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Fix to deal with reduced reads containing a deletion

This commit is contained in:
Eric Banks 2011-11-14 12:23:46 -05:00
parent 3d2970453b
commit 7aee80cd3b
1 changed files with 2 additions and 1 deletions
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3
public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
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@ -99,7 +99,8 @@ public class PileupElement implements Comparable<PileupElement> {
} }
public int getRepresentativeCount() { public int getRepresentativeCount() {
return isReducedRead() ? read.getReducedCount(offset) : 1; // TODO -- if we ever decide to reduce the representation of deletions then this will need to be fixed
return (!isDeletion() && isReducedRead()) ? read.getReducedCount(offset) : 1;
} }
} }