From 404b95183f0a79a412874ada40dd51a19a696826 Mon Sep 17 00:00:00 2001 From: asivache Date: Fri, 15 Jan 2010 20:33:41 +0000 Subject: [PATCH] This is a LocusWalker, not a RodWalker (thanks Mark!!). RodWalkers currently are not capable of attaching alignment contexts (reads) to the ROD-annotated loci they traverse over... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2596 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/annotator/VariantAnnotator.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java index 581682542..29ee8f045 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java @@ -20,7 +20,7 @@ import java.io.*; //@Requires(value={DataSource.READS, DataSource.REFERENCE},referenceMetaData=@RMD(name="variant",type=VariationRod.class)) @Allows(value={DataSource.READS, DataSource.REFERENCE}) @Reference(window=@Window(start=-20,stop=20)) -public class VariantAnnotator extends RodWalker { +public class VariantAnnotator extends LocusWalker { @Argument(fullName="vcfOutput", shortName="vcf", doc="VCF file to which all variants should be written with annotations", required=true) protected File VCF_OUT; @Argument(fullName="sampleName", shortName="sample", doc="The sample (NA-ID) corresponding to the variant input (for non-VCF input only)", required=false)