Package picard.analysis
Class CollectQualityYieldMetrics
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.analysis.SinglePassSamProgram
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- picard.analysis.CollectQualityYieldMetrics
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@DocumentedFeature public class CollectQualityYieldMetrics extends SinglePassSamProgram
Command line program to calibrate quality yield metrics
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
CollectQualityYieldMetrics.QualityYieldMetrics
A set of metrics used to describe the general quality of a BAM filestatic class
CollectQualityYieldMetrics.QualityYieldMetricsCollector
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Field Summary
Fields Modifier and Type Field Description boolean
INCLUDE_SECONDARY_ALIGNMENTS
boolean
INCLUDE_SUPPLEMENTAL_ALIGNMENTS
boolean
USE_ORIGINAL_QUALITIES
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Fields inherited from class picard.analysis.SinglePassSamProgram
ASSUME_SORTED, INPUT, OUTPUT, STOP_AFTER
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Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors Constructor Description CollectQualityYieldMetrics()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected 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
setup(htsjdk.samtools.SAMFileHeader header, File samFile)
Should be implemented by subclasses to do one-time initialization work.protected boolean
usesNoRefReads()
Ensure that we get all reads regardless of alignment status.-
Methods inherited from class picard.analysis.SinglePassSamProgram
doWork, makeItSo, setReferenceSequence
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Methods inherited from class picard.cmdline.CommandLineProgram
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Detail
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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
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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
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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
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Method Detail
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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
protected void setup(htsjdk.samtools.SAMFileHeader header, File samFile)
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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