picard.analysis

Class SinglePassSamProgram

java.lang.Object

picard.cmdline.CommandLineProgram

picard.analysis.SinglePassSamProgram

Direct Known Subclasses:

CollectAlignmentSummaryMetrics, CollectBaseDistributionByCycle, CollectGcBiasMetrics, CollectInsertSizeMetrics, CollectQualityYieldMetrics, CollectRnaSeqMetrics, CollectSequencingArtifactMetrics, MeanQualityByCycle, QualityScoreDistribution

public abstract class SinglePassSamProgram
extends CommandLineProgram

Super class that is designed to provide some consistent structure between subclasses that simply iterate once over a coordinate sorted BAM and collect information from the records as the go in order to produce some kind of output.

Field Summary

Fields

Modifier and Type	Field and Description
boolean	ASSUME_SORTED
java.io.File	INPUT
java.io.File	OUTPUT
long	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, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY

Constructor Summary

Constructors

Constructor and Description
SinglePassSamProgram()

Method Summary

Modifier and Type	Method and Description
protected abstract void	acceptRead(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref) Should be implemented by subclasses to accept SAMRecords one at a time.
protected int	doWork() Final implementation of doWork() that checks and loads the input and optionally reference sequence files and the runs the sublcass through the setup() acceptRead() and finish() steps.
protected abstract void	finish() Should be implemented by subclasses to do one-time finalization work.
static void	makeItSo(java.io.File input, java.io.File referenceSequence, boolean assumeSorted, long stopAfter, java.util.Collection<SinglePassSamProgram> programs)
void	setReferenceSequence(java.io.File referenceFile) Set the reference File.
protected abstract void	setup(htsjdk.samtools.SAMFileHeader header, java.io.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.cmdline.CommandLineProgram

customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser

Methods inherited from class java.lang.Object

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

Field Detail

INPUT

@Argument(shortName="I",
          doc="Input SAM or BAM file.")
public java.io.File INPUT

OUTPUT

@Argument(shortName="O",
          doc="File to write the output to.")
public java.io.File OUTPUT

ASSUME_SORTED

@Argument(doc="If true (default), then the sort order in the header file will be ignored.",
          shortName="AS")
public boolean ASSUME_SORTED

STOP_AFTER

@Argument(doc="Stop after processing N reads, mainly for debugging.")
public long STOP_AFTER

Constructor Detail

SinglePassSamProgram

public SinglePassSamProgram()

Method Detail

setReferenceSequence

public void setReferenceSequence(java.io.File referenceFile)

Set the reference File.

doWork

protected final int doWork()

Final implementation of doWork() that checks and loads the input and optionally reference sequence files and the runs the sublcass through the setup() acceptRead() and finish() steps.

Specified by:

doWork in class CommandLineProgram

Returns:

program exit status.

makeItSo

public static void makeItSo(java.io.File input,
                            java.io.File referenceSequence,
                            boolean assumeSorted,
                            long stopAfter,
                            java.util.Collection<SinglePassSamProgram> programs)

usesNoRefReads

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.

setup

protected abstract void setup(htsjdk.samtools.SAMFileHeader header,
                              java.io.File samFile)

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

acceptRead

protected abstract void acceptRead(htsjdk.samtools.SAMRecord rec,
                                   htsjdk.samtools.reference.ReferenceSequence ref)

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.

finish

protected abstract void finish()

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