picard.analysis

Class CollectQualityYieldMetrics

java.lang.Object

picard.cmdline.CommandLineProgram

picard.analysis.SinglePassSamProgram

picard.analysis.CollectQualityYieldMetrics

public class CollectQualityYieldMetrics
extends SinglePassSamProgram

Command line program to calibrate quality yield metrics

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	CollectQualityYieldMetrics.QualityYieldMetrics A set of metrics used to describe the general quality of a BAM file

Field Summary

Fields

Modifier and Type	Field and Description
boolean	INCLUDE_SECONDARY_ALIGNMENTS
boolean	INCLUDE_SUPPLEMENTAL_ALIGNMENTS
boolean	USE_ORIGINAL_QUALITIES

Fields inherited from class picard.analysis.SinglePassSamProgram

ASSUME_SORTED, INPUT, OUTPUT, STOP_AFTER

Fields inherited from class picard.cmdline.CommandLineProgram

COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, TMP_DIR, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
CollectQualityYieldMetrics()

Method Summary

Modifier and Type	Method and 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, java.io.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

Methods inherited from class picard.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getMetricsFile, getNestedOptions, getNestedOptionsForHelp, getStandardUsagePreamble, getVersion, instanceMain, instanceMainWithExit, parseArgs, setDefaultHeaders

Methods inherited from class java.lang.Object

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

Field Detail

USE_ORIGINAL_QUALITIES

@Option(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

@Option(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

@Option(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

Constructor Detail

CollectQualityYieldMetrics

public CollectQualityYieldMetrics()

Method Detail

usesNoRefReads

protected boolean usesNoRefReads()

Ensure that we get all reads regardless of alignment status.

Overrides:

usesNoRefReads in class SinglePassSamProgram

setup

protected void setup(htsjdk.samtools.SAMFileHeader header,
                     java.io.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