From b1dc6d65e4132406bb1cf862d23cce79457934d0 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 21 Sep 2009 21:15:04 +0000
Subject: [PATCH] interval merging is now blazingly fast

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1674 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/indels/IntervalMergerWalker.java    | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java
index cf1a1f2d2..2c6b3986b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java
@@ -118,10 +118,7 @@ public class IntervalMergerWalker extends ReadWalker<Integer,Integer> {
      */
     private LinkedList<GenomeLoc> parseIntervals(List<String> intervalsSource) {
         List<GenomeLoc> parsedIntervals = GenomeAnalysisEngine.parseIntervalRegion(intervalsSource);
-        GenomeLocSortedSet intervalSortedSet = new GenomeLocSortedSet();
-        for ( GenomeLoc parsedInterval : parsedIntervals )
-            intervalSortedSet.addRegion(parsedInterval);
-
-        return new LinkedList<GenomeLoc>( intervalSortedSet );
+	Collections.sort(parsedIntervals);
+	return new LinkedList<GenomeLoc>(GenomeLocParser.mergeOverlappingLocations(parsedIntervals));
     }
 }