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Query for stop locations because we don't have that information in the reference

This commit is contained in:
Joel Thibault 2012-04-12 16:17:42 -04:00
parent 1cda87a4ad
commit ca737479cf
1 changed files with 1 additions and 1 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -556,7 +556,6 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
private Collection<VariantContext> getMongoVariants(ReferenceContext ref, GenomeLoc location) {
String contig = location.getContig();
long start = location.getStart();
long stop = location.getStop();
ArrayList<VariantContext> vcs = new ArrayList<VariantContext>();
@ -642,6 +641,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
String source = (String)result.get("source");
String id = (String)result.get("id");
Double error = (Double)result.get("error");
Long stop = (Long)result.get("stop");
VariantContextBuilder builder = new VariantContextBuilder(source, contig, start, stop, sourceRodAllelePair.getSecond());