From 1bd0c3c14544238bf2a3b024ca7a2b6222702b12 Mon Sep 17 00:00:00 2001 From: depristo Date: Tue, 6 Oct 2009 13:04:26 +0000 Subject: [PATCH] variant eval allows non Variation rod objects git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1768 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/varianteval/VariantEvalWalker.java | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java index 7fd685696..3fbcbc056 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java @@ -25,9 +25,8 @@ import java.util.*; * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality. * */ -@By(DataSource.REFERENCE) -@Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="eval",type=VariationRod.class)}) // right now we have no base variant class for rods, this should change -@Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="eval",type=VariationRod.class), @RMD(name="dbsnp",type=rodDbSNP.class),@RMD(name="hapmap-chip",type=RodGenotypeChipAsGFF.class), @RMD(name="interval",type=IntervalRod.class)}) +@Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="eval",type=ReferenceOrderedDatum.class)}) // right now we have no base variant class for rods, this should change +@Allows(value={DataSource.REFERENCE},referenceMetaData = {@RMD(name="eval",type=ReferenceOrderedDatum.class), @RMD(name="dbsnp",type=rodDbSNP.class),@RMD(name="hapmap-chip",type=ReferenceOrderedDatum.class), @RMD(name="interval",type=IntervalRod.class)}) public class VariantEvalWalker extends RefWalker { @Argument(shortName="minConfidenceScore", doc="Minimum confidence score to consider an evaluation SNP a variant", required=false) public int minConfidenceScore = -1;