From 45f70de6df40c358b5957301796687398e584311 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 15 Mar 2010 04:45:55 +0000
Subject: [PATCH] Fixed bug that failed to reset an accumulator when crossing
 contig boundaries, meaning that in special cases of shallow coverage, an
 interval might get dropped.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2999 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/datasources/shards/IntervalSharder.java      | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java
index 76fbdec92..d152b24ff 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java
@@ -24,6 +24,12 @@ public class IntervalSharder {
         FilePointer filePointer = null;
 
         for(GenomeLoc location: loci) {
+            // If crossing contigs, be sure to reset the filepointer that's been accumulating shard data.
+            if(filePointer != null && filePointer.bin.referenceSequence != location.getContigIndex()) {
+                filePointers.add(filePointer);
+                filePointer = null;
+            }
+
             int locationStart = (int)location.getStart();
             final int locationStop = (int)location.getStop();