Package org.broadinstitute.hellbender.utils.variant.writers

Class ReblockingGVCFBlockCombiner

java.lang.Object

org.broadinstitute.hellbender.utils.variant.writers.GVCFBlockCombiner

org.broadinstitute.hellbender.utils.variant.writers.ReblockingGVCFBlockCombiner

All Implemented Interfaces:

PushPullTransformer<htsjdk.variant.variantcontext.VariantContext>

public class ReblockingGVCFBlockCombiner
extends GVCFBlockCombiner
implements PushPullTransformer<htsjdk.variant.variantcontext.VariantContext>

Combines variants into GVCF blocks.

Method Summary

Modifier and Type	Method	Description
protected htsjdk.variant.variantcontext.VariantContext	addHomRefSite(htsjdk.variant.variantcontext.VariantContext vc, htsjdk.variant.variantcontext.Genotype g)	Add hom-ref site from vc to this gVCF hom-ref state tracking, emitting any pending states if appropriate
int	getBufferEnd()
int	getBufferStart()
String	getCurrentContig()
int	getVcfOutputEnd()
boolean	isBufferEmpty()
static void	moveBuilderStart(htsjdk.variant.variantcontext.VariantContextBuilder builder, int newStart, CachingIndexedFastaSequenceFile referenceReader)	Modifies ref block builder to change start position and update ref allele accordingly in VC and genotypes
void	signalEndOfInput()	Used to tell the transformer that no more items will be submitted to it, and that it should finalize any pending items.
void	submit(htsjdk.variant.variantcontext.VariantContext variantContextToOutput)	Add the input as a new reference block or write and remove ref blocks that end before the variantContext if it is variant Trim ref block if the variant occurs in the middle of a block

Methods inherited from class org.broadinstitute.hellbender.utils.variant.writers.GVCFBlockCombiner

addRangesToHeader, consumeFinalizedItems, hasFinalizedItems

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.broadinstitute.hellbender.utils.iterators.PushPullTransformer

consumeFinalizedItems, hasFinalizedItems, submit

Method Details

addHomRefSite

protected htsjdk.variant.variantcontext.VariantContext addHomRefSite(htsjdk.variant.variantcontext.VariantContext vc,
 htsjdk.variant.variantcontext.Genotype g)

Add hom-ref site from vc to this gVCF hom-ref state tracking, emitting any pending states if appropriate

Overrides:

addHomRefSite in class GVCFBlockCombiner

Parameters:

vc - a non-null VariantContext

g - a non-null genotype from VariantContext

Returns:

a VariantContext to be emitted, or null if non is appropriate

submit

public void submit(htsjdk.variant.variantcontext.VariantContext variantContextToOutput)

Add the input as a new reference block or write and remove ref blocks that end before the variantContext if it is variant Trim ref block if the variant occurs in the middle of a block

Specified by:

submit in interface PushPullTransformer<htsjdk.variant.variantcontext.VariantContext>

Overrides:

submit in class GVCFBlockCombiner

Parameters:

variantContextToOutput - may be variant or reference, can overlap existing ref blocks in buffer, but should never start before vcfOutputEnd

moveBuilderStart

public static void moveBuilderStart(htsjdk.variant.variantcontext.VariantContextBuilder builder,
 int newStart,
 CachingIndexedFastaSequenceFile referenceReader)

Modifies ref block builder to change start position and update ref allele accordingly in VC and genotypes

Parameters:

builder - a builder for a reference block, contains only NON_REF, no other ALTs

newStart - the new position for the reference block

getVcfOutputEnd

public int getVcfOutputEnd()

getCurrentContig

public String getCurrentContig()

getBufferEnd

public int getBufferEnd()

isBufferEmpty

public boolean isBufferEmpty()

getBufferStart

public int getBufferStart()

signalEndOfInput

public void signalEndOfInput()

Description copied from interface: PushPullTransformer

Used to tell the transformer that no more items will be submitted to it, and that it should finalize any pending items.

Specified by:

signalEndOfInput in interface PushPullTransformer<htsjdk.variant.variantcontext.VariantContext>

Overrides:

signalEndOfInput in class GVCFBlockCombiner