From 7aee80cd3b909c4982d932f2a9bea6ab762b408d Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Mon, 14 Nov 2011 12:23:46 -0500 Subject: [PATCH] Fix to deal with reduced reads containing a deletion --- .../org/broadinstitute/sting/utils/pileup/PileupElement.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) 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