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interval merging is now blazingly fast 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1674 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-09-21 21:15:04 +00:00
parent 15135788ca
commit b1dc6d65e4
1 changed files with 2 additions and 5 deletions
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7
java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalMergerWalker.java
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@ -118,10 +118,7 @@ public class IntervalMergerWalker extends ReadWalker<Integer,Integer> {
*/ */
private LinkedList<GenomeLoc> parseIntervals(List<String> intervalsSource) { private LinkedList<GenomeLoc> parseIntervals(List<String> intervalsSource) {
List<GenomeLoc> parsedIntervals = GenomeAnalysisEngine.parseIntervalRegion(intervalsSource); List<GenomeLoc> parsedIntervals = GenomeAnalysisEngine.parseIntervalRegion(intervalsSource);
GenomeLocSortedSet intervalSortedSet = new GenomeLocSortedSet(); Collections.sort(parsedIntervals);
for ( GenomeLoc parsedInterval : parsedIntervals ) return new LinkedList<GenomeLoc>(GenomeLocParser.mergeOverlappingLocations(parsedIntervals));
intervalSortedSet.addRegion(parsedInterval);
return new LinkedList<GenomeLoc>( intervalSortedSet );
} }
} }