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set SAM file header's sorting order to unsorted, hopefully it will help to speed things up 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@468 348d0f76-0448-11de-a6fe-93d51630548a
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asivache 2009-04-17 19:32:24 +00:00
parent 03ec3452f2
commit 2a937fa8d3
1 changed files with 1 additions and 0 deletions
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java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelInspector.java
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@ -49,6 +49,7 @@ public class IndelInspector extends ReadWalker<Integer, Integer> {
}
SAMFileHeader header = getToolkit().getSamReader().getFileHeader();
header.setSortOrder(SAMFileHeader.SortOrder.unsorted);
ptWriter = new PassThroughWriter(OUT1, header);
if ( ! CONTROL_RUN ) pileBuilder = new PileBuilder(OUT2, header, ptWriter);