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Reverting the last reversal. bestConsensus points to something also kept in a set, so just reassigning it will NOT automatically destroy the underlying data; explicit clearing of unneeded data reinstated. STUPIDO!!! 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2796 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2010-02-05 18:08:53 +00:00
parent cf7e6d0c0b
commit a1d5a384f4
2 changed files with 2 additions and 0 deletions
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1
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -460,6 +460,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
//logger.debug(consensus.str + " " + consensus.mismatchSum);
if ( bestConsensus == null || bestConsensus.mismatchSum > consensus.mismatchSum) {
if ( bestConsensus != null ) bestConsensus.readIndexes.clear();
bestConsensus = consensus;
//logger.debug(consensus.str + " " + consensus.mismatchSum);
} else {

1
java/src/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerWalker.java
View File

@ -365,6 +365,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
//logger.debug(consensus.str + " " + consensus.mismatchSum);
if ( bestConsensus == null || bestConsensus.mismatchSum > consensus.mismatchSum) {
if ( bestConsensus != null ) bestConsensus.readIndexes.clear();
bestConsensus = consensus;
//logger.debug(consensus.str + " " + consensus.mismatchSum);
} else {