Package org.broadinstitute.hellbender.utils.haplotype

Class SAMFileDestination

java.lang.Object

org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMDestination

org.broadinstitute.hellbender.utils.haplotype.SAMFileDestination

public final class SAMFileDestination
extends HaplotypeBAMDestination

Class used to direct output from a HaplotypeBAMWriter to a bam/sam file.

Constructor Summary

Constructors

Constructor	Description
SAMFileDestination(Path outPath, boolean createBamOutIndex, boolean createBamOutMD5, htsjdk.samtools.SAMFileHeader sourceHeader, Optional<String> haplotypeReadGroupID)	Create a new file destination.

Method Summary

Modifier and Type	Method	Description
void	add(GATKRead read)	Write a read to the output file specified by this destination.

Methods inherited from class org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMDestination

getBAMOutputHeader, getHaplotypeReadGroupID, getHaplotypeSampleTag

Methods inherited from class java.lang.Object

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

Constructor Details

SAMFileDestination

public SAMFileDestination(Path outPath,
 boolean createBamOutIndex,
 boolean createBamOutMD5,
 htsjdk.samtools.SAMFileHeader sourceHeader,
 Optional<String> haplotypeReadGroupID)

Create a new file destination.

Parameters:

outPath - path where output is written (doesn't have to be local)

createBamOutIndex - true to create an index file for the bamout

createBamOutMD5 - true to create an md5 file for the bamout

sourceHeader - SAMFileHeader used to seed the output SAMFileHeader for this destination, must not be null

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

Method Details

add

public void add(GATKRead read)

Write a read to the output file specified by this destination.

Specified by:

add in class HaplotypeBAMDestination

Parameters:

read - the read to write out, must not be null