org.broadinstitute.hellbender.engine

Interface AssemblyRegionEvaluator

All Known Implementing Classes:

HaplotypeCallerEngine, Mutect2Engine

Functional Interface:

This is a functional interface and can therefore be used as the assignment target for a lambda expression or method reference.

@FunctionalInterface
public interface AssemblyRegionEvaluator

Classes that implement this interface have the ability to evaluate how likely it is that a site is "active" (contains potential real variation).

Method Summary

Modifier and Type	Method and Description
ActivityProfileState	isActive(AlignmentContext locusPileup, ReferenceContext referenceContext, FeatureContext featureContext) Given a pileup over a single locus, returns an ActivityProfileState containing the probability (0.0 to 1.0) that the locus is an "active" site.

Method Detail

isActive

ActivityProfileState isActive(AlignmentContext locusPileup,
                              ReferenceContext referenceContext,
                              FeatureContext featureContext)

Given a pileup over a single locus, returns an ActivityProfileState containing the probability (0.0 to 1.0) that the locus is an "active" site.

Parameters:

locusPileup - reads pileup to examine

referenceContext - reference base overlapping the pileup locus

featureContext - features overlapping the pileup locus

Returns:

ActivityProfileState containing the probability between 0.0 and 1.0 that the site is active