org.broadinstitute.hellbender.utils.variant.writers

Class SomaticGVCFBlockCombiner

java.lang.Object

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

org.broadinstitute.hellbender.utils.variant.writers.SomaticGVCFBlockCombiner

All Implemented Interfaces:

PushPullTransformer<htsjdk.variant.variantcontext.VariantContext>

public class SomaticGVCFBlockCombiner
extends GVCFBlockCombiner

Field Summary

Fields

Modifier and Type	Field and Description
protected int	partitionPrecision

Constructor Summary

Constructors

Constructor and Description
SomaticGVCFBlockCombiner(java.util.List<java.lang.Number> gqPartitions, int defaultPloidy)
SomaticGVCFBlockCombiner(java.util.List<java.lang.Number> gqPartitions, int defaultPloidy, int partitionPrecision)

Method Summary

Modifier and Type	Method and Description
protected static int	convertLODtoInt(double LOD, int partitionPrecision)

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

addHomRefSite, addRangesToHeader, consumeFinalizedItems, hasFinalizedItems, signalEndOfInput, submit

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

Field Detail

partitionPrecision

protected int partitionPrecision

Constructor Detail

SomaticGVCFBlockCombiner

public SomaticGVCFBlockCombiner(java.util.List<java.lang.Number> gqPartitions,
                                int defaultPloidy)

SomaticGVCFBlockCombiner

public SomaticGVCFBlockCombiner(java.util.List<java.lang.Number> gqPartitions,
                                int defaultPloidy,
                                int partitionPrecision)

Method Detail

convertLODtoInt

protected static int convertLODtoInt(double LOD,
                                     int partitionPrecision)