From 663175e8686e51d16c7e15e2b316964366695097 Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 25 Sep 2009 22:24:34 +0000
Subject: [PATCH] Bug fix: when jumping onto next contig (chromosome), the
 walker was erasing last mismatch interval from the previous chr it was still
 holding without printing it; now it gets printed.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1733 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/indels/MismatchIntervalWalker.java        | 1 +
 1 file changed, 1 insertion(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/MismatchIntervalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/MismatchIntervalWalker.java
index 4817e05df..af226c9ae 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/MismatchIntervalWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/MismatchIntervalWalker.java
@@ -71,6 +71,7 @@ public class MismatchIntervalWalker extends LocusWalker<Pair<GenomeLoc, Boolean>
     public Pair<LinkedList<Boolean>, GenomeLoc> reduce(Pair<GenomeLoc, Boolean> value, Pair<LinkedList<Boolean>, GenomeLoc> sum) {
         // if we hit a new contig, clear the list
         if ( sum.second != null && sum.second.getContigIndex() != value.first.getContigIndex() ) {
+            out.println(sum.second);
             sum.first.clear();
             sum.second = null;
         }