Package picard.analysis
Class CollectQualityYieldMetrics
java.lang.Object
picard.cmdline.CommandLineProgram
picard.analysis.SinglePassSamProgram
picard.analysis.CollectQualityYieldMetrics
Command line program to calculate quality yield metrics
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic class
A set of metrics used to describe the general quality of a BAM filestatic class
static class
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Field Summary
FieldsModifier and TypeFieldDescriptionboolean
boolean
boolean
boolean
Fields inherited from class picard.analysis.SinglePassSamProgram
ASSUME_SORTED, INPUT, output, OUTPUT, STOP_AFTER
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 void
acceptRead
(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref) Should be implemented by subclasses to accept SAMRecords one at a time.protected void
finish()
Should be implemented by subclasses to do one-time finalization work.protected void
Should be implemented by subclasses to do one-time initialization work.protected boolean
Ensure that we get all reads regardless of alignment status.Methods inherited from class picard.analysis.SinglePassSamProgram
doWork, getOutputArgumentCollection, makeItSo, setReferenceSequence
Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Details
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USE_ORIGINAL_QUALITIES
@Argument(shortName="OQ", doc="If available in the OQ tag, use the original quality scores as inputs instead of the quality scores in the QUAL field.") public boolean USE_ORIGINAL_QUALITIES -
INCLUDE_SECONDARY_ALIGNMENTS
@Argument(doc="If true, include bases from secondary alignments in metrics. Setting to true may cause double-counting of bases if there are secondary alignments in the input file.") public boolean INCLUDE_SECONDARY_ALIGNMENTS -
INCLUDE_SUPPLEMENTAL_ALIGNMENTS
@Argument(doc="If true, include bases from supplemental alignments in metrics. Setting to true may cause double-counting of bases if there are supplemental alignments in the input file.") public boolean INCLUDE_SUPPLEMENTAL_ALIGNMENTS -
FLOW_MODE
@Argument(doc="If true, calculates flow-specific READ_LENGTH_AVG_Q metrics.") public boolean FLOW_MODE
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Constructor Details
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CollectQualityYieldMetrics
public CollectQualityYieldMetrics()
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Method Details
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usesNoRefReads
protected boolean usesNoRefReads()Ensure that we get all reads regardless of alignment status.- Overrides:
usesNoRefReads
in classSinglePassSamProgram
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setup
Description copied from class:SinglePassSamProgram
Should be implemented by subclasses to do one-time initialization work.- Specified by:
setup
in classSinglePassSamProgram
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acceptRead
protected void acceptRead(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref) Description copied from class:SinglePassSamProgram
Should be implemented by subclasses to accept SAMRecords one at a time. If the read has a reference sequence and a reference sequence file was supplied to the program it will be passed as 'ref'. Otherwise 'ref' may be null.- Specified by:
acceptRead
in classSinglePassSamProgram
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finish
protected void finish()Description copied from class:SinglePassSamProgram
Should be implemented by subclasses to do one-time finalization work.- Specified by:
finish
in classSinglePassSamProgram
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