From 7fda409f4eeb38448d71b93a4c7224f012a37690 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 30 Mar 2009 23:43:12 +0000
Subject: [PATCH] Fixed bug where read traversals would fail with an exception
 when not called with a genome_region (-L) argument.  From TraversalEngine,
 line 455, looks like Mark intended an invariant where the list of locations
 is 0 length if not specified.  Made GenomeLoc code compliant with that.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@230 348d0f76-0448-11de-a6fe-93d51630548a
---
 java/src/org/broadinstitute/sting/utils/GenomeLoc.java | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
index 521ca0cf2..5e1c7869b 100644
--- a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
@@ -252,7 +252,7 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
      * @return true if we are past the last location to process
      */
     public static boolean pastFinalLocation(GenomeLoc curr, ArrayList<GenomeLoc> locs) {
-        if ( locs == null )
+        if ( locs.size() == 0 )
             return false;
         else {
             GenomeLoc last = locs.get(locs.size() - 1);
@@ -268,7 +268,7 @@ public class GenomeLoc implements Comparable<GenomeLoc> {
      * @return true if we should process GenomeLoc curr, otherwise false
      */
     public static boolean inLocations(GenomeLoc curr, ArrayList<GenomeLoc> locs) {
-        if (locs == null) {
+        if ( locs.size() == 0 ) {
             return true;
         } else {
             for ( GenomeLoc loc : locs ) {