Merged bug fix from Stable into Unstable

2011-06-29 15:59:27 -04:00 · 2011-06-29 15:59:27 -04:00 · dcd520a42e
parent 0b622e8d67 70ba851478
commit dcd520a42e
1 changed files with 2 additions and 0 deletions
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@ -1010,6 +1010,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
            for ( byte b : indelStr )
                sb.append((char)b);
            cigar.add(new CigarElement(indelStr.length, CigarOperator.I));
+        } else {
+            throw new ReviewedStingException("Creating an alternate consensus from a complex indel is not allowed");
        }

        if ( reference.length - refIdx > 0 )