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Add referenceBaseForIndel to the Mongo VariantContext objects

This commit is contained in:
Joel Thibault 2012-04-11 16:11:07 -04:00
parent 7ed0ee7ed0
commit 11ed8e61c9
1 changed files with 9 additions and 2 deletions
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11
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
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@ -479,7 +479,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
return 0; return 0;
//Collection<VariantContext> vcs = tracker.getValues(variantCollection.variants, context.getLocation()); //Collection<VariantContext> vcs = tracker.getValues(variantCollection.variants, context.getLocation());
Collection<VariantContext> vcs = getMongoVariants(context.getLocation()); Collection<VariantContext> vcs = getMongoVariants(ref, context.getLocation());
if ( vcs == null || vcs.size() == 0) { if ( vcs == null || vcs.size() == 0) {
return 0; return 0;
@ -552,7 +552,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
return 1; return 1;
} }
private Collection<VariantContext> getMongoVariants(GenomeLoc location) { private Collection<VariantContext> getMongoVariants(ReferenceContext ref, GenomeLoc location) {
String contig = location.getContig(); String contig = location.getContig();
long start = location.getStart(); long start = location.getStart();
long stop = location.getStop(); long stop = location.getStop();
@ -639,6 +639,13 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
builder.attributes(attributes); builder.attributes(attributes);
builder.filters(filters); builder.filters(filters);
long index = start - ref.getWindow().getStart() - 1;
if ( index >= 0 ) {
// we were given enough reference context to create the VariantContext
builder.referenceBaseForIndel(ref.getBases()[(int)index]);
}
builder.referenceBaseForIndel(ref.getBases()[0]);
vcs.add(builder.make()); vcs.add(builder.make());
} }