diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java index bab20b9e8..2d13d6e59 100755 --- a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java +++ b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java @@ -99,7 +99,8 @@ public class PileupElement implements Comparable { } 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; } } \ No newline at end of file