Memory-saving change, same as in old IntervalCleaner (if alt consensus does not beat the best one, destroy its data immediately)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2795 348d0f76-0448-11de-a6fe-93d51630548a
2010-02-05 18:05:04 +00:00 · 2010-02-05 18:05:04 +00:00 · cf7e6d0c0b
parent df0be25afb
commit cf7e6d0c0b
1 changed files with 2 additions and 0 deletions
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@ -462,6 +462,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
            if ( bestConsensus == null || bestConsensus.mismatchSum > consensus.mismatchSum) {
                bestConsensus = consensus;
                //logger.debug(consensus.str +  " " + consensus.mismatchSum);
+            } else {
+                consensus.readIndexes.clear(); // we do not need this alt consensus, release memory right away!!
            }
        }