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

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));
-    }
-}

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
      *