Package org.broadinstitute.hellbender.utils.haplotype

Class HaplotypeBAMWriter

java.lang.Object

org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMWriter

All Implemented Interfaces:

AutoCloseable

public class HaplotypeBAMWriter
extends Object
implements AutoCloseable

A BAMWriter that aligns reads to haplotypes and emits their best alignments to a destination.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	HaplotypeBAMWriter.WriterType	Possible modes for writing haplotypes to BAMs

Field Summary

Fields

Modifier and Type	Field	Description
static final String	DEFAULT_GATK3_HAPLOTYPE_READ_GROUP_ID
static final String	DEFAULT_HAPLOTYPE_READ_GROUP_ID

Constructor Summary

Constructors

Constructor	Description
HaplotypeBAMWriter(HaplotypeBAMWriter.WriterType type, Path outputPath, boolean createBamOutIndex, boolean createBamOutMD5, htsjdk.samtools.SAMFileHeader sourceHeader)	Create a new HaplotypeBAMWriter of type "type" for writing SAMRecords to an output file
HaplotypeBAMWriter(HaplotypeBAMWriter.WriterType type, HaplotypeBAMDestination destination)	Create a new HaplotypeBAMWriter of type "type" for writing SAMRecords to and output destination

Method Summary

Modifier and Type	Method	Description
void	close()	Close any output resource associated with this writer.
void	setAddSpecialTag(boolean addSpecialTag)
void	writeReadsAlignedToHaplotypes(Collection<Haplotype> haplotypes, htsjdk.samtools.util.Locatable paddedReferenceLoc, Collection<Haplotype> bestHaplotypes, Set<Haplotype> calledHaplotypes, AlleleLikelihoods<GATKRead,Haplotype> readLikelihoods)
void	writeReadsAlignedToHaplotypes(Collection<Haplotype> haplotypes, htsjdk.samtools.util.Locatable paddedReferenceLoc, Collection<Haplotype> bestHaplotypes, Set<Haplotype> calledHaplotypes, AlleleLikelihoods<GATKRead,Haplotype> readLikelihoods, htsjdk.samtools.util.Locatable callableRegion)	Write out a BAM representing for the haplotype caller at this site writerType (ALL_POSSIBLE_HAPLOTYPES or CALLED_HAPLOTYPES) determines inputs to writeHaplotypesAsReads Write out a BAM representing the haplotypes at this site, based on the value for writerType used when the writer was constructed (ALL_POSSIBLE_HAPLOTYPES or CALLED_HAPLOTYPES).

Methods inherited from class java.lang.Object

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

Field Details

DEFAULT_HAPLOTYPE_READ_GROUP_ID

public static final String DEFAULT_HAPLOTYPE_READ_GROUP_ID

See Also:

• Constant Field Values

DEFAULT_GATK3_HAPLOTYPE_READ_GROUP_ID

public static final String DEFAULT_GATK3_HAPLOTYPE_READ_GROUP_ID

See Also:

• Constant Field Values

Constructor Details

HaplotypeBAMWriter

public HaplotypeBAMWriter(HaplotypeBAMWriter.WriterType type,
 Path outputPath,
 boolean createBamOutIndex,
 boolean createBamOutMD5,
 htsjdk.samtools.SAMFileHeader sourceHeader)

Create a new HaplotypeBAMWriter of type "type" for writing SAMRecords to an output file

Parameters:

type - the type of the writer we want to create, must not be null

outputPath - the destination, must not be null

createBamOutIndex - true to create an index for the bamout

createBamOutMD5 - true to create an MD5 file for the bamout

sourceHeader - the header of the input BAMs used to make calls, must not be null.

HaplotypeBAMWriter

public HaplotypeBAMWriter(HaplotypeBAMWriter.WriterType type,
 HaplotypeBAMDestination destination)

Create a new HaplotypeBAMWriter of type "type" for writing SAMRecords to and output destination

Parameters:

type - the type of the writer we want to create

destination - the destination, must not be null. Note that SAM writer associated with the destination must have its presorted bit set to false, as reads may come in out of order during writing.

Method Details

close

public void close()

Close any output resource associated with this writer.

Specified by:

close in interface AutoCloseable

writeReadsAlignedToHaplotypes

public void writeReadsAlignedToHaplotypes(Collection<Haplotype> haplotypes,
 htsjdk.samtools.util.Locatable paddedReferenceLoc,
 Collection<Haplotype> bestHaplotypes,
 Set<Haplotype> calledHaplotypes,
 AlleleLikelihoods<GATKRead,Haplotype> readLikelihoods,
 htsjdk.samtools.util.Locatable callableRegion)

Write out a BAM representing for the haplotype caller at this site writerType (ALL_POSSIBLE_HAPLOTYPES or CALLED_HAPLOTYPES) determines inputs to writeHaplotypesAsReads Write out a BAM representing the haplotypes at this site, based on the value for writerType used when the writer was constructed (ALL_POSSIBLE_HAPLOTYPES or CALLED_HAPLOTYPES).

Parameters:

haplotypes - a list of all possible haplotypes at this loc, cannot be null

paddedReferenceLoc - the span of the based reference here, cannot be null

bestHaplotypes - a list of the best (a subset of all) haplotypes that actually went forward into genotyping, cannot be null

calledHaplotypes - a list of the haplotypes that where actually called as non-reference, cannot be null

readLikelihoods - a map from sample -> likelihoods for each read for each of the best haplotypes, cannot be null

callableRegion - the region over which variants are being called

writeReadsAlignedToHaplotypes

public void writeReadsAlignedToHaplotypes(Collection<Haplotype> haplotypes,
 htsjdk.samtools.util.Locatable paddedReferenceLoc,
 Collection<Haplotype> bestHaplotypes,
 Set<Haplotype> calledHaplotypes,
 AlleleLikelihoods<GATKRead,Haplotype> readLikelihoods)

setAddSpecialTag

public void setAddSpecialTag(boolean addSpecialTag)