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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
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asivache 2010-01-15 20:33:41 +00:00
parent 7078219b89
commit 404b95183f
1 changed files with 1 additions and 1 deletions
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2
java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
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@ -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<Integer, Integer> {
public class VariantAnnotator extends LocusWalker<Integer, Integer> {
@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)