From 3434a611461209108667eb2997f6717e2fcfc07a Mon Sep 17 00:00:00 2001 From: ebanks Date: Sun, 11 Apr 2010 02:59:11 +0000 Subject: [PATCH] Don't trigger when ref=N (which can happen when a dbsnp track is provided) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3150 348d0f76-0448-11de-a6fe-93d51630548a --- .../org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java b/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java index 68aff5cd7..5ce7c1f3f 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/VariantsToVCF.java @@ -7,6 +7,7 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext; import org.broadinstitute.sting.gatk.refdata.*; import org.broadinstitute.sting.utils.cmdLine.Argument; import org.broadinstitute.sting.utils.genotype.vcf.*; +import org.broadinstitute.sting.utils.BaseUtils; import java.util.*; @@ -29,7 +30,7 @@ public class VariantsToVCF extends RodWalker { private String[] ALLOWED_FORMAT_FIELDS = {"GT"}; public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) { - if ( tracker == null ) + if ( tracker == null || !BaseUtils.isRegularBase(ref.getBase()) ) return 0; rodDbSNP dbsnp = rodDbSNP.getFirstRealSNP(tracker.getReferenceMetaData("dbsnp"));