org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup

Class AllelePileupCounter

java.lang.Object

org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup.AllelePileupCounter

public class AllelePileupCounter
extends java.lang.Object

Useful when you know the interval and the alleles of interest ahead of the counting. Supports simple Indels, SNP, and MNP.

Constructor Summary

Constructors

Constructor and Description
AllelePileupCounter(htsjdk.variant.variantcontext.Allele referenceAllele, java.util.List<htsjdk.variant.variantcontext.Allele> alternateAlleles, int minBaseQualityCutoff)
AllelePileupCounter(htsjdk.variant.variantcontext.Allele referenceAllele, java.util.List<htsjdk.variant.variantcontext.Allele> alternateAlleles, int minBaseQualityCutoff, ReadPileup readPileup) See AllelePileupCounter(Allele, List, int), except this will immediately add the given pileup as well.

Method Summary

Modifier and Type	Method and Description
void	addPileup(ReadPileup pileup)
java.util.Map<htsjdk.variant.variantcontext.Allele,org.apache.commons.lang3.mutable.MutableInt>	getCountMap()

Methods inherited from class java.lang.Object

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

Constructor Detail

AllelePileupCounter

public AllelePileupCounter(htsjdk.variant.variantcontext.Allele referenceAllele,
                           java.util.List<htsjdk.variant.variantcontext.Allele> alternateAlleles,
                           int minBaseQualityCutoff)

Parameters:

referenceAllele - allele to treat as reference. Create with Allele.create(String, boolean), where second parameter is true. Never null. If the reference is symbolic, exception will be thrown.

alternateAlleles - List of alleles to treat as the alternates. Easy to create with Allele.create(String, boolean), where second parameter is false. Never null

minBaseQualityCutoff - minimum base quality for the bases that match the allele in order to be counted. Must be positive or zero.

AllelePileupCounter

public AllelePileupCounter(htsjdk.variant.variantcontext.Allele referenceAllele,
                           java.util.List<htsjdk.variant.variantcontext.Allele> alternateAlleles,
                           int minBaseQualityCutoff,
                           ReadPileup readPileup)

See AllelePileupCounter(Allele, List, int), except this will immediately add the given pileup as well.

Parameters:

referenceAllele - See AllelePileupCounter(Allele, List, int)

alternateAlleles - See AllelePileupCounter(Allele, List, int)

minBaseQualityCutoff - See AllelePileupCounter(Allele, List, int)

readPileup - Initial pileup to add to this allele pileup counter

Method Detail

addPileup

public void addPileup(ReadPileup pileup)

Parameters:

pileup - read pileup to base the counts of each allele. If null, it will not be considered.

getCountMap

public java.util.Map<htsjdk.variant.variantcontext.Allele,org.apache.commons.lang3.mutable.MutableInt> getCountMap()