Package picard.sam.markduplicates
Class CollectDuplicateMetrics
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.analysis.SinglePassSamProgram
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- picard.sam.markduplicates.CollectDuplicateMetrics
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@DocumentedFeature public class CollectDuplicateMetrics extends SinglePassSamProgram
Collect DuplicateMark'ing metrics from an input file that was already Duplicate-Marked.
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Field Summary
Fields Modifier and Type Field Description File
METRICS_FILE
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Fields inherited from class picard.analysis.SinglePassSamProgram
ASSUME_SORTED, INPUT, output, 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_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 Constructor Description CollectDuplicateMetrics()
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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 OutputArgumentCollection
getOutputArgumentCollection()
protected boolean
requiresReference()
protected void
setup(htsjdk.samtools.SAMFileHeader header, File samFile)
Should be implemented by subclasses to do one-time initialization work.protected boolean
usesNoRefReads()
Can be overridden and set to false if the section of unmapped reads at the end of the file isn't needed.-
Methods inherited from class picard.analysis.SinglePassSamProgram
doWork, makeItSo, setReferenceSequence
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Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, setDefaultHeaders, useLegacyParser
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Field Detail
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METRICS_FILE
@Argument(shortName="M", doc="File to write duplication metrics to.") public File METRICS_FILE
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Method Detail
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getOutputArgumentCollection
protected OutputArgumentCollection getOutputArgumentCollection()
- Overrides:
getOutputArgumentCollection
in classSinglePassSamProgram
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requiresReference
protected boolean requiresReference()
- Overrides:
requiresReference
in classCommandLineProgram
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usesNoRefReads
protected boolean usesNoRefReads()
Description copied from class:SinglePassSamProgram
Can be overridden and set to false if the section of unmapped reads at the end of the file isn't needed.- 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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