Temporary phasing evalution walker that needs to be incorporated into the newest VariantEval, whenever it is available
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/*
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* Copyright (c) 2010, The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.oneoffprojects.walkers;
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import org.broad.tribble.util.variantcontext.Genotype;
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import org.broad.tribble.util.variantcontext.VariantContext;
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import org.broad.tribble.vcf.VCFHeader;
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import org.broadinstitute.sting.commandline.Argument;
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import org.broadinstitute.sting.commandline.Output;
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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.contexts.variantcontext.VariantContextUtils;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.Requires;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.utils.vcf.VCFUtils;
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import java.io.PrintStream;
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import java.util.*;
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/**
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* Emits specific fields as dictated by the user from one or more VCF files.
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*/
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@Requires(value={})
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public class PhasingEval extends RodWalker<Integer, Integer> {
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@Output(doc="File to which results should be written",required=true)
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protected PrintStream out;
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@Argument(doc="sample to emit", required = false)
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protected String sample = null;
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@Argument(doc="only include physical phased results", required = false)
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protected boolean requirePQ = false;
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@Argument(doc="Analysis to perform", required = true)
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protected Analysis analysis;
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public enum Analysis {
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HAPLOTYPE_SIZES,
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PHASING_BY_AC
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}
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private class Haplotype {
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GenomeLoc start, last;
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List<Genotype> genotypes;
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public Haplotype(GenomeLoc start) {
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this.start = start;
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this.last = null;
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this.genotypes = new ArrayList<Genotype>();
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}
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}
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private class PhasingByAC {
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int myAC = 0;
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int myAN = 0;
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int nHets = 0;
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int nHetsPhased = 0;
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public PhasingByAC(int myAC, int myAN) {
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this.myAC = myAC;
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this.myAN = myAN;
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}
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}
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Map<String, Haplotype> haplotypes = new Hashtable<String, Haplotype>();
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List<PhasingByAC> phasingByACs = new ArrayList<PhasingByAC>();
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public void initialize() {
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if ( analysis == Analysis.HAPLOTYPE_SIZES ) {
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out.println(Utils.join("\t", Arrays.asList("sample", "haplotype.length", "n.genotypes", "start", "stop")));
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}
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Set<String> samples = SampleUtils.getSampleList(VCFUtils.getVCFHeadersFromRods(getToolkit(), null));
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int AN = 2 * samples.size();
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for ( int i = 0; i <= AN; i++ ) {
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phasingByACs.add(new PhasingByAC(i, AN));
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}
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}
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( tracker == null ) // RodWalkers can make funky map calls
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return 0;
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Collection<VariantContext> vcs = tracker.getAllVariantContexts(ref, context.getLocation());
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for ( VariantContext vc : vcs) {
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if ( sample != null )
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vc = vc.subContextFromGenotypes(vc.getGenotype(sample));
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if ( analysis == Analysis.HAPLOTYPE_SIZES) {
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GenomeLoc loc = getToolkit().getGenomeLocParser().parseGenomeLoc(vc.getChr(), vc.getStart(), vc.getEnd());
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for ( Genotype g : vc.getGenotypes().values() ) {
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if ( ! haplotypes.containsKey(g.getSampleName()) )
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haplotypes.put(g.getSampleName(), new Haplotype(loc));
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Haplotype h = haplotypes.get(g.getSampleName());
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if ( g.isPhased() ) {
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h.genotypes.add(g);
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h.last = loc;
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} else {
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if ( ! requirePQ || isPhysicallyPhased(h.genotypes) )
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out.printf("%s %d %d %s %s%n", g.getSampleName(),
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h.last != null ? h.start.distance(h.last) : 0,
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h.genotypes.size(), h.start, h.last);
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haplotypes.put(g.getSampleName(), new Haplotype(loc));
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}
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}
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} else if ( analysis == Analysis.PHASING_BY_AC ) {
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int homref = vc.getHomRefCount();
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int homalt = vc.getHomVarCount();
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int het = vc.getHetCount();
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int ac = 2 * homalt + het;
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//int an = 2 * (homref + homalt + het);
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PhasingByAC data = phasingByACs.get(ac);
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data.nHets += het > 0 ? 1 : 0;
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data.nHetsPhased += isPhysicallyPhased(vc.getGenotypes().values()) ? 1 : 0;
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}
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}
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return 1;
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}
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private boolean isPhysicallyPhased(Collection<Genotype> genotypes) {
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for ( Genotype g : genotypes ) {
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if ( g.isHet() && g.hasAttribute("PQ") )
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return true;
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}
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return false;
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}
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public Integer reduceInit() {
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return 0;
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}
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public Integer reduce(Integer counter, Integer sum) {
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return counter + sum;
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}
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public void onTraversalDone(Integer sum) {
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if ( analysis == Analysis.PHASING_BY_AC ) {
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out.println(Utils.join("\t", Arrays.asList("ac", "nhets", "nhetphased")));
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for ( PhasingByAC pac : phasingByACs ) {
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out.printf("%d\t%d\t%d%n", pac.myAC, pac.nHets, pac.nHetsPhased);
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}
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}
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}
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}
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