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new method to filter out overlapping PE reads 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3002 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kcibul 2010-03-15 15:40:09 +00:00
parent 4bdc3b2784
commit 9f519af06d
1 changed files with 35 additions and 0 deletions
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35
java/src/org/broadinstitute/sting/utils/pileup/ReadBackedPileup.java
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@ -173,6 +173,41 @@ public class ReadBackedPileup implements Iterable<PileupElement> {
}
}
/**
* Returns a new ReadBackedPileup where only one read from an overlapping read
* pair is retained. If the two reads in question disagree to their basecall,
* neither read is retained. If they agree on the base, the read with the higher
* quality observation is retained
*
* @return the newly filtered pileup
*/
public ReadBackedPileup getOverlappingFragementFilteredPileup() {
Map<String, PileupElement> filteredPileup = new HashMap<String, PileupElement>();
for ( PileupElement p : pileup ) {
String readName = p.getRead().getReadName();
// if we've never seen this read before, life is good
if (!filteredPileup.containsKey(readName)) {
filteredPileup.put(readName, p);
} else {
PileupElement existing = filteredPileup.get(readName);
// if the reads disagree at this position, throw them both out. Otherwise
// keep the element with the higher quality score
if (existing.getBase() != p.getBase()) {
filteredPileup.remove(readName);
} else {
if (existing.getQual() < p.getQual()) {
filteredPileup.put(readName, p);
}
}
}
}
return new ReadBackedPileup(loc, new ArrayList<PileupElement>(filteredPileup.values()));
}
/**
* Returns a new ReadBackedPileup that is free of mapping quality zero reads in this pileup. Note that this
* does not copy the data, so both ReadBackedPileups should not be changed. Doesn't make an unnecessary copy