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Bug fix: when jumping onto next contig (chromosome), the walker was erasing last mismatch interval from the previous chr it was still holding without printing it; now it gets printed. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1733 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-09-25 22:24:34 +00:00
parent 92c6efabb7
commit 663175e868
1 changed files with 1 additions and 0 deletions
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java/src/org/broadinstitute/sting/gatk/walkers/indels/MismatchIntervalWalker.java
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@ -71,6 +71,7 @@ public class MismatchIntervalWalker extends LocusWalker<Pair<GenomeLoc, Boolean>
public Pair<LinkedList<Boolean>, GenomeLoc> reduce(Pair<GenomeLoc, Boolean> value, Pair<LinkedList<Boolean>, GenomeLoc> sum) { public Pair<LinkedList<Boolean>, GenomeLoc> reduce(Pair<GenomeLoc, Boolean> value, Pair<LinkedList<Boolean>, GenomeLoc> sum) {
// if we hit a new contig, clear the list // if we hit a new contig, clear the list
if ( sum.second != null && sum.second.getContigIndex() != value.first.getContigIndex() ) { if ( sum.second != null && sum.second.getContigIndex() != value.first.getContigIndex() ) {
out.println(sum.second);
sum.first.clear(); sum.first.clear();
sum.second = null; sum.second = null;
} }