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Fix to deal with 'proper' options of casting

This commit is contained in:
Menachem Fromer 2012-11-22 01:45:18 -05:00
parent d33a412b5f
commit 2306518ab6
1 changed files with 17 additions and 5 deletions
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22
public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
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@ -1022,7 +1022,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
* @return
*/
@Override
public ReadBackedPileup getStartSortedPileup() {
public RBP getStartSortedPileup() {
final TreeSet<PE> sortedElements = new TreeSet<PE>(new Comparator<PE>() {
@Override
@ -1031,15 +1031,27 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
return difference != 0 ? difference : element1.getRead().getReadName().compareTo(element2.getRead().getReadName());
}
});
UnifiedPileupElementTracker<PE> tracker = (UnifiedPileupElementTracker<PE>) pileupElementTracker;
for (PE pile : tracker)
sortedElements.add(pile);
if (pileupElementTracker instanceof PerSamplePileupElementTracker) {
PerSamplePileupElementTracker<PE> tracker = (PerSamplePileupElementTracker<PE>) pileupElementTracker;
for (final String sample : tracker.getSamples()) {
PileupElementTracker<PE> perSampleElements = tracker.getElements(sample);
for (PE pile : perSampleElements)
sortedElements.add(pile);
}
}
else {
UnifiedPileupElementTracker<PE> tracker = (UnifiedPileupElementTracker<PE>) pileupElementTracker;
for (PE pile : tracker)
sortedElements.add(pile);
}
UnifiedPileupElementTracker<PE> sortedTracker = new UnifiedPileupElementTracker<PE>();
for (PE pile : sortedElements)
sortedTracker.add(pile);
return (RBP) createNewPileup(this.getLocation(), sortedTracker);
return (RBP) createNewPileup(loc, sortedTracker);
}
@Override