bug fix for known-indels used as consenses

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3245 348d0f76-0448-11de-a6fe-93d51630548a
2010-04-23 13:52:51 +00:00 · 2010-04-23 13:52:51 +00:00 · 3adf7fbf64
parent f050beada6
commit 3adf7fbf64
1 changed files with 7 additions and 6 deletions
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@ -759,7 +759,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
            cigar.add(new CigarElement(indelStr.length, CigarOperator.D));
        }
        else {
-            sb.append(indelStr);
+            for ( byte b : indelStr )
+                sb.append((char)b);
            cigar.add(new CigarElement(indelStr.length, CigarOperator.I));
        }