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Fixed ReadBackedPileup downsampling 

Downsampling in the PerSampleReadBackedPileup was broken, it didn't downsample anything, always returning a copy the original pileup.
This commit is contained in:
Mauricio Carneiro 2012-11-29 22:10:25 -05:00
parent 0e1287a843
commit fc7fab5f3b
1 changed files with 5 additions and 9 deletions
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14
public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
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@ -652,23 +652,19 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
PerSamplePileupElementTracker<PE> tracker = (PerSamplePileupElementTracker<PE>) pileupElementTracker;
PerSamplePileupElementTracker<PE> filteredTracker = new PerSamplePileupElementTracker<PE>();
int current = 0;
for (final String sample : tracker.getSamples()) {
PileupElementTracker<PE> perSampleElements = tracker.getElements(sample);
List<PileupElement> filteredPileup = new ArrayList<PileupElement>();
for (PileupElement p : perSampleElements) {
int current = 0;
UnifiedPileupElementTracker<PE> filteredPileup = new UnifiedPileupElementTracker<PE>();
for (PE p : perSampleElements) {
if (positions.contains(current))
filteredPileup.add(p);
}
current++;
if (!filteredPileup.isEmpty()) {
AbstractReadBackedPileup<RBP, PE> pileup = createNewPileup(loc, perSampleElements);
filteredTracker.addElements(sample, pileup.pileupElementTracker);
}
current++;
filteredTracker.addElements(sample, filteredPileup);
}
return (RBP) createNewPileup(loc, filteredTracker);