From 40f0320a1c44248ed595e3db341204ee5576e478 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Fri, 10 Aug 2012 14:58:29 -0400
Subject: [PATCH] When adding a unit test to LIBS for X and = CIGAR operators,
 I uncovered a bug with the implementation of the
 ReadBackedPileup.depthOfCoverage() method.

---
 .../sting/utils/pileup/AbstractReadBackedPileup.java            | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java b/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
index e71cd01be..3d986f666 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
@@ -155,7 +155,7 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
 
     protected void addPileupToCumulativeStats(AbstractReadBackedPileup<RBP, PE> pileup) {
         size += pileup.getNumberOfElements();
-        abstractSize += pileup.depthOfCoverage();
+        abstractSize = pileup.depthOfCoverage() + (abstractSize == -1 ? 0 : abstractSize);
         nDeletions += pileup.getNumberOfDeletions();
         nMQ0Reads += pileup.getNumberOfMappingQualityZeroReads();
     }