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

Class AlleleCount

java.lang.Object

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

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

All Implemented Interfaces:

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

public class AlleleCount
extends VariantStratifier

Stratifies the eval RODs by the allele count of the alternate allele Looks first at the MLEAC value in the INFO field, and uses that value if present. If not present, it then looks for the AC value in the INFO field. If both are absent, it computes the AC from the genotypes themselves. If no AC can be computed, 0 is used.

Field Summary

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

states

Constructor Summary

Constructors

Constructor and Description
AlleleCount()

Method Summary

Modifier and Type	Method and Description
java.lang.String	getFormat()
java.util.Set<java.lang.Class<? extends VariantEvaluator>>	getIncompatibleEvaluators() The way for a stratifier to specify that it's incompatible with specific evaluations.
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, getName, getVariantEvalWalker, setVariantEvalWalker, toString

Methods inherited from class java.lang.Object

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

Constructor Detail

AlleleCount

public AlleleCount()

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

getIncompatibleEvaluators

public java.util.Set<java.lang.Class<? extends VariantEvaluator>> getIncompatibleEvaluators()

Description copied from class: VariantStratifier

The way for a stratifier to specify that it's incompatible with specific evaluations. For example, VariantSummary includes a per-sample metric, and so cannot be used safely with Sample or AlleleCount stratifications as this introduces an O(n^2) memory and cpu cost.

Overrides:

getIncompatibleEvaluators in class VariantStratifier

Returns:

the set of VariantEvaluators that cannot be active with this Stratification

getFormat

public java.lang.String getFormat()

Overrides:

getFormat in class VariantStratifier