Package picard.analysis
Class CollectWgsMetricsWithNonZeroCoverage
java.lang.Object
picard.cmdline.CommandLineProgram
picard.analysis.CollectWgsMetrics
picard.analysis.CollectWgsMetricsWithNonZeroCoverage
@DocumentedFeature
@ExperimentalFeature
public class CollectWgsMetricsWithNonZeroCoverage
extends CollectWgsMetrics
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic class
Metrics for evaluating the performance of whole genome sequencing experiments.protected class
Nested classes/interfaces inherited from class picard.analysis.CollectWgsMetrics
CollectWgsMetrics.CollectWgsMetricsIntervalArgumentCollection, CollectWgsMetrics.WgsMetricsCollector
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Field Summary
FieldsFields inherited from class picard.analysis.CollectWgsMetrics
ALLELE_FRACTION, COUNT_UNPAIRED, COVERAGE_CAP, INCLUDE_BQ_HISTOGRAM, INPUT, intervalArgumentCollection, INTERVALS, LOCUS_ACCUMULATION_CAP, MINIMUM_BASE_QUALITY, MINIMUM_MAPPING_QUALITY, OUTPUT, READ_LENGTH, SAMPLE_SIZE, STOP_AFTER, THEORETICAL_SENSITIVITY_OUTPUT, USE_FAST_ALGORITHM
Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected String[]
Put any custom command-line validation in an override of this method.protected int
doWork()
Do the work after command line has been parsed.protected WgsMetrics
generateWgsMetrics
(htsjdk.samtools.util.IntervalList intervals, htsjdk.samtools.util.Histogram<Integer> highQualityDepthHistogram, htsjdk.samtools.util.Histogram<Integer> unfilteredDepthHistogram, double pctExcludedByAdapter, double pctExcludedByMapq, double pctExcludedByDupes, double pctExcludedByPairing, double pctExcludedByBaseq, double pctExcludedByOverlap, double pctExcludedByCapping, double pctTotal, int coverageCap, htsjdk.samtools.util.Histogram<Integer> unfilteredBaseQHistogram, int sampleSize) protected CollectWgsMetrics.WgsMetricsCollector
getCollector
(int coverageCap, htsjdk.samtools.util.IntervalList intervals) CreatesAbstractWgsMetricsCollector
implementation according toCollectWgsMetrics.USE_FAST_ALGORITHM
value.protected htsjdk.samtools.SamReader
Gets the SamReader from which records will be examined.Methods inherited from class picard.analysis.CollectWgsMetrics
getBasesExcludedBy, getIntervalsToExamine, getLocusIterator, getSamFileHeader, makeIntervalArgumentCollection, requiresReference
Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, setDefaultHeaders, useLegacyParser
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Field Details
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CHART_OUTPUT
@Argument(shortName="CHART", doc="A file (with .pdf extension) to write the chart to.") public File CHART_OUTPUT
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Constructor Details
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CollectWgsMetricsWithNonZeroCoverage
public CollectWgsMetricsWithNonZeroCoverage()
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Method Details
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customCommandLineValidation
Description copied from class:CommandLineProgram
Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.- Overrides:
customCommandLineValidation
in classCommandLineProgram
- Returns:
- null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.
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getSamReader
protected htsjdk.samtools.SamReader getSamReader()Description copied from class:CollectWgsMetrics
Gets the SamReader from which records will be examined. This will also set the header so that it is available in- Overrides:
getSamReader
in classCollectWgsMetrics
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doWork
protected int doWork()Description copied from class:CommandLineProgram
Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.- Overrides:
doWork
in classCollectWgsMetrics
- Returns:
- program exit status.
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generateWgsMetrics
protected WgsMetrics generateWgsMetrics(htsjdk.samtools.util.IntervalList intervals, htsjdk.samtools.util.Histogram<Integer> highQualityDepthHistogram, htsjdk.samtools.util.Histogram<Integer> unfilteredDepthHistogram, double pctExcludedByAdapter, double pctExcludedByMapq, double pctExcludedByDupes, double pctExcludedByPairing, double pctExcludedByBaseq, double pctExcludedByOverlap, double pctExcludedByCapping, double pctTotal, int coverageCap, htsjdk.samtools.util.Histogram<Integer> unfilteredBaseQHistogram, int sampleSize) - Overrides:
generateWgsMetrics
in classCollectWgsMetrics
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getCollector
protected CollectWgsMetrics.WgsMetricsCollector getCollector(int coverageCap, htsjdk.samtools.util.IntervalList intervals) Description copied from class:CollectWgsMetrics
CreatesAbstractWgsMetricsCollector
implementation according toCollectWgsMetrics.USE_FAST_ALGORITHM
value.- Overrides:
getCollector
in classCollectWgsMetrics
- Parameters:
coverageCap
- the maximum depth/coverage to consider.intervals
- the intervals over which metrics are collected.- Returns:
- if
CollectWgsMetrics.USE_FAST_ALGORITHM
is enabled, returnsFastWgsMetricsCollector
implementation, otherwise default algorithm is used andCollectWgsMetrics.WgsMetricsCollector
is returned.
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