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Compares RBP phasing to a simple trio phasing model that can phase a child het iff both parental genotypes are known and at least one of them is not het [at EACH of the sites in the pair to be phased] 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5092 348d0f76-0448-11de-a6fe-93d51630548a
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fromer 2011-01-26 23:43:29 +00:00
parent 68729045ca
commit 466f8f8a3c
1 changed files with 187 additions and 0 deletions
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187
java/src/org/broadinstitute/sting/oneoffprojects/phasing/ComparePhasingToTrioPhasingNoRecombinationWalker.java 100755
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/*
* Copyright (c) 2010, 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.oneoffprojects.phasing;
import org.broad.tribble.util.variantcontext.Allele;
import org.broad.tribble.util.variantcontext.Genotype;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.filters.ZeroMappingQualityReadFilter;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
import java.io.PrintStream;
import java.util.LinkedList;
import java.util.Map;
import java.util.TreeSet;
/**
* Walks along all variant ROD loci and verifies the phasing from the reads for user-defined pairs of sites.
*/
@Allows(value = {DataSource.REFERENCE})
@Requires(value = {DataSource.REFERENCE}, referenceMetaData = {@RMD(name = ComparePhasingToTrioPhasingNoRecombinationWalker.TRIO_ROD_NAME, type = ReferenceOrderedDatum.class), @RMD(name = ComparePhasingToTrioPhasingNoRecombinationWalker.PHASING_ROD_NAME, type = ReferenceOrderedDatum.class)})
@ReadFilters({ZeroMappingQualityReadFilter.class})
// Filter out all reads with zero mapping quality
public class ComparePhasingToTrioPhasingNoRecombinationWalker extends RodWalker<Integer, Integer> {
public final static String TRIO_ROD_NAME = "trio";
public final static String PHASING_ROD_NAME = "phasing";
private final static int NUM_IN_TRIO = 3;
@Output
protected PrintStream out;
private String phasingSample = null;
private enum TrioStatus {
PRESENT, MISSING, TRIPLE_HET
}
private GenomeLoc prevLoc = null;
private TrioStatus prevTrioStatus = TrioStatus.MISSING;
public void initialize() {
}
public boolean generateExtendedEvents() {
return false;
}
public Integer reduceInit() {
return 0;
}
/**
* @param tracker the meta-data tracker
* @param ref the reference base
* @param context the context for the given locus
* @return statistics of and list of all phased VariantContexts and their base pileup that have gone out of cacheWindow range.
*/
public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
if (tracker == null)
return null;
GenomeLoc curLoc = ref.getLocus();
VariantContext phasingVc = tracker.getVariantContext(ref, PHASING_ROD_NAME, curLoc);
if (phasingVc == null || phasingVc.isFiltered())
return null;
Map<String, Genotype> phasingSampleToGt = phasingVc.getGenotypes();
if (phasingSampleToGt.size() != 1)
throw new UserException("Must provide EXACTLY one sample in " + PHASING_ROD_NAME + " track!");
Map.Entry<String, Genotype> phasingSampGt = phasingSampleToGt.entrySet().iterator().next();
String sample = phasingSampGt.getKey();
if (phasingSample == null)
phasingSample = sample;
if (!sample.equals(phasingSample))
throw new UserException("Must provide EXACTLY one sample!");
Genotype phasingGt = phasingSampGt.getValue();
if (!phasingGt.isHet())
return null;
VariantContext trioVc = tracker.getVariantContext(ref, TRIO_ROD_NAME, curLoc);
boolean useTrioVc = (trioVc != null && !trioVc.isFiltered());
Genotype sampleGtInTrio = null;
if (useTrioVc) {
sampleGtInTrio = trioVc.getGenotype(phasingSample);
if (trioVc.getNSamples() > NUM_IN_TRIO || sampleGtInTrio == null)
throw new UserException("Must provide trio data for sample: " + phasingSample);
if (!new TreeSet<Allele>(phasingGt.getAlleles()).equals(new TreeSet<Allele>(sampleGtInTrio.getAlleles()))) {
logger.warn("Locus " + curLoc + " breaks phase, since " + PHASING_ROD_NAME + " and " + TRIO_ROD_NAME + " tracks have different genotypes for " + phasingSample + "!");
prevLoc = null;
return null;
}
}
// Now, we have a [trio-consistent] het genotype that may be phased or not [and we want to know if it could be phased based on trio information]:
int processed = 1;
TrioStatus currentTrioStatus = TrioStatus.MISSING;
if (useTrioVc && trioVc.getNSamples() == NUM_IN_TRIO) {
boolean allHet = true;
for (int i = 0; i < NUM_IN_TRIO; i++) {
if (!trioVc.getGenotype(i).isHet()) {
allHet = false;
break;
}
}
if (allHet)
currentTrioStatus = TrioStatus.TRIPLE_HET;
else
currentTrioStatus = TrioStatus.PRESENT;
}
if (prevLoc != null && curLoc.onSameContig(prevLoc)) {
String trioPhaseStatus;
if (prevTrioStatus == TrioStatus.TRIPLE_HET || currentTrioStatus == TrioStatus.TRIPLE_HET) {
trioPhaseStatus = "Het3";
}
else if (prevTrioStatus == TrioStatus.MISSING || currentTrioStatus == TrioStatus.MISSING) {
trioPhaseStatus = "Missing";
}
else {
if (prevTrioStatus != TrioStatus.PRESENT || currentTrioStatus != TrioStatus.PRESENT)
throw new ReviewedStingException("LOGICAL error: prevTrioStatus != TrioStatus.PRESENT || currentTrioStatus != TrioStatus.PRESENT");
trioPhaseStatus = "trio_phased";
}
out.println(prevLoc + "\t" + curLoc + "\t" + trioPhaseStatus + "\t" + phasingGt.isPhased());
}
prevLoc = curLoc;
prevTrioStatus = currentTrioStatus;
return processed;
}
public Integer reduce(Integer addIn, Integer runningCount) {
if (addIn == null)
addIn = 0;
return runningCount + addIn;
}
/**
* @param result the number of reads and VariantContexts seen.
*/
public void onTraversalDone(Integer result) {
System.out.println("Processed " + result + " sites.");
}
}