Merge pull request #261 from broadinstitute/md_ad_bugfix
Fixes for genotype-level annotations in HaplotypeCaller / UnifiedGenotyper
This commit is contained in:
Eric Banks
commit
e7c69cb304
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@ -66,10 +66,7 @@ import org.broadinstitute.variant.variantcontext.Genotype;
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import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
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import org.broadinstitute.variant.variantcontext.VariantContext;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Map;
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import java.util.*;
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/**
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@ -135,20 +132,24 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
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}
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private void annotateWithLikelihoods(final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap, final VariantContext vc, final GenotypeBuilder gb) {
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final HashMap<Allele, Integer> alleleCounts = new HashMap<Allele, Integer>();
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final Set<Allele> alleles = new HashSet<>(vc.getAlleles());
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// make sure that there's a meaningful relationship between the alleles in the perReadAlleleLikelihoodMap and our VariantContext
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if ( ! perReadAlleleLikelihoodMap.getAllelesSet().containsAll(alleles) )
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throw new IllegalStateException("VC alleles " + alleles + " not a strict subset of per read allele map alleles " + perReadAlleleLikelihoodMap.getAllelesSet());
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final HashMap<Allele, Integer> alleleCounts = new HashMap<>();
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for ( final Allele allele : vc.getAlleles() ) { alleleCounts.put(allele, 0); }
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for ( final Allele allele : vc.getAlleles() ) {
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alleleCounts.put(allele, 0);
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}
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for (Map.Entry<GATKSAMRecord,Map<Allele,Double>> el : perReadAlleleLikelihoodMap.getLikelihoodReadMap().entrySet()) {
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final MostLikelyAllele a = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue(), alleles);
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if (! a.isInformative() ) continue; // read is non-informative
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final GATKSAMRecord read = el.getKey();
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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.getMostLikelyAllele()))
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continue; // sanity check - shouldn't be needed
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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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final int prevCount = alleleCounts.get(a.getMostLikelyAllele());
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final int incCount = read.isReducedRead() ? read.getReducedCount(ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(read, vc.getStart(), ReadUtils.ClippingTail.RIGHT_TAIL)) : 1;
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alleleCounts.put(a.getMostLikelyAllele(), prevCount + incCount);
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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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for (int i = 0; i < vc.getAlternateAlleles().size(); i++)
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@ -0,0 +1,126 @@
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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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* 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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* 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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*
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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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* 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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* 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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* 7.3 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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*/
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package org.broadinstitute.sting.gatk.walkers.annotator;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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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.sting.utils.sam.GATKSAMRecord;
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import org.broadinstitute.sting.utils.sam.ReadUtils;
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import org.broadinstitute.variant.variantcontext.Allele;
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import org.broadinstitute.variant.variantcontext.Genotype;
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import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
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import org.broadinstitute.variant.variantcontext.VariantContext;
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import org.broadinstitute.variant.vcf.VCFConstants;
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import org.broadinstitute.variant.vcf.VCFFormatHeaderLine;
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import org.broadinstitute.variant.vcf.VCFStandardHeaderLines;
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import java.util.*;
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/**
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* The depth of coverage of each allele per sample
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*
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* the depth for the HC is the sum of the informative alleles at this site. It's not perfect (as we cannot
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* differentiate between reads that align over the event but aren't informative vs. those that aren't even
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* close) but it's a pretty good proxy and it matches with the AD field (i.e., sum(AD) = DP).
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*/
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public class DepthPerSampleHC extends GenotypeAnnotation {
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public void annotate(final RefMetaDataTracker tracker,
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final AnnotatorCompatible walker,
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final ReferenceContext ref,
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final AlignmentContext stratifiedContext,
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final VariantContext vc,
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final Genotype g,
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final GenotypeBuilder gb,
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final PerReadAlleleLikelihoodMap alleleLikelihoodMap) {
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if ( g == null || !g.isCalled() || ( stratifiedContext == null && alleleLikelihoodMap == null) )
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return;
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if (alleleLikelihoodMap == null )
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throw new IllegalStateException("DepthPerSampleHC can only be used with likelihood based annotations in the HaplotypeCaller");
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// the depth for the HC is the sum of the informative alleles at this site. It's not perfect (as we cannot
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// differentiate between reads that align over the event but aren't informative vs. those that aren't even
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// close) but it's a pretty good proxy and it matches with the AD field (i.e., sum(AD) = DP).
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int dp = 0;
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if ( alleleLikelihoodMap.isEmpty() ) {
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// there are no reads
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} else {
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final Set<Allele> alleles = new HashSet<>(vc.getAlleles());
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// make sure that there's a meaningful relationship between the alleles in the perReadAlleleLikelihoodMap and our VariantContext
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if ( ! alleleLikelihoodMap.getAllelesSet().containsAll(alleles) )
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throw new IllegalStateException("VC alleles " + alleles + " not a strict subset of per read allele map alleles " + alleleLikelihoodMap.getAllelesSet());
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for (Map.Entry<GATKSAMRecord,Map<Allele,Double>> el : alleleLikelihoodMap.getLikelihoodReadMap().entrySet()) {
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final MostLikelyAllele a = PerReadAlleleLikelihoodMap.getMostLikelyAllele(el.getValue(), alleles);
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if ( a.isInformative() ) {
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final GATKSAMRecord read = el.getKey();
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final int incCount = read.isReducedRead() ? read.getReducedCount(ReadUtils.getReadCoordinateForReferenceCoordinateUpToEndOfRead(read, vc.getStart(), ReadUtils.ClippingTail.RIGHT_TAIL)) : 1;
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dp += incCount;
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}
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}
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gb.DP(dp);
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}
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}
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public List<String> getKeyNames() {
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return Collections.singletonList(VCFConstants.DEPTH_KEY);
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}
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public List<VCFFormatHeaderLine> getDescriptions() {
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return Collections.singletonList(VCFStandardHeaderLines.getFormatLine(getKeyNames().get(0)));
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}
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}
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@ -543,11 +543,6 @@ public class UnifiedGenotyperEngine {
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builder.attributes(attributes);
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VariantContext vcCall = builder.make();
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// if we are subsetting alleles (either because there were too many or because some were not polymorphic)
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// then we may need to trim the alleles (because the original VariantContext may have had to pad at the end).
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if ( myAlleles.size() != vc.getAlleles().size() && !limitedContext ) // limitedContext callers need to handle allele trimming on their own to keep their perReadAlleleLikelihoodMap alleles in sync
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vcCall = GATKVariantContextUtils.reverseTrimAlleles(vcCall);
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if ( annotationEngine != null && !limitedContext ) { // limitedContext callers need to handle annotations on their own by calling their own annotationEngine
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// Note: we want to use the *unfiltered* and *unBAQed* context for the annotations
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final ReadBackedPileup pileup = rawContext.getBasePileup();
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@ -556,6 +551,11 @@ public class UnifiedGenotyperEngine {
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vcCall = annotationEngine.annotateContext(tracker, refContext, stratifiedContexts, vcCall, perReadAlleleLikelihoodMap);
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}
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// if we are subsetting alleles (either because there were too many or because some were not polymorphic)
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// then we may need to trim the alleles (because the original VariantContext may have had to pad at the end).
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if ( myAlleles.size() != vc.getAlleles().size() && !limitedContext ) // limitedContext callers need to handle allele trimming on their own to keep their perReadAlleleLikelihoodMap alleles in sync
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vcCall = GATKVariantContextUtils.reverseTrimAlleles(vcCall);
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return new VariantCallContext(vcCall, confidentlyCalled(phredScaledConfidence, PoFGT0));
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}
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@ -204,13 +204,12 @@ public class GenotypingEngine {
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convertHaplotypeReadMapToAlleleReadMap( haplotypeReadMap, alleleMapper, 0.0 ) );
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final Map<String, PerReadAlleleLikelihoodMap> stratifiedReadMap = filterToOnlyOverlappingReads( genomeLocParser, alleleReadMap_annotations, perSampleFilteredReadList, call );
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VariantContext annotatedCall = call;
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if( annotatedCall.getAlleles().size() != mergedVC.getAlleles().size() ) { // some alleles were removed so reverseTrimming might be necessary!
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VariantContext annotatedCall = annotationEngine.annotateContext(stratifiedReadMap, call);
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if( call.getAlleles().size() != mergedVC.getAlleles().size() ) { // some alleles were removed so reverseTrimming might be necessary!
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annotatedCall = GATKVariantContextUtils.reverseTrimAlleles(annotatedCall);
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}
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annotatedCall = annotationEngine.annotateContext(stratifiedReadMap, annotatedCall);
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// maintain the set of all called haplotypes
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for ( final Allele calledAllele : call.getAlleles() )
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calledHaplotypes.addAll(alleleMapper.get(calledAllele));
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@ -223,7 +223,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
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*/
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@Advanced
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@Argument(fullName="annotation", shortName="A", doc="One or more specific annotations to apply to variant calls", required=false)
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protected List<String> annotationsToUse = new ArrayList<String>(Arrays.asList(new String[]{"ClippingRankSumTest"}));
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protected List<String> annotationsToUse = new ArrayList<>(Arrays.asList(new String[]{"ClippingRankSumTest", "DepthPerSampleHC"}));
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/**
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* Which annotations to exclude from output in the VCF file. Note that this argument has higher priority than the -A or -G arguments,
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@ -79,6 +79,6 @@ public class UnifiedGenotyperGeneralPloidySuite1IntegrationTest extends WalkerTe
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@Test(enabled = true)
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public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() {
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executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "66a5a3eb657fac5c621bc0c228ea9caf");
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executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "353c97bfb05a939b3838dc8eee50326b");
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}
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}
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@ -58,7 +58,7 @@ public class UnifiedGenotyperGeneralPloidySuite2IntegrationTest extends WalkerTe
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@Test(enabled = true)
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public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() {
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executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","5eabc12fc7b4f9749e6d1be0f5b45d14");
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executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","7e4e1397d5cff68aeba3595e671574fc");
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}
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@Test(enabled = true)
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@ -96,7 +96,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
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public void testMultipleSNPAlleles() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm BOTH --dbsnp " + b37dbSNP129 + " -I " + privateTestDir + "multiallelic.snps.bam -o %s -L " + privateTestDir + "multiallelic.snps.intervals", 1,
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Arrays.asList("1ab95513a3abb5b760578831c61ef94b"));
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Arrays.asList("f576d86656cc37c0a869c7ac911f4c7c"));
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executeTest("test Multiple SNP alleles", spec);
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}
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@ -112,7 +112,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{
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public void testReverseTrim() {
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WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
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"-T UnifiedGenotyper --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1,
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Arrays.asList("314b99eb146de1fdafed872ecbe1cfc2"));
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Arrays.asList("94d7a907fdca7e8c9fd6bb8a87b2bab2"));
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executeTest("test reverse trim", spec);
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}
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@ -74,7 +74,7 @@ public class UnifiedGenotyperReducedReadsIntegrationTest extends WalkerTest {
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@Test
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public void testReducedBamINDELs() {
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testReducedCalling("INDEL", "19bc6a74250ec19efc4e1b4ee6515ac0");
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testReducedCalling("INDEL", "22110b001e2d3dd45d7872334086b2b9");
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}
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@ -64,7 +64,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
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@Test
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public void testHaplotypeCallerMultiSampleComplex1() {
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HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "fc11b553fbf16beac0da04a69f419365");
|
||||
HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "8d7728909b1b8eb3f30f2f1583f054a8");
|
||||
}
|
||||
|
||||
private void HCTestSymbolicVariants(String bam, String args, String md5) {
|
||||
|
|
@ -88,12 +88,12 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa
|
|||
@Test
|
||||
public void testHaplotypeCallerMultiSampleGGAComplex() {
|
||||
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538",
|
||||
"38b4596c3910fdde51ea59aa1a8f848f");
|
||||
"db71826dc798ff1cdf0c5d05b0ede976");
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
|
||||
HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
|
||||
"08147870d73d9749ced8cfc7cdd4714f");
|
||||
"42831d5463552911b7da9de0b4a27289");
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -80,12 +80,12 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
|
||||
@Test
|
||||
public void testHaplotypeCallerMultiSample() {
|
||||
HCTest(CEUTRIO_BAM, "", "37e462379de17bc6c8aeeed6e9735dd3");
|
||||
HCTest(CEUTRIO_BAM, "", "1b15e4647013ab2c3ce7073c420d8640");
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testHaplotypeCallerSingleSample() {
|
||||
HCTest(NA12878_BAM, "", "983a0d122714d4aa0ff7af20cc686703");
|
||||
HCTest(NA12878_BAM, "", "423be27dc2cf7fd10baf465cf93e18e2");
|
||||
}
|
||||
|
||||
@Test(enabled = false) // can't annotate the rsID's yet
|
||||
|
|
@ -96,7 +96,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testHaplotypeCallerMultiSampleGGA() {
|
||||
HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
|
||||
"ffd69c410dca0d2f9fe75f3cb5d08179");
|
||||
"a28e6f14e28708283d61c1e423bbdcb1");
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
@ -112,7 +112,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
|
||||
@Test
|
||||
public void testHaplotypeCallerSingleSampleIndelQualityScores() {
|
||||
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "ce602282e80cca6d4272f940e20e90c3");
|
||||
HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "8344d86751b707c53b296c297eba4bfa");
|
||||
}
|
||||
|
||||
private void HCTestNearbySmallIntervals(String bam, String args, String md5) {
|
||||
|
|
@ -149,7 +149,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
|
||||
@Test
|
||||
public void testHaplotypeCallerNearbySmallIntervals() {
|
||||
HCTestNearbySmallIntervals(NA12878_BAM, "", "09335c01d2e90714af7f4c91156da0b1");
|
||||
HCTestNearbySmallIntervals(NA12878_BAM, "", "dea98f257d39fa1447a12c36a6bbf4a3");
|
||||
}
|
||||
|
||||
// This problem bam came from a user on the forum and it spotted a problem where the ReadClipper
|
||||
|
|
@ -159,14 +159,14 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void HCTestProblematicReadsModifiedInActiveRegions() {
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering -R %s -I %s", REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965";
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("b34ddc93a7b9919e05da499508f44dd9"));
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("7cd1c5e2642ae8ddf38932aba1f51d69"));
|
||||
executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void HCTestStructuralIndels() {
|
||||
final String base = String.format("-T HaplotypeCaller --disableDithering -R %s -I %s", REF, privateTestDir + "AFR.structural.indels.bam") + " --no_cmdline_in_header -o %s -minPruning 6 -L 20:8187565-8187800 -L 20:18670537-18670730";
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("98a78b9f58ab197b827ef2ce3ab043d3"));
|
||||
final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("ee55ff4c6ec1bbef88e21cc0f45d4c47"));
|
||||
executeTest("HCTestStructuralIndels: ", spec);
|
||||
}
|
||||
|
||||
|
|
@ -188,7 +188,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
public void HCTestReducedBam() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T HaplotypeCaller --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
|
||||
Arrays.asList("6e6ef6e0326bee6d20d9fd37349fdb8c"));
|
||||
Arrays.asList("4886a98bf699f4e7f4491160749ada6a"));
|
||||
executeTest("HC calling on a ReducedRead BAM", spec);
|
||||
}
|
||||
|
||||
|
|
@ -196,7 +196,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest {
|
|||
public void testReducedBamWithReadsNotFullySpanningDeletion() {
|
||||
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
|
||||
"-T HaplotypeCaller --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "reduced.readNotFullySpanningDeletion.bam -o %s -L 1:167871297", 1,
|
||||
Arrays.asList("5e535983b2f7e5fb6c84fecffa092324"));
|
||||
Arrays.asList("86bdd07a3ac4f6ce239c30efea8bf5ba"));
|
||||
executeTest("test calling on a ReducedRead BAM where the reads do not fully span a deletion", spec);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -366,4 +366,12 @@ public class PerReadAlleleLikelihoodMap {
|
|||
|
||||
return true;
|
||||
}
|
||||
|
||||
/**
|
||||
* Get an unmodifiable set of the unique alleles in this PerReadAlleleLikelihoodMap
|
||||
* @return a non-null unmodifiable map
|
||||
*/
|
||||
public Set<Allele> getAllelesSet() {
|
||||
return Collections.unmodifiableSet(allelesSet);
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue