From 39dcd4f11f4663953def5579cd2668f09246e53d Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 10 Jun 2009 19:53:50 +0000
Subject: [PATCH] an attempt to bail out when unmapped reads are reached at the
 end of the file(s). still testing...

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@973 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/indels/IndelGenotyperWalker.java      | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java
index c765e799f..b87f13c2a 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java
@@ -77,6 +77,12 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
 	@Override
 	public Integer map(char[] ref, SAMRecord read) {
 		
+		if ( read.getReadUnmappedFlag() && read.getReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX &&
+				read.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START ) {
+			System.out.println("I think I reached unmapped reads at the end of the file(s) and I am done...");
+			return -1;
+		}
+		
 		if ( read.getReadUnmappedFlag() ||
 			 read.getDuplicateReadFlag() ||
 			 read.getNotPrimaryAlignmentFlag() ||
@@ -264,6 +270,10 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
 	
 	@Override
 	public Integer reduce(Integer value, Integer sum) {
+		if ( value == -1 ) {
+			onTraversalDone(sum);
+			System.exit(1);
+		}
 		sum += value;
 		return sum;
 	}