Package picard.sam.markduplicates

Class CollectDuplicateMetrics

java.lang.Object

picard.cmdline.CommandLineProgram

picard.analysis.SinglePassSamProgram

picard.sam.markduplicates.CollectDuplicateMetrics

@DocumentedFeature
public class CollectDuplicateMetrics
extends SinglePassSamProgram

Collect DuplicateMark'ing metrics from an input file that was already Duplicate-Marked.

Field Summary

Fields

Modifier and Type	Field	Description
File	METRICS_FILE

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

Constructor Summary

Constructors

Constructor	Description
CollectDuplicateMetrics()

Method Summary

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

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

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details

METRICS_FILE

@Argument(shortName="M",
          doc="File to write duplication metrics to.")
public File METRICS_FILE

Constructor Details

CollectDuplicateMetrics

public CollectDuplicateMetrics()

Method Details

getOutputArgumentCollection

protected OutputArgumentCollection getOutputArgumentCollection()

Overrides:

getOutputArgumentCollection in class SinglePassSamProgram

requiresReference

protected boolean requiresReference()

Overrides:

requiresReference in class CommandLineProgram

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 class SinglePassSamProgram

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 class SinglePassSamProgram

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 class SinglePassSamProgram

finish

protected void finish()

Description copied from class: SinglePassSamProgram

Should be implemented by subclasses to do one-time finalization work.

Specified by:

finish in class SinglePassSamProgram