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Don't require entropy reduction when cleaning only at known sites; instead we need to trust the known indels. This will improve consistency between lane-level and aggregated cleaning. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4076 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-08-22 02:44:38 +00:00
parent b6989289fc
commit 30a104228a
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -533,7 +533,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
if ( !updateRead(bestConsensus.cigar, bestConsensus.positionOnReference, indexPair.second, aRead, (int)leftmostIndex) )
return;
}
if ( !alternateReducesEntropy(altReads, reference, leftmostIndex) ) {
if ( !USE_KNOWN_INDELS_ONLY && !alternateReducesEntropy(altReads, reference, leftmostIndex) ) {
if ( statsOutput != null ) {
try {
statsOutput.write(currentInterval.toString());