Added walker to calculate haplotype lengths for ALL fragments produced by stitching together phased sites (actually, stitching together everything BUT unphased het sites)
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5104 348d0f76-0448-11de-a6fe-93d51630548a
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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.phasing;
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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.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.datasources.sample.Sample;
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import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
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import java.io.PrintStream;
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import java.util.*;
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import static org.broadinstitute.sting.utils.vcf.VCFUtils.getVCFHeadersFromRods;
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/**
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* Walks along all variant ROD loci and verifies the phasing from the reads for user-defined pairs of sites.
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*/
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@Allows(value = {DataSource.REFERENCE})
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@Requires(value = {DataSource.REFERENCE})
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public class CalcFullHaplotypesWalker extends RodWalker<Integer, Integer> {
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private Map<String, Haplotype> waitingHaplotypes = null;
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@Output
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protected PrintStream out;
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public void initialize() {
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this.waitingHaplotypes = new HashMap<String, Haplotype>();
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Map<String, VCFHeader> rodNameToHeader = getVCFHeadersFromRods(getToolkit(), null);
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for (VCFHeader header : rodNameToHeader.values()) {
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for (String sample : header.getGenotypeSamples())
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waitingHaplotypes.put(sample, null);
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}
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}
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public boolean generateExtendedEvents() {
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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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/**
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* @param tracker the meta-data tracker
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* @param ref the reference base
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* @param context the context for the given locus
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* @return statistics of and list of all phased VariantContexts and their base pileup that have gone out of cacheWindow range.
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*/
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if (tracker == null)
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return null;
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GenomeLoc curLocus = ref.getLocus();
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outputDoneHaplotypes(curLocus);
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// Extend the haplotypes to include this position:
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for (Map.Entry<String, Haplotype> sampleHapEntry : waitingHaplotypes.entrySet()) {
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Haplotype waitingHaplotype = sampleHapEntry.getValue();
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if (waitingHaplotype == null) {// changed to a new contig:
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// Set the new haplotype to extend from [1, curLocus]
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GenomeLoc startInterval = getToolkit().getGenomeLocParser().parseGenomeLoc(curLocus.getContig(), 1, curLocus.getStop());
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waitingHaplotype = new Haplotype(startInterval, sampleHapEntry.getKey());
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sampleHapEntry.setValue(waitingHaplotype);
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}
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else
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waitingHaplotype.extend(curLocus.getStop());
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}
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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 (vc.isFiltered())
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continue;
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for (Map.Entry<String, Genotype> sampleGtEntry : vc.getGenotypes().entrySet()) {
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String sample = sampleGtEntry.getKey();
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Genotype gt = sampleGtEntry.getValue();
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if (gt.isHet()) {
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Haplotype sampleHap = waitingHaplotypes.get(sample);
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if (sampleHap == null)
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throw new ReviewedStingException("EVERY sample should have a haplotype [by code above and getToolkit().getSamples()]");
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sampleHap.incrementHetCount();
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if (!gt.isPhased()) { // Terminate the haplotype here:
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outputHaplotype(sampleHap);
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// Start a new haplotype from the next position [if it exists]:
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Haplotype nextHaplotype = null;
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int startNext = sampleHap.interval.getStop() + 1;
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if (startNext <= getContigLength(curLocus.getContig())) {
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GenomeLoc nextInterval = getToolkit().getGenomeLocParser().parseGenomeLoc(curLocus.getContig(), startNext, startNext);
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nextHaplotype = new Haplotype(nextInterval, sample);
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}
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waitingHaplotypes.put(sample, nextHaplotype);
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}
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}
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}
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}
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return 1;
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}
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public Integer reduce(Integer addIn, Integer runningCount) {
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if (addIn == null)
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addIn = 0;
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return runningCount + addIn;
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}
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private void outputDoneHaplotypes(GenomeLoc curLocus) {
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for (Map.Entry<String, Haplotype> sampleHapEntry : waitingHaplotypes.entrySet()) {
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Haplotype waitingHaplotype = sampleHapEntry.getValue();
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if (waitingHaplotype != null) {
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if (curLocus == null || !waitingHaplotype.interval.onSameContig(curLocus)) {
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sampleHapEntry.setValue(null);
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// Set the output haplotype to terminate at the end of its contig:
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int contigLength = getContigLength(waitingHaplotype.interval.getContig());
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waitingHaplotype.extend(contigLength);
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outputHaplotype(waitingHaplotype);
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}
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}
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}
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}
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private int getContigLength(String contig) {
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return getToolkit().getGenomeLocParser().getContigInfo(contig).getSequenceLength();
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}
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private void outputHaplotype(Haplotype h) {
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out.println(h);
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}
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/**
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* @param result the number of reads and VariantContexts seen.
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*/
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public void onTraversalDone(Integer result) {
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outputDoneHaplotypes(null);
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System.out.println("map was called " + result + " times.");
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}
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private class Haplotype {
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public GenomeLoc interval;
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public String sample;
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public int hetCount;
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public Haplotype(GenomeLoc interval, String sample) {
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this.interval = interval;
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this.sample = sample;
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this.hetCount = 0;
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}
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public void extend(int stop) {
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if (stop > interval.getStop())
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interval = getToolkit().getGenomeLocParser().parseGenomeLoc(interval.getContig(), interval.getStart(), stop);
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}
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public void incrementHetCount() {
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hetCount++;
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}
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public String toString() {
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return sample + "\t" + interval.toString() + "\t" + interval.size() + "\t" + hetCount;
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}
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}
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}
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@ -22,7 +22,7 @@
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.oneoffprojects.phasing;
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package org.broadinstitute.sting.oneoffprojects.walkers.phasing;
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import org.broad.tribble.util.variantcontext.Allele;
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import org.broad.tribble.util.variantcontext.Genotype;
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@ -22,7 +22,7 @@
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.oneoffprojects.phasing;
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package org.broadinstitute.sting.oneoffprojects.walkers.phasing;
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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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@ -22,7 +22,7 @@
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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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package org.broadinstitute.sting.oneoffprojects.walkers.phasing;
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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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