From 4e0019b04fe52620f5ca84c55a63a2f05a519893 Mon Sep 17 00:00:00 2001
From: hanna <hanna@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 6 May 2010 22:37:25 +0000
Subject: [PATCH] Repair code that sorts and merges intervals.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3317 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/GenomeAnalysisEngine.java           |  2 +-
 .../sting/utils/interval/IntervalUtils.java        | 14 ++++++--------
 2 files changed, 7 insertions(+), 9 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 65d044664..9493b2a0e 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -227,7 +227,7 @@ public class GenomeAnalysisEngine {
         if (rawIntervals.size() == 0)
             return null;
 
-        return IntervalUtils.sortAndMergeIntervals(GenomeLocSortedSet.createSetFromList(rawIntervals),mergingRule);
+        return IntervalUtils.sortAndMergeIntervals(rawIntervals,mergingRule);
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java b/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
index 81cba6416..9924266fd 100644
--- a/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/interval/IntervalUtils.java
@@ -27,7 +27,7 @@ public class IntervalUtils {
      * @param argList A list of strings containing interval data.
      * @return an unsorted, unmerged representation of the given intervals.  Null is used to indicate that all intervals should be used. 
      */
-    public static GenomeLocSortedSet parseIntervalArguments(List<String> argList) {
+    public static List<GenomeLoc> parseIntervalArguments(List<String> argList) {
         List<GenomeLoc> rawIntervals = new ArrayList<GenomeLoc>();    // running list of raw GenomeLocs
 
         if (argList != null) { // now that we can be in this function if only the ROD-to-Intervals was provided, we need to
@@ -58,7 +58,7 @@ public class IntervalUtils {
             }
         }
 
-        return GenomeLocSortedSet.createSetFromList(rawIntervals);
+        return rawIntervals;
     }
 
     /**
@@ -70,15 +70,13 @@ public class IntervalUtils {
      * @param mergingRule A descriptor for the type of merging to perform.
      * @return A sorted, merged version of the intervals passed in.
      */
-    public static GenomeLocSortedSet sortAndMergeIntervals(GenomeLocSortedSet intervals, IntervalMergingRule mergingRule) {
-        List<GenomeLoc> intervalList = intervals.toList();
-
+    public static GenomeLocSortedSet sortAndMergeIntervals(List<GenomeLoc> intervals, IntervalMergingRule mergingRule) {
         // sort raw interval list
-        Collections.sort(intervalList);
+        Collections.sort(intervals);
         // now merge raw interval list
-        intervalList = GenomeLocParser.mergeIntervalLocations(intervalList, mergingRule);
+        intervals = GenomeLocParser.mergeIntervalLocations(intervals, mergingRule);
 
-        return GenomeLocSortedSet.createSetFromList(intervalList);
+        return GenomeLocSortedSet.createSetFromList(intervals);
     }
 
     /**