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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1795 348d0f76-0448-11de-a6fe-93d51630548a
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kiran 2009-10-08 18:47:20 +00:00
parent 94d82d1915
commit 29ad6cd876
1 changed files with 0 additions and 65 deletions
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65
java/src/org/broadinstitute/sting/gatk/walkers/filters/IVFDuplicateReads.java
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package org.broadinstitute.sting.gatk.walkers.filters;
import net.sf.samtools.SAMRecord;
import java.util.List;
import java.util.HashSet;
import java.util.ArrayList;
import org.broadinstitute.sting.gatk.walkers.genotyper.SingleSampleGenotyper;
import org.broadinstitute.sting.gatk.walkers.genotyper.SSGenotypeCall;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
public class IVFDuplicateReads implements IndependentVariantFeature {
private SingleSampleGenotyper SSG;
private double[] likelihoods = new double[10];
public void initialize(String arguments) {
SSG = new SingleSampleGenotyper();
SSG.initialize();
}
public void compute(VariantContextWindow contextWindow) {
List<SAMRecord> reads = contextWindow.getContext().getAlignmentContext(useZeroQualityReads()).getReads();
List<Integer> offsets = contextWindow.getContext().getAlignmentContext(useZeroQualityReads()).getOffsets();
HashSet<Integer> alignmentStarts = new HashSet<Integer>();
ArrayList<SAMRecord> dupeRemovedReads = new ArrayList<SAMRecord>();
ArrayList<Integer> dupeRemovedOffsets = new ArrayList<Integer>();
for (int readIndex = 0; readIndex < reads.size(); readIndex++) {
SAMRecord read = reads.get(readIndex);
Integer offset = offsets.get(readIndex);
Integer start = read.getAlignmentStart();
if (!alignmentStarts.contains(start)) {
dupeRemovedReads.add(read);
dupeRemovedOffsets.add(offset);
}
alignmentStarts.add(start);
}
AlignmentContext ac = new AlignmentContext(contextWindow.getContext().getAlignmentContext(useZeroQualityReads()).getLocation(), dupeRemovedReads, dupeRemovedOffsets);
SSGenotypeCall ssgcall = SSG.map(contextWindow.getContext().getTracker(), contextWindow.getContext().getReferenceContext(), ac);
double[] newlikelihoods = ssgcall.getLikelihoods();
for (int likelihoodIndex = 0; likelihoodIndex < newlikelihoods.length; likelihoodIndex++) {
likelihoods[likelihoodIndex] = newlikelihoods[likelihoodIndex] - contextWindow.getContext().getVariant().getGenotypeLikelihoods()[likelihoodIndex];
}
}
public double[] getLikelihoods() {
return likelihoods;
}
public String getStudyHeader() {
return "";
}
public String getStudyInfo() {
return "";
}
public boolean useZeroQualityReads() { return false; }
}