From df5744bcd336c2d6b99fccd3bd21142781fc0d0b Mon Sep 17 00:00:00 2001 From: ebanks Date: Mon, 17 Aug 2009 16:30:39 +0000 Subject: [PATCH] update this walker so any variants can be passed in git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1426 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/indels/SNPClusterWalker.java | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/SNPClusterWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/SNPClusterWalker.java index 1f0b607b6..1ced3f714 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/SNPClusterWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/SNPClusterWalker.java @@ -9,9 +9,7 @@ import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.cmdLine.Argument; @WalkerName("SNPClusters") -@By(DataSource.REFERENCE) -@Requires(DataSource.REFERENCE) -@Allows(DataSource.REFERENCE) +@Requires(value={DataSource.REFERENCE},referenceMetaData={@RMD(name="snps",type=AllelicVariant.class)}) public class SNPClusterWalker extends RefWalker { @Argument(fullName="windowSize", shortName="window", doc="window size for calculating clusters", required=false) int windowSize = 10; @@ -22,10 +20,8 @@ public class SNPClusterWalker extends RefWalker { } public GenomeLoc map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - AllelicVariant eval = (AllelicVariant)tracker.lookup("eval", null); - if ( eval instanceof SNPCallFromGenotypes ) - return context.getLocation(); - return null; + AllelicVariant snp = (AllelicVariant)tracker.lookup("snps", null); + return (snp != null && snp.isSNP()) ? context.getLocation() : null; } public void onTraversalDone(GenomeLoc sum) {