org.broadinstitute.hellbender.tools.walkers.readorientation

Class LearnReadOrientationModelEngine

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.readorientation.LearnReadOrientationModelEngine

public class LearnReadOrientationModelEngine
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description

LearnReadOrientationModelEngine(htsjdk.samtools.util.Histogram<java.lang.Integer> refHistogram, java.util.List<htsjdk.samtools.util.Histogram<java.lang.Integer>> altDepthOneHistograms, java.util.List<AltSiteRecord> altDesignMatrixForContext, double convergenceThreshold, int maxEMIterations, int maxDepth, org.apache.logging.log4j.Logger logger) Contract: the reference contexts must be combined with its reverse complements prior to instantiating this class

Method Summary

Modifier and Type	Method and Description
static double[]	computeResponsibilities(Nucleotide refAllele, Nucleotide altAllele, int altDepth, int f1r2AltCount, int depth, double[] artifactPrior, boolean givenNotHomRef) Return normalized probabilities
double[]	getAltDepth1Resonsibilities(int rowNum)
double[]	getAltResonsibilities(int rowNum)
org.apache.commons.math3.linear.RealVector	getEffectiveCounts()
double	getEffectiveCounts(ArtifactState state)
static double[]	getFlatPrior(Nucleotide refAllele)
double[]	getRefResonsibilities(int rowNum)
ArtifactPrior	learnPriorForArtifactStates()

Methods inherited from class java.lang.Object

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

Constructor Detail

LearnReadOrientationModelEngine

public LearnReadOrientationModelEngine(htsjdk.samtools.util.Histogram<java.lang.Integer> refHistogram,
                                       java.util.List<htsjdk.samtools.util.Histogram<java.lang.Integer>> altDepthOneHistograms,
                                       java.util.List<AltSiteRecord> altDesignMatrixForContext,
                                       double convergenceThreshold,
                                       int maxEMIterations,
                                       int maxDepth,
                                       org.apache.logging.log4j.Logger logger)

Contract: the reference contexts must be combined with its reverse complements prior to instantiating this class

Method Detail

learnPriorForArtifactStates

public ArtifactPrior learnPriorForArtifactStates()

computeResponsibilities

public static double[] computeResponsibilities(Nucleotide refAllele,
                                               Nucleotide altAllele,
                                               int altDepth,
                                               int f1r2AltCount,
                                               int depth,
                                               double[] artifactPrior,
                                               boolean givenNotHomRef)

Return normalized probabilities

getRefResonsibilities

public double[] getRefResonsibilities(int rowNum)

getAltResonsibilities

public double[] getAltResonsibilities(int rowNum)

getAltDepth1Resonsibilities

public double[] getAltDepth1Resonsibilities(int rowNum)

getEffectiveCounts

public org.apache.commons.math3.linear.RealVector getEffectiveCounts()

getEffectiveCounts

public double getEffectiveCounts(ArtifactState state)

getFlatPrior

public static double[] getFlatPrior(Nucleotide refAllele)