From 5ce42cbab3dfdc3ca8462c758ff591935243b4b8 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 22 Sep 2009 01:32:35 +0000
Subject: [PATCH] After thinking about this a bit more, it makes sense to pull
 this functionality out of my walker and into the GenomeLocParser where
 everyone else can benefit from it...

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1677 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/indels/IntervalMergerWalker.java | 15 ++-------------
 .../sting/utils/GenomeLocParser.java              | 11 +++++++++++
 2 files changed, 13 insertions(+), 13 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 2c6b3986b..ef9459fac 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java
@@ -56,7 +56,7 @@ public class IntervalMergerWalker extends ReadWalker<Integer,Integer> {
 
     @Override
     public void initialize() {
-        intervals = parseIntervals(intervalsSource);
+        intervals = new LinkedList<GenomeLoc>(GenomeLocParser.parseIntervals(intervalsSource));
         currentInterval = (intervals.size() > 0 ? intervals.removeFirst() : null);
     }
 
@@ -109,16 +109,5 @@ public class IntervalMergerWalker extends ReadWalker<Integer,Integer> {
              currentInterval.getStop() - currentInterval.getStart() < maxIntervalSize)
             out.println(currentInterval);
     }
-
-    /**
-     * Load the intervals directly from the command-line or from file, as appropriate.
-     * Merge overlapping intervals.
-     * @param intervalsSource Source of intervals.
-     * @return a linked list of sorted, merged intervals.
-     */
-    private LinkedList<GenomeLoc> parseIntervals(List<String> intervalsSource) {
-        List<GenomeLoc> parsedIntervals = GenomeAnalysisEngine.parseIntervalRegion(intervalsSource);
-	Collections.sort(parsedIntervals);
-	return new LinkedList<GenomeLoc>(GenomeLocParser.mergeOverlappingLocations(parsedIntervals));
-    }
 }
+
diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
index 084f8c997..c49f3a28a 100644
--- a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
@@ -130,6 +130,17 @@ public class GenomeLocParser {
         return true;
     }
 
+    /**
+     * Load one or more intervals sources, sorting and merging overlapping intervals.
+     * @param intervalsSource Source of intervals.
+     * @return a list of sorted, merged intervals.
+     */
+    public static List<GenomeLoc> parseIntervals(List<String> intervalsSource) {
+        List<GenomeLoc> parsedIntervals = GenomeAnalysisEngine.parseIntervalRegion(intervalsSource);
+	Collections.sort(parsedIntervals);
+	return GenomeLocParser.mergeOverlappingLocations(parsedIntervals);
+    }
+
     /**
      * parse a genome location, from a location string
      *