From 15b8c08132c59cfa08ed0e7b5a08f1d893da8029 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 6 Nov 2012 20:53:33 -0800
Subject: [PATCH] Apparently CIGAR elements can have 0 length according to the
 spec, but 0Ms were causing left alignment of indels to fail.  Fixed.

---
 .../src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
index 4f1e66ba2..585578958 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
@@ -646,7 +646,7 @@ public class AlignmentUtils {
 
         // get the indel element and move it left one base
         CigarElement ce = cigar.getCigarElement(indexOfIndel - 1);
-        elements.add(new CigarElement(ce.getLength() - 1, ce.getOperator()));
+        elements.add(new CigarElement(Math.max(ce.getLength() - 1, 0), ce.getOperator()));
         elements.add(cigar.getCigarElement(indexOfIndel));
         if (indexOfIndel + 1 < cigar.numCigarElements()) {
             ce = cigar.getCigarElement(indexOfIndel + 1);