From 4d880477d65cc25de8ee6705efeb545543a1a393 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 4 Jun 2009 20:09:53 +0000
Subject: [PATCH] Deal with ends of contigs

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@900 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/indels/MismatchIntervalWalker.java         | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/MismatchIntervalWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/MismatchIntervalWalker.java
index 11a442b0b..b9fd32055 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/MismatchIntervalWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/MismatchIntervalWalker.java
@@ -61,6 +61,12 @@ 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() ) {
+            sum.first.clear();
+            sum.second = null;
+        }
+        
         sum.first.addLast(value.second);
         if ( sum.first.size() <= windowSize )
             return sum;