From 710d34633e951ea6261890652401924175af7ba7 Mon Sep 17 00:00:00 2001
From: Andrey Sivachenko <asivache@broadinstitute.org>
Date: Wed, 17 Aug 2011 15:16:23 -0400
Subject: [PATCH] now the reads that are too long are truly ignored (fix of the
 fix)

---
 .../sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java    | 1 +
 1 file changed, 1 insertion(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
index 7e8985e03..b2d30235a 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
@@ -482,6 +482,7 @@ public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
                                              "  Read length="+read.getReadLength()+"; cigar="+read.getCigarString()+"; start="+
                                              read.getAlignmentStart()+"; end="+read.getAlignmentEnd()+
                                              "; window start (after trying to accomodate the read)="+normal_context.getStart()+"; window end="+normal_context.getStop());
+                    return 1;
                 }
             }