Package org.broadinstitute.hellbender.tools.walkers.featuremapping

Class SNVMapper

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.featuremapping.SNVMapper

All Implemented Interfaces:

FeatureMapper

public class SNVMapper
extends Object
implements FeatureMapper

An implementation of a feature mapper that finds SNPs (SVN) This class only finds SNP that are surrounded by a specific number of bases identical to the reference.

Constructor Summary

Constructors

Constructor	Description
SNVMapper(FlowFeatureMapperArgumentCollection fmArgs)

Method Summary

Modifier and Type	Method	Description
void	forEachOnRead(GATKRead read, ReferenceContext referenceContext, Consumer<? super FlowFeatureMapper.MappedFeature> action)
boolean	noFeatureButFilterAt(GATKRead read, ReferenceContext referenceContext, int start)

Methods inherited from class java.lang.Object

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

Constructor Details

SNVMapper

public SNVMapper(FlowFeatureMapperArgumentCollection fmArgs)

Method Details

forEachOnRead

public void forEachOnRead(GATKRead read,
 ReferenceContext referenceContext,
 Consumer<? super FlowFeatureMapper.MappedFeature> action)

Specified by:

forEachOnRead in interface FeatureMapper

noFeatureButFilterAt

public boolean noFeatureButFilterAt(GATKRead read,
 ReferenceContext referenceContext,
 int start)

Specified by:

noFeatureButFilterAt in interface FeatureMapper