org.broadinstitute.hellbender.utils.variant.writers

Class GVCFBlockCombiner

java.lang.Object

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

All Implemented Interfaces:

PushPullTransformer<htsjdk.variant.variantcontext.VariantContext>

Direct Known Subclasses:

SomaticGVCFBlockCombiner

public class GVCFBlockCombiner
extends java.lang.Object
implements PushPullTransformer<htsjdk.variant.variantcontext.VariantContext>

Combines variants into GVCF blocks.

Constructor Summary

Constructors

Constructor and Description
GVCFBlockCombiner(java.util.List<java.lang.Number> gqPartitions, int defaultPloidy, boolean floorBlocks)

Method Summary

Modifier and Type	Method and 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
void	addRangesToHeader(htsjdk.variant.vcf.VCFHeader header)
java.util.List<htsjdk.variant.variantcontext.VariantContext>	consumeFinalizedItems() Return (and *remove*) all items that have survived transformation and are waiting to be retrieved.
boolean	hasFinalizedItems() Are there items that have survived the transformation process waiting to be retrieved?
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 vc) Submit one item to the transformer for consideration.

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

submit

Constructor Detail

GVCFBlockCombiner

public GVCFBlockCombiner(java.util.List<java.lang.Number> gqPartitions,
                         int defaultPloidy,
                         boolean floorBlocks)

Method Detail

addRangesToHeader

public void addRangesToHeader(htsjdk.variant.vcf.VCFHeader header)

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

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 vc)

Description copied from interface: PushPullTransformer

Submit one item to the transformer for consideration. Some transformers will be able to determine immediately whether the item survives the transformation process, while others will need to see more items before making that determination.

Specified by:

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

Parameters:

vc - the individual item to submit to the transformer for consideration

hasFinalizedItems

public boolean hasFinalizedItems()

Description copied from interface: PushPullTransformer

Are there items that have survived the transformation process waiting to be retrieved?

Specified by:

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

Returns:

true if this transformer has > 0 finalized items, otherwise false

consumeFinalizedItems

public java.util.List<htsjdk.variant.variantcontext.VariantContext> consumeFinalizedItems()

Description copied from interface: PushPullTransformer

Return (and *remove*) all items that have survived transformation and are waiting to be retrieved.

Specified by:

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

Returns:

a list of all finalized items this transformer contains, or an empty list if there are none

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>