Rescores a variant after removing duplicates (defined very strictly as reads with the same start points).

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1782 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/filters/IVFDuplicateReads.java

@@ -0,0 +1,65 @@
+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; }
+}