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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
This commit is contained in:
chartl 2010-05-21 15:59:42 +00:00
parent 7910a6a7cb
commit 4e834b5e35
1 changed files with 2 additions and 3 deletions
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5
java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
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@ -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<Integer, Integer> {
@Argument(fullName="filterExpression", shortName="filter", doc="One or more expression used with INFO fields to filter (see wiki docs for more info)", required=false)