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updates for VCF; we can no longer cache genotypes or alleles in a static array, this is bad for sharred memory parallel runs. One instance per codec was better for performance than using ThreadLocal code. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4063 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-08-19 19:34:44 +00:00
parent 8054b6b295
commit 04e5b28f6d
1 changed files with 3 additions and 1 deletions
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4
java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRodWalker.java
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@ -57,11 +57,13 @@ public class CountRodWalker extends RodWalker<CountRodWalker.Datum, Pair<Expandi
ExpandingArrayList<Long> nt = new ExpandingArrayList<Long>();
nt.addAll(lhs.first);
int index = 0;
for (Long l : rhs.first)
for (Long l : rhs.first) {
if (nt.get(index) == null)
nt.add(l);
else
nt.set(index,nt.get(index) + l);
index++;
}
return new Pair<ExpandingArrayList<Long>, Long>(nt, lhs.second + rhs.second);
}