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Minor optimization 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4817 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-12-10 18:56:35 +00:00
parent 56433ebf6b
commit 491a599b59
1 changed files with 2 additions and 4 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -449,9 +449,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
} }
private void abortCleanForCurrentInterval() { private void abortCleanForCurrentInterval() {
// merge the two sets for emission
readsNotToClean.addAll(readsToClean.getReads());
emit(readsNotToClean); emit(readsNotToClean);
emit(readsToClean.getReads());
readsToClean.clear(); readsToClean.clear();
readsNotToClean.clear(); readsNotToClean.clear();
currentInterval = intervals.hasNext() ? intervals.next() : null; currentInterval = intervals.hasNext() ? intervals.next() : null;
@ -471,9 +470,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
clean(readsToClean); clean(readsToClean);
knownIndelsToTry.clear(); knownIndelsToTry.clear();
// merge the two sets for emission
readsNotToClean.addAll(readsToClean.getReads());
emit(readsNotToClean); emit(readsNotToClean);
emit(readsToClean.getReads());
readsToClean.clear(); readsToClean.clear();
readsNotToClean.clear(); readsNotToClean.clear();