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LOD checks for normal and brute force versions 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@732 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-05-17 02:56:03 +00:00
parent 527df6e57b
commit 81fac73c01
1 changed files with 2 additions and 2 deletions
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4
java/src/org/broadinstitute/sting/playground/gatk/walkers/IntervalCleanerWalker.java
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@ -225,8 +225,8 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
}
// if the best alternate consensus has a smaller sum of quality score mismatches, then clean!
if ( bestConsensus != null && bestConsensus.mismatchSum < totalMismatchSum ) {
logger.info("CLEAN: " + bestConsensus.str);
if ( bestConsensus != null && ((double)(totalMismatchSum - bestConsensus.mismatchSum))/10.0 >= LOD_THRESHOLD ) {
logger.info("CLEAN: " + bestConsensus.str );
if ( indelOutput != null && bestConsensus.cigar.numCigarElements() > 1 ) {
StringBuffer str = new StringBuffer();
str.append(reads.get(0).getReferenceName());