From b363eedd2c989cb9f2a6844775e49aa36ea43804 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 14 Apr 2009 19:13:16 +0000
Subject: [PATCH] Deal with screwy reads by changing logic to determine whether
 we are past the last interval

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@409 348d0f76-0448-11de-a6fe-93d51630548a
---
 java/src/org/broadinstitute/sting/utils/GenomeLoc.java | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
index f18aceb28..24961e8b0 100644
--- a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
@@ -281,12 +281,7 @@ 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.size() == 0 )
-            return false;
-        else {
-            GenomeLoc last = locs.get(locs.size() - 1);
-            return last.compareTo(curr) == -1 && ! last.overlapsP(curr);
-        }
+        return (locs.size() > 0 && curr.isPast(locs.get(locs.size() - 1)));
     }
 
     /**