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

Class JexlExpression

java.lang.Object

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

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

All Implemented Interfaces:

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

public class JexlExpression
extends VariantStratifier
implements StandardStratification

Stratifies the eval RODs by user-supplied JEXL expressions See http://gatkforums.broadinstitute.org/discussion/1255/what-are-jexl-expressions-and-how-can-i-use-them-with-the-gatk for more details

Field Summary

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

states

Constructor Summary

Constructors

Constructor and Description
JexlExpression()

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

JexlExpression

public JexlExpression()

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