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Bug fix: when getting variant contexts at a site, we need to get only variants that start at current location, otherwise we get duplicated records when filtering indels. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4830 348d0f76-0448-11de-a6fe-93d51630548a
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delangel 2010-12-13 19:23:10 +00:00
parent d34c5640d2
commit a5008faca8
1 changed files with 8 additions and 1 deletions
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9
java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
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@ -37,6 +37,7 @@ import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.vcf.VCFUtils;
@ -146,7 +147,13 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
if ( rods.size() == 0 )
return 0;
VariantContext vc = VariantContextAdaptors.toVariantContext( INPUT_VARIANT_ROD_BINDING_NAME, rods.get(0), ref );
//VariantContext vc = VariantContextAdaptors.toVariantContext( INPUT_VARIANT_ROD_BINDING_NAME, rods.get(0), ref );
VariantContext vc = tracker.getVariantContext( ref, INPUT_VARIANT_ROD_BINDING_NAME, null, context.getLocation(), true );
// protect against case where we have a variant in context but we're not at the beginning of location
if (vc == null)
return 0;
FiltrationContext varContext = new FiltrationContext(tracker, ref, vc);
// if we're still initializing the context, do so