
Returns true if the buffer is closed, false otherwise.
- isClusterRecord() - Method in class picard.illumina.parser.readers.TileMetricsOutReader.IlluminaTileMetrics
- isComment(byte[]) - Method in class picard.util.AbstractInputParser
-
Determines whether a given line is a comment
- isContaminant(HitsForInsert) - Method in class picard.sam.AbstractAlignmentMerger
- isContaminant(HitsForInsert) - Method in class picard.sam.SamAlignmentMerger
-
Criteria for contaminant reads: 1.
- isDbSnpSite(String, int) - Method in class picard.util.DbSnpBitSetUtil
-
Returns true if there is a dbSnp entry at pos in sequenceName, otherwise false
- isDelimiter(byte) - Method in class picard.util.AbstractInputParser
-
Determines whether a given character is a delimiter
- isDelimiter(byte) - Method in class picard.util.CsvInputParser
-
Determines whether a given character is a delimiter
- isDelimiter(byte) - Method in class picard.util.TabbedInputParser
-
Determines whether a given character is a delimiter
- isDupe() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- isEmpty() - Method in class picard.illumina.parser.ReadStructure.Substructure
- isEmpty() - Method in class picard.sam.markduplicates.util.MarkQueue
- isExpected() - Method in enum class picard.fingerprint.CrosscheckMetric.FingerprintResult
- isFail() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- isGzipped(File) - Static method in class picard.illumina.parser.readers.BclReader
- isHeterozygous() - Method in enum class picard.fingerprint.DiploidGenotype
- isHomomozygous() - Method in enum class picard.fingerprint.DiploidGenotype
- isIndel() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- isIntensityOnly() - Method in class picard.arrays.illumina.IlluminaBPMLocusEntry
- isKeepAlignerProperPairFlags() - Method in class picard.sam.AbstractAlignmentMerger
- isKeepValid() - Method in enum class picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
- isLegacyPicardStyle(String[]) - Static method in class picard.cmdline.CommandLineSyntaxTranslater
- isMatch() - Method in enum class picard.fingerprint.CrosscheckMetric.FingerprintResult
- isMatched() - Method in class picard.illumina.BarcodeExtractor.BarcodeMatch
- isMissing(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns true if EITHER the truth or call state is MISSING.
- isOpticalDuplicate - Variable in class picard.sam.markduplicates.util.ReadEnds
-
A *transient* flag marking this read end as being an optical duplicate.
- isPaired() - Method in class picard.sam.markduplicates.util.ReadEnds
- isPaired() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
- isPf() - Method in class picard.illumina.parser.CbclData
- isPf() - Method in class picard.illumina.parser.ClusterData
- isPhasing(IlluminaMetricsCode) - Static method in enum class picard.illumina.parser.IlluminaMetricsCode
- isPopulateOaTag() - Method in enum class picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
- isQualityClipped(SAMRecord) - Static method in class picard.sam.markduplicates.MarkDuplicatesForFlowHelper
- isRefStrandDefinedInManifest() - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
- isReservedTag(String) - Method in class picard.sam.AbstractAlignmentMerger
- isResetMappingInformation() - Method in enum class picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
- isSingleEndReadKnownFragment(SAMRecord) - Static method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
-
This method is used to generate the following two metrics: UNPAIRED_DUPS_WITH_TLEN UNPAIRED_DUPS_WITHOUT_TLEN It will return true if and only if the read is single ended and the exact fragment length is known (i.e.
- isSkipBlankLines() - Method in class picard.util.AbstractInputParser
- isSnp() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- isSoloTranscript() - Method in class picard.annotation.Gene.Transcript
- isTreatGroupedDelimitersAsOne() - Method in class picard.util.AbstractInputParser
- isValidBase(byte) - Static method in enum class picard.fingerprint.DiploidGenotype
- isVar(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns true if EITHER the truth or call state is a VAR.
- isVariantFile(File) - Static method in class picard.vcf.VcfUtils
-
Checks if the suffix is one of those that are allowed for the various formats that contain variants (currently vcf and bcf)
- isWGT - Variable in class picard.arrays.illumina.InfiniumEGTFile
- iterator - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
- iterator() - Method in class picard.annotation.Gene
- iterator() - Method in class picard.arrays.illumina.IlluminaManifest
- iterator() - Method in class picard.illumina.parser.BaseIlluminaDataProvider
- iterator() - Method in class picard.illumina.parser.ReadStructure.Substructure
- iterator() - Method in class picard.illumina.parser.TileIndex
- iterator() - Method in class picard.util.AbstractInputParser
- iterator() - Method in class picard.util.IntervalList.IntervalListScatter
- iterator() - Method in class picard.util.TabbedTextFileWithHeaderParser
-
Creates the iterator object.
- iterators() - Method in class picard.vcf.processor.VariantIteratorProducer
-
Renders the embodied regions of the VCF files in the form of
CloseableIterator
s overVariantContext
s. - Iterators - Class in picard.util
- Iterators() - Constructor for class picard.util.Iterators
- IUPAC_NUCLEOTIDE_CODES - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
J
- JAVASCRIPT_FILE - Variable in class picard.sam.FilterSamReads
- JAVASCRIPT_FILE - Variable in class picard.vcf.filter.FilterVcf
- JUMP_DUPLICATE_PAIRS - Variable in class picard.analysis.JumpingLibraryMetrics
-
The number of outward-facing pairs that are duplicates
- JUMP_DUPLICATE_PCT - Variable in class picard.analysis.JumpingLibraryMetrics
-
The fraction of outward-facing pairs that are marked as duplicates
- JUMP_LIBRARY_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
-
The estimated library size for outward-facing pairs
- JUMP_MEAN_INSERT_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
-
The mean insert size for outward-facing pairs
- JUMP_PAIRS - Variable in class picard.analysis.JumpingLibraryMetrics
-
The number of outward-facing pairs in the SAM file
- JUMP_SIZE - Variable in class picard.sam.MergeBamAlignment
-
Deprecated.
- JUMP_STDEV_INSERT_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
-
The standard deviation on the insert size for outward-facing pairs
- JumpingLibraryMetrics - Class in picard.analysis
-
High level metrics about the presence of outward- and inward-facing pairs within a SAM file generated with a jumping library, produced by the CollectJumpingLibraryMetrics program and usually stored in a file with the extension ".jump_metrics".
- JumpingLibraryMetrics() - Constructor for class picard.analysis.JumpingLibraryMetrics
K
- KEEP_FIRST_DUPLICATE - Variable in class picard.sam.RevertSam
- KEY - Variable in class picard.analysis.CompareMetrics
- KEY - Variable in class picard.analysis.CompareMetrics.MetricComparisonDifferences
- klDivergance(double[], double[]) - Static method in class picard.util.MathUtil
-
Calculate the KL divergence from measured to distribution // https://en.wikipedia.org/wiki/Kullback%E2%80%93Leibler_divergence
L
- lane - Variable in class picard.illumina.parser.BaseIlluminaDataProvider
- lane - Variable in class picard.illumina.parser.ParameterizedFileUtil
- lane - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
-
The lane, which is determined from the file name
- LANE - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
- LANE - Variable in class picard.illumina.ExtractBarcodesProgram
- LANE - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The lane for which the metrics were calculated.
- LANE - Variable in class picard.illumina.IlluminaLaneMetrics
-
This lane's number.
- LANE - Variable in class picard.illumina.IlluminaPhasingMetrics
-
Illumina flowcell lane number
- LANE - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
- LANE_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- laneFactories - Variable in class picard.illumina.BasecallsConverter
- laneIsSet() - Method in class picard.illumina.parser.ClusterData
- LanePhasingMetricsCollector - Class in picard.illumina
-
Helper class used to transform tile data for a lane into a collection of IlluminaPhasingMetrics
- LanePhasingMetricsCollector(Collection<Tile>, boolean) - Constructor for class picard.illumina.LanePhasingMetricsCollector
-
Constructor takes a lane's collection of Tiles and calculates the median phasing/prephasing for the first and second (if available) reads
- LANES - Variable in class picard.illumina.CheckIlluminaDirectory
- laneTileCode - Variable in class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
- LEFT_FILE - Variable in class picard.fingerprint.CrosscheckMetric
-
The LEFT file from which the fingerprint was obtained.
- LEFT_FILE - Variable in class picard.sam.SamComparisonMetric
-
Left file used in comparison
- LEFT_GROUP_VALUE - Variable in class picard.fingerprint.CrosscheckMetric
-
The LEFT group value.
- LEFT_LANE - Variable in class picard.fingerprint.CrosscheckMetric
-
The LEFT lane.
- LEFT_LIBRARY - Variable in class picard.fingerprint.CrosscheckMetric
-
The LEFT library identifier.
- LEFT_MOLECULAR_BARCODE_SEQUENCE - Variable in class picard.fingerprint.CrosscheckMetric
-
The LEFT molecular (sample) barcode.
- LEFT_PRIMER - Variable in class picard.util.BaitDesigner
- LEFT_RUN_BARCODE - Variable in class picard.fingerprint.CrosscheckMetric
-
The LEFT run barcode (PU field) expected to look like : D047KACXX110901.1.ACCAACTG.
- LEFT_SAMPLE - Variable in class picard.fingerprint.CrosscheckMetric
-
The LEFT sample identifier.
- leftAlignVariant(VariantContextBuilder, int, int, List<Allele>, ReferenceSequence) - Static method in class picard.util.LiftoverUtils
-
Normalizes and left aligns a
VariantContextBuilder
. - leftVariantContext - Variable in class picard.vcf.PairedVariantSubContextIterator.VcfTuple
- length - Variable in class picard.illumina.parser.Range
- length - Variable in class picard.illumina.parser.ReadDescriptor
- length() - Method in class picard.annotation.Gene.Transcript
- length() - Method in class picard.illumina.parser.ReadStructure.Substructure
- leniantHammingDistance() - Method in class picard.util.SingleBarcodeDistanceMetric
-
Deprecated.
- LENIENT_DUP - Variable in class picard.sam.util.SAMComparisonArgumentCollection
- LENIENT_HAMMING - Enum constant in enum class picard.illumina.DistanceMetric
- LENIENT_HEADER - Variable in class picard.sam.util.SAMComparisonArgumentCollection
- LENIENT_LOW_MQ_ALIGNMENT - Variable in class picard.sam.util.SAMComparisonArgumentCollection
- LENIENT_UNKNOWN_MQ_ALIGNMENT - Variable in class picard.sam.util.SAMComparisonArgumentCollection
- lenientHammingDistance() - Method in class picard.util.SingleBarcodeDistanceMetric
-
Similar to Hamming distance but this version doesn't penalize matching bases with low quality for the read.
- LIBRARY - Enum constant in enum class picard.analysis.MetricAccumulationLevel
- LIBRARY - Enum constant in enum class picard.fingerprint.CrosscheckMetric.DataType
- LIBRARY - Enum constant in enum class picard.sam.markduplicates.MarkDuplicates.DuplicateType
- LIBRARY - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The name of the library being assayed.
- LIBRARY - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
The name of the library being assayed.
- LIBRARY - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The name of the library being assayed.
- LIBRARY - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
The name of the library being assayed.
- LIBRARY - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The name of the library being assayed.
- LIBRARY - Variable in class picard.metrics.MultilevelMetrics
-
The library to which these metrics apply.
- LIBRARY - Variable in class picard.sam.DuplicationMetrics
-
The library on which the duplicate marking was performed.
- LIBRARY - Variable in class picard.sam.markduplicates.UmiMetrics
-
Library that was used to generate UMI data.
- LIBRARY_NAME - Variable in class picard.illumina.BarcodeMetric
-
The name of the library
- LIBRARY_NAME - Variable in class picard.illumina.IlluminaBasecallsToSam
- LIBRARY_NAME - Variable in class picard.sam.FastqToSam
- LIBRARY_NAME - Variable in class picard.sam.RevertSam
- LIBRARY_NAME_COLUMN - Static variable in class picard.illumina.ExtractBarcodesProgram
-
Column header for the library name.
- LIBRARY_NAME_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- LIBRARY_PARAMS - Variable in class picard.illumina.IlluminaBasecallsToSam
- libraryId - Variable in class picard.sam.markduplicates.util.ReadEnds
- libraryIdGenerator - Variable in class picard.sam.markduplicates.MarkDuplicates
- LibraryIdGenerator - Class in picard.sam.markduplicates.util
-
A class to generate library Ids and keep duplication metrics by library IDs.
- LibraryIdGenerator(SAMFileHeader) - Constructor for class picard.sam.markduplicates.util.LibraryIdGenerator
- LibraryIdGenerator(SAMFileHeader, boolean) - Constructor for class picard.sam.markduplicates.util.LibraryIdGenerator
- LIFTOVER_FAILED - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
- LIFTOVER_FAILED_FOR_ONE_OR_MORE_SNPS - Static variable in class picard.fingerprint.LiftOverHaplotypeMap
- LIFTOVER_MIN_MATCH - Variable in class picard.vcf.LiftoverVcf
- LiftOverHaplotypeMap - Class in picard.fingerprint
-
Liftover SNPs in HaplotypeMaps from one reference to another
- LiftOverHaplotypeMap() - Constructor for class picard.fingerprint.LiftOverHaplotypeMap
- LiftOverIntervalList - Class in picard.util
-
This tool adjusts the coordinates in an interval list on one reference to its homologous interval list on another reference, based on a chain file that describes the correspondence between the two references.
- LiftOverIntervalList() - Constructor for class picard.util.LiftOverIntervalList
- LiftoverUtils - Class in picard.util
- LiftoverUtils() - Constructor for class picard.util.LiftoverUtils
- LiftoverVcf - Class in picard.vcf
-
Summary
- LiftoverVcf() - Constructor for class picard.vcf.LiftoverVcf
- liftSimpleVariantContext(VariantContext, Interval) - Static method in class picard.util.LiftoverUtils
- liftVariant(VariantContext, Interval, ReferenceSequence, boolean, boolean) - Static method in class picard.util.LiftoverUtils
-
This will take an input VariantContext and lift to the provided interval.
- limitingProcessedRegionsTo(IntervalList) - Method in class picard.vcf.processor.VariantProcessor.Builder
- LINE_LENGTH - Variable in class picard.reference.ExtractSequences
- LINE_LENGTH - Variable in class picard.reference.NormalizeFasta
- LINK_LOCS - Variable in class picard.illumina.CheckIlluminaDirectory
-
Deprecated.It is no longer necessary to create locs file symlinks.
- listWeight(IntervalList) - Method in interface picard.util.IntervalList.IntervalListScatterer
-
A method that defines the "weight" of an interval for the purpose of scattering.
- listWeight(IntervalList) - Method in class picard.util.IntervalList.IntervalListScattererByBaseCount
- listWeight(IntervalList) - Method in class picard.util.IntervalList.IntervalListScattererByIntervalCount
- LL_EXPECTED_SAMPLE - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
The Log Likelihood of the sequence data given the expected sample's genotypes.
- LL_RANDOM_SAMPLE - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
The Log Likelihood of the sequence data given a random sample from the human population.
- LLK - Variable in class picard.arrays.VerifyIDIntensityContaminationMetrics
-
The log likelihood
- LLK0 - Variable in class picard.arrays.VerifyIDIntensityContaminationMetrics
-
The log likelihood 0
- loadFingerprints(Path, Path, boolean, String) - Method in class picard.fingerprint.FingerprintChecker
-
Loads genotypes from the supplied file into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
- loadFingerprintsFromIndexedVcf(Path, String) - Method in class picard.fingerprint.FingerprintChecker
-
Loads genotypes from the supplied file into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
- loadFingerprintsFromNonIndexedVcf(Path, String) - Method in class picard.fingerprint.FingerprintChecker
-
Loads genotypes from the supplied file into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
- loadFingerprintsFromQueriableReader(VCFFileReader, String, Path) - Method in class picard.fingerprint.FingerprintChecker
-
Loads genotypes from the supplied reader into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
- loadFingerprintsFromVariantContexts(Iterable<VariantContext>, String, Path) - Method in class picard.fingerprint.FingerprintChecker
-
Loads genotypes from the supplied file into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
- loadPropertiesFile(String, Class<?>) - Static method in class picard.util.PropertyUtils
-
Attempt to load a Properties object from an on-disk properties file.
- loadRefFlat(File, SAMSequenceDictionary) - Static method in class picard.annotation.GeneAnnotationReader
- LOCATION_BIN_SIZE - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- Locs - Enum constant in enum class picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
- LocsFileFaker - Class in picard.illumina.parser.fakers
-
Created by jcarey on 3/13/14.
- LocsFileFaker() - Constructor for class picard.illumina.parser.fakers.LocsFileFaker
- LocsFileReader - Class in picard.illumina.parser.readers
-
The locs file format is one 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively.
- LocsFileReader(File) - Constructor for class picard.illumina.parser.readers.LocsFileReader
- LocsFileReader(File, int, int) - Constructor for class picard.illumina.parser.readers.LocsFileReader
- LOCUS_ACCUMULATION_CAP - Variable in class picard.analysis.CollectWgsMetrics
- LOCUS_MAX_READS - Variable in class picard.fingerprint.ExtractFingerprint
- LOCUS_MAX_READS - Variable in class picard.fingerprint.IdentifyContaminant
- LocusFunction - Enum Class in picard.annotation
-
Describes the behavior of a locus relative to a gene.
- LOD - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The LOD score for OBSERVED_GENOTYPE vs.
- LOD_EXPECTED_SAMPLE - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
The LOD for Expected Sample vs.
- LOD_SCORE - Variable in class picard.fingerprint.CrosscheckMetric
-
The resulting LOD score comparing LEFT and RIGHT data.
- LOD_SCORE_NORMAL_TUMOR - Variable in class picard.fingerprint.CrosscheckMetric
-
The resulting LOD score comparing LEFT as normal and RIGHT as tumor.
- LOD_SCORE_TUMOR_NORMAL - Variable in class picard.fingerprint.CrosscheckMetric
-
The resulting LOD score comparing LEFT as tumor and RIGHT as normal.
- LOD_SELF_CHECK - Variable in class picard.fingerprint.FingerprintMetrics
-
The fingerprinting LOD score this sample gets when compared to itself (big is good)
- LOD_THRESHOLD - Variable in class picard.fingerprint.ClusterCrosscheckMetrics
- LOD_THRESHOLD - Variable in class picard.fingerprint.CrosscheckFingerprints
- log - Static variable in class picard.illumina.SortedBasecallsConverter
- log - Static variable in class picard.util.LiftoverUtils
- LOG - Static variable in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
- LOG - Static variable in class picard.vcf.VcfFormatConverter
- LOG - Static variable in class picard.vcf.VcfToIntervalList
- LOG_10_MATH - Static variable in class picard.util.MathUtil
- LOG_2_MATH - Static variable in class picard.util.MathUtil
- LOG_4_BASE_E - Static variable in class picard.util.MathUtil
-
Constant to convert between the natural base e and 4.0.
- LOG_FAILED_INTERVALS - Variable in class picard.vcf.LiftoverVcf
- LOG_ODDS_THRESHOLD - Variable in class picard.analysis.TheoreticalSensitivityMetrics
-
Log-likelihood ratio is used as a threshold to distinguish a positive site with a given allele fraction from HOM_REF.
- log10_1p(double) - Static method in class picard.util.MathUtil
-
this function mimics the behavior of log_1p but resulting in log _base 10_ of (1+x) instead of natural log of 1+x
- LOG10_CHI_SQUARED_PVALUE - Variable in class picard.fingerprint.FingerprintMetrics
-
The log10 of the Chi-squared pvalue
- LOG10_HET_CHI_SQUARED_PVALUE - Variable in class picard.fingerprint.FingerprintMetrics
-
The log10 of the Chi-squared pvalue for the number of HETs and HOMs
- LOG10_HOM_CHI_SQUARED_PVALUE - Variable in class picard.fingerprint.FingerprintMetrics
-
The log10 of the Chi-squared pvalue for
FingerprintMetrics.NUM_HOM_ALLELE1
andFingerprintMetrics.NUM_HOM_ALLELE2
- LOG10_PVAL - Variable in class picard.arrays.BafRegressMetrics
-
The log p-value of the estimate
- logLikelihoodsToProbs(double[]) - Static method in class picard.util.MathUtil
-
Deprecated.
- logMemoryStats(Log) - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
- logRRatio - Variable in class picard.arrays.illumina.InfiniumGTCRecord
- LONG_HOMOPOLYMER - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymer
- LONG_HOMOPOLYMER - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- longLaneStr(int) - Static method in class picard.illumina.parser.IlluminaFileUtil
- LOSS_OF_HET_RATE - Variable in class picard.fingerprint.CrosscheckFingerprints
- LOW_DP - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- LOW_DP - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- LOW_DP_CODE - Enum constant in enum class picard.vcf.GenotypeConcordanceStateCodes
- LOW_GQ - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- LOW_GQ - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- LOW_GQ_CODE - Enum constant in enum class picard.vcf.GenotypeConcordanceStateCodes
- LOW_MQ_THRESHOLD - Variable in class picard.sam.util.SAMComparisonArgumentCollection
- LRR - Static variable in class picard.arrays.illumina.InfiniumVcfFields
M
- M - Enum constant in enum class picard.illumina.parser.ReadType
- MACHINE_NAME - Variable in class picard.illumina.IlluminaBasecallsToFastq
- MAD_COVERAGE - Variable in class picard.analysis.WgsMetrics
-
The median absolute deviation of coverage of the genome after all filters are applied.
- MAD_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The median absolute deviation of the distribution of all read lengths.
- main(String[]) - Static method in class picard.cmdline.PicardCommandLine
-
Override this if you want to include different java packages to search for classes that extend CommandLineProgram.
- main(String[]) - Static method in class picard.sam.DuplicationMetrics
- main(String[]) - Static method in class picard.Test
- make() - Method in enum class picard.util.IntervalList.IntervalListScatterMode
-
Create the scatterer
- makeAllReadCollector() - Method in class picard.analysis.directed.TargetMetricsCollector
- makeAllReadCollector() - Method in class picard.metrics.MultiLevelCollector
- makeArg(SAMRecord, ReferenceSequence) - Method in class picard.analysis.directed.InsertSizeMetricsCollector
- makeArg(SAMRecord, ReferenceSequence) - Method in class picard.analysis.GcBiasMetricsCollector
- makeArg(SAMRecord, ReferenceSequence) - Method in class picard.metrics.MultiLevelCollector
- makeArg(SAMRecord, ReferenceSequence) - Method in class picard.metrics.SAMRecordAndReferenceMultiLevelCollector
- makeArg(SAMRecord, ReferenceSequence) - Method in class picard.metrics.SAMRecordMultiLevelCollector
- makeBarcodeRegex(int) - Static method in class picard.illumina.parser.ParameterizedFileUtil
- makeChildCollector(String, String, String) - Method in class picard.analysis.AlignmentSummaryMetricsCollector
- makeChildCollector(String, String, String) - Method in class picard.analysis.directed.InsertSizeMetricsCollector
-
Make an InsertSizeCollector with the given arguments
- makeChildCollector(String, String, String) - Method in class picard.analysis.directed.RnaSeqMetricsCollector
- makeChildCollector(String, String, String) - Method in class picard.analysis.directed.TargetMetricsCollector
- makeChildCollector(String, String, String) - Method in class picard.analysis.GcBiasMetricsCollector
- makeChildCollector(String, String, String) - Method in class picard.analysis.RrbsMetricsCollector
- makeChildCollector(String, String, String) - Method in class picard.metrics.MultiLevelCollector
-
Construct a PerUnitMetricCollector with the given arguments.
- makeCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int) - Method in class picard.analysis.directed.CollectHsMetrics
- makeCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int) - Method in class picard.analysis.directed.CollectTargetedMetrics
-
A factory method for the TargetMetricsCollector to use this time.
- makeCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int) - Method in class picard.analysis.directed.CollectTargetedPcrMetrics
- makeCycleFileParser(List<File>) - Method in class picard.illumina.parser.MultiTileBclParser
- makeCycleFileParser(List<File>, PerTileCycleParser.CycleFilesParser<BclData>) - Method in class picard.illumina.parser.MultiTileBclParser
- makeDataProvider() - Method in class picard.illumina.parser.IlluminaDataProviderFactory
- makeDataProvider(Integer) - Method in class picard.illumina.parser.IlluminaDataProviderFactory
- makeDataProvider(List<Integer>) - Method in class picard.illumina.parser.IlluminaDataProviderFactory
-
Call this method to create a ClusterData iterator over the specified tiles.
- makeExceptionMsg() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
-
Create a string that will be included in any NoSuchElementException thrown by the next() method
- makeExceptionMsg() - Method in class picard.illumina.parser.readers.ClocsFileReader
- makeExceptionMsg() - Method in class picard.illumina.parser.readers.LocsFileReader
- makeExceptionMsg() - Method in class picard.illumina.parser.readers.PosFileReader
- makeIgnoredSequenceIndicesSet(SAMFileHeader, Set<String>) - Static method in class picard.analysis.directed.RnaSeqMetricsCollector
- makeInstance(String, String, File, File, Set<MetricAccumulationLevel>, File, File, File, Set<String>) - Method in interface picard.analysis.CollectMultipleMetrics.ProgramInterface
- makeInstance(String, String, File, File, Set<MetricAccumulationLevel>, File, File, File, Set<String>, boolean) - Method in interface picard.analysis.CollectMultipleMetrics.ProgramInterface
-
By default, this method calls the
CollectMultipleMetrics.ProgramInterface.makeInstance(String, String, File, File, Set, File, File, File, Set)
method without 'includeUnpaired' parameter. - makeIntervalArgumentCollection() - Method in class picard.analysis.CollectWgsMetrics
- makeItSo(FastqReader, FastqReader, SAMFileWriter) - Method in class picard.sam.FastqToSam
-
Handles the FastqToSam execution on the FastqReader(s).
- makeItSo(File, File, boolean, long, Collection<SinglePassSamProgram>) - Static method in class picard.analysis.SinglePassSamProgram
- makeLaneTileRegex(String, int) - Static method in class picard.illumina.parser.ParameterizedFileUtil
-
Return a regex string for finding Lane and Tile given a file extension pattern
- makeLibraryCollector(SAMReadGroupRecord) - Method in class picard.metrics.MultiLevelCollector
- makeOverlapDetector(File, SAMFileHeader, File, Log) - Static method in class picard.analysis.directed.RnaSeqMetricsCollector
- makePhredBinaryFromSolexaQualityAscii_1_3(String) - Static method in class picard.util.IlluminaUtil
-
Convert from Solexa-scaled ASCII qualities to Phred-scaled binary.
- makePhredBinaryFromSolexaQualityAscii_1_3(String, int, int) - Static method in class picard.util.IlluminaUtil
-
Convert from Solexa-scaled ASCII qualities to Phred-scaled binary.
- makeReadGroupCollector(SAMReadGroupRecord) - Method in class picard.metrics.MultiLevelCollector
- makeReferenceArgumentCollection() - Method in class picard.analysis.CollectAlignmentSummaryMetrics
- makeReferenceArgumentCollection() - Method in class picard.analysis.CollectRrbsMetrics
- makeReferenceArgumentCollection() - Method in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- makeReferenceArgumentCollection() - Method in class picard.cmdline.CommandLineProgram
- makeReferenceArgumentCollection() - Method in class picard.sam.CreateSequenceDictionary
- makeReferenceArgumentCollection() - Method in class picard.sam.DownsampleSam
- makeReferenceArgumentCollection() - Method in class picard.util.ScatterIntervalsByNs
- makeReferenceArgumentCollection() - Method in class picard.vcf.LiftoverVcf
- makeSampleCollector(SAMReadGroupRecord) - Method in class picard.metrics.MultiLevelCollector
- makeSeekable(List<File>, BclQualityEvaluationStrategy, int[]) - Static method in class picard.illumina.parser.readers.BclReader
- makeSequenceDictionary(File) - Method in class picard.sam.CreateSequenceDictionary
-
Read all the sequences from the given reference file, and convert into SAMSequenceRecords
- MakeSitesOnlyVcf - Class in picard.vcf
-
Creates a VCF that contains all the site-level information for all records in the input VCF but no genotype information.
- MakeSitesOnlyVcf() - Constructor for class picard.vcf.MakeSitesOnlyVcf
- makeSortingCollection() - Static method in class picard.util.SequenceDictionaryUtils
- makeTileIterator(File) - Method in class picard.illumina.parser.PerTileParser
-
Factory method for the iterator of each tile
- makeTileIterator(File) - Method in class picard.illumina.parser.PosParser
-
Make an CloseableIterator
based on the given file and fileType specified at construction. - MakeVcfSampleNameMap - Class in picard.vcf
-
Creates a TSV from sample name to VCF/GVCF path, with one line per input.
- MakeVcfSampleNameMap() - Constructor for class picard.vcf.MakeVcfSampleNameMap
- Male - Enum constant in enum class picard.pedigree.Sex
- MALE_CHROMS - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
- MANIFEST_FILE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- MANIFEST_FILE_HEADER_NAMES - Static variable in class picard.arrays.illumina.IlluminaManifest
- manifestFileParser - Variable in class picard.arrays.illumina.IlluminaManifest
- manifestName - Variable in class picard.arrays.illumina.InfiniumEGTFile
- MAP_FILE - Variable in class picard.arrays.MergePedIntoVcf
- MAP_INFO_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- mappingQualityStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies into the mapping-quality of the read under consideration
- MAPPINGS_DIFFER - Enum constant in enum class picard.sam.util.SamComparison.AlignmentComparison
- MAPPINGS_DIFFER - Variable in class picard.sam.SamComparisonMetric
-
The number of primary records which are mapped in both files but do not meet criteria to be counted in MAPPINGS_MATCH.
- MAPPINGS_MATCH - Enum constant in enum class picard.sam.util.SamComparison.AlignmentComparison
- MAPPINGS_MATCH - Variable in class picard.sam.SamComparisonMetric
-
The number of primary records for which mappings match in files.
- markDuplicateFragments(List<ReadEndsForMarkDuplicates>, boolean) - Method in class picard.sam.markduplicates.MarkDuplicates
-
Takes a list of ReadEndsForMarkDuplicates objects and removes from it all objects that should not be marked as duplicates.
- MarkDuplicates - Class in picard.sam.markduplicates
-
A better duplication marking algorithm that handles all cases including clipped and gapped alignments.
- MarkDuplicates() - Constructor for class picard.sam.markduplicates.MarkDuplicates
- MarkDuplicates.DuplicateTaggingPolicy - Enum Class in picard.sam.markduplicates
-
Enum used to control how duplicates are flagged in the DT optional tag on each read.
- MarkDuplicates.DuplicateType - Enum Class in picard.sam.markduplicates
-
Enum for the possible values that a duplicate read can be tagged with in the DT attribute.
- MarkDuplicatesForFlowArgumentCollection - Class in picard.sam.markduplicates
- MarkDuplicatesForFlowArgumentCollection() - Constructor for class picard.sam.markduplicates.MarkDuplicatesForFlowArgumentCollection
- MarkDuplicatesForFlowHelper - Class in picard.sam.markduplicates
-
MarkDuplicates calculation helper class for flow based mode The class extends the behavior of MarkDuplicates which contains the complete code for the non-flow based mode.
- MarkDuplicatesForFlowHelper(MarkDuplicates) - Constructor for class picard.sam.markduplicates.MarkDuplicatesForFlowHelper
- MarkDuplicatesHelper - Interface in picard.sam.markduplicates
- MarkDuplicatesWithMateCigar - Class in picard.sam.markduplicates
-
An even better duplication marking algorithm that handles all cases including clipped and gapped alignments.
- MarkDuplicatesWithMateCigar() - Constructor for class picard.sam.markduplicates.MarkDuplicatesWithMateCigar
- MarkDuplicatesWithMateCigarIterator - Class in picard.sam.markduplicates
-
This will iterate through a coordinate sorted SAM file (iterator) and either mark or remove duplicates as appropriate.
- MarkDuplicatesWithMateCigarIterator(SAMFileHeader, CloseableIterator<SAMRecord>, OpticalDuplicateFinder, DuplicateScoringStrategy.ScoringStrategy, int, boolean, boolean, int, int, List<File>) - Constructor for class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
-
Initializes the mark duplicates iterator.
- MarkIlluminaAdapters - Class in picard.illumina
-
Command line program to mark the location of adapter sequences.
- MarkIlluminaAdapters() - Constructor for class picard.illumina.MarkIlluminaAdapters
- MarkQueue - Class in picard.sam.markduplicates.util
-
This is the mark queue.
- MarkQueue(DuplicateScoringStrategy.ScoringStrategy) - Constructor for class picard.sam.markduplicates.util.MarkQueue
- MASKING_QUALITY - Static variable in class picard.illumina.parser.MultiTileBclParser
- MATCH_BARCODES_INLINE - Variable in class picard.illumina.IlluminaBasecallsToFastq
- MATCH_BARCODES_INLINE - Variable in class picard.illumina.IlluminaBasecallsToSam
- MATCHING_DICTIONARY_TAGS - Variable in class picard.sam.MergeBamAlignment
- matchPattern - Variable in class picard.illumina.parser.ParameterizedFileUtil
-
A pattern that will match files of this type for this lane
- MatchResults - Class in picard.fingerprint
-
Represents the results of a fingerprint comparison between one dataset and a specific fingerprint file.
- MathUtil - Class in picard.util
-
General math utilities
- MathUtil.LogMath - Class in picard.util
-
A collection of common math operations that work with log values.
- MATRIX_OUTPUT - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- MATRIX_OUTPUT - Variable in class picard.fingerprint.CrosscheckFingerprints
- max(double[]) - Static method in class picard.util.MathUtil
-
Returns the largest value stored in the array.
- max(long[]) - Static method in class picard.util.MathUtil
-
Returns the largest value stored in the array.
- MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH - Static variable in class picard.cmdline.CommandLineProgram
-
CommandLineProgramProperties oneLineSummary attribute must be shorted than this in order to maintain reasonable help output formatting.
- MAX_DIFF_RATE - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
- MAX_DISCARD_FRACTION - Variable in class picard.sam.RevertSam
- MAX_EDIT_DISTANCE_TO_JOIN - Variable in class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
- MAX_EFFECT_OF_EACH_HAPLOTYPE_BLOCK - Variable in class picard.fingerprint.CrosscheckFingerprints
- MAX_ERROR_RATE - Static variable in class picard.util.ClippingUtility
-
The default value used for the maximum error rate when matching read bases to clippable sequence.
- MAX_ERROR_RATE_PE - Variable in class picard.illumina.MarkIlluminaAdapters
- MAX_ERROR_RATE_SE - Variable in class picard.illumina.MarkIlluminaAdapters
- MAX_FILE_HANDLES_FOR_READ_ENDS_MAP - Variable in class picard.sam.markduplicates.MarkDuplicates
- MAX_FS - Variable in class picard.vcf.filter.FilterVcf
- MAX_GROUP_RATIO - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
- MAX_INSERT_SIZE - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
- MAX_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
-
The maximum measure insert size by alignment.
- MAX_INSERTIONS_OR_DELETIONS - Variable in class picard.sam.MergeBamAlignment
- MAX_LOCI - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- MAX_MISMATCH_RATE - Variable in class picard.analysis.CollectRrbsMetrics
- MAX_MISMATCHES - Variable in class picard.illumina.ExtractBarcodesProgram
- MAX_NO_CALLS - Variable in class picard.illumina.ExtractBarcodesProgram
- MAX_OPEN_TEMP_FILES - Variable in class picard.sam.ValidateSamFile
- MAX_OPTICAL_DUPLICATE_SET_SIZE - Variable in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
- MAX_OUTPUT - Variable in class picard.sam.ValidateSamFile
- MAX_PE_ERROR_RATE - Static variable in class picard.util.ClippingUtility
-
The default value used for the maximum error rate when matching paired end read bases to clippable sequence.
- MAX_POS - Static variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
- MAX_PROB_BELOW_ONE - Static variable in class picard.util.MathUtil
-
The double value closest to 1 while still being less than 1.
- MAX_Q - Variable in class picard.sam.FastqToSam
- MAX_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The maximum read length.
- MAX_READ_LENGTH - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
- MAX_READS_IN_RAM_PER_TILE - Variable in class picard.illumina.IlluminaBasecallsToFastq
-
Deprecated.
- MAX_READS_IN_RAM_PER_TILE - Variable in class picard.illumina.IlluminaBasecallsToSam
- MAX_RECORDS_IN_RAM - Variable in class picard.cmdline.CommandLineProgram
- MAX_RECORDS_IN_RAM - Static variable in class picard.sam.AbstractAlignmentMerger
- MAX_RECORDS_TO_EXAMINE - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
- MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP - Variable in class picard.sam.markduplicates.MarkDuplicates
-
If more than this many sequences in SAM file, don't spill to disk because there will not be enough file handles.
- MAX_TARGET_COVERAGE - Variable in class picard.analysis.directed.PanelMetricsBase
-
The maximum coverage of reads that mapped to target regions of an experiment.
- MAX_TO_MERGE - Variable in class picard.util.ScatterIntervalsByNs
- MAX_UNSIGNED_SHORT - Static variable in class picard.arrays.illumina.InfiniumDataFile
- maximalInterestingDistance - Variable in class picard.util.BarcodeEditDistanceQuery
-
maximal edit distance between reads and barcodes to be considered
- MAXIMUM_INSERT_SIZE - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- MAXIMUM_INSERT_SIZE - Variable in class picard.analysis.CollectOxoGMetrics
- maybeAdvance() - Method in class picard.illumina.parser.PerTileParser
- maybeDemultiplex(ClusterData, Map<String, BarcodeMetric>, BarcodeMetric, ReadStructure) - Method in class picard.illumina.BasecallsConverter
-
If we are demultiplexing and a barcodeExtractor is defined then this method will perform on-the-fly demuxing.
- mean(double...) - Method in class picard.util.MathUtil.LogMath
-
Computes the mean of the provided log values.
- mean(double[]) - Static method in class picard.util.MathUtil
- mean(double[], int, int) - Static method in class picard.util.MathUtil
-
Calculated the mean of an array of doubles.
- MEAN_ALIGNED_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The mean aligned read length of the set of reads examined.
- MEAN_AMPLICON_COVERAGE - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The mean read coverage of all amplicon regions in the experiment.
- MEAN_BAIT_COVERAGE - Variable in class picard.analysis.directed.HsMetrics
-
The mean coverage of all baits in the experiment.
- MEAN_BASE_QUALITY - Variable in class picard.analysis.GcBiasDetailMetrics
-
The mean quality (determined via the error rate) of all bases of all reads that are assigned to windows of this GC.
- MEAN_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The mean number of clusters per tile.
- MEAN_COVERAGE - Variable in class picard.analysis.WgsMetrics
-
The mean coverage in bases of the genome territory, after all filters are applied.
- MEAN_CPG_COVERAGE - Variable in class picard.analysis.RrbsSummaryMetrics
-
Mean coverage of CpG sites
- MEAN_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
-
The mean insert size of the "core" of the distribution.
- MEAN_PCT_PF_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The mean percentage of pf clusters per tile.
- MEAN_PF_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The mean number of pf clusters per tile.
- MEAN_PROBE_COVERAGE - Variable in class picard.analysis.directed.TargetMetrics
-
The mean coverage of all probes in the experiment, ON_PROBE_BASES/PROBE_TERRITORY.
- MEAN_R - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- MEAN_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The mean read length of the set of reads examined.
- MEAN_TARGET_COVERAGE - Variable in class picard.analysis.directed.PanelMetricsBase
-
The mean coverage of targets.
- MEAN_THETA - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- MEAN_UMI_LENGTH - Variable in class picard.sam.markduplicates.UmiMetrics
-
Number of bases in each UMI
- MEAN_X - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- MEAN_Y - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- MeanQualityByCycle - Class in picard.analysis
-
Program to generate a data table and chart of mean quality by cycle from a BAM file.
- MeanQualityByCycle - Enum constant in enum class picard.analysis.CollectMultipleMetrics.Program
- MeanQualityByCycle() - Constructor for class picard.analysis.MeanQualityByCycle
- meanR - Variable in class picard.arrays.illumina.InfiniumEGTFile
- meanTheta - Variable in class picard.arrays.illumina.InfiniumEGTFile
- median(double...) - Static method in class picard.util.MathUtil
-
Calculate the median of an array of doubles.
- MEDIAN_3PRIME_BIAS - Variable in class picard.analysis.RnaSeqMetrics
-
The median 3 prime bias of the 1000 most highly expressed transcripts that have a length greater than the END_BIAS_BASES parameter, where 3 prime bias is calculated per transcript as: mean coverage of the 3 prime-most number of bases, divided by the mean coverage of the whole transcript.
- MEDIAN_5PRIME_BIAS - Variable in class picard.analysis.RnaSeqMetrics
-
The median 5 prime bias of the 1000 most highly expressed transcripts that have a length greater than the END_BIAS_BASES parameter.
- MEDIAN_5PRIME_TO_3PRIME_BIAS - Variable in class picard.analysis.RnaSeqMetrics
-
The ratio of coverage at the 5 prime end to the 3 prime end based on the 1000 most highly expressed transcripts that have a length greater than the END_BIAS_BASES parameter.
- MEDIAN_ABSOLUTE_DEVIATION - Variable in class picard.analysis.InsertSizeMetrics
-
The median absolute deviation of the distribution.
- MEDIAN_COVERAGE - Variable in class picard.analysis.WgsMetrics
-
The median coverage in bases of the genome territory, after all filters are applied.
- MEDIAN_CPG_COVERAGE - Variable in class picard.analysis.RrbsSummaryMetrics
-
Median coverage of CpG sites
- MEDIAN_CV_COVERAGE - Variable in class picard.analysis.RnaSeqMetrics
-
The median coefficient of variation (CV) or stdev/mean for coverage values of the 1000 most highly expressed transcripts that have a length greater than the END_BIAS_BASES parameter.
- MEDIAN_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
-
The MEDIAN insert size of all paired end reads where both ends mapped to the same chromosome.
- MEDIAN_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The median read length of the set of reads examined.
- MEDIAN_TARGET_COVERAGE - Variable in class picard.analysis.directed.PanelMetricsBase
-
The median coverage of targets.
- MemoryBasedReadEndsForMarkDuplicatesMap - Class in picard.sam.markduplicates.util
-
Map from String to ReadEnds object.
- MemoryBasedReadEndsForMarkDuplicatesMap() - Constructor for class picard.sam.markduplicates.util.MemoryBasedReadEndsForMarkDuplicatesMap
- MendelianViolationMetrics - Class in picard.vcf.MendelianViolations
-
Describes the type and number of mendelian violations found within a Trio.
- MendelianViolationMetrics() - Constructor for class picard.vcf.MendelianViolations.MendelianViolationMetrics
- MendelianViolationsByFamily - Class in picard.vcf.MendelianViolations
-
Created by farjoun on 6/25/16.
- MendelianViolationsByFamily() - Constructor for class picard.vcf.MendelianViolations.MendelianViolationsByFamily
- merge(Collection<? extends MergeableMetricBase>) - Method in class picard.analysis.MergeableMetricBase
-
for a collection of MergeableMetricBase, merge them all into "this" one.
- merge(Collection<CallingMetricAccumulator.Result>) - Static method in class picard.vcf.CallingMetricAccumulator.Result
- merge(Collection<RESULT>) - Method in interface picard.vcf.processor.VariantProcessor.ResultMerger
- merge(List<VariantContext>) - Static method in class picard.arrays.CombineGenotypingArrayVcfs
-
Merges multiple VariantContexts all for the same locus into a single hybrid.
- merge(MergeableMetricBase) - Method in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
- merge(MergeableMetricBase) - Method in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsFlow
- merge(MergeableMetricBase) - Method in class picard.analysis.MergeableMetricBase
-
Merge another metric into this one
- merge(MergeableMetricBase) - Method in class picard.analysis.WgsMetrics
-
Merges the various PCT_EXC_* metrics.
- merge(Fingerprint) - Method in class picard.fingerprint.Fingerprint
-
Merges the likelihoods from the supplied Fingerprint into the likelihoods for this fingerprint.
- merge(FingerprintIdDetails) - Method in class picard.fingerprint.FingerprintIdDetails
- merge(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilities
-
Merges in the likelihood information from the supplied haplotype probabilities object.
- merge(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromContaminatorSequence
- merge(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotype
- merge(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
-
Merges information from another haplotype probabilities object for the same haplotype into this object.
- merge(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
-
Merges information from another haplotype probabilities object for the same haplotype into this object.
- merge(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilityOfNormalGivenTumor
- merge(BarcodeMetric) - Method in class picard.illumina.BarcodeMetric
-
Adds the non-calculated
- merge(CollectHiSeqXPfFailMetrics.PFFailSummaryMetric) - Method in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
Adds the non-calculated fields from the other metric to this one.
- MERGE_NEARBY_TARGETS - Variable in class picard.util.BaitDesigner
- MERGE_SEQUENCE_DICTIONARIES - Variable in class picard.sam.MergeSamFiles
- MergeableMetricBase - Class in picard.analysis
-
An extension of MetricBase that knows how to merge-by-adding fields that are appropriately annotated (
MergeByAdding
). - MergeableMetricBase() - Constructor for class picard.analysis.MergeableMetricBase
- MergeableMetricBase.MergeByAdding - Annotation Interface in picard.analysis
-
Metrics whose values can be merged by adding.
- MergeableMetricBase.MergeByAssertEquals - Annotation Interface in picard.analysis
-
Metrics whose values should be equal when merging.
- MergeableMetricBase.MergingIsManual - Annotation Interface in picard.analysis
-
Metrics that are merged manually in the
MergeableMetricBase.merge(MergeableMetricBase)
()}. - MergeableMetricBase.NoMergingIsDerived - Annotation Interface in picard.analysis
-
Metrics that are not merged, but are subsequently derived from other metrics, for example by
MergeableMetricBase.calculateDerivedFields()
. - MergeableMetricBase.NoMergingKeepsValue - Annotation Interface in picard.analysis
-
Metrics that are not merged.
- mergeAlignment(File) - Method in class picard.sam.AbstractAlignmentMerger
-
Merges the alignment data with the non-aligned records from the source BAM file.
- mergeAlignment(File) - Method in class picard.sam.SamAlignmentMerger
-
Merges the alignment from the map file with the non-aligned records from the source BAM file.
- MergeBamAlignment - Class in picard.sam
-
Summary
- MergeBamAlignment() - Constructor for class picard.sam.MergeBamAlignment
- mergeFingerprintsBy(Map<FingerprintIdDetails, Fingerprint>, Function<FingerprintIdDetails, String>) - Static method in class picard.fingerprint.Fingerprint
- mergeIfCan(MergeableMetricBase) - Method in class picard.analysis.MergeableMetricBase
-
Merges another MergableMetricBase if possible
- MergePedIntoVcf - Class in picard.arrays
-
Class to take genotype calls from a ped file output from zCall and merge them into a vcf from autocall.
- MergePedIntoVcf() - Constructor for class picard.arrays.MergePedIntoVcf
- MergeSamFiles - Class in picard.sam
-
This tool is used for combining SAM and/or BAM files from different runs or read groups into a single file, similar to the \"merge\" function of Samtools (http://www.htslib.org/doc/samtools.html).
- MergeSamFiles() - Constructor for class picard.sam.MergeSamFiles
- MergeVcfs - Class in picard.vcf
-
Combines multiple variant files into a single variant file.
- MergeVcfs() - Constructor for class picard.vcf.MergeVcfs
- METRIC - Variable in class picard.analysis.CompareMetrics.MetricComparisonDifferences
- METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectAlignmentSummaryMetrics
- METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectGcBiasMetrics
- METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectInsertSizeMetrics
- METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectMultipleMetrics
- METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectRnaSeqMetrics
- METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.CollectRrbsMetrics
- METRIC_ACCUMULATION_LEVEL - Variable in class picard.analysis.directed.CollectTargetedMetrics
- METRIC_ALLOWABLE_RELATIVE_CHANGE - Variable in class picard.analysis.CompareMetrics
- MetricAccumulationLevel - Enum Class in picard.analysis
-
For use with Picard metrics programs that may output metrics for multiple levels of aggregation with an analysis.
- MetricComparisonDifferences() - Constructor for class picard.analysis.CompareMetrics.MetricComparisonDifferences
- metrics - Variable in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
- METRICS - Variable in class picard.illumina.MarkIlluminaAdapters
- METRICS_FILE - Variable in class picard.illumina.ExtractBarcodesProgram
- METRICS_FILE - Variable in class picard.sam.DownsampleSam
- METRICS_FILE - Variable in class picard.sam.markduplicates.CollectDuplicateMetrics
- METRICS_FILE - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- METRICS_FILE_PREFIX - Variable in class picard.analysis.CollectRrbsMetrics
- METRICS_FILE_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- METRICS_NOT_REQUIRED - Variable in class picard.analysis.CompareMetrics
- METRICS_TO_IGNORE - Variable in class picard.analysis.CompareMetrics
- MetricToAllowableRelativeChange - Variable in class picard.analysis.CompareMetrics
- min(byte[]) - Static method in class picard.util.MathUtil
-
Returns the smallest value stored in the array.
- min(double[]) - Static method in class picard.util.MathUtil
-
Returns the smallest value stored in the array.
- min(int[]) - Static method in class picard.util.MathUtil
-
Returns the smallest value stored in the array.
- min(short[]) - Static method in class picard.util.MathUtil
-
Returns the smallest value stored in the array.
- MIN_AB - Variable in class picard.vcf.filter.FilterVcf
- MIN_BASE_Q - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- MIN_DP - Variable in class picard.vcf.filter.FilterVcf
- MIN_DP - Variable in class picard.vcf.GenotypeConcordance
- MIN_DP - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
- MIN_GQ - Variable in class picard.vcf.filter.FilterVcf
- MIN_GQ - Variable in class picard.vcf.GenotypeConcordance
- MIN_GQ - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
- MIN_GROUP_COUNT - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
- MIN_HET_FRACTION - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
- MIN_HISTOGRAM_WIDTH - Variable in class picard.analysis.CollectInsertSizeMetrics
- MIN_IDENTICAL_BASES - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
- MIN_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
-
The minimum measured insert size.
- MIN_LIFTOVER_PCT - Variable in class picard.util.LiftOverIntervalList
- MIN_MAPPING_Q - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- MIN_MATCH_BASES - Static variable in class picard.util.ClippingUtility
-
The default value used for the minimum number of contiguous bases to match against.
- MIN_MATCH_BASES_PE - Variable in class picard.illumina.MarkIlluminaAdapters
- MIN_MATCH_BASES_SE - Variable in class picard.illumina.MarkIlluminaAdapters
- MIN_MATCH_PE_BASES - Static variable in class picard.util.ClippingUtility
-
The default value used for the minimum number of contiguous bases to match against in a paired end read
- MIN_MEAN_QUALITY - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
- MIN_MISMATCH_DELTA - Variable in class picard.illumina.ExtractBarcodesProgram
- MIN_POS - Static variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
-
At least one NextSeq run produced a small negative value for y coordinate (-5), so allow small negative values and see what happens.
- MIN_Q - Variable in class picard.sam.FastqToSam
- MIN_QD - Variable in class picard.vcf.filter.FilterVcf
- MIN_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The minimum read length.
- MIN_TARGET_COVERAGE - Variable in class picard.analysis.directed.PanelMetricsBase
-
The minimum coverage of reads that mapped to target regions of an experiment.
- MIN_TRIMMED_LENGTH - Variable in class picard.illumina.IlluminaBasecallsToFastq
- MIN_UNCLIPPED_BASES - Variable in class picard.sam.MergeBamAlignment
- MINIMUM_BAITS_PER_TARGET - Variable in class picard.util.BaitDesigner
- MINIMUM_BARCODE_BQ - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- MINIMUM_BASE_QUALITY - Variable in class picard.analysis.CollectWgsMetrics
- MINIMUM_BASE_QUALITY - Variable in class picard.analysis.directed.CollectTargetedMetrics
- MINIMUM_BASE_QUALITY - Variable in class picard.illumina.ExtractBarcodesProgram
- MINIMUM_BQ - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- MINIMUM_DISTANCE - Variable in class picard.sam.markduplicates.MarkDuplicatesWithMateCigar
- MINIMUM_GENOME_FRACTION - Variable in class picard.analysis.CollectGcBiasMetrics
- MINIMUM_GQ - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- MINIMUM_INSERT_SIZE - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- MINIMUM_INSERT_SIZE - Variable in class picard.analysis.CollectOxoGMetrics
- MINIMUM_LENGTH - Variable in class picard.analysis.CollectRnaSeqMetrics
- MINIMUM_LOD_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.CollectJumpingLibraryMetrics
- MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.CollectOxoGMetrics
- MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.CollectWgsMetrics
- MINIMUM_MAPPING_QUALITY - Variable in class picard.analysis.directed.CollectTargetedMetrics
- MINIMUM_MAPPING_QUALITY_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- MINIMUM_MQ - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- MINIMUM_PCT - Variable in class picard.analysis.CollectInsertSizeMetrics
- MINIMUM_QUALITY - Variable in class picard.illumina.ExtractBarcodesProgram
- MINIMUM_QUALITY_SCORE - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- MINIMUM_QUALITY_SCORE - Variable in class picard.analysis.CollectOxoGMetrics
- MINIMUM_READ_LENGTH - Variable in class picard.analysis.CollectRrbsMetrics
- minimumBaseQuality - Variable in class picard.util.BarcodeEditDistanceQuery
-
minimal base quality to condiser informative
- MINUS - Enum constant in enum class picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
- MISALIGNED - Enum constant in enum class picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
- mismatchesInReadStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies according to the overall mismatches (from NM) that the read has against the reference, NOT including the current base.
- MismatchesInReadStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.MismatchesInReadStratifier
- MISSING - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- MISSING - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- MISSING_ALLELE_B_PROBESEQ - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Manifest contained no allele B probe sequence
- MISSING_CODE - Enum constant in enum class picard.vcf.GenotypeConcordanceStateCodes
-
These codes allow for constants in the truth state enum and the call state enum to be compared.
- MISSING_LEFT - Variable in class picard.sam.SamComparisonMetric
-
The number of primary records which are found in right file but not found in left file
- MISSING_RIGHT - Variable in class picard.sam.SamComparisonMetric
-
The number of primary records which are found in left file but not found in right file
- MISSING_SITES_HOM_REF - Variable in class picard.vcf.GenotypeConcordance
- MMapBackedIteratorFactory - Class in picard.illumina.parser.readers
-
MMapBackedIteratorFactory a file reader that takes a header size and a binary file, maps the file to a read-only byte buffer and provides methods to retrieve the header as it's own bytebuffer and create iterators of different data types over the values of file (starting after the end of the header).
- MMapBackedIteratorFactory() - Constructor for class picard.illumina.parser.readers.MMapBackedIteratorFactory
- MODE - Variable in class picard.sam.markduplicates.CheckDuplicateMarking
- MODE - Variable in class picard.sam.ValidateSamFile
- MODE_INSERT_SIZE - Variable in class picard.analysis.InsertSizeMetrics
-
The MODE insert size of all paired end reads where both ends mapped to the same chromosome.
- MOLECULAR_BARCODE_NAME - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The barcode name for which the metrics were calculated.
- MOLECULAR_BARCODE_SEQUENCE_1 - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The barcode sequence for which the metrics were calculated.
- MOLECULAR_IDENTIFIER_TAG - Variable in class picard.sam.markduplicates.MarkDuplicates
- MOLECULAR_INDEX_BASE_QUALITY_TAG - Variable in class picard.illumina.IlluminaBasecallsToSam
- MOLECULAR_INDEX_TAG - Variable in class picard.illumina.IlluminaBasecallsToSam
- molecularBarcode - Variable in class picard.illumina.parser.ReadStructure
- MolecularIndex - Static variable in enum class picard.illumina.parser.ReadType
- MostDistantPrimaryAlignmentSelectionStrategy - Class in picard.sam
-
For a paired-end aligner that aligns each end independently, select the pair of alignments that result in the largest insert size.
- MostDistantPrimaryAlignmentSelectionStrategy() - Constructor for class picard.sam.MostDistantPrimaryAlignmentSelectionStrategy
- MOTHER - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The ID of the mother within the trio.
- MOVE_TO_TAG - Enum constant in enum class picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
- MultiLevelCollector<METRIC_TYPE extends htsjdk.samtools.metrics.MetricBase,
Histogram_KEY extends Comparable, ARGTYPE> - Class in picard.metrics -
MultiLevelCollector handles accumulating Metrics at different MetricAccumulationLevels(ALL_READS, SAMPLE, LIBRARY, READ_GROUP).
- MultiLevelCollector() - Constructor for class picard.metrics.MultiLevelCollector
- MultilevelMetrics - Class in picard.metrics
- MultilevelMetrics() - Constructor for class picard.metrics.MultilevelMetrics
- MULTIPLEX_PARAMS - Variable in class picard.illumina.IlluminaBasecallsToFastq
- multiply(double[], double[]) - Static method in class picard.util.MathUtil
-
Calculates the product of two arrays of the same length.
- MultiThreadedChunkBased(int, VariantIteratorProducer, VariantProcessor.AccumulatorGenerator<A, R>) - Constructor for class picard.vcf.processor.VariantAccumulatorExecutor.MultiThreadedChunkBased
- multithreadingBy(int) - Method in class picard.vcf.processor.VariantProcessor.Builder
- MultiTileBcl - Enum constant in enum class picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
- MultiTileBclFileFaker - Class in picard.illumina.parser.fakers
-
Created by jcarey on 3/13/14.
- MultiTileBclFileFaker() - Constructor for class picard.illumina.parser.fakers.MultiTileBclFileFaker
- MultiTileBclFileUtil - Class in picard.illumina.parser
-
NextSeq-style bcl's have all tiles for a cycle in a single file.
- MultiTileBclParser - Class in picard.illumina.parser
-
Parse .bcl.bgzf files that contain multiple tiles in a single file.
- MultiTileBclParser(File, int, CycleIlluminaFileMap, OutputMapping, boolean, BclQualityEvaluationStrategy, TileIndex) - Constructor for class picard.illumina.parser.MultiTileBclParser
- MultiTileFileUtil<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData> - Class in picard.illumina.parser
-
For file types for which there is one file per lane, with fixed record size, and all the tiles in it, so the s_
.bci file can be used to figure out where each tile starts and ends. - MultiTileFilter - Enum constant in enum class picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
- MultiTileFilterParser - Class in picard.illumina.parser
-
Read filter file that contains multiple tiles in a single file.
- MultiTileFilterParser(TileIndex, List<Integer>, File) - Constructor for class picard.illumina.parser.MultiTileFilterParser
- MultiTileLocs - Enum constant in enum class picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
- MultiTileLocsFileFaker - Class in picard.illumina.parser.fakers
-
Created by jcarey on 3/13/14.
- MultiTileLocsFileFaker() - Constructor for class picard.illumina.parser.fakers.MultiTileLocsFileFaker
- MultiTileLocsParser - Class in picard.illumina.parser
-
Read locs file that contains multiple tiles in a single file.
- MultiTileLocsParser(TileIndex, List<Integer>, File, int) - Constructor for class picard.illumina.parser.MultiTileLocsParser
- MultiTileParser<OUTPUT_RECORD extends picard.illumina.parser.IlluminaData> - Class in picard.illumina.parser
-
Abstract class for files with fixed-length records for multiple tiles, e.g.
- MultiTileParser(TileIndex, List<Integer>, Set<IlluminaDataType>) - Constructor for class picard.illumina.parser.MultiTileParser
N
- n - Variable in class picard.arrays.illumina.InfiniumEGTFile
- N - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- N_CYCLES - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
- NA - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.ContingencyState
- NA - Static variable in class picard.vcf.GenotypeConcordanceScheme
-
These are convenience variables for defining a scheme.
- nAlternateAllelesBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of doubletons where the two reads matched the alternate.
- nAlternateAllelesTriDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of tripletons where the two reads matched the alternate.
- nAlternateReads - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of alternate alleles in the reads.
- name - Variable in class picard.annotation.Gene.Transcript
- NAME - Variable in class picard.util.FifoBuffer
- NAME_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- NATURAL_LOG_MATH - Static variable in class picard.util.MathUtil
- nBadBarcodes - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of sets where the UMIs had poor quality bases and were not used for any comparisons.
- NCBI_35 - Static variable in class picard.arrays.illumina.IlluminaManifest
- NCBI_36 - Static variable in class picard.arrays.illumina.IlluminaManifest
- NCBI_37 - Static variable in class picard.arrays.illumina.IlluminaManifest
- nDeletedBases - Variable in class picard.sam.SamErrorMetric.IndelErrorCalculator
-
Total number of deleted bases
- nDeletions - Variable in class picard.sam.SamErrorMetric.IndelErrorCalculator
-
Total number of deletions
- nDifferentAllelesBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of doubletons where the two reads had different bases in the locus.
- nDifferentAllelesTriDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of tripletons where at least one of the reads didn't match either allele of the het site.
- nDuplicateSets - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of duplicate sets examined.
- NEAR_AMPLICON_BASES - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The number of PF_BASES_ALIGNED that mapped to within a fixed interval of an amplified region, but not on a baited region.
- NEAR_BAIT_BASES - Variable in class picard.analysis.directed.HsMetrics
-
The number of PF_BASES_ALIGNED that are mapped to within a fixed interval containing a baited region, but not within the baited section per se.
- NEAR_DISTANCE - Variable in class picard.analysis.directed.CollectTargetedMetrics
- NEAR_PROBE_BASES - Variable in class picard.analysis.directed.TargetMetrics
-
The number of PF aligned bases that mapped to within a fixed interval of a probed region, but not on a probed region.
- NEAR_PROBE_DISTANCE_DEFAULT - Static variable in class picard.analysis.directed.TargetMetricsCollector
-
Default distance for a read to be considered "selected".
- needsReferenceSequence() - Method in interface picard.analysis.CollectMultipleMetrics.ProgramInterface
- needsRefflatFile() - Method in interface picard.analysis.CollectMultipleMetrics.ProgramInterface
- NEGATIVE - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ReadDirection
- NEW_SAMPLE_NAME - Variable in class picard.vcf.RenameSampleInVcf
- newCounter() - Method in class picard.analysis.CounterManager
-
Creates a new Counter object and adds it to the list of managed Counters.
- nExactlyDouble - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of sets of size exactly 2 found.
- nExactlyTriple - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of sets of size exactly 3 found.
- next() - Method in class picard.illumina.parser.MultiTileBclParser
- next() - Method in class picard.illumina.parser.MultiTileParser
- next() - Method in class picard.illumina.parser.PerTileParser
- next() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
-
Return the next set of coordinates in a given file.
- next() - Method in class picard.illumina.parser.readers.BarcodeFileReader
- next() - Method in class picard.illumina.parser.readers.BclReader
- next() - Method in class picard.illumina.parser.readers.CbclReader
- next() - Method in class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader
- next() - Method in class picard.illumina.parser.readers.FilterFileReader
- next() - Method in class picard.illumina.parser.readers.TileMetricsOutReader
- next() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
- next() - Method in class picard.util.AsyncIterator
- next() - Method in interface picard.util.AtomicIterator
-
Produces the next element from the iterator, if there is one; otherwise, produces
Optional.EMPTY
- next() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
- next() - Method in class picard.util.SequenceDictionaryUtils.SamSequenceRecordsIterator
- next() - Method in class picard.vcf.ByIntervalListVariantContextIterator
- next() - Method in class picard.vcf.filter.FilterApplyingVariantIterator
-
Provides the next record from the underlying iterator after applying filter strings generated by the set of filters in use by the iterator.
- next() - Method in class picard.vcf.PairedVariantSubContextIterator
- next() - Method in class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
- NEXT_BASE_QUALITY_THRESHOLD - Variable in class picard.analysis.CollectRrbsMetrics
- NEXTERA_V1 - Enum constant in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- NEXTERA_V2 - Enum constant in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- nextReadBaseStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies bases into the following (uppercase) base as it was read from the sequencer (i.e.
- nGoodBarcodes - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
the number of sets where the UMIs had good quality bases and were used for any comparisons.
- NHOM - Variable in class picard.arrays.BafRegressMetrics
-
The number of homozygous genotypes used to fit the model
- nInsertedBases - Variable in class picard.sam.SamErrorMetric.IndelErrorCalculator
-
Total number of inserted bases
- nInsertions - Variable in class picard.sam.SamErrorMetric.IndelErrorCalculator
-
Total number of inserts
- nMatchingUMIsInDiffBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of UMIs that are match within Bi-sets that come from different alleles.
- nMatchingUMIsInSameBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of UMIs that are match within Bi-sets that come from the same alleles.
- nMismatchingAllelesBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of tripletons where the two reads had different bases in the locus.
- nMismatchingAllelesTriDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of tripletons where at least one of the reads didn't match either allele of the het site.
- nMismatchingBases - Variable in class picard.sam.SamErrorMetric.SimpleErrorCalculator
- nMismatchingUMIsInContraOrientedBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of bi-sets with mismatching UMIs and opposite orientation.
- nMismatchingUMIsInCoOrientedBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of bi-sets with mismatching UMIs and same orientation.
- nMismatchingUMIsInDiffBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of UMIs that are different within Bi-sets that come from different alleles.
- nMismatchingUMIsInSameBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of UMIs that are different within Bi-sets that come from the same alleles.
- NN - Enum constant in enum class picard.arrays.illumina.IlluminaGenotype
- NO_CALL - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- NO_CALL - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- NO_CALL - Static variable in class picard.arrays.illumina.InfiniumGTCFile
- NO_CALL_BASE - Static variable in class picard.illumina.parser.readers.BaseBclReader
- NO_CALL_CODE - Enum constant in enum class picard.vcf.GenotypeConcordanceStateCodes
- NO_LIBRARIES_SPECIFIED_IN_HEADER - Static variable in class picard.sam.SplitSamByLibrary
- NO_MATCH - Static variable in class picard.util.ClippingUtility
-
The value returned by methods returning int when no match is found.
- NO_PHENO - Static variable in class picard.pedigree.PedFile
- NO_VALUE - Static variable in interface picard.sam.util.PhysicalLocation
- noMatchMetric - Variable in class picard.illumina.ExtractBarcodesProgram
- NON_CPG_BASES - Variable in class picard.analysis.RrbsSummaryMetrics
-
Number of times a non-CpG cytosine was encountered
- NON_CPG_CONVERTED_BASES - Variable in class picard.analysis.RrbsSummaryMetrics
-
Number of times a non-CpG cytosine was converted (C->T for +, G->A for -)
- NON_REF_GENOTYPE_CONCORDANCE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The non-ref genotype concordance, ie for all var states only.
- NON_ZERO_REGIONS - Enum constant in enum class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
- NONE - Enum constant in enum class picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
- NONE - Enum constant in enum class picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
- NONJUMP_DUPLICATE_PAIRS - Variable in class picard.analysis.JumpingLibraryMetrics
-
The number of inward-facing pais that are duplicates
- NONJUMP_DUPLICATE_PCT - Variable in class picard.analysis.JumpingLibraryMetrics
-
The fraction of inward-facing pairs that are marked as duplicates
- NONJUMP_LIBRARY_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
-
The estimated library size for inward-facing pairs
- NONJUMP_MEAN_INSERT_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
-
The mean insert size for inward-facing pairs
- NONJUMP_PAIRS - Variable in class picard.analysis.JumpingLibraryMetrics
-
The number of inward-facing pairs in the SAM file
- NONJUMP_STDEV_INSERT_SIZE - Variable in class picard.analysis.JumpingLibraryMetrics
-
The standard deviation on the insert size for inward-facing pairs
- NonNFastaSize - Class in picard.reference
-
A tool to count the number of non-N bases in a fasta file
- NonNFastaSize() - Constructor for class picard.reference.NonNFastaSize
- NonPF - Enum constant in enum class picard.sam.ViewSam.PfStatus
- nonSkips - Variable in class picard.illumina.parser.ReadStructure
- nonStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
A constant stratifier which places all the reads into a single stratum.
- normalizationVersion - Variable in class picard.arrays.illumina.InfiniumEGTFile
- normalizeAlleles(VariantContext, String, VariantContext, String, Boolean) - Static method in class picard.vcf.GenotypeConcordance
-
Gets the alleles for the truth and call genotypes.
- NORMALIZED_COVERAGE - Variable in class picard.analysis.GcBiasDetailMetrics
-
The ratio of "coverage" in this GC bin vs.
- normalizedXIntensity - Variable in class picard.arrays.illumina.InfiniumGTCRecord
- normalizedYIntensity - Variable in class picard.arrays.illumina.InfiniumGTCRecord
- NormalizeFasta - Class in picard.reference
-
Little program to "normalize" a fasta file to ensure that all line of sequence are the same length, and are a reasonable length!
- NormalizeFasta() - Constructor for class picard.reference.NormalizeFasta
- normalizeHistogram(Histogram<Integer>) - Static method in class picard.analysis.TheoreticalSensitivity
- NORMX - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- NORMY - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- NOT_ALIGNED_ERROR - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
- NotReported - Enum constant in enum class picard.pedigree.Sex
- NOVEL_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of passing indels called that were not found in dbSNP
- NOVEL_INS_DEL_RATIO - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The Insertion/Deletion ratio of the indel calls made at non-dbSNP sites
- NOVEL_SNPS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The number of high confidence SNPS called that were not found in dbSNP
- NOVEL_SNPS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of passing bi-allelic SNPS called that were not found in dbSNP
- NOVEL_TITV - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The Transition/Transversion ratio of the passing bi-allelic SNP calls made at non-dbSNP sites
- nReadsInBigSets - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of reads in duplicate of sizes greater than 3.
- nRecordsInMemory - Variable in class picard.annotation.SortGff
- nReferenceAllelesBiDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of doubletons where the two reads matched the reference.
- nReferenceAllelesTriDups - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of tripletons where the two reads matched the reference.
- nReferenceReads - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The number of reference alleles in the reads.
- nsInReadStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratify by the number of Ns found in the read.
- NsInReadStratifier() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.NsInReadStratifier
- nSites - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The count of sites used.
- nThreeAllelesSites - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The count of sites in which a third allele was found.
- nTotalReads - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
The total number of reads over the het sites.
- NUM_ADAPTERS_TO_KEEP - Variable in class picard.illumina.MarkIlluminaAdapters
- NUM_ASSAYS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The total number of assays (SNP and indels) in the VCF
- NUM_AUTOCALL_CALLS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The number of passing autocall calls
- NUM_BASES_WITH_OVERLAPPING_READS - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
-
The number of bases for which an overlapping base from the mate read was found
- NUM_CALLS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The number of passing calls
- NUM_CHANNELS - Static variable in enum class picard.illumina.parser.IntensityChannel
- NUM_DELETED_BASES - Variable in class picard.sam.SamErrorMetric.IndelErrorMetric
-
The number of deleted bases.
- NUM_DELETIONS - Variable in class picard.sam.SamErrorMetric.IndelErrorMetric
-
The number of deletions.
- NUM_DIPLOID_DENOVO - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The number of diploid sites at which a potential de-novo mutation was observed (i.e.
- NUM_DISAGREES_WITH_REF_AND_MATE - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
-
The number of bases that disagree with both the reference and their mate (which agree with each other)
- NUM_DISAGREES_WITH_REFERENCE_ONLY - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
-
The number of bases that disagree with the reference, but agree with their mate
- NUM_FILTERED_ASSAYS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The total number of filtered assays in the VCF
- NUM_HAPLOID_DENOVO - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The number of sites at which the offspring is haploid, the parent is homozygous reference and the offspring is non-reference.
- NUM_HAPLOID_OTHER - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The number of sites at which the offspring is haploid and exhibits a reference allele that is not present in the parent.
- NUM_HET - Variable in class picard.fingerprint.FingerprintMetrics
-
Number of heterozygous calls
- NUM_HOM_ALLELE1 - Variable in class picard.fingerprint.FingerprintMetrics
-
Number of major allele homozygous calls
- NUM_HOM_ALLELE2 - Variable in class picard.fingerprint.FingerprintMetrics
-
Number of minor allele homozygous calls
- NUM_HOM_ANY - Variable in class picard.fingerprint.FingerprintMetrics
-
Number of homozygous calls of either allele (might not be the sum of
FingerprintMetrics.NUM_HOM_ALLELE1
andFingerprintMetrics.NUM_HOM_ALLELE1
due to rounding - NUM_HOM_HET_HOM - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The number of sites at which one parent is homozygous, the other is heterozygous and the offspring is the alternative homozygote.
- NUM_HOMREF_HOMVAR_HOM - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The number of sites at which the one parent is homozygous reference, the other homozygous variant and the offspring is homozygous.
- NUM_HOMVAR_HOMVAR_HET - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The number of sites at which both parents are homozygous for a non-reference allele and the offspring is heterozygous.
- NUM_IN_DB_SNP - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The number of high confidence SNPs found in dbSNP
- NUM_IN_DB_SNP - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of passing bi-allelic SNPs found in dbSNP
- NUM_IN_DB_SNP_COMPLEX_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of passing complex indels found in dbSNP
- NUM_IN_DB_SNP_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of passing indels found in dbSNP
- NUM_IN_DB_SNP_MULTIALLELIC - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of passing multi-allelic SNPs found in dbSNP
- NUM_INDELS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The number of indel calls
- NUM_INSERTED_BASES - Variable in class picard.sam.SamErrorMetric.IndelErrorMetric
-
The number of inserted bases.
- NUM_INSERTIONS - Variable in class picard.sam.SamErrorMetric.IndelErrorMetric
-
The number of insertions.
- NUM_MARKERS_FILE - Variable in class picard.arrays.VcfToAdpc
- NUM_N - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
-
The number of Ns found in this read
- NUM_NO_CALLS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The number of no-calls
- NUM_NON_FILTERED_ASSAYS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The total number of NON-filtered assays in the VCF
- NUM_OTHER - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The number of otherwise unclassified events.
- NUM_PROCESSORS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics
- NUM_PROCESSORS - Variable in class picard.illumina.ExtractIlluminaBarcodes
- NUM_PROCESSORS - Variable in class picard.illumina.IlluminaBasecallsToFastq
- NUM_PROCESSORS - Variable in class picard.illumina.IlluminaBasecallsToSam
- NUM_PROCESSORS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
- NUM_Q_GT_TWO - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
-
The number of Quality scores greater than 2 found in this read
- NUM_R1_TRANSCRIPT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
-
The number of reads that support the model where R1 is on the strand of transcription and R2 is on the opposite strand.
- NUM_R2_TRANSCRIPT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
-
The fraction of reads that support the model where R2 is on the strand of transcription and R1 is on the opposite strand.
- NUM_SEQUENCES - Variable in class picard.sam.CreateSequenceDictionary
- NUM_SINGLETONS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
For summary metrics, the number of variants that appear in only one sample.
- NUM_SINGLETONS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
For summary metrics, the number of variants that appear in only one sample.
- NUM_SNPS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The number of bi-allelic SNP calls
- NUM_THREADS - Variable in class picard.fingerprint.CrosscheckFingerprints
- NUM_THREE_WAYS_DISAGREEMENT - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
-
The number of bases that disagree with both the reference and their mate (which also disagree)
- NUM_UNEXPLAINED_READS - Variable in class picard.analysis.RnaSeqMetrics
-
The fraction of reads for which the transcription strand model could not be inferred.
- NUM_VARIANT_SITES - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The number of biallelic, SNP sites at which all relevant samples exceeded the minimum genotype quality and depth and at least one of the samples was variant.
- NUM_ZEROED_OUT_ASSAYS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The total number of zeroed-out (filtered out by Illumina in chip design) assays in the VCF
- NUMBER_OF_SAMPLING - Variable in class picard.fingerprint.CalculateFingerprintMetrics
- numClusters - Variable in class picard.illumina.parser.readers.FilterFileReader
-
The number of cluster's pf values stored in this file
- numCodes - Variable in class picard.arrays.illumina.InfiniumEGTFile
- numOutputReads() - Method in class picard.illumina.parser.OutputMapping
- numProcessors(int) - Method in class picard.illumina.BasecallsConverterBuilder
-
Configures how many processors this converter will use.
O
- OBS_A - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The number of observations of the first, or A, allele of the SNP in the sequencing data.
- OBS_B - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The number of observations of the second, or B, allele of the SNP in the sequencing data.
- obsAllele1 - Variable in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
- obsAllele2 - Variable in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
- obsAlleleOther - Variable in class picard.fingerprint.HaplotypeProbabilitiesFromSequence
- OBSERVED_BASE_ERRORS - Variable in class picard.sam.markduplicates.UmiMetrics
-
Number of errors inferred by comparing the observed and inferred UMIs
- OBSERVED_GENOTYPE - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The most likely genotype given the observed evidence at the SNP locus in the sequencing data.
- OBSERVED_SAMPLE_ALIAS - Variable in class picard.fingerprint.CheckFingerprint
- OBSERVED_UMI_ENTROPY - Variable in class picard.sam.markduplicates.UmiMetrics
-
Entropy (in base 4) of the observed UMI sequences, indicating the effective number of bases in the UMIs.
- OBSERVED_UNIQUE_UMIS - Variable in class picard.sam.markduplicates.UmiMetrics
-
Number of different UMI sequences observed
- of(SAMRecord) - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
- of(SAMRecord) - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
- of(SAMRecord) - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ReadDirection
- of(SAMRecord) - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ReadOrdinality
- OFF_AMPLICON_BASES - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The number of PF_BASES_ALIGNED that mapped neither on or near an amplicon.
- OFF_BAIT_BASES - Variable in class picard.analysis.directed.HsMetrics
-
The number of PF_BASES_ALIGNED that are mapped away from any baited region.
- OFF_PROBE_BASES - Variable in class picard.analysis.directed.TargetMetrics
-
The number of PF aligned bases that mapped to neither on or near a probe.
- OFFSPRING - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The ID of the offspring within the trio.
- OFFSPRING_SEX - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The sex of the offspring.
- OLD_SAMPLE_NAME - Variable in class picard.vcf.RenameSampleInVcf
- ON_AMPLICON_BASES - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The number of PF_BASES_ALIGNED that mapped to an amplified region of the genome.
- ON_AMPLICON_VS_SELECTED - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The fraction of bases mapping to regions on or near amplicons, which mapped directly to but not near amplicons, ON_AMPLICON_BASES/(NEAR_AMPLICON_BASES + ON_AMPLICON_BASES)
- ON_BAIT_BASES - Variable in class picard.analysis.directed.HsMetrics
-
The number of PF_BASES_ALIGNED that are mapped to the baited regions of the genome.
- ON_BAIT_VS_SELECTED - Variable in class picard.analysis.directed.HsMetrics
-
The fraction of bases on or near baits that are covered by baits, ON_BAIT_BASES/(ON_BAIT_BASES + NEAR_BAIT_BASES).
- ON_PROBE_BASES - Variable in class picard.analysis.directed.TargetMetrics
-
The number of PF aligned probed bases that mapped to a baited region of the genome.
- ON_PROBE_VS_SELECTED - Variable in class picard.analysis.directed.TargetMetrics
-
The fraction of on+near probe bases that are on as opposed to near, ON_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES).
- ON_TARGET_BASES - Variable in class picard.analysis.directed.PanelMetricsBase
-
The number of PF aligned bases that mapped to a targeted region of the genome.
- ON_TARGET_FROM_PAIR_BASES - Variable in class picard.analysis.directed.TargetMetricsBase
-
The number of PF aligned bases that are mapped in pair to a targeted region of the genome.
- ONE_MISMATCH_MATCHES - Variable in class picard.illumina.BarcodeMetric
-
The number of all reads matching this barcode that matched with 1 error or no-call.
- oneBasePaddedContextStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies into the one base context of the base, which includes one read-base on each side and the reference base from where the current base is the bases will be reverse-complemented so that the bases are in the original order they were read from the sequencer
- openInputs(boolean) - Method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
-
Since this may read its inputs more than once this method does all the opening and checking of the inputs.
- OPTICAL_DUPLICATE_PIXEL_DISTANCE - Variable in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
- opticalDuplicateFinder - Variable in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
- OpticalDuplicateFinder - Class in picard.sam.markduplicates.util
-
Contains methods for finding optical/co-localized/sequencing duplicates.
- OpticalDuplicateFinder() - Constructor for class picard.sam.markduplicates.util.OpticalDuplicateFinder
-
Uses the default duplicate distance
OpticalDuplicateFinder.DEFAULT_OPTICAL_DUPLICATE_DISTANCE
(100) and the default read name regexReadNameParser.DEFAULT_READ_NAME_REGEX
. - OpticalDuplicateFinder(String, int, long, Log) - Constructor for class picard.sam.markduplicates.util.OpticalDuplicateFinder
- OpticalDuplicateFinder(String, int, Log) - Constructor for class picard.sam.markduplicates.util.OpticalDuplicateFinder
- opticalDuplicateIndexes - Variable in class picard.sam.markduplicates.MarkDuplicates
- opticalDuplicatePixelDistance - Variable in class picard.sam.markduplicates.util.OpticalDuplicateFinder
- OpticalOnly - Enum constant in enum class picard.sam.markduplicates.MarkDuplicates.DuplicateTaggingPolicy
- OptionalReferenceArgumentCollection - Class in picard.cmdline.argumentcollections
-
Picard default argument collection for an optional reference.
- OptionalReferenceArgumentCollection() - Constructor for class picard.cmdline.argumentcollections.OptionalReferenceArgumentCollection
- orientation - Variable in class picard.sam.markduplicates.util.ReadEnds
- orientationForOpticalDuplicates - Variable in class picard.sam.markduplicates.util.ReadEnds
-
For optical duplicate detection the orientation matters regard to 1st or 2nd end of a mate
- ORIGINAL_ALLELES - Static variable in class picard.vcf.LiftoverVcf
-
Attribute used to store the list of original alleles (including REF), in the original order prior to liftover.
- ORIGINAL_CONTIG - Static variable in class picard.vcf.LiftoverVcf
-
Attribute used to store the name of the source contig/chromosome prior to liftover.
- ORIGINAL_START - Static variable in class picard.vcf.LiftoverVcf
-
Attribute used to store the position of the variant on the source contig prior to liftover.
- ORIGINAL_VCF - Variable in class picard.arrays.MergePedIntoVcf
- OtherProgramGroup - Class in picard.cmdline.programgroups
-
Miscellaneous tools, e.g.
- OtherProgramGroup() - Constructor for class picard.cmdline.programgroups.OtherProgramGroup
- out - Variable in class picard.sam.FixMateInformation
- out - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
- out - Variable in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
- OUT_PREFIX - Variable in class picard.sam.SplitSamByNumberOfReads
- output - Variable in class picard.analysis.SinglePassSamProgram
- OUTPUT - Variable in class picard.analysis.CollectJumpingLibraryMetrics
- OUTPUT - Variable in class picard.analysis.CollectMultipleMetrics
- OUTPUT - Variable in class picard.analysis.CollectOxoGMetrics
- OUTPUT - Variable in class picard.analysis.CollectWgsMetrics
- OUTPUT - Variable in class picard.analysis.CompareMetrics
- OUTPUT - Variable in class picard.analysis.directed.CollectTargetedMetrics
- OUTPUT - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- OUTPUT - Variable in class picard.analysis.SinglePassSamProgram
- OUTPUT - Variable in class picard.annotation.SortGff
- OUTPUT - Variable in class picard.arrays.CollectArraysVariantCallingMetrics
- OUTPUT - Variable in class picard.arrays.CombineGenotypingArrayVcfs
- OUTPUT - Variable in class picard.arrays.CreateBafRegressMetricsFile
- OUTPUT - Variable in class picard.arrays.CreateVerifyIDIntensityContaminationMetricsFile
- OUTPUT - Variable in class picard.arrays.GtcToVcf
- OUTPUT - Variable in class picard.arrays.illumina.BpmToNormalizationManifestCsv
- OUTPUT - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- OUTPUT - Variable in class picard.arrays.MergePedIntoVcf
- OUTPUT - Variable in class picard.arrays.VcfToAdpc
- OUTPUT - Variable in class picard.cmdline.argumentcollections.RequiredOutputArgumentCollection
- OUTPUT - Variable in class picard.fingerprint.CalculateFingerprintMetrics
- OUTPUT - Variable in class picard.fingerprint.CheckFingerprint
- OUTPUT - Variable in class picard.fingerprint.ClusterCrosscheckMetrics
- OUTPUT - Variable in class picard.fingerprint.ConvertHaplotypeDatabaseToVcf
- OUTPUT - Variable in class picard.fingerprint.CrosscheckFingerprints
- OUTPUT - Variable in class picard.fingerprint.ExtractFingerprint
- OUTPUT - Variable in class picard.fingerprint.IdentifyContaminant
- OUTPUT - Variable in class picard.fingerprint.LiftOverHaplotypeMap
- OUTPUT - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
- OUTPUT - Variable in class picard.illumina.IlluminaBasecallsToSam
- OUTPUT - Variable in class picard.illumina.MarkIlluminaAdapters
- OUTPUT - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
- OUTPUT - Variable in class picard.reference.ExtractSequences
- OUTPUT - Variable in class picard.reference.NonNFastaSize
- OUTPUT - Variable in class picard.reference.NormalizeFasta
- OUTPUT - Variable in class picard.sam.AddCommentsToBam
- OUTPUT - Variable in class picard.sam.AddOATag
- OUTPUT - Variable in class picard.sam.AddOrReplaceReadGroups
- OUTPUT - Variable in class picard.sam.BuildBamIndex
- OUTPUT - Variable in class picard.sam.CalculateReadGroupChecksum
- OUTPUT - Variable in class picard.sam.CleanSam
- OUTPUT - Variable in class picard.sam.CompareSAMs
- OUTPUT - Variable in class picard.sam.CreateSequenceDictionary
- OUTPUT - Variable in class picard.sam.DownsampleSam
- OUTPUT - Variable in class picard.sam.FastqToSam
- OUTPUT - Variable in class picard.sam.FilterSamReads
- OUTPUT - Variable in class picard.sam.FixMateInformation
- OUTPUT - Variable in class picard.sam.GatherBamFiles
- OUTPUT - Variable in class picard.sam.markduplicates.CheckDuplicateMarking
- OUTPUT - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
- OUTPUT - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- OUTPUT - Variable in class picard.sam.MergeBamAlignment
- OUTPUT - Variable in class picard.sam.MergeSamFiles
- OUTPUT - Variable in class picard.sam.PositionBasedDownsampleSam
- OUTPUT - Variable in class picard.sam.ReorderSam
- OUTPUT - Variable in class picard.sam.ReplaceSamHeader
- OUTPUT - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
- OUTPUT - Variable in class picard.sam.RevertSam
- OUTPUT - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- OUTPUT - Variable in class picard.sam.SamFormatConverter
- OUTPUT - Variable in class picard.sam.SetNmMdAndUqTags
- OUTPUT - Variable in class picard.sam.SortSam
- OUTPUT - Variable in class picard.sam.SplitSamByLibrary
- OUTPUT - Variable in class picard.sam.SplitSamByNumberOfReads
- OUTPUT - Variable in class picard.sam.ValidateSamFile
- OUTPUT - Variable in class picard.util.AccumulateQualityYieldMetrics
- OUTPUT - Variable in class picard.util.BedToIntervalList
- OUTPUT - Variable in class picard.util.IntervalListToBed
- OUTPUT - Variable in class picard.util.IntervalListTools
- OUTPUT - Variable in class picard.util.LiftOverIntervalList
- OUTPUT - Variable in class picard.util.ScatterIntervalsByNs
- OUTPUT - Variable in class picard.vcf.AccumulateVariantCallingMetrics
- OUTPUT - Variable in class picard.vcf.CollectVariantCallingMetrics
- OUTPUT - Variable in class picard.vcf.filter.FilterVcf
- OUTPUT - Variable in class picard.vcf.FixVcfHeader
- OUTPUT - Variable in class picard.vcf.GatherVcfs
- OUTPUT - Variable in class picard.vcf.GenotypeConcordance
- OUTPUT - Variable in class picard.vcf.LiftoverVcf
- OUTPUT - Variable in class picard.vcf.MakeSitesOnlyVcf
- OUTPUT - Variable in class picard.vcf.MakeVcfSampleNameMap
- OUTPUT - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
- OUTPUT - Variable in class picard.vcf.MergeVcfs
- OUTPUT - Variable in class picard.vcf.RenameSampleInVcf
- OUTPUT - Variable in class picard.vcf.SortVcf
- OUTPUT - Variable in class picard.vcf.UpdateVcfSequenceDictionary
- OUTPUT - Variable in class picard.vcf.VcfFormatConverter
- OUTPUT - Variable in class picard.vcf.VcfToIntervalList
- OUTPUT_AGILENT_FILES - Variable in class picard.util.BaitDesigner
- OUTPUT_ALL_ROWS - Variable in class picard.vcf.GenotypeConcordance
- OUTPUT_BASE - Variable in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
- OUTPUT_BY_READGROUP - Variable in class picard.sam.RevertSam
- OUTPUT_BY_READGROUP_FILE_FORMAT - Variable in class picard.sam.RevertSam
- OUTPUT_DIR - Variable in class picard.illumina.ExtractIlluminaBarcodes
- OUTPUT_DIR - Variable in class picard.sam.SamToFastq
- OUTPUT_DIRECTORY - Variable in class picard.illumina.CollectIlluminaLaneMetrics
- OUTPUT_DIRECTORY - Variable in class picard.util.BaitDesigner
- OUTPUT_ERRORS_ONLY - Variable in class picard.fingerprint.CrosscheckFingerprints
- OUTPUT_MAP - Variable in class picard.sam.RevertSam
- OUTPUT_PER_RG - Variable in class picard.sam.SamToFastq
- OUTPUT_PREFIX - Variable in class picard.illumina.CollectIlluminaLaneMetrics
- OUTPUT_PREFIX - Variable in class picard.illumina.IlluminaBasecallsToFastq
- OUTPUT_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- OUTPUT_TABLE - Variable in class picard.analysis.CompareMetrics
- OUTPUT_TYPE - Variable in class picard.util.ScatterIntervalsByNs
- OUTPUT_VALUE - Variable in class picard.util.IntervalListTools
- OUTPUT_VCF - Variable in class picard.vcf.GenotypeConcordance
- OUTPUT_VCF_CALL_SAMPLE_NAME - Static variable in class picard.vcf.GenotypeConcordance
- OUTPUT_VCF_FILE_EXTENSION - Static variable in class picard.vcf.GenotypeConcordance
- OUTPUT_VCF_TRUTH_SAMPLE_NAME - Static variable in class picard.vcf.GenotypeConcordance
- OutputArgumentCollection - Interface in picard.cmdline.argumentcollections
-
Base interface for an output argument collection.
- outputDetailMetricsFile(VariantContext.Type, MetricsFile<GenotypeConcordanceDetailMetrics, ?>, GenotypeConcordanceCounts, String, String, boolean, boolean) - Static method in class picard.vcf.GenotypeConcordance
-
Outputs the detailed statistics tables for SNP and Indel match categories.
- OutputMapping - Class in picard.illumina.parser
-
In multiple locations we need to know what cycles are output, as of now we output all non-skip cycles, but rather than sprinkle this knowledge throughout the parser code, instead OutputMapping provides all the data a client might want about the cycles to be output including what ReadType they are.
- OutputMapping(ReadStructure) - Constructor for class picard.illumina.parser.OutputMapping
-
Create an OutputMapping from a readStructure, currently the outputSubstructure just references the readStructure.nonSkips Substructure
- outputMetrics() - Method in class picard.illumina.ExtractBarcodesProgram
- OverlappingErrorMetric - Class in picard.sam.SamErrorMetric
-
An error metric for the errors invovling bases in the overlapping region of a read-pair.
- OverlappingErrorMetric() - Constructor for class picard.sam.SamErrorMetric.OverlappingErrorMetric
- OverlappingErrorMetric(String, long, long, long, long, long) - Constructor for class picard.sam.SamErrorMetric.OverlappingErrorMetric
- OverlappingReadsErrorCalculator - Class in picard.sam.SamErrorMetric
-
A calculator that estimates the error rate of the bases it observes, assuming that the reference is truth.
- OverlappingReadsErrorCalculator() - Constructor for class picard.sam.SamErrorMetric.OverlappingReadsErrorCalculator
- OVERLAPS - Enum constant in enum class picard.util.IntervalListTools.Action
- OXIDATION_ERROR_RATE - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The oxo error rate, calculated as max(ALT_OXO_BASES - ALT_NONOXO_BASES, 1) / TOTAL_BASES
- OXIDATION_Q - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
-10 * log10(OXIDATION_ERROR_RATE)
- OXOG_METRICS_EXT - Static variable in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
- OXOG_OUT - Variable in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
P
- P_95_GREEN - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- P_95_RED - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- P95_GREEN - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The 95th Intensity Percentile for the green color channel for this sample
- P95_RED - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The 95th Intensity Percentile for the red color channel for this sample
- PADDING - Variable in class picard.util.BaitDesigner
- PADDING - Variable in class picard.util.IntervalListTools
- Pair<X extends Comparable<X>,
Y extends Comparable<Y>> - Class in picard.sam.util -
Simple Pair class.
- Pair(X, Y) - Constructor for class picard.sam.util.Pair
- PAIR - Enum constant in enum class picard.analysis.AlignmentSummaryMetrics.Category
- PAIR_ORIENTATION - Variable in class picard.analysis.InsertSizeMetrics
-
The pair orientation of the reads in this data category.
- PAIRED_END - Enum constant in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
-
The following sequences can be found in https://support.illumina.com/content/dam/illumina-support/documents/documentation/chemistry_documentation/experiment-design/illumina-adapter-sequences_1000000002694-01.pdf and are protected by the following copyright notice: Oligonucleotide sequences (c) 2016 Illumina, Inc.
- PAIRED_RUN - Variable in class picard.illumina.MarkIlluminaAdapters
- PAIRED_RUN - Variable in class picard.sam.MergeBamAlignment
-
Deprecated.
- PairedVariantSubContextIterator - Class in picard.vcf
-
An iterator that takes a pair of iterators over VariantContexts and iterates over them in tandem.
- PairedVariantSubContextIterator(Iterator<VariantContext>, String, Iterator<VariantContext>, String, SAMSequenceDictionary) - Constructor for class picard.vcf.PairedVariantSubContextIterator
- PairedVariantSubContextIterator.VcfTuple - Class in picard.vcf
-
Little class to hold a pair of VariantContexts that are in sync with one another.
- pairSort - Variable in class picard.sam.markduplicates.MarkDuplicates
- PairStratifier(ReadBaseStratification.RecordAndOffsetStratifier<T>, ReadBaseStratification.RecordAndOffsetStratifier<R>) - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification.PairStratifier
- PairStratifierFactory(ReadBaseStratification.RecordAndOffsetStratifier<T>, ReadBaseStratification.RecordAndOffsetStratifier<S>, String) - Static method in class picard.sam.SamErrorMetric.ReadBaseStratification
-
A factory for generating "pair" stratifier instances from two stratifiers and a string
- PanelMetricsBase - Class in picard.analysis.directed
-
A base class for Metrics for targeted panels.
- PanelMetricsBase() - Constructor for class picard.analysis.directed.PanelMetricsBase
- PARAMETER_DOC - Static variable in class picard.illumina.parser.ReadStructure
- ParameterizedFileUtil - Class in picard.illumina.parser
- ParameterizedFileUtil(boolean, String, File, FileFaker, int) - Constructor for class picard.illumina.parser.ParameterizedFileUtil
- ParameterizedFileUtil(boolean, String, File, FileFaker, int, boolean) - Constructor for class picard.illumina.parser.ParameterizedFileUtil
- ParameterizedFileUtil(String, String, File, FileFaker, int) - Constructor for class picard.illumina.parser.ParameterizedFileUtil
- parseArgs(String[]) - Method in class picard.cmdline.CommandLineProgram
- parseClusterRecordsFromTileMetrics(Collection<File>, Map<Integer, File>, ReadStructure) - Static method in class picard.illumina.parser.TileMetricsUtil
- parseDirective(String) - Static method in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
-
Parses a "Directive" of the form "ERROR,STRATIFIER,STRATIFIER...etc." into a
BaseErrorAggregation
consisting of the appropriateBaseCalculator
and theCollectionStratifier
constructed from the various individual stratifiers. - parseInputFile(File, ReadStructure) - Static method in class picard.illumina.ExtractBarcodesProgram
-
Parses any one of the following types of files: ExtractIlluminaBarcodes BARCODE_FILE IlluminaBasecallsToFastq MULTIPLEX_PARAMS IlluminaBasecallsToSam LIBRARY_PARAMS This will validate to file format as well as populate a Map of barcodes to metrics.
- parseTileMetrics(File, ReadStructure, ValidationStringency) - Static method in class picard.illumina.parser.TileMetricsUtil
-
Returns an unmodifiable collection of tile data read from the provided file.
- PASS - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
The record in the manifest passes validation and will be used in VCF generation
- PASS_FILTER - Static variable in class picard.vcf.filter.FilterApplyingVariantIterator
-
The "PASS"ing filter String.
- PathProvider - Enum Class in picard.nio
-
A class whose purpose is to initialize the various plugins that provide Path support.
- PCT_100X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 100X sequence coverage in post-filtering bases.
- PCT_10X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 10X sequence coverage in post-filtering bases.
- PCT_15X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 15X sequence coverage in post-filtering bases.
- PCT_1X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 1X sequence coverage in post-filtering bases.
- PCT_20X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 20X sequence coverage in post-filtering bases.
- PCT_25X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 25X sequence coverage in post-filtering bases.
- PCT_30X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 30X sequence coverage in post-filtering bases.
- PCT_40X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 40X sequence coverage in post-filtering bases.
- PCT_50X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 50X sequence coverage in post-filtering bases.
- PCT_5X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 5X sequence coverage in post-filtering bases.
- PCT_60X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 60X sequence coverage in post-filtering bases.
- PCT_70X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 70X sequence coverage in post-filtering bases.
- PCT_80X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 80X sequence coverage in post-filtering bases.
- PCT_90X - Variable in class picard.analysis.WgsMetrics
-
The fraction of bases that attained at least 90X sequence coverage in post-filtering bases.
- PCT_A - Variable in class picard.analysis.BaseDistributionByCycleMetrics
- PCT_ADAPTER - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The fraction of PF reads that are unaligned or aligned with MQ0 and match to a known adapter sequence right from the start of the read (indication of adapter-dimer pairs).
- PCT_AMPLIFIED_BASES - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The fraction of PF_BASES_ALIGNED that mapped to or near an amplicon, (ON_AMPLICON_BASES + NEAR_AMPLICON_BASES)/PF_BASES_ALIGNED.
- PCT_C - Variable in class picard.analysis.BaseDistributionByCycleMetrics
- PCT_CHIMERAS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The fraction of reads that map outside of a maximum insert size (usually 100kb) or that have the two ends mapping to different chromosomes.
- PCT_CHIMERAS - Variable in class picard.analysis.JumpingLibraryMetrics
-
The number of chimeric pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
- PCT_CODING_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
Fraction of PF_ALIGNED_BASES that mapped to protein coding regions of genes, CODING_BASES/PF_ALIGNED_BASES
- PCT_CONVERTED - Variable in class picard.analysis.RrbsCpgDetailMetrics
-
CpG CONVERTED_BASES / CpG TOTAL_BASES (fraction)
- PCT_CORRECT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
-
Fraction of reads corresponding to mRNA transcripts which map to the correct strand of a reference genome = CORRECT_STRAND_READS/(CORRECT_STRAND_READS + INCORRECT_STRAND_READS).
- PCT_CPG_BASES_CONVERTED - Variable in class picard.analysis.RrbsSummaryMetrics
-
CPG_BASES_CONVERTED / CPG_BASES_SEEN (fraction)
- PCT_DBSNP - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
-
The fraction of high confidence SNPs in dbSNP
- PCT_DBSNP - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The fraction of passing bi-allelic SNPs in dbSNP
- PCT_DBSNP_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The fraction of passing indels in dbSNP
- PCT_EXC_ADAPTER - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of aligned bases in reads that have MQ=0 and whose 5' end consists of adapter sequence.
- PCT_EXC_ADAPTER - Variable in class picard.analysis.WgsMetrics
-
The fraction of aligned bases that were filtered out because they were in reads with mapping quality 0 and the looked like adapter reads.
- PCT_EXC_BASEQ - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of aligned bases that were filtered out because they were of low base quality.
- PCT_EXC_BASEQ - Variable in class picard.analysis.WgsMetrics
-
The fraction of aligned bases that were filtered out because they were of low base quality (lower than MIN_BASE_QUALITY).
- PCT_EXC_CAPPED - Variable in class picard.analysis.WgsMetrics
-
The fraction of aligned bases that were filtered out because they would have raised coverage above COVERAGE_CAP.
- PCT_EXC_DUPE - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.
- PCT_EXC_DUPE - Variable in class picard.analysis.WgsMetrics
-
The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.
- PCT_EXC_MAPQ - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of aligned bases that were filtered out because they were in reads with low mapping quality.
- PCT_EXC_MAPQ - Variable in class picard.analysis.WgsMetrics
-
The fraction of aligned bases that were filtered out because they were in reads with low mapping quality (lower than MIN_MAPPING_QUALITY).
- PCT_EXC_OFF_TARGET - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of aligned bases that were filtered out because they did not align over a target base.
- PCT_EXC_OVERLAP - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads.
- PCT_EXC_OVERLAP - Variable in class picard.analysis.WgsMetrics
-
The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads.
- PCT_EXC_TOTAL - Variable in class picard.analysis.WgsMetrics
-
The total fraction of aligned bases excluded due to all filters.
- PCT_EXC_UNPAIRED - Variable in class picard.analysis.WgsMetrics
-
The fraction of aligned bases that were filtered out because they were in reads without a mapped mate pair.
- PCT_G - Variable in class picard.analysis.BaseDistributionByCycleMetrics
- PCT_GQ0_VARIANTS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
-
The percentage of variants in a particular sample that have a GQ score of 0.
- PCT_HARDCLIP - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The fraction of PF bases that are (on primary, aligned reads and) hard-clipped, as a fraction of the PF_ALIGNED_BASES (even though these are not aligned!)
- PCT_INTERGENIC_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
Fraction of PF_ALIGNED_BASES that mapped to intergenic regions of genomic DNA, INTERGENIC_BASES/PF_ALIGNED_BASES
- PCT_INTRONIC_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
Fraction of PF_ALIGNED_BASES that correspond to gene introns, INTRONIC_BASES/PF_ALIGNED_BASES
- PCT_JUMPS - Variable in class picard.analysis.JumpingLibraryMetrics
-
The number of outward-facing pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
- PCT_MATCHES - Variable in class picard.illumina.BarcodeMetric
-
The fraction of all reads in the lane that matched to this barcode.
- PCT_MIX - Variable in class picard.arrays.VerifyIDIntensityContaminationMetrics
-
The percent mixture (contamination) of the sample for ID
- PCT_MRNA_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
Sum of bases mapped to regions corresponding to UTRs and coding regions of mRNA transcripts, PCT_UTR_BASES + PCT_CODING_BASES
- PCT_N - Variable in class picard.analysis.BaseDistributionByCycleMetrics
- PCT_NON_CPG_BASES_CONVERTED - Variable in class picard.analysis.RrbsSummaryMetrics
-
NON_CPG_CONVERTED_BASES / NON_CPG_BASES (fraction)
- PCT_NONJUMPS - Variable in class picard.analysis.JumpingLibraryMetrics
-
The number of inward-facing pairs expressed as a fraction of the total of all outward facing pairs, inward-facing pairs, and chimeric pairs.
- PCT_OFF_AMPLICON - Variable in class picard.analysis.directed.TargetedPcrMetrics
-
The fraction of PF_BASES_ALIGNED that mapped neither onto or near an amplicon, OFF_AMPLICON_BASES/PF_BASES_ALIGNED
- PCT_OFF_BAIT - Variable in class picard.analysis.directed.HsMetrics
-
The fraction of PF_BASES_ALIGNED that are mapped away from any baited region, OFF_BAIT_BASES/PF_BASES_ALIGNED.
- PCT_OFF_PROBE - Variable in class picard.analysis.directed.TargetMetrics
-
The fraction of aligned PF bases that mapped neither on or near a probe, OFF_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES).
- PCT_PF_FAIL_EMPTY - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The fraction of non-PF reads in this tile that are deemed empty (as fraction of all non-PF reads).
- PCT_PF_FAIL_MISALIGNED - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The fraction of non-PF reads in this tile that are deemed "misaligned" (as fraction of all non-PF reads).
- PCT_PF_FAIL_POLYCLONAL - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The fraction of non-PF reads in this tile that are deemed multiclonal (as fraction of all non-PF reads).
- PCT_PF_FAIL_READS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The fraction of PF_READS
- PCT_PF_FAIL_UNKNOWN - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The fraction of non-PF reads in this tile that have not been classified (as fraction of all non-PF reads).
- PCT_PF_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The fraction of reads that are PF (PF_READS / TOTAL_READS)
- PCT_PF_READS - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of reads passing filter, PF_READS/TOTAL_READS.
- PCT_PF_READS_ALIGNED - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The percentage of PF reads that aligned to the reference sequence.
- PCT_PF_READS_IMPROPER_PAIRS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The fraction of (primary) reads that are *not* "properly" aligned in pairs (as per SAM flag 0x2).
- PCT_PF_UQ_READS - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of unique reads passing filter, PF_UNIQUE_READS/TOTAL_READS.
- PCT_PF_UQ_READS_ALIGNED - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of unique reads passing filter that align to the reference, PF_UQ_READS_ALIGNED/PF_UNIQUE_READS.
- PCT_R1_TRANSCRIPT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
-
The fraction of reads that support the model where R1 is on the strand of transcription and R2 is on the opposite strand.
- PCT_R2_TRANSCRIPT_STRAND_READS - Variable in class picard.analysis.RnaSeqMetrics
-
The fraction of reads that support the model where R2 is on the strand of transcription and R1 is on the opposite strand.
- PCT_READS_ALIGNED_IN_PAIRS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The fraction of aligned reads whose mate pair was also aligned to the reference.
- PCT_RIBOSOMAL_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
Fraction of PF_ALIGNED_BASES that mapped to regions encoding ribosomal RNA, RIBOSOMAL_BASES/PF_ALIGNED_BASES
- PCT_SELECTED_BASES - Variable in class picard.analysis.directed.HsMetrics
-
The fraction of PF_BASES_ALIGNED located on or near a baited region (ON_BAIT_BASES + NEAR_BAIT_BASES)/PF_BASES_ALIGNED.
- PCT_SELECTED_BASES - Variable in class picard.analysis.directed.TargetMetrics
-
The fraction of bases that map on or near a probe (ON_PROBE_BASES + NEAR_PROBE_BASES)/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES).
- PCT_SOFTCLIP - Variable in class picard.analysis.AlignmentSummaryMetrics
-
the fraction of PF bases that are on (primary) aligned reads and are soft-clipped, as a fraction of the PF_ALIGNED_BASES (even though these are not aligned!)
- PCT_T - Variable in class picard.analysis.BaseDistributionByCycleMetrics
- PCT_TARGET_BASES_100000X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 100000X or greater coverage.
- PCT_TARGET_BASES_10000X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 10000X or greater coverage.
- PCT_TARGET_BASES_1000X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 1000X or greater coverage.
- PCT_TARGET_BASES_100X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 100X or greater coverage.
- PCT_TARGET_BASES_10X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 10X or greater coverage.
- PCT_TARGET_BASES_1X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 1X or greater coverage.
- PCT_TARGET_BASES_20X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 20X or greater coverage.
- PCT_TARGET_BASES_25000X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 25000X or greater coverage.
- PCT_TARGET_BASES_2500X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 2500X or greater coverage.
- PCT_TARGET_BASES_250X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 250X or greater coverage.
- PCT_TARGET_BASES_2X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 2X or greater coverage.
- PCT_TARGET_BASES_30X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 30X or greater coverage.
- PCT_TARGET_BASES_40X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 40X or greater coverage.
- PCT_TARGET_BASES_50000X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 50000X or greater coverage.
- PCT_TARGET_BASES_5000X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 5000X or greater coverage.
- PCT_TARGET_BASES_500X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 500X or greater coverage.
- PCT_TARGET_BASES_50X - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of all target bases achieving 50X or greater coverage.
- PCT_UMI_WITH_N - Variable in class picard.sam.markduplicates.UmiMetrics
-
The percentage of reads that contain an UMI that contains at least one N
- PCT_USABLE_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
The fraction of bases mapping to mRNA divided by the total number of PF bases, (CODING_BASES + UTR_BASES)/PF_BASES.
- PCT_USABLE_BASES_ON_BAIT - Variable in class picard.analysis.directed.HsMetrics
-
The number of aligned, de-duped, on-bait bases out of the PF bases available.
- PCT_USABLE_BASES_ON_TARGET - Variable in class picard.analysis.directed.HsMetrics
-
The number of aligned, de-duped, on-target bases out of all of the PF bases available.
- PCT_UTR_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
Fraction of PF_ALIGNED_BASES that mapped to untranslated regions (UTR) of genes, UTR_BASES/PF_ALIGNED_BASES
- PDF_FILE_EXTENSION - Static variable in class picard.analysis.CollectRrbsMetrics
- PED_FILE - Variable in class picard.arrays.MergePedIntoVcf
- PedFile - Class in picard.pedigree
-
Represents a .ped file of family information as documented here: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml Stores the information in memory as a map of individualId -> Pedigree information for that individual
- PedFile(boolean) - Constructor for class picard.pedigree.PedFile
- PedFile.PedTrio - Class in picard.pedigree
- PedTrio(String, String, String, String, Sex, Number) - Constructor for class picard.pedigree.PedFile.PedTrio
-
Constructs a TRIO that cannot be modified after the fact.
- peek() - Method in class picard.sam.markduplicates.util.MarkQueue
-
Returns the first element in this queue
- PER_BASE_COVERAGE - Variable in class picard.analysis.directed.CollectTargetedMetrics
- PER_TARGET_COVERAGE - Variable in class picard.analysis.directed.CollectTargetedMetrics
- PER_TILE_PATTERN_STRING - Static variable in class picard.illumina.parser.ParameterizedFileUtil
- PERCENT_DUPLICATION - Variable in class picard.sam.DuplicationMetrics
-
The fraction of mapped sequence that is marked as duplicate.
- percentageOrNull(Long, Long) - Static method in class picard.util.MathUtil
-
Obtains percentage of two Longs
- PERFECT_MATCHES - Variable in class picard.illumina.BarcodeMetric
-
The number of all reads matching this barcode that matched with 0 errors or no-calls.
- permute(double[], RandomDataGenerator) - Static method in class picard.util.MathUtil
-
permute the input array randomly (using a RandomDataGenerator)
- PerTileBarcodeExtractor(int, File, IlluminaDataProviderFactory, BarcodeExtractor) - Constructor for class picard.illumina.ExtractIlluminaBarcodes.PerTileBarcodeExtractor
-
Constructor
- PerTileFileUtil - Class in picard.illumina.parser
- PerTileFileUtil(String, File, FileFaker, int) - Constructor for class picard.illumina.parser.PerTileFileUtil
- PerTileFileUtil(String, File, FileFaker, int, boolean) - Constructor for class picard.illumina.parser.PerTileFileUtil
- PerTileOrPerRunFileUtil - Class in picard.illumina.parser
- PerTileOrPerRunFileUtil(String, File, FileFaker, int) - Constructor for class picard.illumina.parser.PerTileOrPerRunFileUtil
- PerTileParser<ILLUMINA_DATA extends picard.illumina.parser.IlluminaData> - Class in picard.illumina.parser
-
Abstract base class for Parsers that open a single tile file at a time and iterate through them.
- PerTileParser(IlluminaFileMap) - Constructor for class picard.illumina.parser.PerTileParser
- PerTileParser(IlluminaFileMap, int) - Constructor for class picard.illumina.parser.PerTileParser
- PerTilePerCycleFileUtil - Class in picard.illumina.parser
- PerTilePerCycleFileUtil(String, File, FileFaker, int) - Constructor for class picard.illumina.parser.PerTilePerCycleFileUtil
- PerUnitGcBiasMetricsCollector(String, String, String) - Constructor for class picard.analysis.GcBiasMetricsCollector.PerUnitGcBiasMetricsCollector
- PerUnitInsertSizeMetricsCollector(String, String, String) - Constructor for class picard.analysis.directed.InsertSizeMetricsCollector.PerUnitInsertSizeMetricsCollector
- PerUnitMetricCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,
HKEY extends Comparable, ARGTYPE> - Interface in picard.metrics -
PerRecordCollector - An interface for classes that collect data in order to generate one or more metrics.
- PerUnitRnaSeqMetricsCollector(String, String, String, Long) - Constructor for class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
- PerUnitRnaSeqMetricsCollector(RnaSeqMetrics, String, String, String, Long) - Constructor for class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
-
Derived classes that need to capture some additional metrics can use this ctor to supply a metrics instance that is a subclass of RnaSeqMetrics.
- PerUnitTargetMetricCollector(String, Set<Interval>, String, String, String, long, long, long, Map<Interval, Double>, int, int, boolean, boolean) - Constructor for class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
-
Constructor that parses the squashed reference to genome reference file and stores the information in a map for later use.
- PF - Enum constant in enum class picard.illumina.parser.IlluminaDataType
- PF - Enum constant in enum class picard.sam.ViewSam.PfStatus
- PF_ALIGNED_BASES - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The total number of aligned bases, in all mapped PF reads, that are aligned to the reference sequence.
- PF_ALIGNED_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
The total number of aligned PF bases.
- PF_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The total number of bases in all PF reads
- PF_BASES - Variable in class picard.analysis.directed.PanelMetricsBase
-
The number of bases in the PF_READS of a SAM or BAM file
- PF_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
The total number of PF bases including non-aligned reads.
- PF_BASES - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The total number of passing-filter bases assigned to the index.
- PF_BASES_ALIGNED - Variable in class picard.analysis.directed.PanelMetricsBase
-
The number of PF_BASES that are aligned with mapping score > 0 to the reference genome.
- PF_CLUSTERS - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The total number of PF clusters assigned to the index.
- PF_FAIL_EMPTY - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The number of non-PF reads in this tile that are deemed empty.
- PF_FAIL_MISALIGNED - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The number of non-PF reads in this tile that are deemed "misaligned".
- PF_FAIL_POLYCLONAL - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The number of non-PF reads in this tile that are deemed multiclonal.
- PF_FAIL_READS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The number of non-PF reads in this tile.
- PF_FAIL_UNKNOWN - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The number of non-PF reads in this tile that have not been classified.
- PF_HQ_ALIGNED_BASES - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of bases aligned to the reference sequence in reads that were mapped at high quality.
- PF_HQ_ALIGNED_Q20_BASES - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The subset of PF_HQ_ALIGNED_BASES where the base call quality was Q20 or higher.
- PF_HQ_ALIGNED_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of PF reads that were aligned to the reference sequence with a mapping quality of Q20 or higher signifying that the aligner estimates a 1/100 (or smaller) chance that the alignment is wrong.
- PF_HQ_ERROR_RATE - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The fraction of bases that mismatch the reference in PF HQ aligned reads.
- PF_HQ_MEDIAN_MISMATCHES - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The median number of mismatches versus the reference sequence in reads that were aligned to the reference at high quality (i.e.
- PF_INDEL_RATE - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of insertion and deletion events per 100 aligned bases.
- PF_MISMATCH_RATE - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The rate of bases mismatching the reference for all bases aligned to the reference sequence.
- PF_NOISE_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of PF reads that are marked as noise reads.
- PF_NORMALIZED_MATCHES - Variable in class picard.illumina.BarcodeMetric
-
The "normalized" matches to each barcode.
- PF_ONE_MISMATCH_MATCHES - Variable in class picard.illumina.BarcodeMetric
-
The number of PF reads matching this barcode that matched with 1 error or no-call.
- PF_PCT_MATCHES - Variable in class picard.illumina.BarcodeMetric
-
The fraction of PF reads in the lane that matched to this barcode.
- PF_PERFECT_MATCHES - Variable in class picard.illumina.BarcodeMetric
-
The number of PF reads matching this barcode that matched with 0 errors or no-calls.
- PF_Q20_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The number of bases in PF reads that achieve quality score 20 or higher
- PF_Q20_EQUIVALENT_YIELD - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The sum of quality scores of all bases in PF reads divided by 20
- PF_Q30_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The number of bases in PF reads that achieve quality score 30 or higher
- PF_RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT - Variable in class picard.illumina.BarcodeMetric
-
The rate of PF reads matching this barcode to PF reads matching the most prevalent barcode.
- PF_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of PF reads where PF is defined as passing Illumina's filter.
- PF_READS - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The number of reads that are PF - pass filter
- PF_READS - Variable in class picard.analysis.directed.PanelMetricsBase
-
The number of passing filter reads (PF).
- PF_READS - Variable in class picard.illumina.BarcodeMetric
-
The number of PF reads matching this barcode (always less than or equal to READS).
- PF_READS - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The total number of passing-filter reads assigned to the index.
- PF_READS_ALIGNED - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of PF reads that were aligned to the reference sequence.
- PF_READS_IMPROPER_PAIRS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of (primary) aligned reads that are **not** "properly" aligned in pairs (as per SAM flag 0x2).
- PF_READS_ONLY - Variable in class picard.analysis.CollectBaseDistributionByCycle
- PF_READS_ONLY - Variable in class picard.analysis.MeanQualityByCycle
- PF_READS_ONLY - Variable in class picard.analysis.QualityScoreDistribution
- PF_READS_ONLY_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- PF_SELECTED_PAIRS - Variable in class picard.analysis.directed.TargetMetricsBase
-
Tracks the number of read pairs that we see that are PF (used to calculate library size)
- PF_SELECTED_UNIQUE_PAIRS - Variable in class picard.analysis.directed.TargetMetricsBase
-
Tracks the number of unique PF_SELECTED_PAIRS we see (used to calc library size)
- PF_STATUS - Variable in class picard.sam.ViewSam
- PF_UNIQUE_READS - Variable in class picard.analysis.directed.PanelMetricsBase
-
The number of PF_READS that are not marked as duplicates.
- PF_UQ_BASES_ALIGNED - Variable in class picard.analysis.directed.PanelMetricsBase
-
The number of PF unique bases that are aligned with mapping score > 0 to the reference genome.
- PF_UQ_READS_ALIGNED - Variable in class picard.analysis.directed.PanelMetricsBase
-
The number of PF_UNIQUE_READS that are aligned with mapping score > 0 to the reference genome.
- PFFailDetailedMetric() - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
-
This ctor is necessary for when reading metrics from file
- PFFailDetailedMetric(Integer, int, int, int, int, CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason) - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
- PFFailSummaryMetric() - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
This ctor is necessary for when reading metrics from file
- PFFailSummaryMetric(String) - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
- PG_PROGRAM_NAME - Static variable in class picard.sam.PositionBasedDownsampleSam
- pgIdsSeen - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
-
The program groups that have been seen during the course of examining the input records.
- pgTagArgumentCollection - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- pgTagArgumentCollection - Variable in class picard.sam.MergeBamAlignment
- PGTagArgumentCollection - Class in picard.sam.util
-
Argument Collection which holds parameters common to classes that want to add PG tags to reads in SAM/BAM files
- PGTagArgumentCollection() - Constructor for class picard.sam.util.PGTagArgumentCollection
- PHASESET_PREFIX - Static variable in class picard.fingerprint.HaplotypeMap
- PHASING_APPLIED - Variable in class picard.illumina.IlluminaPhasingMetrics
-
Median phasing value across all tiles in a lane, applied to the first and second template reads
- PHASING_BASE - Enum constant in enum class picard.illumina.parser.IlluminaMetricsCode
- phasingWeight - Variable in class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
- PhysicalLocation - Interface in picard.sam.util
-
Small interface that provides access to the physical location information about a cluster.
- PhysicalLocationForMateCigar - Class in picard.sam.markduplicates.util
-
Stores the minimal information needed for optical duplicate detection.
- PhysicalLocationForMateCigar(PhysicalLocation) - Constructor for class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
- PhysicalLocationForMateCigarSet - Class in picard.sam.markduplicates.util
-
This stores records that are comparable for detecting optical duplicates.
- PhysicalLocationForMateCigarSet() - Constructor for class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
- PhysicalLocationInt - Class in picard.sam.util
-
Small class that provides access to the physical location information about a cluster.
- PhysicalLocationInt() - Constructor for class picard.sam.util.PhysicalLocationInt
- PhysicalLocationShort - Class in picard.sam.util
-
Small class that provides access to the physical location information about a cluster.
- PhysicalLocationShort() - Constructor for class picard.sam.util.PhysicalLocationShort
- picard - package picard
- picard.analysis - package picard.analysis
- picard.analysis.artifacts - package picard.analysis.artifacts
- picard.analysis.directed - package picard.analysis.directed
- picard.analysis.replicates - package picard.analysis.replicates
- picard.annotation - package picard.annotation
- picard.arrays - package picard.arrays
- picard.arrays.illumina - package picard.arrays.illumina
- picard.cmdline - package picard.cmdline
- picard.cmdline.argumentcollections - package picard.cmdline.argumentcollections
- picard.cmdline.programgroups - package picard.cmdline.programgroups
- picard.fastq - package picard.fastq
- picard.filter - package picard.filter
- picard.fingerprint - package picard.fingerprint
- picard.illumina - package picard.illumina
- picard.illumina.parser - package picard.illumina.parser
- picard.illumina.parser.fakers - package picard.illumina.parser.fakers
- picard.illumina.parser.readers - package picard.illumina.parser.readers
- picard.illumina.quality - package picard.illumina.quality
- picard.metrics - package picard.metrics
- picard.nio - package picard.nio
- picard.pedigree - package picard.pedigree
- picard.reference - package picard.reference
- picard.sam - package picard.sam
- picard.sam.markduplicates - package picard.sam.markduplicates
- picard.sam.markduplicates.util - package picard.sam.markduplicates.util
- picard.sam.SamErrorMetric - package picard.sam.SamErrorMetric
- picard.sam.util - package picard.sam.util
- picard.util - package picard.util
- picard.util.help - package picard.util.help
- picard.util.IntervalList - package picard.util.IntervalList
- picard.vcf - package picard.vcf
- picard.vcf.filter - package picard.vcf.filter
- picard.vcf.MendelianViolations - package picard.vcf.MendelianViolations
- picard.vcf.processor - package picard.vcf.processor
- picard.vcf.processor.util - package picard.vcf.processor.util
- PicardCommandLine - Class in picard.cmdline
-
This is the main class of Picard and is the way of executing individual command line programs.
- PicardCommandLine() - Constructor for class picard.cmdline.PicardCommandLine
- PicardException - Exception in picard
-
Basic Picard runtime exception that, for now, does nothing much
- PicardException(String) - Constructor for exception picard.PicardException
- PicardException(String, Throwable) - Constructor for exception picard.PicardException
- PicardHtsPath - Class in picard.nio
- PicardHtsPath(HtsPath) - Constructor for class picard.nio.PicardHtsPath
-
Create a PicardHtsPath from an existing
HtsPath
or subclass. - PicardHtsPath(File) - Constructor for class picard.nio.PicardHtsPath
-
Create a PicardHtsPath from a
File
reference. - PicardHtsPath(String) - Constructor for class picard.nio.PicardHtsPath
-
Create a PicardHtsPath from a raw input path string.
- pickPrimaryAlignment(HitsForInsert) - Method in class picard.sam.BestEndMapqPrimaryAlignmentStrategy
-
Primary alignment was filtered out.
- pickPrimaryAlignment(HitsForInsert) - Method in class picard.sam.BestMapqPrimaryAlignmentSelectionStrategy
-
Primary alignment was filtered out.
- pickPrimaryAlignment(HitsForInsert) - Method in class picard.sam.EarliestFragmentPrimaryAlignmentSelectionStrategy
- pickPrimaryAlignment(HitsForInsert) - Method in class picard.sam.MostDistantPrimaryAlignmentSelectionStrategy
- pickPrimaryAlignment(HitsForInsert) - Method in interface picard.sam.PrimaryAlignmentSelectionStrategy
-
When this method returns, one alignment has been marked as primary according to the implementation's strategy.
- pickTranscripts(Map<Gene.Transcript, int[]>) - Method in class picard.analysis.directed.RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector
-
Picks the set of transcripts on which the coverage metrics are to be calculated.
- PIPELINE_VERSION - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The version of the pipeline used for this sample
- PIPELINE_VERSION - Variable in class picard.arrays.GtcToVcf
- PIPELINE_VERSION - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- PLATFORM - Variable in class picard.illumina.IlluminaBasecallsToSam
- PLATFORM - Variable in class picard.sam.FastqToSam
- PLATFORM_MODEL - Variable in class picard.sam.FastqToSam
- PLATFORM_UNIT - Variable in class picard.sam.FastqToSam
- PLOIDY_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- PLUS - Enum constant in enum class picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
- pNormalizeLogProbability(double[]) - Static method in class picard.util.MathUtil
-
Takes a complete set of mutually exclusive logPosteriors and converts them to probabilities that sum to 1 with as much fidelity as possible.
- pNormalizeVector(double[]) - Static method in class picard.util.MathUtil
-
Takes a vector of numbers and converts it to a vector of probabilities that sum to 1 with as much fidelity as possible.
- poll(SamRecordTrackingBuffer, SAMFileHeader, OpticalDuplicateFinder, LibraryIdGenerator) - Method in class picard.sam.markduplicates.util.MarkQueue
-
The poll method will return the read end that is *not* the duplicate of all comparable read ends that have been seen.
- POLYCLONAL - Enum constant in enum class picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
- POOL_SIZE - Variable in class picard.util.BaitDesigner
- Pos - Enum constant in enum class picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
- PosFileFaker - Class in picard.illumina.parser.fakers
-
Created by jcarey on 3/13/14.
- PosFileFaker() - Constructor for class picard.illumina.parser.fakers.PosFileFaker
- PosFileReader - Class in picard.illumina.parser.readers
-
The pos file format is one 3 Illumina formats(pos, locs, and clocs) that stores position data exclusively.
- PosFileReader(File) - Constructor for class picard.illumina.parser.readers.PosFileReader
- Position - Enum constant in enum class picard.illumina.parser.IlluminaDataType
- POSITION - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The position of the SNP on the chromosome.
- POSITION - Variable in class picard.analysis.RrbsCpgDetailMetrics
-
Position within the sequence of the CpG site
- PositionBasedDownsampleSam - Class in picard.sam
-
Summary
- PositionBasedDownsampleSam() - Constructor for class picard.sam.PositionBasedDownsampleSam
- PositionInfo(float, float, int, int) - Constructor for class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
- POSITIVE - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ReadDirection
- PosParser - Class in picard.illumina.parser
-
PosParser parses multiple files formatted as one of the three file formats that contain position information only (pos, locs, and clocs).
- PosParser(IlluminaFileMap, int, IlluminaFileUtil.SupportedIlluminaFormat) - Constructor for class picard.illumina.parser.PosParser
- PosParser(IlluminaFileMap, IlluminaFileUtil.SupportedIlluminaFormat) - Constructor for class picard.illumina.parser.PosParser
- postDiNucleotideStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies a base onto the reference base that it covers and the following base, possibly reverse complemented if the read has been reversed by the aligner.
- Ppv(GenotypeConcordanceScheme, GenotypeConcordanceStates.CallState[]) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Returns the PPV defined by the scheme across the subset of call states.
- PRE_ADAPTER_DETAILS_EXT - Static variable in class picard.analysis.artifacts.SequencingArtifactMetrics
- PRE_ADAPTER_IN - Variable in class picard.analysis.artifacts.ConvertSequencingArtifactToOxoG
- PRE_ADAPTER_SUMMARY_EXT - Static variable in class picard.analysis.artifacts.SequencingArtifactMetrics
- PRE_INDEL_SEQUENCE - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
- PreAdapterDetailMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
- PreAdapterSummaryMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
- PredicateFilterDecoratingClosableIterator<T> - Class in picard.vcf.processor.util
-
Performs on-the-fly filtering of the provided
VariantContext
Iterator
such that only variants that satisfy all predicates are emitted. - PredicateFilterDecoratingClosableIterator(CloseableIterator<T>, Collection<Predicate<T>>) - Constructor for class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
- PREDICTED_INSERT_SIZE - Variable in class picard.sam.FastqToSam
- preDiNucleotideStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies a base onto the reference base that it covers and the preceding base, possibly reverse complemented if the read has been reversed by the aligner.
- PREPHASING_APPLIED - Variable in class picard.illumina.IlluminaPhasingMetrics
-
Median pre-phasing value across all tiles in a lane, applied to the first and second template reads
- PREPHASING_BASE - Enum constant in enum class picard.illumina.parser.IlluminaMetricsCode
- prephasingWeight - Variable in class picard.illumina.parser.readers.EmpiricalPhasingMetricsOutReader.IlluminaPhasingMetrics
- preprocessIntervalList(IntervalList) - Method in interface picard.util.IntervalList.IntervalListScatterer
-
A function that will be called on an IntervalList prior to splitting it into sub-lists, and is a point where implementations can chose to impose some conditions on the lists, for example, merging overlapping/abutting intervals, removing duplicates, etc.
- preprocessIntervalList(IntervalList) - Method in class picard.util.IntervalList.IntervalListScattererWithSubdivision
- previousReadBaseStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies bases into the previous (uppercase) base as it was read from the sequencer (i.e.
- PRIMARY_ALIGNMENT_STRATEGY - Variable in class picard.sam.MergeBamAlignment
- PRIMARY_MAPPED_ONLY - Enum constant in enum class picard.sam.markduplicates.CheckDuplicateMarking.Mode
- PRIMARY_ONLY - Enum constant in enum class picard.sam.markduplicates.CheckDuplicateMarking.Mode
- PRIMARY_PROPER_PAIR_ONLY - Enum constant in enum class picard.sam.markduplicates.CheckDuplicateMarking.Mode
- PrimaryAlignmentKey - Class in picard.sam.util
-
It is useful to define a key such that the key will occur at most once among the primary alignments in a given file (assuming the file is valid).
- PrimaryAlignmentKey(SAMRecord) - Constructor for class picard.sam.util.PrimaryAlignmentKey
- PrimaryAlignmentSelectionStrategy - Interface in picard.sam
-
Given a set of alignments for a read or read pair, mark one alignment as primary, according to whatever strategy is appropriate.
- printUnknown(Set<Class<?>>, String) - Static method in class picard.cmdline.PicardCommandLine
-
When a command does not match any known command, searches for similar commands, using the same method as GIT
- PRIOR_ERROR - Static variable in class picard.sam.SamErrorMetric.ErrorMetric
- PRIOR_Q - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- PRO_ALT_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The number of REF_BASE:ALT_BASE alignments having a read number and orientation that supports the presence of this artifact.
- PRO_REF_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The number of REF_BASE:REF_BASE alignments having a read number and orientation that supports the presence of this artifact.
- PROB_EXPLICIT_READS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
- PROBABILITY - Variable in class picard.sam.DownsampleSam
- PROBABILITY - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- PROBE_A - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- PROBE_B - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- PROBE_SEQUENCE_MISMATCH - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Probe sequence not found in reference.
- PROBE_SEQUENCE_STRAND_INVALID - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Deprecated.- but used in existing extended manifest files.
- PROBE_SET - Variable in class picard.analysis.directed.TargetMetrics
-
The name of the PROBE_SET (BAIT_SET, AMPLICON_SET, ...) used in this metrics collection run
- PROBE_TERRITORY - Variable in class picard.analysis.directed.TargetMetrics
-
The number of unique bases covered by the intervals of all probes in the probe set
- process() - Method in class picard.vcf.processor.VariantProcessor
- PROCESS_SINGLE_TILE - Variable in class picard.illumina.IlluminaBasecallsToSam
- processAllCommandLinePrograms(List<String>, BiConsumer<Class<CommandLineProgram>, CommandLineProgramProperties>) - Static method in class picard.cmdline.PicardCommandLine
-
Process each
CommandLineProgram
-derived class given a list of packages. - processDeletionLocus(SamLocusIterator.RecordAndOffset, SamLocusIterator.LocusInfo) - Method in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
-
Checks if the same record has been seen at the previous locus already, thereby determining whether or not a deletion has already been processed.
- processFile() - Method in interface picard.analysis.WgsMetricsProcessor
-
Method processes the input data and accumulates result data
- processFile() - Method in class picard.analysis.WgsMetricsProcessorImpl
-
Method gets the data from iterator for each locus and processes it with the help of collector.
- processTilesAndWritePerSampleOutputs(Set<String>) - Method in class picard.illumina.BasecallsConverter
-
Abstract method for processing tiles of data and outputting records for each barcode.
- processTilesAndWritePerSampleOutputs(Set<String>) - Method in class picard.illumina.SortedBasecallsConverter
-
Set up tile processing and record writing threads for this converter.
- processTilesAndWritePerSampleOutputs(Set<String>) - Method in class picard.illumina.UnsortedBasecallsConverter
-
Set up tile processing and record writing threads for this converter.
- product(double...) - Method in class picard.util.MathUtil.LogMath
-
Computes the sum of the provided log values.
- PROGRAM - Variable in class picard.analysis.CollectMultipleMetrics
- PROGRAM_GROUP - Variable in class picard.sam.FastqToSam
- PROGRAM_GROUP_COMMAND_LINE - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- PROGRAM_GROUP_COMMAND_LINE - Variable in class picard.sam.MergeBamAlignment
- PROGRAM_GROUP_NAME - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- PROGRAM_GROUP_NAME - Variable in class picard.sam.MergeBamAlignment
- PROGRAM_GROUP_VERSION - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- PROGRAM_GROUP_VERSION - Variable in class picard.sam.MergeBamAlignment
- PROGRAM_RECORD_ID - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- PROGRAM_RECORD_ID - Variable in class picard.sam.MergeBamAlignment
- PROGRAM_RECORD_ID_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- PROGRESS_STEP_INTERVAL - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- PROGRESS_STEP_INTERVAL - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- promote(int[]) - Static method in class picard.util.MathUtil
-
"Promotes" an int[] into a double array with the same values (or as close as precision allows).
- PROPER - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
- PropertyUtils - Class in picard.util
-
Utility for loading properties files from resources.
- PropertyUtils() - Constructor for class picard.util.PropertyUtils
- proportionsAboveThresholds(List<ArrayList<Integer>>, List<Double>) - Static method in class picard.analysis.TheoreticalSensitivity
- PRUNE_ADAPTER_LIST_AFTER_THIS_MANY_ADAPTERS_SEEN - Variable in class picard.illumina.MarkIlluminaAdapters
- pSameAlleleWhenMismatchingUmi - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
When the UMIs mismatch, we expect about the same number of different alleles as the same (assuming that different UMI implies biological duplicate) thus, this value should be near 0.5
- pSameUmiInIndependentBiDup - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
When the alleles are different, we know that this is a biological duplication, thus we expect nearly all the UMIs to be different (allowing for equality due to chance).
- PSEUDO_AUTOSOMAL_REGIONS - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
- put(int, String, ReadEndsForMarkDuplicates) - Method in class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
- put(int, String, ReadEndsForMarkDuplicates) - Method in class picard.sam.markduplicates.util.MemoryBasedReadEndsForMarkDuplicatesMap
- put(int, String, ReadEndsForMarkDuplicates) - Method in interface picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap
-
Store the element in the map with the given key.
- PVAL - Variable in class picard.arrays.BafRegressMetrics
-
The p-value of the estimate
Q
- Q_SCORE - Variable in class picard.sam.SamErrorMetric.BaseErrorMetric
-
The (phred) rate of bases that disagree with the reference
- Q20_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The number of bases in all reads that achieve quality score 20 or higher
- Q20_EQUIVALENT_YIELD - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The sum of quality scores of all bases divided by 20
- Q30_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The number of bases in all reads that achieve quality score 30 or higher
- QdFilter - Class in picard.vcf.filter
-
Filters out sites that have a QD annotation applied to them and where the QD value is lower than a lower limit.
- QdFilter(double) - Constructor for class picard.vcf.filter.QdFilter
- QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The Phred-scaled quality score of the artifact, calculated as -10 * log10(ERROR_RATE).
- QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The Phred-scaled quality score of the artifact, calculated as -10 * log10(ERROR_RATE).
- qualities - Variable in class picard.illumina.parser.BclData
- qualities - Variable in class picard.util.BarcodeEditDistanceQuery
-
list of quality scores for reads
- QUALITY - Variable in class picard.sam.SamToFastq
- QUALITY_FORMAT - Variable in class picard.sam.FastqToSam
- QUALITY_TAG_GROUP - Variable in class picard.sam.SamToFastqWithTags
- QualityScoreDistribution - Class in picard.analysis
-
Charts quality score distribution within a BAM file.
- QualityScoreDistribution - Enum constant in enum class picard.analysis.CollectMultipleMetrics.Program
- QualityScoreDistribution() - Constructor for class picard.analysis.QualityScoreDistribution
- QualityScores - Enum constant in enum class picard.illumina.parser.IlluminaDataType
- QualityYieldMetrics() - Constructor for class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
- QualityYieldMetrics(boolean) - Constructor for class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
- QualityYieldMetricsCollector(boolean, boolean, boolean) - Constructor for class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsCollector
- QualityYieldMetricsCollector(boolean, boolean, boolean, boolean) - Constructor for class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsCollector
- QualityYieldMetricsFlow() - Constructor for class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsFlow
- QualityYieldMetricsFlow(boolean) - Constructor for class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsFlow
- QualityYieldMetricsFlow(boolean, HistogramGenerator) - Constructor for class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsFlow
- QuerySortedReadPairIteratorUtil - Class in picard.util
-
A collection of helper utilities for iterating through reads that are in query-name sorted read order as pairs
- QuerySortedReadPairIteratorUtil() - Constructor for class picard.util.QuerySortedReadPairIteratorUtil
- QuerySortedReadPairIteratorUtil.ReadPair - Class in picard.util
- QUIET - Variable in class picard.cmdline.CommandLineProgram
- QUINTILE_1 - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
- QUINTILE_2 - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
- QUINTILE_3 - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
- QUINTILE_4 - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
- QUINTILE_5 - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
R
- R - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- R - Static variable in class picard.sam.markduplicates.util.ReadEnds
- R1R2 - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
- RANDOM_SEED - Variable in class picard.sam.DownsampleSam
- RANDOM_SEED_TAG - Static variable in class picard.sam.DownsampleSam
- randomSublist(List<T>, int, Random) - Static method in class picard.util.MathUtil
-
A small utility function to choose n random elements (un-shuffled) from a list
- Range - Class in picard.illumina.parser
-
While structurally identical to CompositeIndex, this class is maintained as it makes code more readable when the two are used together (see QSeqParser)
- Range(int, int) - Constructor for class picard.illumina.parser.Range
- rapidParseInt(String) - Static method in class picard.sam.util.ReadNameParser
-
Very specialized method to rapidly parse a sequence of digits from a String up until the first non-digit character.
- RATIO_THIS_BARCODE_TO_BEST_BARCODE_PCT - Variable in class picard.illumina.BarcodeMetric
-
The rate of all reads matching this barcode to all reads matching the most prevalent barcode.
- RawWgsMetrics() - Constructor for class picard.analysis.CollectRawWgsMetrics.RawWgsMetrics
- RawWgsMetrics(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, double, int, Histogram<Integer>, int) - Constructor for class picard.analysis.CollectRawWgsMetrics.RawWgsMetrics
- rawXIntensity - Variable in class picard.arrays.illumina.InfiniumGTCRecord
- rawYIntensity - Variable in class picard.arrays.illumina.InfiniumGTCRecord
- RE_REVERSE - Variable in class picard.sam.SamToFastq
- read(byte[], int, int) - Method in class picard.util.CircularByteBuffer
-
Read bytes from the buffer into the supplied array.
- READ_END - Variable in class picard.analysis.BaseDistributionByCycleMetrics
- READ_GROUP - Enum constant in enum class picard.analysis.MetricAccumulationLevel
- READ_GROUP - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The sequencing read group from which sequence data was fingerprinted.
- READ_GROUP - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
The read group from which sequence data was drawn for comparison.
- READ_GROUP - Variable in class picard.metrics.MultilevelMetrics
-
The read group to which these metrics apply.
- READ_GROUP_ID - Variable in class picard.illumina.IlluminaBasecallsToSam
- READ_GROUP_ID_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- READ_GROUP_NAME - Variable in class picard.sam.FastqToSam
- READ_LENGTH - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The average read length of all the reads
- READ_LENGTH - Variable in class picard.analysis.CollectWgsMetrics
- READ_LENGTH_AVG_Q_ABOVE_25 - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsFlow
-
The length of the longest interval on the reads where the average quality per-base is above (Q25)
- READ_LENGTH_AVG_Q_ABOVE_30 - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetricsFlow
-
The length of the longest interval on the reads where the average quality per-base is above (Q30)
- READ_LIST_FILE - Variable in class picard.sam.FilterSamReads
- READ_NAME_FORMAT - Variable in class picard.illumina.IlluminaBasecallsToFastq
- READ_NAME_REGEX - Variable in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
- READ_NAME_REGEX - Variable in class picard.sam.PositionBasedDownsampleSam
- READ_ONE_BARCODE_TAG - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
- READ_ONE_BARCODE_TAG - Variable in class picard.sam.markduplicates.MarkDuplicates
- READ_PAIR_DUPLICATES - Variable in class picard.sam.DuplicationMetrics
-
The number of read pairs that were marked as duplicates.
- READ_PAIR_OPTICAL_DUPLICATES - Variable in class picard.sam.DuplicationMetrics
-
The number of read pairs duplicates that were caused by optical duplication.
- READ_PAIRS - Variable in class picard.analysis.InsertSizeMetrics
-
The total number of read pairs that were examined in the entire distribution.
- READ_PAIRS_EXAMINED - Variable in class picard.sam.DuplicationMetrics
-
The number of mapped read pairs examined.
- READ_STARTS - Variable in class picard.analysis.GcBiasDetailMetrics
-
The number of reads whose start position is at the start of a window of this GC.
- READ_STRUCTURE - Variable in class picard.illumina.CheckIlluminaDirectory
- READ_STRUCTURE - Variable in class picard.illumina.CollectIlluminaBasecallingMetrics
- READ_STRUCTURE - Variable in class picard.illumina.CollectIlluminaLaneMetrics
- READ_STRUCTURE - Variable in class picard.illumina.ExtractBarcodesProgram
- READ_TWO_BARCODE_TAG - Variable in class picard.sam.markduplicates.EstimateLibraryComplexity
- READ_TWO_BARCODE_TAG - Variable in class picard.sam.markduplicates.MarkDuplicates
- read1 - Variable in class picard.util.QuerySortedReadPairIteratorUtil.ReadPair
- READ1_ALIGNED_BAM - Variable in class picard.sam.MergeBamAlignment
- READ1_MAX_BASES_TO_WRITE - Variable in class picard.sam.SamToFastq
- READ1_TRIM - Variable in class picard.sam.MergeBamAlignment
- READ1_TRIM - Variable in class picard.sam.SamToFastq
- read1Coordinate - Variable in class picard.sam.markduplicates.util.ReadEnds
- read1IndexInFile - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
- read1ReferenceIndex - Variable in class picard.sam.markduplicates.util.ReadEnds
- read2 - Variable in class picard.util.QuerySortedReadPairIteratorUtil.ReadPair
- READ2_ALIGNED_BAM - Variable in class picard.sam.MergeBamAlignment
- READ2_MAX_BASES_TO_WRITE - Variable in class picard.sam.SamToFastq
- READ2_TRIM - Variable in class picard.sam.MergeBamAlignment
- READ2_TRIM - Variable in class picard.sam.SamToFastq
- read2Coordinate - Variable in class picard.sam.markduplicates.util.ReadEnds
- read2IndexInFile - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
- read2ReferenceIndex - Variable in class picard.sam.markduplicates.util.ReadEnds
- ReadBaseStratification - Class in picard.sam.SamErrorMetric
-
Classes, methods, and enums that deal with the stratification of read bases and reference information.
- ReadBaseStratification() - Constructor for class picard.sam.SamErrorMetric.ReadBaseStratification
- ReadBaseStratification.BinnedReadCycleStratifier - Class in picard.sam.SamErrorMetric
-
Stratifies into quintiles of read cycle.
- ReadBaseStratification.CigarOperatorsInReadStratifier - Class in picard.sam.SamErrorMetric
-
Stratifies according to the number of matching cigar operators (from CIGAR string) that the read has.
- ReadBaseStratification.CollectionStratifier - Class in picard.sam.SamErrorMetric
-
A CollectionStratifier is a stratifier that uses a collection of stratifiers to inform the stratification.
- ReadBaseStratification.Consensus - Enum Class in picard.sam.SamErrorMetric
-
Types of consensus reads as determined by the number of duplicates used from first and second strands.
- ReadBaseStratification.ConsensusStratifier - Class in picard.sam.SamErrorMetric
-
Stratify by tags used during duplex and single index consensus calling.
- ReadBaseStratification.CycleBin - Enum Class in picard.sam.SamErrorMetric
-
An enum designed to hold a binned version of any probability-like number (between 0 and 1) in quintiles
- ReadBaseStratification.FlowCellTileStratifier - Class in picard.sam.SamErrorMetric
-
Stratifies base into their read's tile which is parsed from the read-name.
- ReadBaseStratification.FlowCellXStratifier - Class in picard.sam.SamErrorMetric
-
Stratifies base into their read's X coordinate which is parsed from the read-name.
- ReadBaseStratification.FlowCellYStratifier - Class in picard.sam.SamErrorMetric
-
Stratifies base into their read's Y coordinate which is parsed from the read-name.
- ReadBaseStratification.GCContentStratifier - Class in picard.sam.SamErrorMetric
-
A stratifier that uses GC (of the read) to stratify.
- ReadBaseStratification.IndelLengthStratifier - Class in picard.sam.SamErrorMetric
-
Stratifies according to the length of an insertion or deletion.
- ReadBaseStratification.IndelsInReadStratifier - Class in picard.sam.SamErrorMetric
-
Stratifies according to the number of indel bases (from CIGAR string) that the read has.
- ReadBaseStratification.LongShortHomopolymer - Enum Class in picard.sam.SamErrorMetric
- ReadBaseStratification.LongShortHomopolymerStratifier - Class in picard.sam.SamErrorMetric
-
Stratify bases according to the type of Homopolymer that they belong to (repeating element, final reference base and whether the length is "long" or not).
- ReadBaseStratification.MismatchesInReadStratifier - Class in picard.sam.SamErrorMetric
-
Stratifies according to the overall mismatches (from
SAMTag.NM
) that the read has against the reference, NOT including the current base. - ReadBaseStratification.NsInReadStratifier - Class in picard.sam.SamErrorMetric
-
Stratify by the number of Ns found in the read.
- ReadBaseStratification.PairOrientation - Enum Class in picard.sam.SamErrorMetric
-
An enum for holding a reads read-pair's Orientation (i.e.
- ReadBaseStratification.PairStratifier<T extends Comparable<T>,
R extends Comparable<R>> - Class in picard.sam.SamErrorMetric -
A PairStratifier is a stratifier that uses two other stratifiers to inform the stratification.
- ReadBaseStratification.ProperPaired - Enum Class in picard.sam.SamErrorMetric
-
An enum to hold information about the "properness" of a read pair
- ReadBaseStratification.ReadDirection - Enum Class in picard.sam.SamErrorMetric
-
An enum for holding the direction for a read (positive strand or negative strand
- ReadBaseStratification.ReadOrdinality - Enum Class in picard.sam.SamErrorMetric
-
An enum to hold the ordinality of a read
- ReadBaseStratification.RecordAndOffsetStratifier<T extends Comparable<T>> - Interface in picard.sam.SamErrorMetric
-
The main interface for a stratifier.
- ReadClassifier(ReadData) - Constructor for class picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier
-
Heart of CLP.
- readCount - Variable in class picard.analysis.directed.TargetMetricsCollector.Coverage
- ReadData - Class in picard.illumina.parser
-
Data for a single end of a paired-end read, a barcode read, or for the entire read if not paired end.
- ReadData() - Constructor for class picard.illumina.parser.ReadData
- ReadData(ReadType) - Constructor for class picard.illumina.parser.ReadData
- ReadDataManipulationProgramGroup - Class in picard.cmdline.programgroups
-
Tools that manipulate read data in SAM, BAM or CRAM format
- ReadDataManipulationProgramGroup() - Constructor for class picard.cmdline.programgroups.ReadDataManipulationProgramGroup
- ReadDescriptor - Class in picard.illumina.parser
-
Represents one set of cycles in an ReadStructure (e.g.
- ReadDescriptor(int, ReadType) - Constructor for class picard.illumina.parser.ReadDescriptor
- readDirectionStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies bases into their read's Direction (i.e.
- ReadEnds - Class in picard.sam.markduplicates.util
-
Little struct-like class to hold read pair (and fragment) end data for duplicate marking.
- ReadEnds() - Constructor for class picard.sam.markduplicates.util.ReadEnds
- ReadEndsForMarkDuplicates - Class in picard.sam.markduplicates.util
-
Little struct-like class to hold read pair (and fragment) end data for MarkDuplicatesWithMateCigar
- ReadEndsForMarkDuplicates() - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
- ReadEndsForMarkDuplicates(ReadEndsForMarkDuplicates) - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
- ReadEndsForMarkDuplicatesCodec - Class in picard.sam.markduplicates.util
-
Codec for ReadEnds that just outputs the primitive fields and reads them back.
- ReadEndsForMarkDuplicatesCodec() - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
- ReadEndsForMarkDuplicatesMap - Interface in picard.sam.markduplicates.util
-
Interface for storing and retrieving ReadEnds objects.
- ReadEndsForMarkDuplicatesWithBarcodes - Class in picard.sam.markduplicates.util
- ReadEndsForMarkDuplicatesWithBarcodes() - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
- ReadEndsForMarkDuplicatesWithBarcodes(ReadEndsForMarkDuplicates) - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
- ReadEndsForMarkDuplicatesWithBarcodes(ReadEndsForMarkDuplicatesWithBarcodes) - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
- ReadEndsForMarkDuplicatesWithBarcodesCodec - Class in picard.sam.markduplicates.util
-
Created by nhomer on 9/13/15.
- ReadEndsForMarkDuplicatesWithBarcodesCodec() - Constructor for class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodesCodec
- ReadEndsForMateCigar - Class in picard.sam.markduplicates.util
-
A class to store individual records for MarkDuplicatesWithMateCigar.
- ReadEndsForMateCigar(SAMFileHeader, SamRecordWithOrdinal, OpticalDuplicateFinder, short) - Constructor for class picard.sam.markduplicates.util.ReadEndsForMateCigar
-
Builds a read ends object that represents a single read.
- ReadEndsForMateCigar(ReadEndsForMateCigar, SamRecordWithOrdinal) - Constructor for class picard.sam.markduplicates.util.ReadEndsForMateCigar
-
Creates a shallow copy from the "other"
- readGroup - Variable in class picard.sam.markduplicates.util.ReadEnds
- READGROUP - Enum constant in enum class picard.fingerprint.CrosscheckMetric.DataType
- READGROUP_ID_REGEX - Static variable in class picard.sam.AddOrReplaceReadGroups
- readgroupStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies to the readgroup id of the read.
- readHeader(int) - Method in class picard.illumina.parser.readers.CbclReader
-
Reads the Cbcl header and sets up the data streams.
- readIndexInFile - Variable in class picard.sam.util.RepresentativeReadIndexer
- readLaneTiles(File, ReadStructure, ValidationStringency, int) - Static method in class picard.illumina.CollectIlluminaLaneMetrics.IlluminaLaneMetricsCollector
-
Returns a partitioned collection of lane number to Tile objects from the provided basecall directory.
- readLengths - Variable in class picard.illumina.parser.ReadStructure
- ReadNameEncoder - Interface in picard.fastq
- ReadNameParser - Class in picard.sam.util
-
Provides access to the physical location information about a cluster.
- ReadNameParser() - Constructor for class picard.sam.util.ReadNameParser
-
Creates are read name parser using the default read name regex and optical duplicate distance.
- ReadNameParser(String) - Constructor for class picard.sam.util.ReadNameParser
-
Creates are read name parser using the given read name regex.
- ReadNameParser(String, Log) - Constructor for class picard.sam.util.ReadNameParser
-
Creates are read name parser using the given read name regex.
- readNameRegex - Variable in class picard.sam.util.ReadNameParser
- readNextLine() - Method in class picard.util.AbstractInputParser
- readNextLine() - Method in class picard.util.BasicInputParser
-
Workhorse method that reads the next line from the underlying reader
- readOneBarcode - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
- readOrdinalityStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies bases into their read's Ordinality (i.e.
- readOrientationStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies bases into their read-pair's Orientation (i.e.
- ReadPair() - Constructor for class picard.util.QuerySortedReadPairIteratorUtil.ReadPair
- readPairednessStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies bases into their read's Proper-pairedness
- READS - Variable in class picard.illumina.BarcodeMetric
-
The total number of reads matching the barcode.
- READS - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The total number of reads examined
- READS_ALIGNED - Variable in class picard.analysis.RrbsSummaryMetrics
-
Number of mapped reads processed
- READS_ALIGNED_IN_PAIRS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of aligned reads whose mate pair was also aligned to the reference.
- READS_IGNORED_MISMATCHES - Variable in class picard.analysis.RrbsSummaryMetrics
-
Number of reads discarded for exceeding the mismatch threshold
- READS_IGNORED_SHORT - Variable in class picard.analysis.RrbsSummaryMetrics
-
Number of reads discarded due to being too short
- READS_USED - Variable in class picard.analysis.GcBiasDetailMetrics
-
This option is used to mark including or excluding duplicates.
- READS_USED - Variable in class picard.analysis.GcBiasSummaryMetrics
-
This option is used to mark including or excluding duplicates.
- READS_WITH_NO_CPG - Variable in class picard.analysis.RrbsSummaryMetrics
-
Number of reads discarded for having no CpG sites
- ReadStructure - Class in picard.illumina.parser
-
Describes the intended logical output structure of clusters of an Illumina run.
- ReadStructure(String) - Constructor for class picard.illumina.parser.ReadStructure
-
Converts readStructureString into a List
and calls the primary constructor using this List as it's argument. - ReadStructure(List<ReadDescriptor>) - Constructor for class picard.illumina.parser.ReadStructure
-
Copies collection into descriptors (making descriptors unmodifiable) and then calculates relevant statistics about descriptors.
- ReadStructure.Substructure - Class in picard.illumina.parser
-
Represents a subset of ReadDescriptors in the containing ReadStructure, they ARE NOT necessarily contiguous in the containing ReadStructure but they ARE in the order they appear in the containing ReadStructure
- readSubsequence - Variable in class picard.util.BarcodeEditDistanceQuery
-
list of barcode reads
- readTwoBarcode - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesWithBarcodes
- ReadType - Enum Class in picard.illumina.parser
-
A read type describes a stretch of cycles in an ReadStructure (e.g.
- reallyFilterOut(SAMRecord) - Method in class picard.filter.CountingAdapterFilter
- reallyFilterOut(SAMRecord) - Method in class picard.filter.CountingDuplicateFilter
- reallyFilterOut(SAMRecord) - Method in class picard.filter.CountingFilter
-
Return true if we are to filter this record out, false otherwise.
- reallyFilterOut(SAMRecord) - Method in class picard.filter.CountingMapQFilter
- reallyFilterOut(SAMRecord) - Method in class picard.filter.CountingPairedFilter
- Record(int, int, Float, Float, float, IlluminaGenotype) - Constructor for class picard.arrays.illumina.IlluminaAdpcFileWriter.Record
- RECORDS_ONLY - Variable in class picard.sam.ViewSam
- RECOVER_SWAPPED_REF_ALT - Variable in class picard.vcf.LiftoverVcf
- RED - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysControlCodesSummaryMetrics
-
The red intensity value for the control.
- ref() - Method in enum class picard.analysis.artifacts.Transition
-
Gets the reference for the transition.
- REF_BASE - Variable in class picard.analysis.artifacts.ErrorSummaryMetrics
-
The reference base (or it's complement).
- REF_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The (upper-case) original base on the reference strand.
- REF_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
The (upper-case) original base on the reference strand.
- REF_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The (upper-case) original base on the reference strand.
- REF_BASE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
The (upper-case) original base on the reference strand.
- REF_COUNT - Variable in class picard.analysis.artifacts.ErrorSummaryMetrics
-
The number of reference bases observed.
- REF_FLAT - Variable in class picard.analysis.CollectMultipleMetrics
- REF_FLAT - Variable in class picard.analysis.CollectRnaSeqMetrics
- REF_NONOXO_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The number of reference alleles observed as C in read 1 and G in read 2.
- REF_OXO_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The number of reference alleles observed as G in read 1 and C in read 2.
- REF_STRAND_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- REF_TOTAL_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The total number of reference alleles observed
- REFERENCE - Variable in class picard.analysis.CollectRrbsMetrics.CollectRrbsMetricsReferenceArgumentCollection
- REFERENCE - Variable in class picard.sam.CreateSequenceDictionary.CreateSeqDictReferenceArgumentCollection
- REFERENCE - Variable in class picard.util.ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
- REFERENCE_SEQUENCE - Variable in class picard.analysis.CollectAlignmentSummaryMetrics.CollectAlignmentRefArgCollection
- REFERENCE_SEQUENCE - Variable in class picard.cmdline.argumentcollections.OptionalReferenceArgumentCollection
- REFERENCE_SEQUENCE - Variable in class picard.cmdline.argumentcollections.RequiredReferenceArgumentCollection
- REFERENCE_SEQUENCE - Variable in class picard.cmdline.CommandLineProgram
- REFERENCE_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- ReferenceArgumentCollection - Interface in picard.cmdline.argumentcollections
-
Base interface for a reference argument collection.
- referenceBaseStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies a base onto the reference base that it covers, possibly reverse complemented if the read has been reversed by the aligner.
- referenceFasta - Variable in class picard.sam.AbstractAlignmentMerger
- ReferenceProgramGroup - Class in picard.cmdline.programgroups
-
Tools that analyze and manipulate FASTA format references
- ReferenceProgramGroup() - Constructor for class picard.cmdline.programgroups.ReferenceProgramGroup
- referenceSequence - Variable in class picard.cmdline.CommandLineProgram
- RefFlatReader - Class in picard.annotation
-
Loads gene annotations from a refFlat file into an OverlapDetector
. - RefFlatReader.RefFlatColumns - Enum Class in picard.annotation
- ReflectionUtil - Class in picard.util
-
Class which contains utility functions that use reflection.
- ReflectionUtil() - Constructor for class picard.util.ReflectionUtil
- reflectiveCopy(TargetMetrics, MT, String[], String[]) - Static method in class picard.analysis.directed.TargetMetricsCollector
-
Since the targeted metrics (HsMetrics, TargetedPcrMetrics,...) share many of the same values as TargetMetrics, this copy will copy all public attributes in targetMetrics to the outputMetrics' attributes of the same name.
- REJECT - Variable in class picard.util.LiftOverIntervalList
- REJECT - Variable in class picard.vcf.LiftoverVcf
- remove() - Method in class picard.illumina.parser.MultiTileParser
- remove() - Method in class picard.illumina.parser.MultiTileBclParser
- remove() - Method in class picard.illumina.parser.PerTileParser
- remove() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
- remove() - Method in class picard.illumina.parser.readers.BarcodeFileReader
- remove() - Method in class picard.illumina.parser.readers.BclReader
- remove() - Method in class picard.illumina.parser.readers.FilterFileReader
- remove() - Method in class picard.illumina.parser.readers.TileMetricsOutReader
- remove() - Method in class picard.sam.markduplicates.MarkDuplicatesWithMateCigarIterator
- remove() - Method in class picard.util.AsyncIterator
- remove() - Method in class picard.util.DelimitedTextFileWithHeaderIterator
- remove() - Method in class picard.vcf.ByIntervalListVariantContextIterator
- remove() - Method in class picard.vcf.filter.FilterApplyingVariantIterator
- remove() - Method in class picard.vcf.PairedVariantSubContextIterator
- remove() - Method in class picard.vcf.processor.util.PredicateFilterDecoratingClosableIterator
- remove(int, String) - Method in class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
- remove(int, String) - Method in class picard.sam.markduplicates.util.MemoryBasedReadEndsForMarkDuplicatesMap
- remove(int, String) - Method in interface picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap
-
Remove element with given key from the map.
- remove(ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
-
Removes the end from this set, if present
- REMOVE_ALIGNMENT_INFORMATION - Variable in class picard.sam.RevertSam
- REMOVE_DUPLICATE_INFORMATION - Variable in class picard.sam.PositionBasedDownsampleSam
- REMOVE_DUPLICATE_INFORMATION - Variable in class picard.sam.RevertSam
- REMOVE_DUPLICATES - Variable in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
- REMOVE_SEQUENCING_DUPLICATES - Variable in class picard.sam.markduplicates.MarkDuplicates
- removeIncompleteTrios() - Method in class picard.pedigree.PedFile
-
Scans through the pedigrees and removes all entries that do not have both paternal and maternal ids set.
- removeLocationSet() - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
- RenameSampleInVcf - Class in picard.vcf
-
Renames a sample within a VCF or BCF.
- RenameSampleInVcf() - Constructor for class picard.vcf.RenameSampleInVcf
- renderPhasingMetricsFilesFromBasecallingDirectory(File) - Static method in class picard.illumina.parser.TileMetricsUtil
- REORDER_INPUT_BY_FIRST_VARIANT - Variable in class picard.vcf.GatherVcfs
- ReorderSam - Class in picard.sam
-
Reorders a SAM/BAM input file according to the order of contigs in a second reference file.
- ReorderSam() - Constructor for class picard.sam.ReorderSam
- REPEAT_TOLERANCE - Variable in class picard.util.BaitDesigner
- replace(ReadEndsForMateCigar, ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
-
Replaces a given end with the other end.
- ReplaceSamHeader - Class in picard.sam
- ReplaceSamHeader() - Constructor for class picard.sam.ReplaceSamHeader
- replicationRateFromReplicateSets - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
An estimate of the duplication rate that is based on the duplicate sets we observed.
- REPORT_FILE - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- REPORTED_GENDER - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The sex, as reported by the collaborator
- RepresentativeReadIndexer - Class in picard.sam.util
-
Little struct-like class to hold a record index, the index of the corresponding representative read, and duplicate set size information.
- RepresentativeReadIndexer() - Constructor for class picard.sam.util.RepresentativeReadIndexer
- RepresentativeReadIndexerCodec - Class in picard.sam.markduplicates.util
-
Codec for read names and integers that outputs the primitive fields and reads them back.
- RepresentativeReadIndexerCodec() - Constructor for class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
- representativeReadIndexInFile - Variable in class picard.sam.util.RepresentativeReadIndexer
- representativeReadIndicesForDuplicates - Variable in class picard.sam.markduplicates.MarkDuplicates
- REQUIRE_INDEX - Variable in class picard.vcf.VcfFormatConverter
- REQUIRE_INDEX_FILES - Variable in class picard.fingerprint.CrosscheckFingerprints
- RequiredOutputArgumentCollection - Class in picard.cmdline.argumentcollections
- RequiredOutputArgumentCollection() - Constructor for class picard.cmdline.argumentcollections.RequiredOutputArgumentCollection
- RequiredOutputArgumentCollection(File) - Constructor for class picard.cmdline.argumentcollections.RequiredOutputArgumentCollection
- RequiredReferenceArgumentCollection - Class in picard.cmdline.argumentcollections
-
Argument collection for references that are required (and not common).
- RequiredReferenceArgumentCollection() - Constructor for class picard.cmdline.argumentcollections.RequiredReferenceArgumentCollection
- requiresReference() - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- requiresReference() - Method in class picard.analysis.CollectOxoGMetrics
- requiresReference() - Method in class picard.analysis.CollectWgsMetrics
- requiresReference() - Method in class picard.arrays.GtcToVcf
- requiresReference() - Method in class picard.cmdline.CommandLineProgram
- requiresReference() - Method in class picard.fingerprint.ConvertHaplotypeDatabaseToVcf
- requiresReference() - Method in class picard.fingerprint.ExtractFingerprint
- requiresReference() - Method in class picard.fingerprint.IdentifyContaminant
- requiresReference() - Method in class picard.reference.ExtractSequences
- requiresReference() - Method in class picard.sam.markduplicates.CollectDuplicateMetrics
- requiresReference() - Method in class picard.sam.MergeBamAlignment
- requiresReference() - Method in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- requiresReference() - Method in class picard.sam.SetNmMdAndUqTags
- requiresReference() - Method in class picard.util.BaitDesigner
- resetRefSeqFileWalker() - Method in class picard.sam.AbstractAlignmentMerger
- RESTORE_HARDCLIPS - Variable in class picard.sam.RevertSam
- RESTORE_ORIGINAL_QUALITIES - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
- RESTORE_ORIGINAL_QUALITIES - Variable in class picard.sam.RevertSam
- result() - Method in class picard.vcf.CallingMetricAccumulator
- result() - Method in interface picard.vcf.processor.VariantProcessor.Accumulator
- RESULT - Variable in class picard.fingerprint.CrosscheckMetric
-
The overall result of the match.
- REV_COMPED_ALLELES - Static variable in class picard.util.LiftoverUtils
- REV_CXT_ALT_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The number of ~REF_BASE:~ALT_BASE alignments at sites complementary to the given reference context.
- REV_CXT_REF_BASES - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The number of ~REF_BASE:~REF_BASE alignments at sites complementary to the given reference context.
- REV_ERROR_RATE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
-
The substitution rate of ~REF_BASE:~ALT_BASE, calculated as max(1e-10, REV_CXT_ALT_BASES / (REV_CXT_ALT_BASES + REV_CXT_REF_BASES)).
- reverseComplementVariantContext(VariantContext, Interval, ReferenceSequence) - Static method in class picard.util.LiftoverUtils
- RevertOriginalBaseQualitiesAndAddMateCigar - Class in picard.sam
-
This tool reverts the original base qualities (if specified) and adds the mate cigar tag to mapped SAM, BAM or CRAM files.
- RevertOriginalBaseQualitiesAndAddMateCigar() - Constructor for class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
- RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile - Enum Class in picard.sam
-
Used as a return for the canSkipSAMFile function.
- RevertSam - Class in picard.sam
-
Reverts a SAM file by optionally restoring original quality scores and by removing all alignment information.
- RevertSam() - Constructor for class picard.sam.RevertSam
- RevertSam.FileType - Enum Class in picard.sam
- revertSamRecord(SAMRecord) - Method in class picard.sam.RevertSam
-
Takes an individual SAMRecord and applies the set of changes/reversions to it that have been requested by program level options.
- reviseAndConditionallyLogQuality(byte) - Method in class picard.illumina.parser.readers.BclQualityEvaluationStrategy
-
Accepts a quality read from a BCL file and (1) returns a 1 if the value was 0 and (2) makes a note of the provided quality if it is low.
- RExecutor - Class in picard.util
-
Util class for executing R scripts.
- RExecutor() - Constructor for class picard.util.RExecutor
- RF - Static variable in class picard.sam.markduplicates.util.ReadEnds
- RG_TAG - Variable in class picard.sam.SamToFastq
- RGCN - Variable in class picard.sam.AddOrReplaceReadGroups
- RGDS - Variable in class picard.sam.AddOrReplaceReadGroups
- RGDT - Variable in class picard.sam.AddOrReplaceReadGroups
- RGFO - Variable in class picard.sam.AddOrReplaceReadGroups
- RGID - Variable in class picard.sam.AddOrReplaceReadGroups
- RGKS - Variable in class picard.sam.AddOrReplaceReadGroups
- RGLB - Variable in class picard.sam.AddOrReplaceReadGroups
- RGPG - Variable in class picard.sam.AddOrReplaceReadGroups
- RGPI - Variable in class picard.sam.AddOrReplaceReadGroups
- RGPL - Variable in class picard.sam.AddOrReplaceReadGroups
- RGPM - Variable in class picard.sam.AddOrReplaceReadGroups
- RGPU - Variable in class picard.sam.AddOrReplaceReadGroups
- RGSM - Variable in class picard.sam.AddOrReplaceReadGroups
- RIBOSOMAL - Enum constant in enum class picard.annotation.LocusFunction
- RIBOSOMAL_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
Number of bases in primary alignments that align to ribosomal sequence.
- RIBOSOMAL_INTERVALS - Variable in class picard.analysis.CollectRnaSeqMetrics
- ribosomalInitialValue - Variable in class picard.analysis.directed.RnaSeqMetricsCollector
- RIGHT_FILE - Variable in class picard.fingerprint.CrosscheckMetric
-
The RIGHT file from which the fingerprint was obtained.
- RIGHT_FILE - Variable in class picard.sam.SamComparisonMetric
-
Right file used in comparison
- RIGHT_GROUP_VALUE - Variable in class picard.fingerprint.CrosscheckMetric
-
The RIGHT group value.
- RIGHT_LANE - Variable in class picard.fingerprint.CrosscheckMetric
-
The RIGHT lane.
- RIGHT_LIBRARY - Variable in class picard.fingerprint.CrosscheckMetric
-
The RIGHT library identifier.
- RIGHT_MOLECULAR_BARCODE_SEQUENCE - Variable in class picard.fingerprint.CrosscheckMetric
-
The RIGHT molecular (sample) barcode.
- RIGHT_PRIMER - Variable in class picard.util.BaitDesigner
- RIGHT_RUN_BARCODE - Variable in class picard.fingerprint.CrosscheckMetric
-
The RIGHT run barcode (PU field) expected to look like : D047KACXX110901.1.ACCAACTG.
- RIGHT_SAMPLE - Variable in class picard.fingerprint.CrosscheckMetric
-
The RIGHT sample identifier.
- rightVariantContext - Variable in class picard.vcf.PairedVariantSubContextIterator.VcfTuple
- RIlmn - Variable in class picard.arrays.illumina.InfiniumGTCRecord
- RnaSeqMetrics - Class in picard.analysis
-
Metrics about the alignment of RNA-seq reads within a SAM file to genes, produced by the CollectRnaSeqMetrics program and usually stored in a file with the extension ".rna_metrics".
- RnaSeqMetrics - Enum constant in enum class picard.analysis.CollectMultipleMetrics.Program
- RnaSeqMetrics() - Constructor for class picard.analysis.RnaSeqMetrics
- RnaSeqMetricsCollector - Class in picard.analysis.directed
- RnaSeqMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, Long, OverlapDetector<Gene>, OverlapDetector<Interval>, HashSet<Integer>, int, RnaSeqMetricsCollector.StrandSpecificity, double, boolean) - Constructor for class picard.analysis.directed.RnaSeqMetricsCollector
- RnaSeqMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, Long, OverlapDetector<Gene>, OverlapDetector<Interval>, HashSet<Integer>, int, RnaSeqMetricsCollector.StrandSpecificity, double, boolean, int) - Constructor for class picard.analysis.directed.RnaSeqMetricsCollector
- RnaSeqMetricsCollector.PerUnitRnaSeqMetricsCollector - Class in picard.analysis.directed
- RnaSeqMetricsCollector.StrandSpecificity - Enum Class in picard.analysis.directed
- round(double...) - Static method in class picard.util.MathUtil
-
returns a long array containing the rounded values of the input array
- round(double, int) - Static method in class picard.util.MathUtil
-
Round off the value to the specified precision.
- RR - Static variable in class picard.sam.markduplicates.util.ReadEnds
- RrbsCpgDetailMetrics - Class in picard.analysis
-
Holds information about CpG sites encountered for RRBS processing QC
- RrbsCpgDetailMetrics() - Constructor for class picard.analysis.RrbsCpgDetailMetrics
- RrbsMetricsCollector - Class in picard.analysis
- RrbsMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, int, int, int, double) - Constructor for class picard.analysis.RrbsMetricsCollector
- RrbsSummaryMetrics - Class in picard.analysis
-
Holds summary statistics from RRBS processing QC
- RrbsSummaryMetrics() - Constructor for class picard.analysis.RrbsSummaryMetrics
- RRNA_FRAGMENT_PERCENTAGE - Variable in class picard.analysis.CollectRnaSeqMetrics
- RS_ID - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- rsNames - Variable in class picard.arrays.illumina.InfiniumEGTFile
- rsNameToIndex - Variable in class picard.arrays.illumina.InfiniumEGTFile
- run() - Method in class picard.illumina.ExtractIlluminaBarcodes.PerTileBarcodeExtractor
-
run method which extracts barcodes and accumulates metrics for an entire tile
- run() - Method in class picard.Test
- RUN_BARCODE - Variable in class picard.illumina.IlluminaBasecallsToFastq
- RUN_BARCODE - Variable in class picard.illumina.IlluminaBasecallsToSam
- RUN_DATE - Variable in class picard.sam.FastqToSam
- RUN_DIRECTORY - Variable in class picard.illumina.CollectIlluminaLaneMetrics
- RUN_START_DATE - Variable in class picard.illumina.IlluminaBasecallsToSam
- runEamssForReadInPlace(byte[], byte[]) - Static method in class picard.illumina.parser.MultiTileBclParser
-
EAMSS is an Illumina Developed Algorithm for detecting reads whose quality has deteriorated towards their end and revising the quality to the masking quality (2) if this is the case.
S
- S - Enum constant in enum class picard.illumina.parser.ReadType
- S_LOCS_FILE - Static variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
- sam - Enum constant in enum class picard.sam.RevertSam.FileType
- SAM_FILES - Variable in class picard.sam.CompareSAMs
- SamAlignmentMerger - Class in picard.sam
-
Class that takes in a set of alignment information in SAM format and merges it with the set of all reads for which alignment was attempted, stored in an unmapped SAM file.
- SamAlignmentMerger(File, File, File, SAMProgramRecord, boolean, boolean, boolean, List<File>, int, List<String>, List<String>, Integer, Integer, List<File>, List<File>, List<SamPairUtil.PairOrientation>, SAMFileHeader.SortOrder, PrimaryAlignmentSelectionStrategy, boolean, boolean, int) - Constructor for class picard.sam.SamAlignmentMerger
-
Constructor with a default value for unmappingReadStrategy
- SamAlignmentMerger(File, File, File, SAMProgramRecord, boolean, boolean, boolean, List<File>, int, List<String>, List<String>, Integer, Integer, List<File>, List<File>, List<SamPairUtil.PairOrientation>, SAMFileHeader.SortOrder, PrimaryAlignmentSelectionStrategy, boolean, boolean, int, AbstractAlignmentMerger.UnmappingReadStrategy, List<String>) - Constructor for class picard.sam.SamAlignmentMerger
-
Constructor
- SamComparison - Class in picard.sam.util
-
Compare two SAM/BAM files.
- SamComparison(SamReader, SamReader) - Constructor for class picard.sam.util.SamComparison
-
Note: the caller must make sure the SamReaders are closed properly.
- SamComparison(SamReader, SamReader, String, String, SAMComparisonArgumentCollection) - Constructor for class picard.sam.util.SamComparison
- SamComparison.AlignmentComparison - Enum Class in picard.sam.util
- samComparisonArgumentCollection - Variable in class picard.sam.CompareSAMs
- SAMComparisonArgumentCollection - Class in picard.sam.util
-
Argument collection for SAM comparison
- SAMComparisonArgumentCollection() - Constructor for class picard.sam.util.SAMComparisonArgumentCollection
- SamComparisonMetric - Class in picard.sam
-
Metric for results of SamComparison.
- SamComparisonMetric() - Constructor for class picard.sam.SamComparisonMetric
- SamFormatConverter - Class in picard.sam
-
Converts a BAM file to human-readable SAM output or vice versa
- SamFormatConverter() - Constructor for class picard.sam.SamFormatConverter
- SamHeaderAndIterator(SAMFileHeader, CloseableIterator<SAMRecord>) - Constructor for class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
- SAMPLE - Enum constant in enum class picard.analysis.MetricAccumulationLevel
- SAMPLE - Enum constant in enum class picard.fingerprint.CrosscheckMetric.DataType
- SAMPLE - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The name of the sample who's genotypes the sequence data was compared to.
- SAMPLE - Variable in class picard.analysis.FingerprintingSummaryMetrics
-
The sample whose known genotypes the sequence data was compared to.
- SAMPLE - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- SAMPLE - Variable in class picard.arrays.BafRegressMetrics
-
The sample name
- SAMPLE - Variable in class picard.metrics.MultilevelMetrics
-
The sample to which these metrics apply.
- SAMPLE - Variable in class picard.vcf.MakeSitesOnlyVcf
- SAMPLE_ALIAS - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasDetailMetrics
- SAMPLE_ALIAS - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
The name of the sample being assayed.
- SAMPLE_ALIAS - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterDetailMetrics
-
The name of the sample being assayed.
- SAMPLE_ALIAS - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
The name of the sample being assayed.
- SAMPLE_ALIAS - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The name of the sample being assayed.
- SAMPLE_ALIAS - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The name of the sample
- SAMPLE_ALIAS - Variable in class picard.arrays.GtcToVcf
- SAMPLE_ALIAS - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- SAMPLE_ALIAS - Variable in class picard.fingerprint.ExtractFingerprint
- SAMPLE_ALIAS - Variable in class picard.fingerprint.FingerprintMetrics
-
The Sample alias taken from RG header or #CHROME line
- SAMPLE_ALIAS - Variable in class picard.fingerprint.IdentifyContaminant
- SAMPLE_ALIAS - Variable in class picard.illumina.IlluminaBasecallsToSam
- SAMPLE_ALIAS - Variable in class picard.sam.RevertSam
- SAMPLE_ALIAS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
-
The name of the sample being assayed
- SAMPLE_ALIAS_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- SAMPLE_INDIVIDUAL_MAP - Variable in class picard.fingerprint.CrosscheckFingerprints
- SAMPLE_NAME - Variable in class picard.sam.FastqToSam
- SAMPLE_SIZE - Variable in class picard.analysis.CollectWgsMetrics
- SAMPLE_SIZE - Variable in class picard.analysis.directed.CollectTargetedMetrics
- SAMPLE_SIZE - Variable in class picard.analysis.TheoreticalSensitivityMetrics
-
Number of samples drawn at each depth in the depth distribution.
- sampleBarcodes - Variable in class picard.illumina.parser.ReadStructure
- sampleCumulativeSums(int, int, boolean) - Method in class picard.analysis.TheoreticalSensitivity.RouletteWheel
- SAMPLES_FILE - Variable in class picard.arrays.VcfToAdpc
- SAMRecordAndReference - Class in picard.metrics
- SAMRecordAndReference(SAMRecord, ReferenceSequence) - Constructor for class picard.metrics.SAMRecordAndReference
- SAMRecordAndReferenceMultiLevelCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,
HKEY extends Comparable> - Class in picard.metrics - SAMRecordAndReferenceMultiLevelCollector() - Constructor for class picard.metrics.SAMRecordAndReferenceMultiLevelCollector
- SAMRecordMultiLevelCollector<BEAN extends htsjdk.samtools.metrics.MetricBase,
HKEY extends Comparable> - Class in picard.metrics -
Defines a MultilevelPerRecordCollector using the argument type of SAMRecord so that this doesn't have to be redefined for each subclass of MultilevelPerRecordCollector
- SAMRecordMultiLevelCollector() - Constructor for class picard.metrics.SAMRecordMultiLevelCollector
- samRecordWithOrdinal - Variable in class picard.sam.markduplicates.util.ReadEndsForMateCigar
- SamRecordWithOrdinalAndSetDuplicateReadFlag - Class in picard.sam.markduplicates.util
-
This class sets the duplicate read flag as the result state when examining sets of records.
- SamRecordWithOrdinalAndSetDuplicateReadFlag() - Constructor for class picard.sam.markduplicates.util.SamRecordWithOrdinalAndSetDuplicateReadFlag
- SamRecordWithOrdinalAndSetDuplicateReadFlag(SAMRecord, long) - Constructor for class picard.sam.markduplicates.util.SamRecordWithOrdinalAndSetDuplicateReadFlag
- SamSequenceRecordsIterator(File, boolean) - Constructor for class picard.util.SequenceDictionaryUtils.SamSequenceRecordsIterator
- SamToBfqWriter - Class in picard.fastq
-
Class to take unmapped reads in SAM/BAM/CRAM file format and create Maq binary fastq format file(s) -- one or two of them, depending on whether it's a paired-end read.
- SamToBfqWriter(File, File, String, Integer, Integer, boolean, String, boolean, boolean, Integer) - Constructor for class picard.fastq.SamToBfqWriter
-
Constructor
- SamToBfqWriter(File, String, boolean, String, boolean) - Constructor for class picard.fastq.SamToBfqWriter
-
Constructor
- SamToFastq - Class in picard.sam
-
Extracts read sequences and qualities from the input SAM/BAM file and writes them into the output file in Sanger FASTQ format.
- SamToFastq() - Constructor for class picard.sam.SamToFastq
- SamToFastqWithTags - Class in picard.sam
-
Extracts read sequences and qualities from the input SAM/BAM file and SAM/BAM tags and writes them into output files in Sanger FASTQ format.
- SamToFastqWithTags() - Constructor for class picard.sam.SamToFastqWithTags
- SANITIZE - Variable in class picard.sam.RevertSam
- scaledEvidenceProbabilityUsingGenotypeFrequencies(double[]) - Method in class picard.fingerprint.HaplotypeProbabilities
-
This function returns the scaled probability of the evidence collected given a vector of priors on the haplotype using the internal likelihood, which may be scaled by an unknown factor.
- SCAN_WINDOW_SIZE - Variable in class picard.analysis.CollectGcBiasMetrics
- SCANNER_NAME - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The name of the scanner used for this sample
- SCANNER_NAME - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- scatter(IntervalList, int) - Method in interface picard.util.IntervalList.IntervalListScatterer
-
Scatter an
IntervalList
into several IntervalLists. - SCATTER_CONTENT - Variable in class picard.util.IntervalListTools
- SCATTER_COUNT - Variable in class picard.util.IntervalListTools
- ScatterIntervalsByNReferenceArgumentCollection() - Constructor for class picard.util.ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection
- ScatterIntervalsByNs - Class in picard.util
-
A Tool for breaking up a reference into intervals of alternating regions of N and ACGT bases.
- ScatterIntervalsByNs() - Constructor for class picard.util.ScatterIntervalsByNs
- ScatterIntervalsByNs.ScatterIntervalsByNReferenceArgumentCollection - Class in picard.util
- scheme - Variable in class picard.vcf.GenotypeConcordanceScheme
-
The underlying scheme
- score - Variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
- SCORE - Variable in class picard.util.IntervalListToBed
- SD_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The standard deviation of clusters per tile.
- SD_COVERAGE - Variable in class picard.analysis.WgsMetrics
-
The standard deviation of coverage of the genome after all filters are applied.
- SD_PCT_PF_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The standard deviation in percentage of pf clusters per tile.
- SD_PF_CLUSTERS_PER_TILE - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The standard deviation in number of pf clusters per tile.
- SD_READ_LENGTH - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The standard deviation of the read lengths.
- SECOND - Enum constant in enum class picard.illumina.parser.TileTemplateRead
- SECOND - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ReadOrdinality
- SECOND_END_FASTQ - Variable in class picard.sam.SamToFastq
- SECOND_INPUT - Variable in class picard.fingerprint.CrosscheckFingerprints
- SECOND_INPUT - Variable in class picard.util.IntervalListTools
- SECOND_INPUT_INDEX_MAP - Variable in class picard.fingerprint.CrosscheckFingerprints
- SECOND_INPUT_SAMPLE_MAP - Variable in class picard.fingerprint.CrosscheckFingerprints
- SECOND_OF_PAIR - Enum constant in enum class picard.analysis.AlignmentSummaryMetrics.Category
- SECOND_READ_TRANSCRIPTION_STRAND - Enum constant in enum class picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
- SECONDARY_OR_SUPPLEMENTARY_RDS - Variable in class picard.sam.DuplicationMetrics
-
The number of reads that were either secondary or supplementary
- seek(List<File>, TileIndex, int) - Method in class picard.illumina.parser.readers.BclReader
- seekToTile(int) - Method in class picard.illumina.parser.MultiTileParser
- seekToTile(int) - Method in class picard.illumina.parser.MultiTileBclParser
-
Clear the current set of cycleFileParsers and replace them with the ones for the tile indicated by oneBasedTileNumber
- seekToTile(int) - Method in class picard.illumina.parser.PerTileParser
- sensitivityAtConstantDepth(int, Histogram<Integer>, double, int, double, long) - Static method in class picard.analysis.TheoreticalSensitivity
-
Calculates the theoretical sensitivity with a given Phred-scaled quality score distribution at a constant depth.
- seq(double, double, double) - Static method in class picard.util.MathUtil
-
Mimic's R's seq() function to produce a sequence of equally spaced numbers.
- SEQUENCE_DICTIONARY - Variable in class picard.annotation.SortGff
- SEQUENCE_DICTIONARY - Variable in class picard.arrays.CollectArraysVariantCallingMetrics
- SEQUENCE_DICTIONARY - Variable in class picard.fingerprint.LiftOverHaplotypeMap
- SEQUENCE_DICTIONARY - Variable in class picard.sam.ReorderSam
- SEQUENCE_DICTIONARY - Variable in class picard.util.BedToIntervalList
- SEQUENCE_DICTIONARY - Variable in class picard.util.LiftOverIntervalList
- SEQUENCE_DICTIONARY - Variable in class picard.vcf.CollectVariantCallingMetrics
- SEQUENCE_DICTIONARY - Variable in class picard.vcf.MergeVcfs
- SEQUENCE_DICTIONARY - Variable in class picard.vcf.SortVcf
- SEQUENCE_DICTIONARY - Variable in class picard.vcf.SplitVcfs
- SEQUENCE_DICTIONARY - Variable in class picard.vcf.UpdateVcfSequenceDictionary
- SEQUENCE_DICTIONARY_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- SEQUENCE_MISMATCH - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Deprecated.- but used in existing extended manifest files.
- SEQUENCE_NAME - Variable in class picard.analysis.RrbsCpgDetailMetrics
-
Sequence the CpG is seen in
- SEQUENCE_NAMES - Variable in class picard.analysis.CollectRrbsMetrics
- SEQUENCE_TAG_GROUP - Variable in class picard.sam.SamToFastqWithTags
- SequenceDictionaryUtils - Class in picard.util
-
Class with helper methods for generating and writing SequenceDictionary objects.
- SequenceDictionaryUtils() - Constructor for class picard.util.SequenceDictionaryUtils
- SequenceDictionaryUtils.SamSequenceRecordsIterator - Class in picard.util
- SEQUENCING - Enum constant in enum class picard.sam.markduplicates.MarkDuplicates.DuplicateType
- SEQUENCING_CENTER - Variable in class picard.illumina.IlluminaBasecallsToSam
- SEQUENCING_CENTER - Variable in class picard.sam.FastqToSam
- SequencingArtifactMetrics - Class in picard.analysis.artifacts
- SequencingArtifactMetrics() - Constructor for class picard.analysis.artifacts.SequencingArtifactMetrics
- SequencingArtifactMetrics.BaitBiasDetailMetrics - Class in picard.analysis.artifacts
-
Bait bias artifacts broken down by context.
- SequencingArtifactMetrics.BaitBiasSummaryMetrics - Class in picard.analysis.artifacts
-
Summary analysis of a single bait bias artifact, also known as a reference bias artifact.
- SequencingArtifactMetrics.PreAdapterDetailMetrics - Class in picard.analysis.artifacts
-
Pre-adapter artifacts broken down by context.
- SequencingArtifactMetrics.PreAdapterSummaryMetrics - Class in picard.analysis.artifacts
-
Summary analysis of a single pre-adapter artifact.
- SET_ONLY_UQ - Variable in class picard.sam.SetNmMdAndUqTags
- setAddPGTagToReads(boolean) - Method in class picard.sam.AbstractAlignmentMerger
-
Set addPGTagToReads.
- setAllowDuplicateReads(boolean) - Method in class picard.fingerprint.FingerprintChecker
-
Sets whether duplicate reads should be allowed when calling genotypes from SAM files.
- setApplyEamssFiltering(boolean) - Method in class picard.illumina.parser.IlluminaDataProviderFactory
-
Sets whether or not EAMSS filtering will be applied if parsing BCL files for bases and quality scores.
- setAssayFormat(String) - Method in class picard.arrays.illumina.IlluminaManifest
- setAttributesToReverse(Set<String>) - Method in class picard.sam.AbstractAlignmentMerger
-
Sets the set of attributes to be reversed on reads marked as negative strand.
- setAttributesToReverseComplement(Set<String>) - Method in class picard.sam.AbstractAlignmentMerger
-
Sets the set of attributes to be reverse complemented on reads marked as negative strand.
- setBaitSetName(String) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
-
Sets the name of the bait set explicitly instead of inferring it from the bait file.
- setBases(byte[]) - Method in class picard.illumina.parser.ReadData
- setBigDuplicateSetSize(int) - Method in class picard.sam.markduplicates.util.OpticalDuplicateFinder
-
Sets the size of a set that is big enough to log progress about.
- setClipOverlappingReads(boolean) - Method in class picard.sam.AbstractAlignmentMerger
- setConverter(BasecallsConverter.ClusterDataConverter<CLUSTER_OUTPUT_RECORD>) - Method in class picard.illumina.BasecallsConverter
-
Must be called before doTileProcessing.
- setCounter(long) - Method in class picard.analysis.AbstractWgsMetricsCollector
-
Sets the counter to the current number of processed loci.
- setDateManufactured(String) - Method in class picard.arrays.illumina.IlluminaManifest
- setDefaultHeaders(List<Header>) - Method in class picard.cmdline.CommandLineProgram
- setDefaultSampleID(String) - Method in class picard.fingerprint.FingerprintChecker
- setDescriptorFileName(String) - Method in class picard.arrays.illumina.IlluminaManifest
- setDupe(boolean) - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- setGcCacheSize(int) - Static method in class picard.sam.SamErrorMetric.ReadBaseStratification
- setGenomeAssembly(String) - Method in class picard.util.SequenceDictionaryUtils.SamSequenceRecordsIterator
- setGenotypingErrorRate(double) - Method in class picard.fingerprint.FingerprintChecker
-
Sets the assumed genotyping error rate used when accurate error rates are not available.
- setHardClipOverlappingReads(boolean) - Method in class picard.sam.AbstractAlignmentMerger
- setHgGenomeBuild(String) - Method in class picard.arrays.illumina.IlluminaManifestRecord
- setIdentifier(String) - Method in class picard.arrays.illumina.InfiniumDataFile
- setIncludeSecondaryAlignments(boolean) - Method in class picard.sam.AbstractAlignmentMerger
- setInputStream(InputStream) - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
- setInputStream(InputStream) - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
- setKeepAlignerProperPairFlags(boolean) - Method in class picard.sam.AbstractAlignmentMerger
-
If true, keep the aligner's idea of proper pairs rather than letting alignment merger decide.
- setLane(int) - Method in class picard.illumina.parser.ClusterData
- setLibraryId(short) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
- setLibraryId(short) - Method in class picard.sam.markduplicates.util.ReadEnds
- setLibraryId(short) - Method in interface picard.sam.util.PhysicalLocation
- setLibraryId(short) - Method in class picard.sam.util.PhysicalLocationInt
- setLocationBinSize(int) - Static method in class picard.sam.SamErrorMetric.ReadBaseStratification
-
defaults to 2500
- setLocationSet(PhysicalLocationForMateCigarSet) - Method in class picard.sam.markduplicates.util.ReadEndsForMateCigar
- setLociCount(int) - Method in class picard.arrays.illumina.IlluminaManifest
- setLocusMaxReads(int) - Method in class picard.fingerprint.FingerprintChecker
- setLogLikelihoods(double[]) - Method in class picard.fingerprint.HaplotypeProbabilitiesFromGenotypeLikelihoods
- setLongHomopolymer(int) - Static method in class picard.sam.SamErrorMetric.ReadBaseStratification
-
defaults to 6
- setManifestFileParser(CsvInputParser) - Method in class picard.arrays.illumina.IlluminaManifest
- setMatchedBarcode(String) - Method in class picard.illumina.parser.ClusterData
- setMaxDuplicateSetSize(long) - Method in class picard.sam.markduplicates.util.OpticalDuplicateFinder
-
Sets the size of a set that is too big to process.
- setMaxPairErrorRate(double) - Method in class picard.util.AdapterMarker
- setMaxRecordsInRam(int) - Method in class picard.sam.AbstractAlignmentMerger
-
Allows the caller to override the maximum records in RAM.
- setMaxSingleEndErrorRate(double) - Method in class picard.util.AdapterMarker
- setMinimumBaseQuality(int) - Method in class picard.fingerprint.FingerprintChecker
-
Sets the minimum base quality for bases used when computing a fingerprint from sequence data.
- setMinimumMappingQuality(int) - Method in class picard.fingerprint.FingerprintChecker
-
Sets the minimum mapping quality for reads used when computing fingerprints from sequence data.
- setMinPairMatchBases(int) - Method in class picard.util.AdapterMarker
- setMinSingleEndMatchBases(int) - Method in class picard.util.AdapterMarker
- setNearProbeDistance(int) - Method in class picard.analysis.directed.TargetMetricsCollector
-
Sets the distance that is allowed between a read and the nearest probe for it to be considered "near probe" and "selected.
- SetNmAndUqTags - Class in picard.sam
-
Deprecated.
- SetNmAndUqTags() - Constructor for class picard.sam.SetNmAndUqTags
-
Deprecated.
- SetNmMdAndUqTags - Class in picard.sam
-
Fixes the NM, MD, and UQ tags in a SAM or BAM file.
- SetNmMdAndUqTags() - Constructor for class picard.sam.SetNmMdAndUqTags
- setNoSideEffects(boolean) - Method in class picard.analysis.directed.TargetMetricsCollector
-
In the case of ignoring bases in overlapping reads from the same template, we choose to internally modify the SAM record's CIGAR to clip overlapping bases.
- setNumAdaptersToKeep(int) - Method in class picard.util.AdapterMarker
-
After seeing the thresholdForSelectingAdapters number of adapters, keep up to this many of the original adapters.
- setNumAssays(int) - Method in class picard.arrays.illumina.IlluminaManifest
- setOffset(int) - Method in class picard.arrays.illumina.InfiniumFileTOC
- setOffsetX(float) - Method in class picard.arrays.illumina.InfiniumTransformation
- setOffsetY(float) - Method in class picard.arrays.illumina.InfiniumTransformation
- setOrCheckLane(int) - Method in class picard.illumina.parser.ClusterData
-
Either set this value if not already set, or if already set, throw an exception if new value != current value.
- setOrCheckPf(boolean) - Method in class picard.illumina.parser.ClusterData
-
Either set this value if not already set, or if already set, throw an exception if new value != current value.
- setOrCheckTile(int) - Method in class picard.illumina.parser.ClusterData
-
Either set this value if not already set, or if already set, throw an exception if new value != current value.
- setOrCheckX(int) - Method in class picard.illumina.parser.ClusterData
-
Either set this value if not already set, or if already set, throw an exception if new value != current value.
- setOrCheckY(int) - Method in class picard.illumina.parser.ClusterData
-
Either set this value if not already set, or if already set, throw an exception if new value != current value.
- setOutputStream(OutputStream) - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesCodec
- setOutputStream(OutputStream) - Method in class picard.sam.markduplicates.util.RepresentativeReadIndexerCodec
- setPerBaseOutput(File) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
-
Sets the (optional) File to write per-base coverage information to.
- setPerTargetOutput(File) - Method in class picard.analysis.directed.TargetMetricsCollector.PerUnitTargetMetricCollector
-
Sets the (optional) File to write per-target coverage information to.
- setPf(boolean) - Method in class picard.illumina.parser.ClusterData
- setpLossofHet(double) - Method in class picard.fingerprint.FingerprintChecker
- setPositionInfo(AbstractIlluminaPositionFileReader.PositionInfo) - Method in class picard.illumina.parser.CbclData
- setPriorError(double) - Static method in class picard.sam.SamErrorMetric.ErrorMetric
- setProgramRecord(SAMProgramRecord) - Method in class picard.sam.AbstractAlignmentMerger
- setProgramsToRun(Collection<CollectMultipleMetrics.ProgramInterface>) - Method in class picard.analysis.CollectMultipleMetrics
-
Use this method when invoking CollectMultipleMetrics programmatically to run programs other than the ones available via enum.
- setQualities(byte[]) - Method in class picard.illumina.parser.ReadData
- setReadGroup(short) - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigar
- setReadGroup(short) - Method in class picard.sam.markduplicates.util.ReadEnds
- setReadGroup(short) - Method in interface picard.sam.util.PhysicalLocation
- setReadGroup(short) - Method in class picard.sam.util.PhysicalLocationInt
- setReadType(ReadType) - Method in class picard.illumina.parser.ReadData
- setReferenceFasta(File) - Method in class picard.fingerprint.FingerprintChecker
- setReferenceSequence(File) - Method in class picard.analysis.SinglePassSamProgram
-
Set the reference File.
- setReserved1(float) - Method in class picard.arrays.illumina.InfiniumTransformation
- setReserved2(float) - Method in class picard.arrays.illumina.InfiniumTransformation
- setReserved3(float) - Method in class picard.arrays.illumina.InfiniumTransformation
- setReserved4(float) - Method in class picard.arrays.illumina.InfiniumTransformation
- setReserved5(float) - Method in class picard.arrays.illumina.InfiniumTransformation
- setReserved6(float) - Method in class picard.arrays.illumina.InfiniumTransformation
- setResultState(boolean) - Method in class picard.sam.markduplicates.util.SamRecordWithOrdinalAndSetDuplicateReadFlag
- setRsId(String) - Method in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord
- setScaleX(float) - Method in class picard.arrays.illumina.InfiniumTransformation
- setScaleY(float) - Method in class picard.arrays.illumina.InfiniumTransformation
- setShear(float) - Method in class picard.arrays.illumina.InfiniumTransformation
- setSize - Variable in class picard.sam.util.RepresentativeReadIndexer
- setSkipBlankLines(boolean) - Method in class picard.util.AbstractInputParser
- setSpecies(String) - Method in class picard.util.SequenceDictionaryUtils.SamSequenceRecordsIterator
- setTheta(float) - Method in class picard.arrays.illumina.InfiniumTransformation
- setThresholdForSelectingAdaptersToKeep(int) - Method in class picard.util.AdapterMarker
-
When this number of adapters have been matched, discard the least-frequently matching ones.
- setTile(int) - Method in class picard.illumina.parser.ClusterData
- setTile(short) - Method in interface picard.sam.util.PhysicalLocation
- setTile(short) - Method in class picard.sam.util.PhysicalLocationInt
- setTileLimits(Integer, Integer) - Method in class picard.illumina.BasecallsConverter
-
Uses the firstTile and tileLimit parameters to set which tiles will be processed.
- setTiles(List<Integer>) - Method in class picard.illumina.parser.ParameterizedFileUtil
- setTilesForPerRunFile(List<Integer>) - Method in class picard.illumina.parser.ParameterizedFileUtil
- setTilesForPerRunFile(List<Integer>) - Method in class picard.illumina.parser.PerTileOrPerRunFileUtil
- setToMarkQueueMinimumDistance(int) - Method in class picard.sam.markduplicates.util.MarkQueue
-
Sets the minimum genomic distance such that we can be assured that all duplicates have been considered.
- setTreatGroupedDelimitersAsOne(boolean) - Method in class picard.util.AbstractInputParser
- setup(SAMFileHeader, File) - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- setup(SAMFileHeader, File) - Method in class picard.analysis.CollectAlignmentSummaryMetrics
- setup(SAMFileHeader, File) - Method in class picard.analysis.CollectBaseDistributionByCycle
- setup(SAMFileHeader, File) - Method in class picard.analysis.CollectGcBiasMetrics
- setup(SAMFileHeader, File) - Method in class picard.analysis.CollectInsertSizeMetrics
- setup(SAMFileHeader, File) - Method in class picard.analysis.CollectQualityYieldMetrics
- setup(SAMFileHeader, File) - Method in class picard.analysis.CollectRnaSeqMetrics
- setup(SAMFileHeader, File) - Method in class picard.analysis.MeanQualityByCycle
- setup(SAMFileHeader, File) - Method in class picard.analysis.QualityScoreDistribution
- setup(SAMFileHeader, File) - Method in class picard.analysis.SinglePassSamProgram
-
Should be implemented by subclasses to do one-time initialization work.
- setup(SAMFileHeader, File) - Method in class picard.sam.markduplicates.CollectDuplicateMetrics
- setup(VCFHeader) - Method in class picard.vcf.CallingMetricAccumulator
- setup(VCFHeader) - Method in class picard.vcf.GvcfMetricAccumulator
- setup(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>) - Method in class picard.metrics.MultiLevelCollector
-
Use an init method so that overloaded methods in subclasses can pass use parameters that are initialized in their constructor
- setupOpticalDuplicateFinder() - Method in class picard.sam.markduplicates.util.AbstractOpticalDuplicateFinderCommandLineProgram
- setUri(String) - Method in class picard.util.SequenceDictionaryUtils.SamSequenceRecordsIterator
- setValidationStringency(ValidationStringency) - Method in class picard.fingerprint.FingerprintChecker
- setValuesFromAlignment(SAMRecord, SAMRecord, boolean) - Method in class picard.sam.AbstractAlignmentMerger
-
Sets the values from the alignment record on the unaligned BAM record.
- setVersion(int) - Method in class picard.arrays.illumina.InfiniumTransformation
- setWordCount(int) - Method in class picard.util.AbstractInputParser
- setX(int) - Method in class picard.illumina.parser.ClusterData
- setX(int) - Method in interface picard.sam.util.PhysicalLocation
- setX(int) - Method in class picard.sam.util.PhysicalLocationInt
- setX(int) - Method in class picard.sam.util.PhysicalLocationShort
- setY(int) - Method in class picard.illumina.parser.ClusterData
- setY(int) - Method in interface picard.sam.util.PhysicalLocation
- setY(int) - Method in class picard.sam.util.PhysicalLocationInt
- setY(int) - Method in class picard.sam.util.PhysicalLocationShort
- Sex - Enum Class in picard.pedigree
-
Represents the sex of an individual.
- shiftedLogEvidenceProbability() - Method in class picard.fingerprint.HaplotypeProbabilities
-
Returns log (p(evidence)) + c assuming that the prior on haplotypes is given by the internal haplotypeFrequencies
- shiftedLogEvidenceProbabilityGivenOtherEvidence(HaplotypeProbabilities) - Method in class picard.fingerprint.HaplotypeProbabilities
-
returns the log-probability the evidence, using as priors the posteriors of another object
- shiftedLogEvidenceProbabilityUsingGenotypeFrequencies(double[]) - Method in class picard.fingerprint.HaplotypeProbabilities
- SHORT_HOMOPOLYMER - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymer
- shortToByteArray(short) - Static method in class picard.arrays.illumina.InfiniumDataFile
-
Utility method to convert a short to a byte array
- shouldBeInLocations(ReadEndsForMateCigar) - Method in class picard.sam.markduplicates.util.MarkQueue
-
Returns true if we should track this for optical duplicate detection, false otherwise
- shouldIncludeInterval(long, double, long) - Method in class picard.util.IntervalList.IntervalListScattererWithoutSubdivision
- shouldIncludeInterval(long, double, long) - Method in class picard.util.IntervalList.IntervalListScattererWithoutSubdivisionWithOverflow
- Simple - Enum constant in enum class picard.util.BaitDesigner.DesignStrategy
-
Ultra simple bait design algorithm that just lays down baits starting at the target start position until either the bait start runs off the end of the target or the bait would run off the sequence
- SimpleErrorCalculator - Class in picard.sam.SamErrorMetric
-
A calculator that estimates the error rate of the bases it observes, assuming that the reference is truth.
- SimpleErrorCalculator() - Constructor for class picard.sam.SamErrorMetric.SimpleErrorCalculator
- SimpleMarkDuplicatesWithMateCigar - Class in picard.sam.markduplicates
-
This is a simple tool to mark duplicates using the DuplicateSetIterator, DuplicateSet, and SAMRecordDuplicateComparator.
- SimpleMarkDuplicatesWithMateCigar() - Constructor for class picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar
- SIMPLEX_CONSENSUS - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
-
Read which had multiple observations, but all from the same strand (or the strand could not be determined).
- SIMPLEX_SINGLETON - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
-
Read which only one observation is made.
- SINGLE_END - Enum constant in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- SingleBarcodeDistanceMetric - Class in picard.util
-
A class for finding the distance between a single barcode and a barcode-read (with base qualities)
- SingleBarcodeDistanceMetric(byte[], byte[], byte[], int, int) - Constructor for class picard.util.SingleBarcodeDistanceMetric
- SinglePassSamProgram - Class in picard.analysis
-
Super class that is designed to provide some consistent structure between subclasses that simply iterate once over a coordinate sorted BAM and collect information from the records as the go in order to produce some kind of output.
- SinglePassSamProgram() - Constructor for class picard.analysis.SinglePassSamProgram
- size() - Method in class picard.fingerprint.HaplotypeBlock
-
Returns the number of SNPs within the haplotype block.
- size() - Method in class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
- size() - Method in class picard.sam.markduplicates.util.MarkQueue
-
The number of records currently in this queue.
- size() - Method in class picard.sam.markduplicates.util.MemoryBasedReadEndsForMarkDuplicatesMap
- size() - Method in class picard.sam.markduplicates.util.PhysicalLocationForMateCigarSet
-
The number of records in this set
- size() - Method in interface picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap
- SIZE_OF - Static variable in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
- sizeInRam() - Method in class picard.sam.markduplicates.util.DiskBasedReadEndsForMarkDuplicatesMap
- sizeInRam() - Method in class picard.sam.markduplicates.util.MemoryBasedReadEndsForMarkDuplicatesMap
- sizeInRam() - Method in interface picard.sam.markduplicates.util.ReadEndsForMarkDuplicatesMap
- Skip - Static variable in enum class picard.illumina.parser.ReadType
- SKIP_CHROMS - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
- SKIP_MATE_VALIDATION - Variable in class picard.sam.ValidateSamFile
- skipEmptyFiles - Variable in class picard.illumina.parser.ParameterizedFileUtil
- skipRecords(int) - Method in class picard.illumina.parser.readers.FilterFileReader
- skipRecords(int) - Method in class picard.illumina.parser.readers.LocsFileReader
- skips - Variable in class picard.illumina.parser.ReadStructure
- Snp - Class in picard.fingerprint
-
Class to represent a SNP in context of a haplotype block that is used in fingerprinting.
- Snp(String, String, int, byte, byte, double, List<String>) - Constructor for class picard.fingerprint.Snp
- SNP - Enum constant in enum class picard.util.VariantType
- SNP - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The name of a representative SNP within the haplotype that was compared.
- SNP_ALLELES - Variable in class picard.analysis.FingerprintingDetailMetrics
-
The possible alleles for the SNP.
- SNP_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- SNP_OUTPUT - Variable in class picard.vcf.SplitVcfs
- SNP_REFERENCE_BIAS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The rate at which reference bases are observed at ref/alt heterozygous SNP sites.
- snpCounter - Variable in class picard.vcf.GenotypeConcordance
- snps - Variable in class picard.util.DbSnpBitSetUtil.DbSnpBitSets
- softClipsLengthStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies into the number of soft-clipped bases that the read has in its alignment, or -1 if not aligned.
- SORT - Variable in class picard.illumina.IlluminaBasecallsToFastq
- SORT - Variable in class picard.illumina.IlluminaBasecallsToSam
- SORT - Variable in class picard.util.BedToIntervalList
- SORT - Variable in class picard.util.IntervalListToBed
- SORT - Variable in class picard.util.IntervalListTools
- SORT_ORDER - Variable in class picard.sam.AddOrReplaceReadGroups
- SORT_ORDER - Variable in class picard.sam.FastqToSam
- SORT_ORDER - Variable in class picard.sam.FilterSamReads
- SORT_ORDER - Variable in class picard.sam.FixMateInformation
- SORT_ORDER - Variable in class picard.sam.MergeBamAlignment
- SORT_ORDER - Variable in class picard.sam.MergeSamFiles
- SORT_ORDER - Variable in class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar
- SORT_ORDER - Variable in class picard.sam.RevertSam
- SORT_ORDER - Variable in class picard.sam.SortSam
- SORT_ORDER_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- SortedBasecallsConverter<CLUSTER_OUTPUT_RECORD> - Class in picard.illumina
-
SortedBasecallsConverter utilizes an underlying IlluminaDataProvider to convert parsed and decoded sequencing data from standard Illumina formats to specific output records (FASTA records/SAM records).
- SortedBasecallsConverter(File, File, int[], ReadStructure, Map<String, ? extends Writer<CLUSTER_OUTPUT_RECORD>>, boolean, int, List<File>, int, Integer, Integer, Comparator<CLUSTER_OUTPUT_RECORD>, SortingCollection.Codec<CLUSTER_OUTPUT_RECORD>, Class<CLUSTER_OUTPUT_RECORD>, BclQualityEvaluationStrategy, boolean, boolean, boolean, AsyncWriterPool, BarcodeExtractor) - Constructor for class picard.illumina.SortedBasecallsConverter
-
Constructs a new SortedBaseCallsConverter.
- SortGff - Class in picard.annotation
-
Summary
- SortGff() - Constructor for class picard.annotation.SortGff
- SORTING_COLLECTION_SIZE_RATIO - Variable in class picard.sam.markduplicates.MarkDuplicates
- SortSam - Class in picard.sam
-
Sorts a SAM or BAM file.
- SortSam() - Constructor for class picard.sam.SortSam
- SortVcf - Class in picard.vcf
-
Sorts one or more VCF files according to the order of the contigs in the header/sequence dictionary and then by coordinate.
- SortVcf() - Constructor for class picard.vcf.SortVcf
- SOURCE - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- SOURCE - Variable in class picard.fingerprint.FingerprintMetrics
-
The originating file (if available) for this fingerprint
- SOURCE_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- SOURCE_SEQ_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- SOURCE_SEQUENCE_INVALID - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Source sequence is invalid (contains invalid character).
- SOURCE_SEQUENCE_MISMATCH - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Deprecated.- but used in existing extended manifest files.
- SOURCE_SEQUENCE_STRAND_INVALID - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Deprecated.- but used in existing extended manifest files.
- SOURCE_STRAND_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- SOURCE_VERSION_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- specialArgumentsCollection - Variable in class picard.cmdline.CommandLineProgram
- SPECIES - Variable in class picard.sam.CreateSequenceDictionary
- SPECIES_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- split(String, String[], String) - Method in class picard.Test
- SPLIT_TO_N_FILES - Variable in class picard.sam.SplitSamByNumberOfReads
- SPLIT_TO_N_READS - Variable in class picard.sam.SplitSamByNumberOfReads
- SplitSamByLibrary - Class in picard.sam
-
Command-line program to split a SAM/BAM/CRAM file into separate files based on library name.
- SplitSamByLibrary() - Constructor for class picard.sam.SplitSamByLibrary
- SplitSamByNumberOfReads - Class in picard.sam
-
Splits the input queryname sorted or query-grouped SAM/BAM/CRAM file and writes it into multiple BAM files, each with an approximately equal number of reads.
- SplitSamByNumberOfReads() - Constructor for class picard.sam.SplitSamByNumberOfReads
- SplitVcfs - Class in picard.vcf
-
Splits the input VCF file into two, one for indels and one for SNPs.
- SplitVcfs() - Constructor for class picard.vcf.SplitVcfs
- STANDARD_DEVIATION - Variable in class picard.analysis.InsertSizeMetrics
-
Standard deviation of insert sizes over the "core" of the distribution.
- StandardOptionDefinitions - Class in picard.cmdline
-
A set of String constants in which the name of the constant (minus the _SHORT_NAME suffix) is the standard long Option name, and the value of the constant is the standard shortName.
- StandardOptionDefinitions() - Constructor for class picard.cmdline.StandardOptionDefinitions
- start - Variable in class picard.annotation.Gene.Transcript.Exon
- start - Variable in class picard.illumina.parser.Range
- start() - Method in class picard.annotation.Gene.Transcript
- start() - Method in class picard.vcf.processor.VariantAccumulatorExecutor.MultiThreadedChunkBased
- start() - Method in interface picard.vcf.processor.VariantAccumulatorExecutor
-
Starts the work of the executor, returning immediately.
- start() - Method in class picard.vcf.processor.VcfFileSegment
-
Deprecated.
- start() - Method in class picard.vcf.processor.VcfPathSegment
- stddev(double[], double) - Static method in class picard.util.MathUtil
-
Calculated the standard deviation of an array of doubles.
- stddev(double[], int, int) - Static method in class picard.util.MathUtil
-
Calculated the standard deviation of an array of doubles.
- stddev(double[], int, int, double) - Static method in class picard.util.MathUtil
-
Calculated the standard deviation of an array of doubles.
- STDERR - Variable in class picard.arrays.BafRegressMetrics
-
The standard error of the estimate
- stop() - Method in class picard.vcf.processor.VcfFileSegment
-
Deprecated.
- stop() - Method in class picard.vcf.processor.VcfPathSegment
- STOP_AFTER - Variable in class picard.analysis.CollectMultipleMetrics
- STOP_AFTER - Variable in class picard.analysis.CollectOxoGMetrics
- STOP_AFTER - Variable in class picard.analysis.CollectWgsMetrics
- STOP_AFTER - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- STOP_AFTER - Variable in class picard.analysis.SinglePassSamProgram
- STOP_AFTER - Variable in class picard.sam.PositionBasedDownsampleSam
- STRAND - Enum constant in enum class picard.annotation.RefFlatReader.RefFlatColumns
- STRAND_BALANCE - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The number of PF reads aligned to the positive strand of the genome divided by the number of PF reads aligned to the genome.
- STRAND_SPECIFICITY - Variable in class picard.analysis.CollectRnaSeqMetrics
- STRATEGY - Variable in class picard.sam.DownsampleSam
- STRATIFIER_VALUE - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.CigarOperatorsInReadStratifier
- stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.ConsensusStratifier
- stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellTileStratifier
- stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellXStratifier
- stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellYStratifier
- stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.GCContentStratifier
- stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.IndelsInReadStratifier
-
Returns the number of bases associated with I and D CIGAR elements.
- stratify(SAMRecord) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.NsInReadStratifier
- stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.BinnedReadCycleStratifier
- stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.CollectionStratifier
- stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.IndelLengthStratifier
- stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymerStratifier
- stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.MismatchesInReadStratifier
- stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.PairStratifier
- stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.FlowCellXStratifier
- stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in interface picard.sam.SamErrorMetric.ReadBaseStratification.RecordAndOffsetStratifier
- stratify(SamLocusIterator.RecordAndOffset, SamLocusAndReferenceIterator.SAMLocusAndReference) - Method in class picard.sam.SamErrorMetric.ReadBaseStratification.IndelsInReadStratifier
- STRICT - Variable in class picard.vcf.SplitVcfs
- stringSeqsToString(String[], String) - Static method in class picard.util.IlluminaUtil
- STRIP_UNPAIRED_MATE_NUMBER - Variable in class picard.sam.FastqToSam
-
Deprecated.
- SUBDIVISION_MODE - Variable in class picard.util.IntervalListTools
- subsetAlleles(GenotypesContext, List<Allele>, List<Allele>) - Static method in class picard.util.AlleleSubsettingUtils
-
Create the new GenotypesContext with the subsetted PLs and ADs Expects allelesToKeep to be in the same order in which they are in originalAlleles.
- subsetAlleles(VariantContext, List<Allele>) - Static method in class picard.util.AlleleSubsettingUtils
- subsettedPLIndices(List<Allele>, List<Allele>) - Static method in class picard.util.AlleleSubsettingUtils
-
Given a list of original alleles and a subset of new alleles to retain, find the array of old PL indices that correspond to new PL indices i.e.
- subsetVCToMatchSnp(VariantContext, Snp) - Static method in class picard.util.AlleleSubsettingUtils
-
Method to subset the alleles in the VariantContext to those in the input snp.
- SUBSTITUTION - Variable in class picard.analysis.artifacts.ErrorSummaryMetrics
-
A single string representing the substition from REF_BASE to ALT_BASE for convenience.
- SUBSTITUTION_RATE - Variable in class picard.analysis.artifacts.ErrorSummaryMetrics
-
The rate of the substitution in question.
- Substructure(List<Integer>, List<Range>) - Constructor for class picard.illumina.parser.ReadStructure.Substructure
-
Indices into the ReadStructure.descriptors for this specific substructure, indices must be in the order they appear in the descriptors list (but the indices do NOT have to be continuous)
- SUBTRACT - Enum constant in enum class picard.util.IntervalListTools.Action
- subtractMax(double[]) - Static method in class picard.util.MathUtil
- sum(double...) - Method in class picard.util.MathUtil.LogMath
-
Computes the sum of the provided log values.
- sum(double[]) - Static method in class picard.util.MathUtil
-
Returns the sum of the elements in the array.
- sum(double[], double) - Static method in class picard.util.MathUtil
-
calculates the sum of an array and a double.
- sum(double[], double[]) - Static method in class picard.util.MathUtil
-
calculates the sum of the arrays as a third array.
- sum(long[], int, int) - Static method in class picard.util.MathUtil
-
Returns the sum of the elements in the array starting with start and ending before stop.
- SUMMARY - Enum constant in enum class picard.sam.ValidateSamFile.Mode
- SUMMARY - Variable in class picard.metrics.GcBiasMetrics
- SUMMARY_FILE_EXTENSION - Static variable in class picard.analysis.CollectRrbsMetrics
- SUMMARY_METRICS_FILE_EXTENSION - Static variable in class picard.vcf.GenotypeConcordance
- SUMMARY_OUTPUT - Variable in class picard.analysis.CollectGcBiasMetrics
- SUMMARY_OUTPUT - Variable in class picard.fingerprint.CheckFingerprint
- summaryMetricsExtension - Static variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics
- SUPPORTED_BUILD - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- SUPPORTED_CHAIN_FILE - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- SUPPORTED_REFERENCE_FILE - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- supportedTypes() - Method in class picard.illumina.parser.MultiTileBclParser
- supportedTypes() - Method in class picard.illumina.parser.PerTileParser
-
The DataTypes that this parser can provide
- supportedTypes() - Method in class picard.illumina.parser.MultiTileParser
- supportedTypes() - Method in class picard.illumina.parser.PosParser
- supportsMetricAccumulationLevel() - Method in interface picard.analysis.CollectMultipleMetrics.ProgramInterface
- swapAlleles(VariantContext, Allele, Allele) - Static method in class picard.util.AlleleSubsettingUtils
-
Swaps one of the alleles in a VC (and its genotypes) with another.
- SWAPPED_ALLELES - Static variable in class picard.util.LiftoverUtils
-
Attribute used to store the fact that the alt and ref alleles of the variant have been swapped, while all the INFO annotations have not.
- swapRefAlt(VariantContext, Collection<String>, Collection<String>) - Static method in class picard.util.LiftoverUtils
-
method to swap the reference and alt alleles of a bi-allelic, SNP
- SYMDIFF - Enum constant in enum class picard.util.IntervalListTools.Action
- SYNTAX_TRANSITION_URL - Static variable in class picard.cmdline.CommandLineProgram
- SYNTHETIC_PHASESET_PREFIX - Static variable in class picard.fingerprint.HaplotypeMap
T
- T - Enum constant in enum class picard.analysis.artifacts.Transition.Base
- T - Enum constant in enum class picard.illumina.parser.IntensityChannel
- T - Enum constant in enum class picard.illumina.parser.ReadType
- TAB_MODE - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
- TabbedInputParser - Class in picard.util
-
Parser for tab-delimited files
- TabbedInputParser(boolean, File...) - Constructor for class picard.util.TabbedInputParser
-
Constructor
- TabbedInputParser(boolean, InputStream...) - Constructor for class picard.util.TabbedInputParser
-
Constructor
- TabbedTextFileWithHeaderParser - Class in picard.util
-
Parse a tabbed text file in which columns are found by looking at a header line rather than by position.
- TabbedTextFileWithHeaderParser(File) - Constructor for class picard.util.TabbedTextFileWithHeaderParser
- TabbedTextFileWithHeaderParser(File, String[]) - Constructor for class picard.util.TabbedTextFileWithHeaderParser
- TabbedTextFileWithHeaderParser(TabbedInputParser) - Constructor for class picard.util.TabbedTextFileWithHeaderParser
- TabbedTextFileWithHeaderParser.Row - Class in picard.util
- TAG - Variable in class picard.sam.FilterSamReads
- TAG_DUPLICATE_SET_MEMBERS - Variable in class picard.sam.markduplicates.MarkDuplicates
- TAG_GROUP_SEPERATOR - Variable in class picard.sam.SamToFastqWithTags
- TAG_PER_MOLECULAR_INDEX - Variable in class picard.illumina.IlluminaBasecallsToSam
- TAG_VALUE - Variable in class picard.sam.FilterSamReads
- TAGGING_POLICY - Variable in class picard.sam.markduplicates.MarkDuplicates
- TAGS_TO_DROP - Variable in class picard.vcf.LiftoverVcf
- TAGS_TO_REVERSE - Variable in class picard.vcf.LiftoverVcf
- TAIL_LIMIT - Variable in class picard.analysis.CollectJumpingLibraryMetrics
- takeSome(Interval, long, long, double) - Method in interface picard.util.IntervalList.IntervalListScatterer
-
Figure out how much of the input interval to put into current list and how much to leave for the next interval list.
- takeSome(Interval, long, long, double) - Method in class picard.util.IntervalList.IntervalListScattererByIntervalCount
- takeSome(Interval, long, long, double) - Method in class picard.util.IntervalList.IntervalListScattererByIntervalCountWithDistributedRemainder
- takeSome(Interval, long, long, double) - Method in class picard.util.IntervalList.IntervalListScattererWithoutSubdivision
- takeSome(Interval, long, long, double) - Method in class picard.util.IntervalList.IntervalListScattererWithSubdivision
- TANDEM_READS - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- TARGET_BUILD - Variable in class picard.arrays.illumina.CreateExtendedIlluminaManifest
- TARGET_INTERVALS - Variable in class picard.analysis.directed.CollectTargetedMetrics
- TARGET_INTERVALS - Variable in class picard.vcf.CollectVariantCallingMetrics
- TARGET_TERRITORY - Variable in class picard.analysis.directed.PanelMetricsBase
-
The number of unique bases covered by the intervals of all targets that should be covered
- TargetedPcrMetrics - Class in picard.analysis.directed
-
Metrics class for the analysis of reads obtained from targeted pcr experiments e.g.
- TargetedPcrMetrics() - Constructor for class picard.analysis.directed.TargetedPcrMetrics
- TargetedPcrMetricsCollector - Class in picard.analysis.directed
-
Calculates HS metrics for a given SAM or BAM file.
- TargetedPcrMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, boolean, boolean, int, int) - Constructor for class picard.analysis.directed.TargetedPcrMetricsCollector
- TargetedPcrMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, int, int) - Constructor for class picard.analysis.directed.TargetedPcrMetricsCollector
- TargetMetrics - Class in picard.analysis.directed
-
TargetMetrics, are metrics to measure how well we hit specific targets (or baits) when using a targeted sequencing process like hybrid selection or Targeted PCR Techniques (TSCA).
- TargetMetrics() - Constructor for class picard.analysis.directed.TargetMetrics
- TargetMetricsBase - Class in picard.analysis.directed
-
TargetMetrics, are metrics to measure how well we hit specific targets (or baits) when using a targeted sequencing process like hybrid selection or Targeted PCR Techniques (TSCA).
- TargetMetricsBase() - Constructor for class picard.analysis.directed.TargetMetricsBase
- TargetMetricsCollector<METRIC_TYPE extends MultilevelMetrics> - Class in picard.analysis.directed
-
TargetMetrics, are metrics to measure how well we hit specific targets (or baits) when using a targeted sequencing process like hybrid selection or Targeted PCR Techniques (TSCA).
- TargetMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, boolean, boolean, int, int) - Constructor for class picard.analysis.directed.TargetMetricsCollector
- TargetMetricsCollector(Set<MetricAccumulationLevel>, List<SAMReadGroupRecord>, ReferenceSequenceFile, File, File, IntervalList, IntervalList, String, int, int, int, boolean, int, int) - Constructor for class picard.analysis.directed.TargetMetricsCollector
- TargetMetricsCollector.Coverage - Class in picard.analysis.directed
-
A simple class that is used to store the coverage information about an interval.
- TargetMetricsCollector.PerUnitTargetMetricCollector - Class in picard.analysis.directed
-
Collect the Target Metrics for one unit of "accumulation" (i.e.
- TARGETS - Variable in class picard.util.BaitDesigner
- Template - Static variable in enum class picard.illumina.parser.ReadType
- templates - Variable in class picard.illumina.parser.ReadStructure
- Test - Class in picard
- Test() - Constructor for class picard.Test
- TEST_INPUT_READABILITY - Variable in class picard.fingerprint.CalculateFingerprintMetrics
- TEST_INPUT_READABILITY - Variable in class picard.fingerprint.CrosscheckFingerprints
- TEST_INPUT_READABILITY - Variable in class picard.fingerprint.ExtractFingerprint
- TEST_INPUT_READABILITY - Variable in class picard.fingerprint.IdentifyContaminant
- Testing - Class in picard.cmdline.programgroups
-
For internal test purposes only.
- Testing() - Constructor for class picard.cmdline.programgroups.Testing
- THEORETICAL_SENSITIVITY - Variable in class picard.analysis.TheoreticalSensitivityMetrics
-
Estimation of sensitivity at a particular allele fraction.
- THEORETICAL_SENSITIVITY_OUTPUT - Variable in class picard.analysis.CollectWgsMetrics
- THEORETICAL_SENSITIVITY_OUTPUT - Variable in class picard.analysis.directed.CollectTargetedMetrics
- THEORETICAL_SENSITIVITY_Q - Variable in class picard.analysis.TheoreticalSensitivityMetrics
-
Phred-scaled value of 1-THEORETICAL_SENSITIVITY.
- theoreticalHetSensitivitySampleSize - Variable in class picard.analysis.WgsMetrics
-
The sample size used for theoretical het sensitivity.
- theoreticalSensitivity(Histogram<Integer>, Histogram<Integer>, int, double, double) - Static method in class picard.analysis.TheoreticalSensitivity
-
Calculates the theoretical sensitivity with a given Phred-scaled quality score distribution and depth distribution.
- TheoreticalSensitivity - Class in picard.analysis
-
Created by David Benjamin on 5/13/15.
- TheoreticalSensitivity() - Constructor for class picard.analysis.TheoreticalSensitivity
- TheoreticalSensitivity.RouletteWheel - Class in picard.analysis
- TheoreticalSensitivityMetrics - Class in picard.analysis
-
TheoreticalSensitivityMetrics, are metrics calculated from TheoreticalSensitivity and parameters used in the calculation.
- TheoreticalSensitivityMetrics() - Constructor for class picard.analysis.TheoreticalSensitivityMetrics
- THETA - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- thetaIlmn - Variable in class picard.arrays.illumina.InfiniumGTCRecord
- THREAD_COUNT - Variable in class picard.vcf.CollectVariantCallingMetrics
- THREAD_COUNT - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
- ThreadPoolExecutorUtil - Class in picard.util
- ThreadPoolExecutorUtil() - Constructor for class picard.util.ThreadPoolExecutorUtil
- ThreadPoolExecutorWithExceptions - Class in picard.util
-
This version of the thread pool executor will throw an exception if any of the internal jobs have throw exceptions while executing
- ThreadPoolExecutorWithExceptions(int) - Constructor for class picard.util.ThreadPoolExecutorWithExceptions
-
Creates a fixed size thread pool executor that will rethrow exceptions from submitted jobs.
- THREE - Enum constant in enum class picard.illumina.parser.readers.TileMetricsOutReader.TileMetricsVersion
- THREE_PRIME_ADAPTER - Variable in class picard.illumina.IlluminaBasecallsToFastq
- THREE_PRIME_ADAPTER - Variable in class picard.illumina.IlluminaBasecallsToSam
- THREE_PRIME_ADAPTER - Variable in class picard.illumina.MarkIlluminaAdapters
- THREE_PRIME_SEQUENCE - Static variable in class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecordCreator
- THREE_WAYS_DISAGREEMENT_ONLY_Q - Variable in class picard.sam.SamErrorMetric.OverlappingErrorMetric
-
The (phred) rate of bases that disagree with both the reference and their mate (which also disagree)
- tile - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
-
The tile, which is determined from the file name
- tile - Variable in class picard.sam.util.PhysicalLocationInt
- Tile - Class in picard.illumina.parser
-
Represents a tile from TileMetricsOut.bin.
- Tile(int, int, float, float, TilePhasingValue...) - Constructor for class picard.illumina.parser.Tile
- TILE - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
-
The Tile that is described by this metric
- TILE - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailSummaryMetric
-
The Tile that is described by this metric.
- TILE_LIMIT - Variable in class picard.illumina.IlluminaBasecallsToFastq
- TILE_LIMIT - Variable in class picard.illumina.IlluminaBasecallsToSam
- TILE_METRICS_OUT_FILE_NAME - Static variable in class picard.illumina.parser.TileMetricsUtil
-
The expected name of the tile metrics output file.
- TILE_NUMBER_COMPARATOR - Static variable in class picard.illumina.BasecallsConverter
-
A comparator used to sort Illumina tiles in their proper order.
- TILE_NUMBERS - Variable in class picard.illumina.CheckIlluminaDirectory
- tileIndex - Variable in class picard.illumina.parser.MultiTileFileUtil
- TileIndex - Class in picard.illumina.parser
-
Load a file containing 8-byte records like this: tile number: 4-byte int number of clusters in tile: 4-byte int Number of records to read is determined by reaching EOF.
- TileIndex.TileIndexRecord - Class in picard.illumina.parser
- tileIsSet() - Method in class picard.illumina.parser.ClusterData
- tileLimit(Integer) - Method in class picard.illumina.BasecallsConverterBuilder
-
Configures the total number of tiles that the converter will process.
- tileMetricsOut() - Method in class picard.illumina.parser.IlluminaFileUtil
- TileMetricsOutReader - Class in picard.illumina.parser.readers
-
Reads a TileMetricsOut file commonly found in the InterOp directory of an Illumina Run Folder.
- TileMetricsOutReader(File) - Constructor for class picard.illumina.parser.readers.TileMetricsOutReader
-
Return a TileMetricsOutReader for the specified file
- TileMetricsOutReader.IlluminaLaneTileCode - Class in picard.illumina.parser.readers
-
Helper class which captures the combination of a lane, tile & metric code
- TileMetricsOutReader.IlluminaTileMetrics - Class in picard.illumina.parser.readers
-
IlluminaPhasingMetrics corresponds to a single record in a TileMetricsOut file
- TileMetricsOutReader.TileMetricsVersion - Enum Class in picard.illumina.parser.readers
- TileMetricsUtil - Class in picard.illumina.parser
-
Utility for reading the tile data from an Illumina run directory's TileMetricsOut.bin file
- TileMetricsUtil() - Constructor for class picard.illumina.parser.TileMetricsUtil
- TilePhasingValue - Class in picard.illumina.parser
-
Captures information about a phasing value - Which read it corresponds to, which phasing type and a median value
- TilePhasingValue(TileTemplateRead, float, float) - Constructor for class picard.illumina.parser.TilePhasingValue
- tiles - Variable in class picard.illumina.BasecallsConverter
- tiles - Variable in class picard.illumina.parser.ParameterizedFileUtil
- TileTemplateRead - Enum Class in picard.illumina.parser
-
Defines the first or second template read for a tile
- TMP_DIR - Variable in class picard.cmdline.CommandLineProgram
- TN - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.ContingencyState
- TN_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
-
The TN (true negative) count across all variants
- TN_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
- TN_ONLY - Static variable in class picard.vcf.GenotypeConcordanceScheme
- toCode() - Method in enum class picard.pedigree.Sex
-
Returns the code used to encode this sex in a ped/fam file.
- TOP - Enum constant in enum class picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
- TOP_GENOMIC_SEQ_HEADER_NAME - Static variable in class picard.arrays.illumina.IlluminaManifest
- toPath() - Method in class picard.nio.PicardHtsPath
-
Resolve the URI of this object to a
Path
object. - toPaths(Collection<PicardHtsPath>) - Static method in class picard.nio.PicardHtsPath
-
Create a
List<Path>
fromPicardHtsPath
s - toReadStructure() - Method in class picard.illumina.parser.ReadStructure.Substructure
-
Create a ReadStructure from this substructure composed of only the descriptors contained in this substructure, Any ReadDescriptors not in this substructure are treated as if they don't exist (e.g.
- toString() - Method in enum class picard.analysis.artifacts.Transition
- toString() - Method in class picard.analysis.directed.TargetMetricsCollector.Coverage
- toString() - Method in class picard.arrays.illumina.ArraysControlInfo
- toString() - Method in class picard.arrays.illumina.IlluminaManifestRecord
- toString() - Method in class picard.fingerprint.HaplotypeBlock
- toString() - Method in class picard.fingerprint.Snp
- toString() - Method in class picard.illumina.IlluminaBasecallingMetrics
- toString() - Method in class picard.illumina.parser.ClusterData
- toString() - Method in class picard.illumina.parser.Range
- toString() - Method in class picard.illumina.parser.ReadDescriptor
- toString() - Method in class picard.illumina.parser.ReadStructure
-
Converts this object into a String using rules complementary to the single string constructor above.
- toString() - Method in class picard.sam.markduplicates.util.ReadEndsForMarkDuplicates
- toString() - Method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ReadDirection
- toString() - Method in class picard.sam.util.Pair
- toString() - Method in class picard.vcf.processor.VcfFileSegment
-
Deprecated.
- toString() - Method in class picard.vcf.processor.VcfPathSegment
- toSymbol() - Method in enum class picard.pedigree.Sex
-
Returns the single-character symbol used to encode sex in a VCF file
- TOTAL_BASES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The total number of basecalls observed at all sites.
- TOTAL_BASES - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The total number of bases in all reads
- TOTAL_BASES - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The total number of bases assigned to the index.
- TOTAL_BASES - Variable in class picard.sam.SamErrorMetric.ErrorMetric
-
The total number of bases included in the calculation of this metric
- TOTAL_CLUSTERS - Variable in class picard.analysis.GcBiasSummaryMetrics
-
The total number of clusters that were seen in the gc bias calculation.
- TOTAL_CLUSTERS - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The total number of clusters assigned to the index.
- TOTAL_COMPLEX_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of passing complex indel calls that were examined
- TOTAL_GQ0_VARIANTS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
-
The total number of variants in a particular sample that have a GQ score of 0.
- TOTAL_HET_DEPTH - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
-
total number of reads (from AD field) for passing bi-allelic SNP hets for this sample
- TOTAL_INDELS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of passing indel calls that were examined
- TOTAL_MENDELIAN_VIOLATIONS - Variable in class picard.vcf.MendelianViolations.MendelianViolationMetrics
-
The total of all mendelian violations observed.
- TOTAL_MULTIALLELIC_SNPS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of passing multi-allelic SNP calls that were examined
- TOTAL_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
The total Phred-scaled Q-score for this artifact.
- TOTAL_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
The total Phred-scaled Q-score for this artifact.
- TOTAL_READS - Variable in class picard.analysis.AlignmentSummaryMetrics
-
The total number of reads including all PF and non-PF reads.
- TOTAL_READS - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
-
The total number of reads in the input file
- TOTAL_READS - Variable in class picard.analysis.directed.PanelMetricsBase
-
The total number of reads in the SAM or BAM file examined.
- TOTAL_READS - Variable in class picard.illumina.IlluminaBasecallingMetrics
-
The total number of reads assigned to the index.
- TOTAL_READS_IN_INPUT - Variable in class picard.sam.SplitSamByNumberOfReads
- TOTAL_SITES - Variable in class picard.analysis.CollectOxoGMetrics.CpcgMetrics
-
The total number of sites that had at least one base covering them.
- TOTAL_SITES - Variable in class picard.analysis.RrbsCpgDetailMetrics
-
Number of times this CpG site was encountered
- TOTAL_SNPS - Variable in class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
-
The number of passing bi-allelic SNPs calls (i.e.
- totalCycles - Variable in class picard.illumina.parser.ReadStructure
- totalScore - Variable in class picard.arrays.illumina.InfiniumEGTFile
- TP - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.ContingencyState
- TP_COUNT - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
-
The TP (true positive) count across all variants
- TP_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
- TP_FP - Static variable in class picard.vcf.GenotypeConcordanceScheme
- TP_FP_FN - Static variable in class picard.vcf.GenotypeConcordanceScheme
- TP_ONLY - Static variable in class picard.vcf.GenotypeConcordanceScheme
- TP_TN - Static variable in class picard.vcf.GenotypeConcordanceScheme
- trackOpticalDuplicates(List<? extends ReadEnds>, ReadEnds, OpticalDuplicateFinder, LibraryIdGenerator) - Static method in class picard.sam.markduplicates.util.AbstractMarkDuplicatesCommandLineProgram
-
Looks through the set of reads and identifies how many of the duplicates are in fact optical duplicates, and stores the data in the instance level histogram.
- Transcript(String, int, int, int, int, int) - Constructor for class picard.annotation.Gene.Transcript
- TRANSCRIPT_NAME - Enum constant in enum class picard.annotation.RefFlatReader.RefFlatColumns
- transcriptionEnd - Variable in class picard.annotation.Gene.Transcript
- transcriptionStart - Variable in class picard.annotation.Gene.Transcript
- Transition - Enum Class in picard.analysis.artifacts
-
Enum representation of a transition from one base to any other.
- Transition.Base - Enum Class in picard.analysis.artifacts
- transitionOf(char, char) - Static method in enum class picard.analysis.artifacts.Transition
-
Gets a the enum representing the transition from a 'reference' to a 'call' base.
- TRIALLELIC - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- TRIMMING_QUALITY - Variable in class picard.illumina.IlluminaBasecallsToFastq
- TRIOS - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
- triSiteHeterogeneityRate - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
the rate of heterogeneity within tripleton sets
- triSiteHomogeneityRate - Variable in class picard.analysis.replicates.IndependentReplicateMetric
-
the rate of homogeneity within tripleton sets.
- TRUNCATE_NAMES_AT_WHITESPACE - Variable in class picard.sam.CreateSequenceDictionary
- TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE - Variable in class picard.reference.NormalizeFasta
- TRUSEQ_SMALLRNA - Enum constant in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
- TRUTH_SAMPLE - Variable in class picard.vcf.GenotypeConcordance
- TRUTH_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
-
The name of the 'truth' sample
- TRUTH_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
-
The name of the 'truth' sample
- TRUTH_SAMPLE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The name of the 'truth' sample
- TRUTH_STATE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
-
The state of the 'truth' sample (i.e.
- TRUTH_VCF - Variable in class picard.vcf.GenotypeConcordance
- truthAllele1 - Variable in class picard.vcf.GenotypeConcordance.Alleles
- truthAllele2 - Variable in class picard.vcf.GenotypeConcordance.Alleles
- truthAlleles() - Method in class picard.vcf.GenotypeConcordance.Alleles
- TruthAndCallStates(GenotypeConcordanceStates.TruthState, GenotypeConcordanceStates.CallState) - Constructor for class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
- truthState - Variable in class picard.vcf.GenotypeConcordanceStates.TruthAndCallStates
- TT - Enum constant in enum class picard.fingerprint.DiploidGenotype
- TtoA - Enum constant in enum class picard.analysis.artifacts.Transition
- TtoC - Enum constant in enum class picard.analysis.artifacts.Transition
- TtoG - Enum constant in enum class picard.analysis.artifacts.Transition
- TtoT - Enum constant in enum class picard.analysis.artifacts.Transition
- TVAL - Variable in class picard.arrays.BafRegressMetrics
-
The test statistic for the estimate
- TWO - Enum constant in enum class picard.illumina.parser.readers.TileMetricsOutReader.TileMetricsVersion
- twoBasePaddedContextStratifier - Static variable in class picard.sam.SamErrorMetric.ReadBaseStratification
-
Stratifies into the two base context of the base, which includes two read-bases on each side and the reference base from where the current base is the bases will be reverse-complemented so that the bases are in the original order they were read from the sequencer
- TX_END - Enum constant in enum class picard.annotation.RefFlatReader.RefFlatColumns
- TX_START - Enum constant in enum class picard.annotation.RefFlatReader.RefFlatColumns
- type - Variable in class picard.illumina.parser.ReadDescriptor
- TYPE_NAME - Variable in class picard.illumina.IlluminaPhasingMetrics
-
Defines an Illumina template read number (first or second)
U
- uByteToInt(byte) - Static method in class picard.util.UnsignedTypeUtil
-
Convert an unsigned byte to a signed int
- uByteToShort(byte) - Static method in class picard.util.UnsignedTypeUtil
-
Convert an unsigned byte to a signed short
- uIntToFloat(int) - Static method in class picard.util.UnsignedTypeUtil
- uIntToLong(int) - Static method in class picard.util.UnsignedTypeUtil
-
Convert an unsigned int to a long
- UMI_BASE_QUALITIES - Variable in class picard.sam.markduplicates.UmiMetrics
-
Estimation of Phred scaled quality scores for UMIs
- UMI_METRICS_FILE - Variable in class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
- UMI_TAG_NAME - Variable in class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
- UmiAwareMarkDuplicatesWithMateCigar - Class in picard.sam.markduplicates
-
This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA.
- UmiAwareMarkDuplicatesWithMateCigar() - Constructor for class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar
- UmiGraph - Class in picard.sam.markduplicates
-
UmiGraph is used to identify UMIs that come from the same original source molecule.
- UmiMetrics - Class in picard.sam.markduplicates
-
Metrics that are calculated during the process of marking duplicates within a stream of SAMRecords using the UmiAwareDuplicateSetIterator.
- UmiMetrics() - Constructor for class picard.sam.markduplicates.UmiMetrics
- UmiMetrics(String) - Constructor for class picard.sam.markduplicates.UmiMetrics
- UmiMetrics(String, double, int, int, int, int, int, double, double, double, double) - Constructor for class picard.sam.markduplicates.UmiMetrics
- Unaligned - Enum constant in enum class picard.sam.ViewSam.AlignmentStatus
- UNEXPECTED_MATCH - Enum constant in enum class picard.fingerprint.CrosscheckMetric.FingerprintResult
- UNEXPECTED_MISMATCH - Enum constant in enum class picard.fingerprint.CrosscheckMetric.FingerprintResult
- unfilteredBaseQHistogram - Variable in class picard.analysis.WgsMetrics
-
The count of bases observed with a given base quality.
- unfilteredBaseQHistogramArray - Variable in class picard.analysis.AbstractWgsMetricsCollector
-
Count of bases observed with a given base quality.
- unfilteredDepthHistogram - Variable in class picard.analysis.WgsMetrics
-
Count of sites with a given depth of coverage.
- unfilteredDepthHistogramArray - Variable in class picard.analysis.AbstractWgsMetricsCollector
-
Count of sites with a given depth of coverage.
- UNION - Enum constant in enum class picard.util.IntervalListTools.Action
- UNIQUE - Variable in class picard.util.BedToIntervalList
- UNIQUE - Variable in class picard.util.IntervalListTools
- Unknown - Enum constant in enum class picard.pedigree.Sex
- UNKNOWN - Enum constant in enum class picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
- UNKNOWN - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
-
Read whose consensus status cannot be determined.
- UNKNOWN - Enum constant in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
- UNKNOWN - Static variable in class picard.metrics.MultiLevelCollector
- UNKNOWN_SEX - Static variable in class picard.pedigree.PedFile
- UNMAP_CONTAMINANT_READS - Variable in class picard.sam.MergeBamAlignment
- UNMAPPED_BAM - Variable in class picard.sam.MergeBamAlignment
- UNMAPPED_BOTH - Enum constant in enum class picard.sam.util.SamComparison.AlignmentComparison
- UNMAPPED_BOTH - Variable in class picard.sam.SamComparisonMetric
-
The number of primary records which are not mapped in either file.
- UNMAPPED_LEFT - Enum constant in enum class picard.sam.util.SamComparison.AlignmentComparison
- UNMAPPED_LEFT - Variable in class picard.sam.SamComparisonMetric
-
The number of primary records which are mapped in right file and found but not mapped in left file
- UNMAPPED_READ_STRATEGY - Variable in class picard.sam.MergeBamAlignment
- UNMAPPED_READS - Variable in class picard.sam.DuplicationMetrics
-
The total number of unmapped reads examined.
- UNMAPPED_RIGHT - Enum constant in enum class picard.sam.util.SamComparison.AlignmentComparison
- UNMAPPED_RIGHT - Variable in class picard.sam.SamComparisonMetric
-
The number of primary records which are mapped in left file and found but not mapped in right file
- UNPAIRED - Enum constant in enum class picard.analysis.AlignmentSummaryMetrics.Category
- UNPAIRED_DUP_RATE_WITH_TLEN - Variable in class picard.sam.FlowBasedDuplicationMetrics
-
The fraction of duplicated reads out of all reads with exact fragment length known
- UNPAIRED_DUP_RATE_WITHOUT_TLEN - Variable in class picard.sam.FlowBasedDuplicationMetrics
-
The fraction of duplicated reads out of all reads with exact fragment length unknown
- UNPAIRED_DUPS_WITH_TLEN - Variable in class picard.sam.FlowBasedDuplicationMetrics
- UNPAIRED_DUPS_WITHOUT_TLEN - Variable in class picard.sam.FlowBasedDuplicationMetrics
- UNPAIRED_END_UNCERTAINTY - Variable in class picard.sam.markduplicates.MarkDuplicatesForFlowArgumentCollection
- UNPAIRED_FASTQ - Variable in class picard.sam.SamToFastq
- UNPAIRED_READ_DUPLICATES - Variable in class picard.sam.DuplicationMetrics
-
The number of fragments that were marked as duplicates.
- UNPAIRED_READS_EXAMINED - Variable in class picard.sam.DuplicationMetrics
-
The number of mapped reads examined which did not have a mapped mate pair, either because the read is unpaired, or the read is paired to an unmapped mate.
- UNPAIRED_WITH_TLEN - Variable in class picard.sam.FlowBasedDuplicationMetrics
- unsafeNextInfo() - Method in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader
-
Returns the next position info.
- unsafeNextInfo() - Method in class picard.illumina.parser.readers.ClocsFileReader
-
Grab the next set of offset values, decompress them.
- unsafeNextInfo() - Method in class picard.illumina.parser.readers.LocsFileReader
- unsafeNextInfo() - Method in class picard.illumina.parser.readers.PosFileReader
-
Read a line of text and parse it into two float values, create a PositionInfo and return it
- UnsignedTypeUtil - Class in picard.util
-
A utility class for dealing with unsigned types.
- UnsignedTypeUtil() - Constructor for class picard.util.UnsignedTypeUtil
- UnsortedBasecallsConverter<CLUSTER_OUTPUT_RECORD> - Class in picard.illumina
-
UnortedBasecallsConverter utilizes an underlying IlluminaDataProvider to convert parsed and decoded sequencing data from standard Illumina formats to specific output records (FASTA records/SAM records).
- UnsortedBasecallsConverter(File, File, int[], ReadStructure, Map<String, ? extends Writer<CLUSTER_OUTPUT_RECORD>>, boolean, Integer, Integer, BclQualityEvaluationStrategy, boolean, boolean, boolean, AsyncWriterPool, BarcodeExtractor, Integer) - Constructor for class picard.illumina.UnsortedBasecallsConverter
-
Constructs a new BasecallsConverter object.
- UNSUPPORTED_GENOME_BUILD - Enum constant in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
- updateCigarForTrimmedOrClippedBases(SAMRecord, SAMRecord) - Method in class picard.sam.AbstractAlignmentMerger
- updateMetric(SamComparison.AlignmentComparison) - Method in class picard.sam.SamComparisonMetric
- updateMetrics(Map<String, BarcodeMetric>, BarcodeMetric) - Method in class picard.illumina.BasecallsConverter
- UpdateVcfSequenceDictionary - Class in picard.vcf
-
Takes a VCF file and a Sequence Dictionary (from a variety of file types) and updates the Sequence Dictionary in VCF.
- UpdateVcfSequenceDictionary() - Constructor for class picard.vcf.UpdateVcfSequenceDictionary
- URI - Variable in class picard.sam.CreateSequenceDictionary
- USAGE - Static variable in class picard.illumina.IlluminaBasecallsToSam
- USAGE - Variable in class picard.sam.ViewSam
- USAGE_SUMMARY - Static variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- USE_END_IN_UNPAIRED_READS - Variable in class picard.sam.markduplicates.MarkDuplicatesForFlowArgumentCollection
- USE_FAST_ALGORITHM - Variable in class picard.analysis.CollectWgsMetrics
- USE_FIRST - Enum constant in enum class picard.vcf.VcfToIntervalList.VARIANT_ID_TYPES
- USE_JDK_DEFLATER - Variable in class picard.cmdline.CommandLineProgram
- USE_JDK_INFLATER - Variable in class picard.cmdline.CommandLineProgram
- USE_OQ - Variable in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- USE_OQ - Variable in class picard.analysis.CollectOxoGMetrics
- USE_ORIGINAL_QUALITIES - Variable in class picard.analysis.CollectQualityYieldMetrics
- USE_ORIGINAL_QUALITIES_SHORT_NAME - Static variable in class picard.cmdline.StandardOptionDefinitions
- USE_SEQUENTIAL_FASTQS - Variable in class picard.sam.FastqToSam
- USE_THREADING - Variable in class picard.sam.MergeSamFiles
- USE_UNPAIRED_CLIPPED_END - Variable in class picard.sam.markduplicates.MarkDuplicatesForFlowArgumentCollection
- USE_VCF_INDEX - Variable in class picard.vcf.GenotypeConcordance
- useLegacyParser() - Static method in class picard.cmdline.CommandLineProgram
-
Return true if the legacy Picard command line parser should be used in place of the Barclay command line parser, otherwise, false.
- useOriginalQualities - Variable in class picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
- usesNoRefReads() - Method in class picard.analysis.artifacts.CollectSequencingArtifactMetrics
- usesNoRefReads() - Method in class picard.analysis.CollectInsertSizeMetrics
- usesNoRefReads() - Method in class picard.analysis.CollectQualityYieldMetrics
-
Ensure that we get all reads regardless of alignment status.
- usesNoRefReads() - Method in class picard.analysis.SinglePassSamProgram
-
Can be overridden and set to false if the section of unmapped reads at the end of the file isn't needed.
- usesNoRefReads() - Method in class picard.sam.markduplicates.CollectDuplicateMetrics
- uShortToInt(short) - Static method in class picard.util.UnsignedTypeUtil
-
Convert an unsigned short to an Int
- UTR - Enum constant in enum class picard.annotation.LocusFunction
- UTR_BASES - Variable in class picard.analysis.RnaSeqMetrics
-
Number of bases in primary alignments that align to a UTR base for some gene, and not a coding base.
V
- VALID_ALLELES - Static variable in class picard.arrays.illumina.IlluminaManifest
- VALIDATE_INDEX - Variable in class picard.sam.ValidateSamFile
- validateCountsAgainstScheme(GenotypeConcordanceScheme) - Method in class picard.vcf.GenotypeConcordanceCounts
-
Validates that there are no counts for NA states in the underlying scheme
- ValidateSamFile - Class in picard.sam
-
This tool reports on the validity of a SAM or BAM file relative to the SAM format specification.
- ValidateSamFile() - Constructor for class picard.sam.ValidateSamFile
- ValidateSamFile.Mode - Enum Class in picard.sam
- validateScheme() - Method in class picard.vcf.GenotypeConcordanceScheme
-
Check that all cells in the scheme exist.
- VALIDATION_STRINGENCY - Variable in class picard.cmdline.CommandLineProgram
- value - Variable in enum class picard.arrays.illumina.IlluminaGenotype
- VALUE1 - Variable in class picard.analysis.CompareMetrics.MetricComparisonDifferences
- VALUE2 - Variable in class picard.analysis.CompareMetrics.MetricComparisonDifferences
- valueOf(String) - Static method in enum class picard.analysis.AlignmentSummaryMetrics.Category
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.analysis.artifacts.Transition.Base
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.analysis.artifacts.Transition
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.analysis.CollectMultipleMetrics.Program
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.analysis.MetricAccumulationLevel
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.annotation.LocusFunction
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.annotation.RefFlatReader.RefFlatColumns
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.arrays.illumina.IlluminaGenotype
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.arrays.illumina.InfiniumVcfFields.GENOTYPE_VALUES
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.fingerprint.CrosscheckMetric.DataType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.fingerprint.CrosscheckMetric.FingerprintResult
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.fingerprint.DiploidGenotype
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.fingerprint.DiploidHaplotype
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.fingerprint.HaplotypeProbabilities.Genotype
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.illumina.DistanceMetric
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.illumina.IlluminaBasecallsToFastq.ReadNameFormat
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.illumina.parser.IlluminaDataType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.illumina.parser.IlluminaMetricsCode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.illumina.parser.IntensityChannel
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.illumina.parser.readers.TileMetricsOutReader.TileMetricsVersion
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.illumina.parser.ReadType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.illumina.parser.TileTemplateRead
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.nio.PathProvider
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.pedigree.Sex
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.FilterSamReads.Filter
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.markduplicates.CheckDuplicateMarking.Mode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.markduplicates.MarkDuplicates.DuplicateTaggingPolicy
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.markduplicates.MarkDuplicates.DuplicateType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.RevertSam.FileType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymer
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ReadDirection
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ReadOrdinality
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.util.SamComparison.AlignmentComparison
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.ValidateSamFile.Mode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.ViewSam.AlignmentStatus
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.sam.ViewSam.PfStatus
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.util.BaitDesigner.DesignStrategy
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.util.IntervalList.IntervalListScatterMode
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.util.IntervalListTools.Action
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.util.VariantType
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.vcf.GenotypeConcordanceStateCodes
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.vcf.GenotypeConcordanceStates.CallState
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.vcf.GenotypeConcordanceStates.ContingencyState
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.vcf.GenotypeConcordanceStates.TruthState
-
Returns the enum constant of this class with the specified name.
- valueOf(String) - Static method in enum class picard.vcf.VcfToIntervalList.VARIANT_ID_TYPES
-
Returns the enum constant of this class with the specified name.
- values() - Static method in enum class picard.analysis.AlignmentSummaryMetrics.Category
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.analysis.artifacts.Transition.Base
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.analysis.artifacts.Transition
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.analysis.CollectMultipleMetrics.Program
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.analysis.directed.RnaSeqMetricsCollector.StrandSpecificity
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.analysis.MetricAccumulationLevel
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.annotation.LocusFunction
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.annotation.RefFlatReader.RefFlatColumns
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.arrays.illumina.Build37ExtendedIlluminaManifestRecord.Flag
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.arrays.illumina.IlluminaGenotype
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.arrays.illumina.IlluminaManifestRecord.IlluminaStrand
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.arrays.illumina.InfiniumVcfFields.GENOTYPE_VALUES
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.fingerprint.CrosscheckMetric.DataType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.fingerprint.CrosscheckMetric.FingerprintResult
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.fingerprint.DiploidGenotype
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.fingerprint.DiploidHaplotype
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.fingerprint.HaplotypeProbabilities.Genotype
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.illumina.DistanceMetric
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.illumina.IlluminaBasecallsToFastq.ReadNameFormat
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.illumina.parser.IlluminaDataType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.illumina.parser.IlluminaFileUtil.SupportedIlluminaFormat
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.illumina.parser.IlluminaMetricsCode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.illumina.parser.IntensityChannel
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.illumina.parser.readers.TileMetricsOutReader.TileMetricsVersion
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.illumina.parser.ReadType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.illumina.parser.TileTemplateRead
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.illumina.quality.CollectHiSeqXPfFailMetrics.ReadClassifier.PfFailReason
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.nio.PathProvider
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.pedigree.Sex
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.AbstractAlignmentMerger.UnmappingReadStrategy
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.FilterSamReads.Filter
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.markduplicates.CheckDuplicateMarking.Mode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.markduplicates.MarkDuplicates.DuplicateTaggingPolicy
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.markduplicates.MarkDuplicates.DuplicateType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.RevertOriginalBaseQualitiesAndAddMateCigar.CanSkipSamFile
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.RevertSam.FileType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.Consensus
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.CycleBin
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.LongShortHomopolymer
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.PairOrientation
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ProperPaired
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ReadDirection
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.SamErrorMetric.ReadBaseStratification.ReadOrdinality
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.util.SamComparison.AlignmentComparison
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.ValidateSamFile.Mode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.ViewSam.AlignmentStatus
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.sam.ViewSam.PfStatus
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.util.BaitDesigner.DesignStrategy
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.util.IlluminaUtil.IlluminaAdapterPair
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.util.IntervalList.IntervalListScatterMode
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.util.IntervalListTools.Action
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.util.VariantType
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.vcf.GenotypeConcordanceStateCodes
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.vcf.GenotypeConcordanceStates.CallState
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.vcf.GenotypeConcordanceStates.ContingencyState
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.vcf.GenotypeConcordanceStates.TruthState
-
Returns an array containing the constants of this enum class, in the order they are declared.
- values() - Static method in enum class picard.vcf.VcfToIntervalList.VARIANT_ID_TYPES
-
Returns an array containing the constants of this enum class, in the order they are declared.
- VAR_PPV - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The ppv (positive predictive value) for all (heterozygous and homozygous) variants (PPV is the TP / (TP + FP))
- VAR_SENSITIVITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The sensitivity for all (heterozygous and homozygous) variants (Sensitivity is TP / (TP + FN))
- VAR_SPECIFICITY - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The specificity for all (heterozygous and homozygous) variants (Specificity is TN / (FP + TN))
- VARIANT_ID_METHOD - Static variable in class picard.vcf.VcfToIntervalList
- VARIANT_TYPE - Variable in class picard.vcf.GenotypeConcordanceContingencyMetrics
-
The type of the event (i.e.
- VARIANT_TYPE - Variable in class picard.vcf.GenotypeConcordanceDetailMetrics
-
The type of the event (i.e.
- VARIANT_TYPE - Variable in class picard.vcf.GenotypeConcordanceSummaryMetrics
-
The type of the event (i.e.
- VariantAccumulatorExecutor<ACCUMULATOR extends VariantProcessor.Accumulator<RESULT>,
RESULT> - Interface in picard.vcf.processor -
Describes the functionality for an executor that manages the delegation of work to
VariantProcessor.Accumulator
s. - VariantAccumulatorExecutor.MultiThreadedChunkBased<A extends VariantProcessor.Accumulator<R>,
R> - Class in picard.vcf.processor -
A
VariantAccumulatorExecutor
that breaks down work into chunks described by the providedVariantIteratorProducer
and spreads them over the indicated number of threads. - VariantCallingDetailMetrics() - Constructor for class picard.vcf.CollectVariantCallingMetrics.VariantCallingDetailMetrics
- VariantCallingSummaryMetrics() - Constructor for class picard.vcf.CollectVariantCallingMetrics.VariantCallingSummaryMetrics
- VariantEvaluationProgramGroup - Class in picard.cmdline.programgroups
-
Tools that evaluate and refine variant calls, e.g.
- VariantEvaluationProgramGroup() - Constructor for class picard.cmdline.programgroups.VariantEvaluationProgramGroup
- VariantFilter - Interface in picard.vcf.filter
-
Interface for classes that can generate filters for VariantContexts.
- VariantFilteringProgramGroup - Class in picard.cmdline.programgroups
-
Tools that filter variants
- VariantFilteringProgramGroup() - Constructor for class picard.cmdline.programgroups.VariantFilteringProgramGroup
- VariantIteratorProducer - Class in picard.vcf.processor
-
A mechanism for iterating over
CloseableIterator
ofVariantContext
s in in some fashion, given VCF files and optionally an interval list. - VariantIteratorProducer() - Constructor for class picard.vcf.processor.VariantIteratorProducer
- VariantManipulationProgramGroup - Class in picard.cmdline.programgroups
-
Tools that manipulate variant call format (VCF) data
- VariantManipulationProgramGroup() - Constructor for class picard.cmdline.programgroups.VariantManipulationProgramGroup
- VariantProcessor<RESULT,
ACCUMULATOR extends VariantProcessor.Accumulator<RESULT>> - Class in picard.vcf.processor -
Describes an object that processes variants and produces a result.
- VariantProcessor.Accumulator<RESULT> - Interface in picard.vcf.processor
-
Handles
VariantContext
s, and accumulates their data in some fashion internally. - VariantProcessor.AccumulatorGenerator<ACCUMULATOR extends VariantProcessor.Accumulator<RESULT>,
RESULT> - Interface in picard.vcf.processor -
Generates instances of
VariantProcessor.Accumulator
s. - VariantProcessor.Builder<A extends VariantProcessor.Accumulator<R>,
R> - Class in picard.vcf.processor -
Simple builder of
VariantProcessor
s. - VariantProcessor.ResultMerger<RESULT> - Interface in picard.vcf.processor
-
Takes a collection of results produced by
VariantProcessor.Accumulator.result()
and merges them into a single RESULT. - VariantType - Enum Class in picard.util
-
Enum to hold the possible types of dbSnps.
- VC_FILTERED - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.CallState
- VC_FILTERED - Enum constant in enum class picard.vcf.GenotypeConcordanceStates.TruthState
- VC_FILTERED_CODE - Enum constant in enum class picard.vcf.GenotypeConcordanceStateCodes
- vcf() - Method in class picard.vcf.processor.VcfFileSegment
-
Deprecated.
- vcf() - Method in class picard.vcf.processor.VcfPathSegment
- VCF - Variable in class picard.analysis.replicates.CollectIndependentReplicateMetrics
- VCF - Variable in class picard.arrays.VcfToAdpc
- VCF - Variable in class picard.sam.SamErrorMetric.CollectSamErrorMetrics
- VCF_DIR - Variable in class picard.vcf.MendelianViolations.FindMendelianViolations
- VcfFileSegment - Class in picard.vcf.processor
-
Deprecated.from 2022-03-17, Use VcfPathSegment
- VcfFileSegment() - Constructor for class picard.vcf.processor.VcfFileSegment
-
Deprecated.
- VcfFileSegmentGenerator - Class in picard.vcf.processor
-
Deprecated.from 2022-03-17, Use
VcfPathSegmentGenerator
- VcfFileSegmentGenerator() - Constructor for class picard.vcf.processor.VcfFileSegmentGenerator
-
Deprecated.
- VcfFormatConverter - Class in picard.vcf
-
Converts an ASCII VCF file to a binary BCF or vice versa.
- VcfFormatConverter() - Constructor for class picard.vcf.VcfFormatConverter
- VcfPathSegment - Class in picard.vcf.processor
-
Describes a segment of a particular VCF file.
- VcfPathSegment() - Constructor for class picard.vcf.processor.VcfPathSegment
- VcfPathSegmentGenerator - Class in picard.vcf.processor
-
Describes a mechanism for producing
VcfPathSegment
s from a VCF file path. - VcfPathSegmentGenerator() - Constructor for class picard.vcf.processor.VcfPathSegmentGenerator
- VcfToAdpc - Class in picard.arrays
-
A simple program to convert a Genotyping Arrays VCF to an ADPC file (Illumina intensity data file).
- VcfToAdpc() - Constructor for class picard.arrays.VcfToAdpc
- VcfToIntervalList - Class in picard.vcf
-
Converts a VCF or BCF file to a Picard Interval List.
- VcfToIntervalList() - Constructor for class picard.vcf.VcfToIntervalList
- VcfToIntervalList.VARIANT_ID_TYPES - Enum Class in picard.vcf
- VcfUtils - Class in picard.vcf
-
Created by farjoun on 4/1/17.
- VcfUtils() - Constructor for class picard.vcf.VcfUtils
- VERBOSE - Enum constant in enum class picard.sam.ValidateSamFile.Mode
- VERBOSITY - Variable in class picard.cmdline.CommandLineProgram
- verify(List<Integer>) - Method in class picard.illumina.parser.TileIndex
- verify(List<Integer>, int[]) - Method in class picard.illumina.parser.MultiTileBclFileUtil
- verify(List<Integer>, int[]) - Method in class picard.illumina.parser.MultiTileFileUtil
-
expectedCycles are not checked in this implementation.
- verify(List<Integer>, int[]) - Method in class picard.illumina.parser.ParameterizedFileUtil
-
Given the expected tiles/expected cycles for this file type, return a list of error messages describing any missing/or malformed files
- verify(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTileFileUtil
- verify(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTileOrPerRunFileUtil
- verify(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTilePerCycleFileUtil
- verifyData(List<Integer>, int[]) - Method in class picard.illumina.parser.MultiTileParser
- verifyData(List<Integer>, int[]) - Method in class picard.illumina.parser.MultiTileBclParser
- verifyData(List<Integer>, int[]) - Method in class picard.illumina.parser.PerTileParser
- VerifyIDIntensityContaminationMetrics - Class in picard.arrays
- VerifyIDIntensityContaminationMetrics() - Constructor for class picard.arrays.VerifyIDIntensityContaminationMetrics
- version - Variable in class picard.illumina.parser.readers.FilterFileReader
-
Version number found in the FilterFile, this should equal 3
- version - Variable in enum class picard.illumina.parser.readers.TileMetricsOutReader.TileMetricsVersion
- ViewSam - Class in picard.sam
-
Prints a SAM or BAM file to the screen.
- ViewSam() - Constructor for class picard.sam.ViewSam
- ViewSam.AlignmentStatus - Enum Class in picard.sam
- ViewSam.PfStatus - Enum Class in picard.sam
W
- WARN_ON_MISSING_CONTIG - Variable in class picard.vcf.LiftoverVcf
- WgsMetrics - Class in picard.analysis
-
Metrics for evaluating the performance of whole genome sequencing experiments.
- WgsMetrics() - Constructor for class picard.analysis.WgsMetrics
-
Create an instance of this metric that is not mergeable.
- WgsMetrics(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, double, int, Histogram<Integer>, int) - Constructor for class picard.analysis.WgsMetrics
-
Create an instance of this metric that is mergeable.
- WgsMetricsCollector(CollectWgsMetrics, int, IntervalList) - Constructor for class picard.analysis.CollectWgsMetrics.WgsMetricsCollector
- WgsMetricsProcessor - Interface in picard.analysis
-
Interface for processing data and generate result for CollectWgsMetrics
- WgsMetricsProcessorImpl<T extends htsjdk.samtools.util.AbstractRecordAndOffset> - Class in picard.analysis
-
Implementation of
WgsMetricsProcessor
that gets input data from a given iterator and processes it with a help of collector - WgsMetricsProcessorImpl(AbstractLocusIterator<T, AbstractLocusInfo<T>>, ReferenceSequenceFileWalker, AbstractWgsMetricsCollector<T>, ProgressLogger) - Constructor for class picard.analysis.WgsMetricsProcessorImpl
- WgsMetricsWithNonZeroCoverage() - Constructor for class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
- WgsMetricsWithNonZeroCoverage(IntervalList, Histogram<Integer>, Histogram<Integer>, double, double, double, double, double, double, double, double, int, Histogram<Integer>, int) - Constructor for class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
- WgsMetricsWithNonZeroCoverageCollector(CollectWgsMetricsWithNonZeroCoverage, int, IntervalList) - Constructor for class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverageCollector
- WHOLE_GENOME - Enum constant in enum class picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage.Category
- WIDTH_OF_10_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 10% of all read pairs.
- WIDTH_OF_20_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 20% of all read pairs.
- WIDTH_OF_30_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 30% of all read pairs.
- WIDTH_OF_40_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 40% of all read pairs.
- WIDTH_OF_50_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 50% of all read pairs.
- WIDTH_OF_60_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 60% of all read pairs.
- WIDTH_OF_70_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 70% of all read pairs.
- WIDTH_OF_80_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 80% of all read pairs.
- WIDTH_OF_90_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 90% of all read pairs.
- WIDTH_OF_95_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 95% of all read pairs.
- WIDTH_OF_99_PERCENT - Variable in class picard.analysis.InsertSizeMetrics
-
The "width" of the bins, centered around the median, that encompass 100% of all read pairs.
- WINDOW_SIZE - Variable in class picard.analysis.GcBiasSummaryMetrics
-
The window size on the genome used to calculate the GC of the sequence.
- WINDOWS - Variable in class picard.analysis.GcBiasDetailMetrics
-
The number of windows on the reference genome that have this G+C content.
- withApplyEamssFiltering(boolean) - Method in class picard.illumina.BasecallsConverterBuilder
-
Configures whether or not the converter will apply EAMSS filtering.
- withAsyncWriterPool(AsyncWriterPool) - Method in class picard.illumina.BasecallsConverterBuilder
- withBarcodeExtractor(BarcodeExtractor) - Method in class picard.illumina.BasecallsConverterBuilder
- withBarcodesDir(File) - Method in class picard.illumina.BasecallsConverterBuilder
-
Configure the director used to find barcode files created by ExtractIlluminaBarcodes.
- withBclQualityEvaluationStrategy(BclQualityEvaluationStrategy) - Method in class picard.illumina.BasecallsConverterBuilder
-
Configures the bcl quality evaluation strategy that the converter will apply.
- withDemultiplex(boolean) - Method in class picard.illumina.BasecallsConverterBuilder
-
Configures whether or not the converter will demultiplex reads by barcode.
- withIgnoreUnexpectedBarcodes(boolean) - Method in class picard.illumina.BasecallsConverterBuilder
-
Configures whether or not the converter will ignore unexpected barcodes or throw an exception if one is found.
- withIncludeNonPfReads(boolean) - Method in class picard.illumina.BasecallsConverterBuilder
-
Configures whether or not the converter will ignore non-PF reads.
- withInput(File...) - Method in class picard.vcf.processor.VariantProcessor.Builder
- withInput(PicardHtsPath...) - Method in class picard.vcf.processor.VariantProcessor.Builder
- withMaxRecordsInRam(int) - Method in class picard.illumina.BasecallsConverterBuilder
-
Specify the max number of records in RAM.
- withMolecularIndexQualityTag(String) - Method in class picard.illumina.ClusterDataToSamConverter
-
Sets the SAM tag to use to store the molecular index base qualities.
- withMolecularIndexTag(String) - Method in class picard.illumina.ClusterDataToSamConverter
-
Sets the SAM tag to use to store the molecular index bases.
- withoutChromosomes(Set<String>) - Method in class picard.fingerprint.HaplotypeMap
-
Returns a copy of this haplotype map that excludes haplotypes on the chromosomes provided.
- withSorting(Comparator<CLUSTER_OUTPUT_RECORD>, SortingCollection.Codec<CLUSTER_OUTPUT_RECORD>, Class<CLUSTER_OUTPUT_RECORD>, List<File>) - Method in class picard.illumina.BasecallsConverterBuilder
-
Builds a new sorting basecalls converter.
- withTagPerMolecularIndex(List<String>) - Method in class picard.illumina.ClusterDataToSamConverter
-
Sets the SAM tags to use to store the bases each molecular index.
- WORST_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
The sequence context (reference bases surrounding the locus of interest) having the lowest Q-score among all contexts for this artifact.
- WORST_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
The sequence context (reference bases surrounding the locus of interest) having the lowest Q-score among all contexts for this artifact.
- WORST_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
The Q-score for the worst context.
- WORST_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
The Q-score for the worst context.
- WORST_POST_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
The post-context (reference bases trailing after the locus of interest) with the lowest Q-score.
- WORST_POST_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
The post-context (reference bases trailing after the locus of interest) with the lowest Q-score.
- WORST_POST_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
The Q-score for the worst post-context.
- WORST_POST_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
The Q-score for the worst post-context.
- WORST_PRE_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
The pre-context (reference bases leading up to the locus of interest) with the lowest Q-score.
- WORST_PRE_CXT - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
The pre-context (reference bases leading up to the locus of interest) with the lowest Q-score.
- WORST_PRE_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.BaitBiasSummaryMetrics
-
The Q-score for the worst pre-context.
- WORST_PRE_CXT_QSCORE - Variable in class picard.analysis.artifacts.SequencingArtifactMetrics.PreAdapterSummaryMetrics
-
The Q-score for the worst pre-context.
- write(byte[], int, int) - Method in class picard.util.CircularByteBuffer
-
Write bytes into the buffer from the supplied array.
- write(DataOutputStream) - Method in class picard.arrays.illumina.IlluminaAdpcFileWriter.Record
- write(File) - Method in class picard.pedigree.PedFile
-
Writes a set of pedigrees out to disk.
- write(Iterable<IlluminaAdpcFileWriter.Record>) - Method in class picard.arrays.illumina.IlluminaAdpcFileWriter
- write(OUTPUT_RECORD) - Method in interface picard.illumina.BasecallsConverter.ConvertedClusterDataWriter
-
Write out a single record of type OUTPUT_RECORD.
- write(IlluminaAdpcFileWriter.Record) - Method in class picard.arrays.illumina.IlluminaAdpcFileWriter
- WRITE_ORIGINAL_ALLELES - Variable in class picard.vcf.LiftoverVcf
- WRITE_ORIGINAL_POSITION - Variable in class picard.vcf.LiftoverVcf
- WRITE_READS_FILES - Variable in class picard.sam.FilterSamReads
- writeAlignment(SAMRecord) - Method in class picard.sam.FixMateInformation
- writeAsVcf(File, File) - Method in class picard.fingerprint.HaplotypeMap
- writeBfqFiles() - Method in class picard.fastq.SamToBfqWriter
-
Writes the binary fastq file(s) to the output directory
- writeFingerPrint(Fingerprint, File, File, String, String) - Static method in class picard.fingerprint.FingerprintUtils
-
A function that takes a Fingerprint and writes it as a VCF to a file
- writeReport(File) - Method in class picard.sam.util.SamComparison
- writeReport(File, List<Header>) - Method in class picard.sam.util.SamComparison
- writerPool - Variable in class picard.illumina.BasecallsConverter
- writeToFile(File) - Method in class picard.fingerprint.HaplotypeMap
-
Writes out a HaplotypeMap file with the contents of this map.
X
- x - Variable in class picard.sam.util.PhysicalLocationInt
- X - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- X - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
-
The X coordinate of the read within the tile
- xIsSet() - Method in class picard.illumina.parser.ClusterData
- xPos - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
-
The x-position as it occurs in the file being read
- xQseqCoord - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
-
The QSeq style x-coordinat, an integer = Math.round(xPos*10 + 1000)
Y
- y - Variable in class picard.sam.util.PhysicalLocationInt
- Y - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- Y - Variable in class picard.illumina.quality.CollectHiSeqXPfFailMetrics.PFFailDetailedMetric
-
The Y coordinate of the read within the tile
- yIsSet() - Method in class picard.illumina.parser.ClusterData
- yPos - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
-
The y-position as it occurs in the file being read
- yQseqCoord - Variable in class picard.illumina.parser.readers.AbstractIlluminaPositionFileReader.PositionInfo
-
The QSeq style y-coordinates, an integer = Math.round(yPos*10 + 1000)
Z
- ZCALL_THRESHOLDS - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- ZCALL_THRESHOLDS_FILE - Variable in class picard.arrays.MergePedIntoVcf
- ZCALL_VERSION - Variable in class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
-
The version of ZCall used for calling this sample
- ZCALL_VERSION - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- ZCALL_VERSION - Variable in class picard.arrays.MergePedIntoVcf
- ZERO_CVG_TARGETS_PCT - Variable in class picard.analysis.directed.PanelMetricsBase
-
The fraction of targets that did not reach coverage=1 over any base.
- ZEROED_OUT_ASSAY - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- ZTHRESH_X - Static variable in class picard.arrays.illumina.InfiniumVcfFields
- ZTHRESH_Y - Static variable in class picard.arrays.illumina.InfiniumVcfFields
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