org.broadinstitute.hellbender.tools.walkers.mutect.clustering

Class SomaticClusteringModel

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.mutect.clustering.SomaticClusteringModel

public class SomaticClusteringModel
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
SomaticClusteringModel(M2FiltersArgumentCollection MTFAC, java.util.List<MutectStats> mutectStats)

Method Summary

Modifier and Type	Method and Description
java.util.List<org.apache.commons.lang3.tuple.Pair<java.lang.String,java.lang.String>>	clusteringMetadata()
double	getLogPriorOfSomaticVariant(htsjdk.variant.variantcontext.VariantContext vc, int altIndex)
double	getLogPriorOfVariantVersusArtifact()
static int	indelLength(htsjdk.variant.variantcontext.VariantContext vc, int altIndex)
void	learnAndClearAccumulatedData()
double	logLikelihoodGivenSomatic(int totalCount, int altCount)
double	probabilityOfSequencingError(Datum datum)
void	record(int[] tumorADs, double[] tumorLogOdds, double artifactProbability, double nonSomaticProbability, htsjdk.variant.variantcontext.VariantContext vc)

Methods inherited from class java.lang.Object

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

Constructor Detail

SomaticClusteringModel

public SomaticClusteringModel(M2FiltersArgumentCollection MTFAC,
                              java.util.List<MutectStats> mutectStats)

Method Detail

getLogPriorOfSomaticVariant

public double getLogPriorOfSomaticVariant(htsjdk.variant.variantcontext.VariantContext vc,
                                          int altIndex)

getLogPriorOfVariantVersusArtifact

public double getLogPriorOfVariantVersusArtifact()

probabilityOfSequencingError

public double probabilityOfSequencingError(Datum datum)

record

public void record(int[] tumorADs,
                   double[] tumorLogOdds,
                   double artifactProbability,
                   double nonSomaticProbability,
                   htsjdk.variant.variantcontext.VariantContext vc)

learnAndClearAccumulatedData

public void learnAndClearAccumulatedData()

logLikelihoodGivenSomatic

public double logLikelihoodGivenSomatic(int totalCount,
                                        int altCount)

clusteringMetadata

public java.util.List<org.apache.commons.lang3.tuple.Pair<java.lang.String,java.lang.String>> clusteringMetadata()

indelLength

public static int indelLength(htsjdk.variant.variantcontext.VariantContext vc,
                              int altIndex)