org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications

Class OneBPIndel

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.VariantStratifier

org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.OneBPIndel

All Implemented Interfaces:

java.lang.Comparable<VariantStratifier>, Stratifier<java.lang.Object>

public class OneBPIndel
extends VariantStratifier

Stratifies the eval RODs into sites where the indel is 1 bp in length and those where the event is 2+. all non indel events go into all bins, so that SNP counts can be used as contrasts in eval modules.

Field Summary

Fields inherited from class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.VariantStratifier

states

Constructor Summary

Constructors

Constructor and Description
OneBPIndel()

Method Summary

Modifier and Type	Method and Description
java.util.List<java.lang.Object>	getRelevantStates(ReferenceContext referenceContext, ReadsContext readsContext, FeatureContext featureContext, htsjdk.variant.variantcontext.VariantContext comp, java.lang.String compName, htsjdk.variant.variantcontext.VariantContext eval, java.lang.String evalName, java.lang.String sampleName, java.lang.String FamilyName)
void	initialize()

Methods inherited from class org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.VariantStratifier

compareTo, getAllStates, getFormat, getIncompatibleEvaluators, getName, getVariantEvalWalker, setVariantEvalWalker, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

OneBPIndel

public OneBPIndel()

Method Detail

initialize

public void initialize()

Specified by:

initialize in class VariantStratifier

getRelevantStates

public java.util.List<java.lang.Object> getRelevantStates(ReferenceContext referenceContext,
                                                          ReadsContext readsContext,
                                                          FeatureContext featureContext,
                                                          htsjdk.variant.variantcontext.VariantContext comp,
                                                          java.lang.String compName,
                                                          htsjdk.variant.variantcontext.VariantContext eval,
                                                          java.lang.String evalName,
                                                          java.lang.String sampleName,
                                                          java.lang.String FamilyName)

Specified by:

getRelevantStates in class VariantStratifier