PerReadAlleleLikelihoodMap getMostLikelyAllele returns an MostLikelyAllele objects now
-- This new functionality allows the client to make decisions about how to handle non-informative reads, rather than having a single enforced constant that isn't really appropriate for all users. The previous functionality is maintained now and used by all of the updated pieces of code, except the BAM writers, which now emit reads to display to their best allele, regardless of whether this is particularly informative or not. That way you can see all of your data realigned to the new HC structure, rather than just those that are specifically informative. -- This all makes me concerned that the informative thresholding isn't appropriately used in the annotations themselves. There are many cases where nearby variation makes specific reads non-informative about one event, due to not being informative about the second. For example, suppose you have two SNPs A/B and C/D that are in the same active region but separated by more than the read length of the reads. All reads would be non-informative as no read provides information about the full combination of 4 haplotypes, as they reads only span a single event. In this case our annotations will all fall apart, returning their default values. Added a JIRA to address this (should be discussed in group meeting)
This commit is contained in:
Mark DePristo
parent
2472828e1c
commit
ad04fdb233
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@ -47,6 +47,7 @@
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package org.broadinstitute.sting.gatk.walkers.annotator;
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import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
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import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele;
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import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
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import org.broadinstitute.variant.vcf.VCFHeaderLineType;
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import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
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@ -90,13 +91,13 @@ public class BaseQualityRankSumTest extends RankSumTest implements StandardAnnot
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}
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for (Map<Allele,Double> el : alleleLikelihoodMap.getLikelihoodMapValues()) {
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final Allele a = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el);
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if (a.isNoCall())
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final MostLikelyAllele a = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el);
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if (! a.isInformative())
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continue; // read is non-informative
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if (a.isReference())
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refQuals.add(-10.0*(double)el.get(a));
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else if (allAlleles.contains(a))
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altQuals.add(-10.0*(double)el.get(a));
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if (a.getMostLikelyAllele().isReference())
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refQuals.add(-10.0*(double)el.get(a.getMostLikelyAllele()));
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else if (allAlleles.contains(a.getMostLikelyAllele()))
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altQuals.add(-10.0*(double)el.get(a.getMostLikelyAllele()));
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}
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@ -46,6 +46,7 @@
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package org.broadinstitute.sting.gatk.walkers.annotator;
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import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele;
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import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
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import org.broadinstitute.variant.vcf.VCFHeaderLineType;
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import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
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@ -84,12 +85,12 @@ public class ClippingRankSumTest extends RankSumTest {
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for (Map.Entry<GATKSAMRecord,Map<Allele,Double>> el : likelihoodMap.getLikelihoodReadMap().entrySet()) {
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final Allele a = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue());
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if (a.isNoCall())
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final MostLikelyAllele a = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue());
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if (! a.isInformative())
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continue; // read is non-informative
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if (a.isReference())
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if (a.getMostLikelyAllele().isReference())
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refQuals.add((double)AlignmentUtils.getNumHardClippedBases(el.getKey()));
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else if (allAlleles.contains(a))
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else if (allAlleles.contains(a.getMostLikelyAllele()))
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altQuals.add((double)AlignmentUtils.getNumHardClippedBases(el.getKey()));
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}
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@ -52,6 +52,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
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import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
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import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
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import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele;
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import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
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import org.broadinstitute.variant.vcf.VCFConstants;
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import org.broadinstitute.variant.vcf.VCFFormatHeaderLine;
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@ -141,12 +142,12 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
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}
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for (Map.Entry<GATKSAMRecord,Map<Allele,Double>> el : perReadAlleleLikelihoodMap.getLikelihoodReadMap().entrySet()) {
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final GATKSAMRecord read = el.getKey();
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final Allele a = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue());
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if (a.isNoCall())
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final MostLikelyAllele a = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue());
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if (! a.isInformative() )
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continue; // read is non-informative
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if (!vc.getAlleles().contains(a))
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if (!vc.getAlleles().contains(a.getMostLikelyAllele()))
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continue; // sanity check - shouldn't be needed
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alleleCounts.put(a, alleleCounts.get(a) + (read.isReducedRead() ? read.getReducedCount(ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(read, vc.getStart(), ReadUtils.ClippingTail.RIGHT_TAIL)) : 1));
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alleleCounts.put(a.getMostLikelyAllele(), alleleCounts.get(a.getMostLikelyAllele()) + (read.isReducedRead() ? read.getReducedCount(ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(read, vc.getStart(), ReadUtils.ClippingTail.RIGHT_TAIL)) : 1));
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}
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final int[] counts = new int[alleleCounts.size()];
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counts[0] = alleleCounts.get(vc.getReference());
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@ -55,6 +55,7 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ActiveRegionBa
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import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
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import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
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import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
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import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele;
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import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
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import org.broadinstitute.sting.utils.QualityUtils;
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import org.broadinstitute.variant.vcf.VCFHeaderLineType;
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@ -273,10 +274,10 @@ public class FisherStrand extends InfoFieldAnnotation implements StandardAnnotat
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for (PerReadAlleleLikelihoodMap maps : stratifiedPerReadAlleleLikelihoodMap.values() ) {
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for (Map.Entry<GATKSAMRecord,Map<Allele,Double>> el : maps.getLikelihoodReadMap().entrySet()) {
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final Allele mostLikelyAllele = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue());
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final MostLikelyAllele mostLikelyAllele = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue());
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final GATKSAMRecord read = el.getKey();
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final int representativeCount = read.isReducedRead() ? read.getReducedCount(ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(read, vc.getStart(), ReadUtils.ClippingTail.RIGHT_TAIL)) : 1;
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updateTable(table, mostLikelyAllele, read, ref, alt, representativeCount);
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updateTable(table, mostLikelyAllele.getAlleleIfInformative(), read, ref, alt, representativeCount);
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}
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}
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@ -47,6 +47,7 @@
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package org.broadinstitute.sting.gatk.walkers.annotator;
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import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
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import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele;
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import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
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import org.broadinstitute.variant.vcf.VCFHeaderLineType;
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import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
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@ -92,13 +93,13 @@ public class MappingQualityRankSumTest extends RankSumTest implements StandardAn
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return;
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}
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for (Map.Entry<GATKSAMRecord,Map<Allele,Double>> el : likelihoodMap.getLikelihoodReadMap().entrySet()) {
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final Allele a = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue());
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final MostLikelyAllele a = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue());
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// BUGBUG: There needs to be a comparable isUsableBase check here
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if (a.isNoCall())
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if (! a.isInformative())
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continue; // read is non-informative
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if (a.isReference())
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if (a.getMostLikelyAllele().isReference())
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refQuals.add((double)el.getKey().getMappingQuality());
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else if (allAlleles.contains(a))
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else if (allAlleles.contains(a.getMostLikelyAllele()))
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altQuals.add((double)el.getKey().getMappingQuality());
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}
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}
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@ -51,6 +51,7 @@ import net.sf.samtools.CigarElement;
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import net.sf.samtools.CigarOperator;
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import net.sf.samtools.SAMRecord;
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import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
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import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele;
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import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
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import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
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import org.broadinstitute.variant.vcf.VCFHeaderLineType;
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@ -107,8 +108,8 @@ public class ReadPosRankSumTest extends RankSumTest implements StandardAnnotatio
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}
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for (Map.Entry<GATKSAMRecord,Map<Allele,Double>> el : alleleLikelihoodMap.getLikelihoodReadMap().entrySet()) {
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final Allele a = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue());
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if (a.isNoCall())
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final MostLikelyAllele a = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue());
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if (! a.isInformative() )
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continue; // read is non-informative
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final GATKSAMRecord read = el.getKey();
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@ -123,9 +124,9 @@ public class ReadPosRankSumTest extends RankSumTest implements StandardAnnotatio
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if (readPos > numAlignedBases / 2)
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readPos = numAlignedBases - (readPos + 1);
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if (a.isReference())
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if (a.getMostLikelyAllele().isReference())
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refQuals.add((double)readPos);
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else if (allAlleles.contains(a))
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else if (allAlleles.contains(a.getMostLikelyAllele()))
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altQuals.add((double)readPos);
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}
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}
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@ -0,0 +1,114 @@
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/*
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* By downloading the PROGRAM you agree to the following terms of use:
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*
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* BROAD INSTITUTE - SOFTWARE LICENSE AGREEMENT - FOR ACADEMIC NON-COMMERCIAL RESEARCH PURPOSES ONLY
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*
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* This Agreement is made between the Broad Institute, Inc. with a principal address at 7 Cambridge Center, Cambridge, MA 02142 (BROAD) and the LICENSEE and is effective at the date the downloading is completed (EFFECTIVE DATE).
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*
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* WHEREAS, LICENSEE desires to license the PROGRAM, as defined hereinafter, and BROAD wishes to have this PROGRAM utilized in the public interest, subject only to the royalty-free, nonexclusive, nontransferable license rights of the United States Government pursuant to 48 CFR 52.227-14; and
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* WHEREAS, LICENSEE desires to license the PROGRAM and BROAD desires to grant a license on the following terms and conditions.
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* NOW, THEREFORE, in consideration of the promises and covenants made herein, the parties hereto agree as follows:
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*
|
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* 1. DEFINITIONS
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* 1.1 PROGRAM shall mean copyright in the object code and source code known as GATK2 and related documentation, if any, as they exist on the EFFECTIVE DATE and can be downloaded from http://www.broadinstitute/GATK on the EFFECTIVE DATE.
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*
|
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* 2. LICENSE
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* 2.1 Grant. Subject to the terms of this Agreement, BROAD hereby grants to LICENSEE, solely for academic non-commercial research purposes, a non-exclusive, non-transferable license to: (a) download, execute and display the PROGRAM and (b) create bug fixes and modify the PROGRAM.
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* The LICENSEE may apply the PROGRAM in a pipeline to data owned by users other than the LICENSEE and provide these users the results of the PROGRAM provided LICENSEE does so for academic non-commercial purposes only. For clarification purposes, academic sponsored research is not a commercial use under the terms of this Agreement.
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* 2.2 No Sublicensing or Additional Rights. LICENSEE shall not sublicense or distribute the PROGRAM, in whole or in part, without prior written permission from BROAD. LICENSEE shall ensure that all of its users agree to the terms of this Agreement. LICENSEE further agrees that it shall not put the PROGRAM on a network, server, or other similar technology that may be accessed by anyone other than the LICENSEE and its employees and users who have agreed to the terms of this agreement.
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* 2.3 License Limitations. Nothing in this Agreement shall be construed to confer any rights upon LICENSEE by implication, estoppel, or otherwise to any computer software, trademark, intellectual property, or patent rights of BROAD, or of any other entity, except as expressly granted herein. LICENSEE agrees that the PROGRAM, in whole or part, shall not be used for any commercial purpose, including without limitation, as the basis of a commercial software or hardware product or to provide services. LICENSEE further agrees that the PROGRAM shall not be copied or otherwise adapted in order to circumvent the need for obtaining a license for use of the PROGRAM.
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*
|
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* 3. OWNERSHIP OF INTELLECTUAL PROPERTY
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* LICENSEE acknowledges that title to the PROGRAM shall remain with BROAD. The PROGRAM is marked with the following BROAD copyright notice and notice of attribution to contributors. LICENSEE shall retain such notice on all copies. LICENSEE agrees to include appropriate attribution if any results obtained from use of the PROGRAM are included in any publication.
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* Copyright 2012 Broad Institute, Inc.
|
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* Notice of attribution: The GATK2 program was made available through the generosity of Medical and Population Genetics program at the Broad Institute, Inc.
|
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* LICENSEE shall not use any trademark or trade name of BROAD, or any variation, adaptation, or abbreviation, of such marks or trade names, or any names of officers, faculty, students, employees, or agents of BROAD except as states above for attribution purposes.
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*
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* 4. INDEMNIFICATION
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* LICENSEE shall indemnify, defend, and hold harmless BROAD, and their respective officers, faculty, students, employees, associated investigators and agents, and their respective successors, heirs and assigns, (Indemnitees), against any liability, damage, loss, or expense (including reasonable attorneys fees and expenses) incurred by or imposed upon any of the Indemnitees in connection with any claims, suits, actions, demands or judgments arising out of any theory of liability (including, without limitation, actions in the form of tort, warranty, or strict liability and regardless of whether such action has any factual basis) pursuant to any right or license granted under this Agreement.
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*
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* 5. NO REPRESENTATIONS OR WARRANTIES
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* THE PROGRAM IS DELIVERED AS IS. BROAD MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE PROGRAM OR THE COPYRIGHT, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE. BROAD EXTENDS NO WARRANTIES OF ANY KIND AS TO PROGRAM CONFORMITY WITH WHATEVER USER MANUALS OR OTHER LITERATURE MAY BE ISSUED FROM TIME TO TIME.
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* IN NO EVENT SHALL BROAD OR ITS RESPECTIVE DIRECTORS, OFFICERS, EMPLOYEES, AFFILIATED INVESTIGATORS AND AFFILIATES BE LIABLE FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES OF ANY KIND, INCLUDING, WITHOUT LIMITATION, ECONOMIC DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER BROAD SHALL BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE FOREGOING.
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* 6. ASSIGNMENT
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* This Agreement is personal to LICENSEE and any rights or obligations assigned by LICENSEE without the prior written consent of BROAD shall be null and void.
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*
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* 7. MISCELLANEOUS
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* 7.1 Export Control. LICENSEE gives assurance that it will comply with all United States export control laws and regulations controlling the export of the PROGRAM, including, without limitation, all Export Administration Regulations of the United States Department of Commerce. Among other things, these laws and regulations prohibit, or require a license for, the export of certain types of software to specified countries.
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* 7.3 Survival. The following provisions shall survive the expiration or termination of this Agreement: Articles 1, 3, 4, 5 and Sections 2.2, 2.3, 7.3, and 7.4.
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* 7.4 Notice. Any notices under this Agreement shall be in writing, shall specifically refer to this Agreement, and shall be sent by hand, recognized national overnight courier, confirmed facsimile transmission, confirmed electronic mail, or registered or certified mail, postage prepaid, return receipt requested. All notices under this Agreement shall be deemed effective upon receipt.
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* 7.5 Amendment and Waiver; Entire Agreement. This Agreement may be amended, supplemented, or otherwise modified only by means of a written instrument signed by all parties. Any waiver of any rights or failure to act in a specific instance shall relate only to such instance and shall not be construed as an agreement to waive any rights or fail to act in any other instance, whether or not similar. This Agreement constitutes the entire agreement among the parties with respect to its subject matter and supersedes prior agreements or understandings between the parties relating to its subject matter.
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* 7.6 Binding Effect; Headings. This Agreement shall be binding upon and inure to the benefit of the parties and their respective permitted successors and assigns. All headings are for convenience only and shall not affect the meaning of any provision of this Agreement.
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* 7.7 Governing Law. This Agreement shall be construed, governed, interpreted and applied in accordance with the internal laws of the Commonwealth of Massachusetts, U.S.A., without regard to conflict of laws principles.
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*/
|
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|
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package org.broadinstitute.sting.utils.genotyper;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.variant.variantcontext.Allele;
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import org.testng.Assert;
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import org.testng.annotations.Test;
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public class MostLikelyAlleleUnitTest extends BaseTest {
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final Allele a = Allele.create("A");
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@Test
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public void testBasicCreation() {
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final double second = -1 - MostLikelyAllele.INFORMATIVE_LIKELIHOOD_THRESHOLD - 1;
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MostLikelyAllele mla = new MostLikelyAllele(a, -1.0, second);
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Assert.assertEquals(mla.getMostLikelyAllele(), a);
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Assert.assertEquals(mla.getLog10LikelihoodOfMostLikely(), -1.0);
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Assert.assertEquals(mla.getLog10LikelihoodOfSecondBest(), second);
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Assert.assertEquals(mla.isInformative(), true);
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Assert.assertEquals(mla.isInformative(10), false);
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Assert.assertEquals(mla.isInformative(0), true);
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Assert.assertEquals(mla.getAlleleIfInformative(), a);
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Assert.assertEquals(mla.getAlleleIfInformative(10), Allele.NO_CALL);
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Assert.assertEquals(mla.getAlleleIfInformative(0), a);
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}
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@Test
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public void testNotDefaultInformative() {
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final double second = -1.0 - (MostLikelyAllele.INFORMATIVE_LIKELIHOOD_THRESHOLD - 1e-2);
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MostLikelyAllele mla = new MostLikelyAllele(a, -1.0, second);
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Assert.assertEquals(mla.isInformative(), false);
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Assert.assertEquals(mla.isInformative(10), false);
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Assert.assertEquals(mla.isInformative(0), true);
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Assert.assertEquals(mla.getAlleleIfInformative(), Allele.NO_CALL);
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Assert.assertEquals(mla.getAlleleIfInformative(10), Allele.NO_CALL);
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Assert.assertEquals(mla.getAlleleIfInformative(0), a);
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}
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@Test
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public void testCreationNoGoodSecond() {
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MostLikelyAllele mla = new MostLikelyAllele(a, -1.0, Double.NEGATIVE_INFINITY);
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Assert.assertEquals(mla.getMostLikelyAllele(), a);
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Assert.assertEquals(mla.getLog10LikelihoodOfMostLikely(), -1.0);
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Assert.assertEquals(mla.getLog10LikelihoodOfSecondBest(), Double.NEGATIVE_INFINITY);
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Assert.assertEquals(mla.isInformative(), true);
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Assert.assertEquals(mla.isInformative(10), true);
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Assert.assertEquals(mla.isInformative(0), true);
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Assert.assertEquals(mla.getAlleleIfInformative(), a);
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Assert.assertEquals(mla.getAlleleIfInformative(10), a);
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Assert.assertEquals(mla.getAlleleIfInformative(0), a);
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}
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@Test
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public void testCreationNoAllele() {
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MostLikelyAllele mla = new MostLikelyAllele(Allele.NO_CALL, Double.NEGATIVE_INFINITY, Double.NEGATIVE_INFINITY);
|
||||
Assert.assertEquals(mla.getMostLikelyAllele(), Allele.NO_CALL);
|
||||
Assert.assertEquals(mla.getLog10LikelihoodOfMostLikely(), Double.NEGATIVE_INFINITY);
|
||||
Assert.assertEquals(mla.getLog10LikelihoodOfSecondBest(), Double.NEGATIVE_INFINITY);
|
||||
|
||||
Assert.assertEquals(mla.isInformative(), false);
|
||||
Assert.assertEquals(mla.isInformative(10), false);
|
||||
Assert.assertEquals(mla.isInformative(0), false);
|
||||
Assert.assertEquals(mla.getAlleleIfInformative(), Allele.NO_CALL);
|
||||
Assert.assertEquals(mla.getAlleleIfInformative(10), Allele.NO_CALL);
|
||||
Assert.assertEquals(mla.getAlleleIfInformative(0), Allele.NO_CALL);
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,127 @@
|
|||
/*
|
||||
* Copyright (c) 2012 The Broad Institute
|
||||
*
|
||||
* Permission is hereby granted, free of charge, to any person
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* files (the "Software"), to deal in the Software without
|
||||
* restriction, including without limitation the rights to use,
|
||||
* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||
* copies of the Software, and to permit persons to whom the
|
||||
* Software is furnished to do so, subject to the following
|
||||
* conditions:
|
||||
*
|
||||
* The above copyright notice and this permission notice shall be
|
||||
* included in all copies or substantial portions of the Software.
|
||||
*
|
||||
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
||||
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
||||
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
||||
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
||||
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
|
||||
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
|
||||
*/
|
||||
|
||||
package org.broadinstitute.sting.utils.genotyper;
|
||||
|
||||
import org.broadinstitute.sting.utils.MathUtils;
|
||||
import org.broadinstitute.variant.variantcontext.Allele;
|
||||
|
||||
/**
|
||||
* Stores the most likely and second most likely alleles, along with a threshold
|
||||
* for assuming computing that a read is informative.
|
||||
*
|
||||
* If the difference between the most-likely allele and the next-most-likely allele is < INFORMATIVE_LIKELIHOOD_THRESHOLD
|
||||
* then the most likely allele is set to "no call", and isInformative will return false. This constant can be
|
||||
* overridden simply by using one of the version of these calls that accepts informative threshold as an argument.
|
||||
*
|
||||
* For convenience, there are functions called getAlleleIfInformative that return either the most likely allele, or
|
||||
* NO_CALL if two or more alleles have likelihoods within INFORMATIVE_LIKELIHOOD_THRESHOLD of one another.
|
||||
*
|
||||
* By default empty allele maps will return NO_CALL, and allele maps with a single entry will return the
|
||||
* corresponding key
|
||||
*
|
||||
* User: depristo
|
||||
* Date: 3/24/13
|
||||
* Time: 1:39 PM
|
||||
*/
|
||||
public final class MostLikelyAllele {
|
||||
public static final double INFORMATIVE_LIKELIHOOD_THRESHOLD = 0.2;
|
||||
|
||||
final Allele mostLikely;
|
||||
final double log10LikelihoodOfMostLikely;
|
||||
final double log10LikelihoodOfSecondBest;
|
||||
|
||||
/**
|
||||
* Create a new MostLikelyAllele
|
||||
*
|
||||
* If there's a meaningful most likely allele, allele should be a real allele. If none can be determined,
|
||||
* mostLikely should be a NO_CALL allele.
|
||||
*
|
||||
* @param mostLikely the most likely allele
|
||||
* @param log10LikelihoodOfMostLikely the log10 likelihood of the most likely allele
|
||||
* @param log10LikelihoodOfSecondBest the log10 likelihood of the next most likely allele (should be NEGATIVE_INFINITY if none is available)
|
||||
*/
|
||||
public MostLikelyAllele(Allele mostLikely, double log10LikelihoodOfMostLikely, double log10LikelihoodOfSecondBest) {
|
||||
if ( mostLikely == null ) throw new IllegalArgumentException("mostLikely allele cannot be null");
|
||||
if ( log10LikelihoodOfMostLikely != Double.NEGATIVE_INFINITY && ! MathUtils.goodLog10Probability(log10LikelihoodOfMostLikely) )
|
||||
throw new IllegalArgumentException("log10LikelihoodOfMostLikely must be either -Infinity or a good log10 prob but got " + log10LikelihoodOfMostLikely);
|
||||
if ( log10LikelihoodOfSecondBest != Double.NEGATIVE_INFINITY && ! MathUtils.goodLog10Probability(log10LikelihoodOfSecondBest) )
|
||||
throw new IllegalArgumentException("log10LikelihoodOfSecondBest must be either -Infinity or a good log10 prob but got " + log10LikelihoodOfSecondBest);
|
||||
if ( log10LikelihoodOfMostLikely < log10LikelihoodOfSecondBest )
|
||||
throw new IllegalArgumentException("log10LikelihoodOfMostLikely must be <= log10LikelihoodOfSecondBest but got " + log10LikelihoodOfMostLikely + " vs 2nd " + log10LikelihoodOfSecondBest);
|
||||
|
||||
this.mostLikely = mostLikely;
|
||||
this.log10LikelihoodOfMostLikely = log10LikelihoodOfMostLikely;
|
||||
this.log10LikelihoodOfSecondBest = log10LikelihoodOfSecondBest;
|
||||
}
|
||||
|
||||
public Allele getMostLikelyAllele() {
|
||||
return mostLikely;
|
||||
}
|
||||
|
||||
public double getLog10LikelihoodOfMostLikely() {
|
||||
return log10LikelihoodOfMostLikely;
|
||||
}
|
||||
|
||||
public double getLog10LikelihoodOfSecondBest() {
|
||||
return log10LikelihoodOfSecondBest;
|
||||
}
|
||||
|
||||
/**
|
||||
* @see #isInformative(double) with threshold of INFORMATIVE_LIKELIHOOD_THRESHOLD
|
||||
*/
|
||||
public boolean isInformative() {
|
||||
return isInformative(INFORMATIVE_LIKELIHOOD_THRESHOLD);
|
||||
}
|
||||
|
||||
/**
|
||||
* Was this allele selected from an object that was specifically informative about the allele?
|
||||
*
|
||||
* The calculation that implements this is whether the likelihood of the most likely allele is larger
|
||||
* than the second most likely by at least the log10ThresholdForInformative
|
||||
*
|
||||
* @return true if so, false if not
|
||||
*/
|
||||
public boolean isInformative(final double log10ThresholdForInformative) {
|
||||
return getLog10LikelihoodOfMostLikely() - getLog10LikelihoodOfSecondBest() > log10ThresholdForInformative;
|
||||
}
|
||||
|
||||
/**
|
||||
* @see #getAlleleIfInformative(double) with threshold of INFORMATIVE_LIKELIHOOD_THRESHOLD
|
||||
*/
|
||||
public Allele getAlleleIfInformative() {
|
||||
return getAlleleIfInformative(INFORMATIVE_LIKELIHOOD_THRESHOLD);
|
||||
}
|
||||
|
||||
/**
|
||||
* Get the most likely allele if isInformative(log10ThresholdForInformative) is true, or NO_CALL otherwise
|
||||
*
|
||||
* @param log10ThresholdForInformative a log10 threshold to determine if the most likely allele was informative
|
||||
* @return a non-null allele
|
||||
*/
|
||||
public Allele getAlleleIfInformative(final double log10ThresholdForInformative) {
|
||||
return isInformative(log10ThresholdForInformative) ? getMostLikelyAllele() : Allele.NO_CALL;
|
||||
}
|
||||
}
|
||||
|
|
@ -41,10 +41,6 @@ import java.util.*;
|
|||
* For each read, this holds underlying alleles represented by an aligned read, and corresponding relative likelihood.
|
||||
*/
|
||||
public class PerReadAlleleLikelihoodMap {
|
||||
|
||||
|
||||
public static final double INFORMATIVE_LIKELIHOOD_THRESHOLD = 0.2;
|
||||
|
||||
protected List<Allele> alleles;
|
||||
protected Map<GATKSAMRecord, Map<Allele, Double>> likelihoodReadMap;
|
||||
|
||||
|
|
@ -119,9 +115,9 @@ public class PerReadAlleleLikelihoodMap {
|
|||
for ( final Map.Entry<GATKSAMRecord, Map<Allele, Double>> entry : likelihoodReadMap.entrySet() ) {
|
||||
// do not remove reduced reads!
|
||||
if ( !entry.getKey().isReducedRead() ) {
|
||||
final Allele bestAllele = getMostLikelyAllele(entry.getValue());
|
||||
if ( bestAllele != Allele.NO_CALL )
|
||||
alleleReadMap.get(bestAllele).add(entry.getKey());
|
||||
final MostLikelyAllele bestAllele = getMostLikelyAllele(entry.getValue());
|
||||
if ( bestAllele.isInformative() )
|
||||
alleleReadMap.get(bestAllele.getMostLikelyAllele()).add(entry.getKey());
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -194,32 +190,25 @@ public class PerReadAlleleLikelihoodMap {
|
|||
|
||||
/**
|
||||
* Given a map from alleles to likelihoods, find the allele with the largest likelihood.
|
||||
* If the difference between the most-likely allele and the next-most-likely allele is < INFORMATIVE_LIKELIHOOD_THRESHOLD
|
||||
* then the most likely allele is set to "no call"
|
||||
*
|
||||
* @param alleleMap - a map from alleles to likelihoods
|
||||
* @return - the most likely allele, or NO_CALL if two or more alleles have likelihoods within INFORMATIVE_LIKELIHOOD_THRESHOLD
|
||||
* of one another. By default empty allele maps will return NO_CALL, and allele maps with a single entry will return the
|
||||
* corresponding key
|
||||
* @return - a MostLikelyAllele object
|
||||
*/
|
||||
@Ensures("result != null")
|
||||
public static Allele getMostLikelyAllele( final Map<Allele,Double> alleleMap ) {
|
||||
public static MostLikelyAllele getMostLikelyAllele( final Map<Allele,Double> alleleMap ) {
|
||||
return getMostLikelyAllele(alleleMap, null);
|
||||
}
|
||||
|
||||
/**
|
||||
* Given a map from alleles to likelihoods, find the allele with the largest likelihood.
|
||||
* If the difference between the most-likely allele and the next-most-likely allele is < INFORMATIVE_LIKELIHOOD_THRESHOLD
|
||||
* then the most likely allele is set to "no call"
|
||||
*
|
||||
* @param alleleMap - a map from alleles to likelihoods
|
||||
* @param onlyConsiderTheseAlleles if not null, we will only consider alleles in this set for being one of the best.
|
||||
* this is useful for the case where you've selected a subset of the alleles that
|
||||
* the reads have been computed for further analysis. If null totally ignored
|
||||
* @return - the most likely allele, or NO_CALL if two or more alleles have likelihoods within INFORMATIVE_LIKELIHOOD_THRESHOLD
|
||||
* of one another. By default empty allele maps will return NO_CALL, and allele maps with a single entry will return the
|
||||
* corresponding key
|
||||
* @return - a MostLikelyAllele object
|
||||
*/
|
||||
public static Allele getMostLikelyAllele( final Map<Allele,Double> alleleMap, final Set<Allele> onlyConsiderTheseAlleles ) {
|
||||
public static MostLikelyAllele getMostLikelyAllele( final Map<Allele,Double> alleleMap, final Set<Allele> onlyConsiderTheseAlleles ) {
|
||||
if ( alleleMap == null ) throw new IllegalArgumentException("The allele to likelihood map cannot be null");
|
||||
double maxLike = Double.NEGATIVE_INFINITY;
|
||||
double prevMaxLike = Double.NEGATIVE_INFINITY;
|
||||
|
|
@ -237,7 +226,8 @@ public class PerReadAlleleLikelihoodMap {
|
|||
prevMaxLike = el.getValue();
|
||||
}
|
||||
}
|
||||
return (maxLike - prevMaxLike > INFORMATIVE_LIKELIHOOD_THRESHOLD ? mostLikelyAllele : Allele.NO_CALL );
|
||||
|
||||
return new MostLikelyAllele(mostLikelyAllele, maxLike, prevMaxLike);
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
|
|||
|
|
@ -1,27 +1,27 @@
|
|||
/*
|
||||
* Copyright (c) 2012 The Broad Institute
|
||||
*
|
||||
* Permission is hereby granted, free of charge, to any person
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* files (the "Software"), to deal in the Software without
|
||||
* restriction, including without limitation the rights to use,
|
||||
* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||
* copies of the Software, and to permit persons to whom the
|
||||
* Software is furnished to do so, subject to the following
|
||||
* conditions:
|
||||
*
|
||||
* The above copyright notice and this permission notice shall be
|
||||
* included in all copies or substantial portions of the Software.
|
||||
*
|
||||
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
||||
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
||||
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
||||
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
||||
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
|
||||
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
|
||||
*/
|
||||
* Copyright (c) 2012 The Broad Institute
|
||||
*
|
||||
* Permission is hereby granted, free of charge, to any person
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* files (the "Software"), to deal in the Software without
|
||||
* restriction, including without limitation the rights to use,
|
||||
* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||
* copies of the Software, and to permit persons to whom the
|
||||
* Software is furnished to do so, subject to the following
|
||||
* conditions:
|
||||
*
|
||||
* The above copyright notice and this permission notice shall be
|
||||
* included in all copies or substantial portions of the Software.
|
||||
*
|
||||
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
||||
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
||||
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
||||
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
||||
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
|
||||
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
|
||||
*/
|
||||
|
||||
package org.broadinstitute.sting.utils.haplotypeBAMWriter;
|
||||
|
||||
|
|
@ -31,6 +31,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
|
|||
import org.broadinstitute.sting.utils.Haplotype;
|
||||
import org.broadinstitute.sting.utils.SWPairwiseAlignment;
|
||||
import org.broadinstitute.sting.utils.Utils;
|
||||
import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele;
|
||||
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
|
||||
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
|
||||
import org.broadinstitute.variant.variantcontext.Allele;
|
||||
|
|
@ -71,9 +72,8 @@ class AllHaplotypeBAMWriter extends HaplotypeBAMWriter {
|
|||
// next, output the interesting reads for each sample aligned against the appropriate haplotype
|
||||
for ( final PerReadAlleleLikelihoodMap readAlleleLikelihoodMap : stratifiedReadMap.values() ) {
|
||||
for ( Map.Entry<GATKSAMRecord, Map<Allele, Double>> entry : readAlleleLikelihoodMap.getLikelihoodReadMap().entrySet() ) {
|
||||
final Allele bestAllele = PerReadAlleleLikelihoodMap.getMostLikelyAllele(entry.getValue());
|
||||
if ( bestAllele != Allele.NO_CALL )
|
||||
writeReadAgainstHaplotype(entry.getKey(), alleleToHaplotypeMap.get(bestAllele), paddedReferenceLoc.getStart());
|
||||
final MostLikelyAllele bestAllele = PerReadAlleleLikelihoodMap.getMostLikelyAllele(entry.getValue());
|
||||
writeReadAgainstHaplotype(entry.getKey(), alleleToHaplotypeMap.get(bestAllele.getMostLikelyAllele()), paddedReferenceLoc.getStart());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,33 +1,34 @@
|
|||
/*
|
||||
* Copyright (c) 2012 The Broad Institute
|
||||
*
|
||||
* Permission is hereby granted, free of charge, to any person
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* files (the "Software"), to deal in the Software without
|
||||
* restriction, including without limitation the rights to use,
|
||||
* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||
* copies of the Software, and to permit persons to whom the
|
||||
* Software is furnished to do so, subject to the following
|
||||
* conditions:
|
||||
*
|
||||
* The above copyright notice and this permission notice shall be
|
||||
* included in all copies or substantial portions of the Software.
|
||||
*
|
||||
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
||||
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
||||
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
||||
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
||||
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
|
||||
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
|
||||
*/
|
||||
* Copyright (c) 2012 The Broad Institute
|
||||
*
|
||||
* Permission is hereby granted, free of charge, to any person
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* files (the "Software"), to deal in the Software without
|
||||
* restriction, including without limitation the rights to use,
|
||||
* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||
* copies of the Software, and to permit persons to whom the
|
||||
* Software is furnished to do so, subject to the following
|
||||
* conditions:
|
||||
*
|
||||
* The above copyright notice and this permission notice shall be
|
||||
* included in all copies or substantial portions of the Software.
|
||||
*
|
||||
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
||||
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
||||
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
||||
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
||||
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
|
||||
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
|
||||
*/
|
||||
|
||||
package org.broadinstitute.sting.utils.haplotypeBAMWriter;
|
||||
|
||||
import net.sf.samtools.SAMFileWriter;
|
||||
import org.broadinstitute.sting.utils.GenomeLoc;
|
||||
import org.broadinstitute.sting.utils.Haplotype;
|
||||
import org.broadinstitute.sting.utils.genotyper.MostLikelyAllele;
|
||||
import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
|
||||
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
|
||||
import org.broadinstitute.variant.variantcontext.Allele;
|
||||
|
|
@ -77,9 +78,8 @@ class CalledHaplotypeBAMWriter extends HaplotypeBAMWriter {
|
|||
for ( final PerReadAlleleLikelihoodMap readAlleleLikelihoodMap : stratifiedReadMap.values() ) {
|
||||
for ( Map.Entry<GATKSAMRecord, Map<Allele, Double>> entry : readAlleleLikelihoodMap.getLikelihoodReadMap().entrySet() ) {
|
||||
if ( entry.getKey().getMappingQuality() > 0 ) {
|
||||
final Allele bestAllele = PerReadAlleleLikelihoodMap.getMostLikelyAllele(entry.getValue(), allelesOfCalledHaplotypes);
|
||||
if ( bestAllele != Allele.NO_CALL )
|
||||
writeReadAgainstHaplotype(entry.getKey(), alleleToHaplotypeMap.get(bestAllele), paddedReferenceLoc.getStart());
|
||||
final MostLikelyAllele bestAllele = PerReadAlleleLikelihoodMap.getMostLikelyAllele(entry.getValue(), allelesOfCalledHaplotypes);
|
||||
writeReadAgainstHaplotype(entry.getKey(), alleleToHaplotypeMap.get(bestAllele.getMostLikelyAllele()), paddedReferenceLoc.getStart());
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue