Package org.broadinstitute.hellbender.utils.haplotype

Class HaplotypeBAMDestination

java.lang.Object

org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMDestination

Direct Known Subclasses:

SAMFileDestination

public abstract class HaplotypeBAMDestination
extends Object

Utility class that allows easy creation of destinations for the HaplotypeBAMWriters

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	HaplotypeBAMDestination(htsjdk.samtools.SAMFileHeader sourceHeader, Optional<String> haplotypeReadGroupID)	Create a new HaplotypeBAMDestination

Method Summary

Modifier and Type	Method	Description
abstract void	add(GATKRead read)	Write a read to the output specified by this destination.
htsjdk.samtools.SAMFileHeader	getBAMOutputHeader()	Get the SAMFileHeader that is used for writing the output for this destination.
Optional<String>	getHaplotypeReadGroupID()	Get the read group ID that is used by this writer when writing halpotypes as reads.
String	getHaplotypeSampleTag()	Get the sample tag that is used by this writer when writing halpotypes as reads.

Methods inherited from class java.lang.Object

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

Constructor Details

HaplotypeBAMDestination

protected HaplotypeBAMDestination(htsjdk.samtools.SAMFileHeader sourceHeader,
 Optional<String> haplotypeReadGroupID)

Create a new HaplotypeBAMDestination

Parameters:

sourceHeader - SAMFileHeader used to seed the output SAMFileHeader for this destination.

haplotypeReadGroupID - read group ID used when writing haplotypes as reads. Empty if HaplotypeBAMWriter.WriterType == NO_HAPLOTYPES.

Method Details

add

public abstract void add(GATKRead read)

Write a read to the output specified by this destination.

Parameters:

read - the read to write out

getHaplotypeReadGroupID

public Optional<String> getHaplotypeReadGroupID()

Get the read group ID that is used by this writer when writing halpotypes as reads. If HaplotypeBAMWriter.WriterType is NO_HAPLOTYPES, then returns Optional.empty()

Returns:

read group ID

getHaplotypeSampleTag

public String getHaplotypeSampleTag()

Get the sample tag that is used by this writer when writing halpotypes as reads.

Returns:

sample tag

getBAMOutputHeader

public htsjdk.samtools.SAMFileHeader getBAMOutputHeader()

Get the SAMFileHeader that is used for writing the output for this destination.

Returns:

output SAMFileHeader