From 4e834b5e35740beb588396a2783cee82a17d74bf Mon Sep 17 00:00:00 2001 From: chartl Date: Fri, 21 May 2010 15:59:42 +0000 Subject: [PATCH] VFW now uses a ref window and thus is compatible with indels. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3412 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/filters/VariantFiltrationWalker.java | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java index 88f0cf4f3..72c8457dc 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java @@ -35,9 +35,7 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrde import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum; import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors; -import org.broadinstitute.sting.gatk.walkers.RMD; -import org.broadinstitute.sting.gatk.walkers.Requires; -import org.broadinstitute.sting.gatk.walkers.RodWalker; +import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.utils.genotype.vcf.*; import org.broadinstitute.sting.utils.genotype.vcf.VCFWriter; @@ -49,6 +47,7 @@ import java.util.*; * Filters variant calls using a number of user-selectable, parameterizable criteria. */ @Requires(value={},referenceMetaData=@RMD(name="variant",type= ReferenceOrderedDatum.class)) +@Reference(window=@Window(start=-50,stop=50)) public class VariantFiltrationWalker extends RodWalker { @Argument(fullName="filterExpression", shortName="filter", doc="One or more expression used with INFO fields to filter (see wiki docs for more info)", required=false)