From 29ab59a7b3f9a4dad8b6ebe99c6edb0dd3d1e34f Mon Sep 17 00:00:00 2001 From: depristo Date: Sat, 24 Apr 2010 21:31:03 +0000 Subject: [PATCH] Bug fix for Kiran; insertions now get a null reference allele even if the ref input object is null git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3254 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/refdata/VariantContextAdaptors.java | 6 +++--- .../sting/gatk/walkers/varianteval/VariantEvalWalker.java | 3 ++- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java index 1505f029c..218cef8eb 100755 --- a/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java @@ -239,12 +239,12 @@ public class VariantContextAdaptors { private static Allele determineRefAllele(VCFRecord vcf, ReferenceContext ref) { Allele refAllele; - if ( ref == null ) { + if ( vcf.isInsertion() ) { + refAllele = new Allele(Allele.NULL_ALLELE_STRING, true); + } else if ( ref == null ) { refAllele = new Allele(vcf.getReference(), true); } else if ( !vcf.isIndel() ) { refAllele = new Allele(Character.toString(ref.getBase()), true); - } else if ( vcf.isInsertion() ) { - refAllele = new Allele(Allele.NULL_ALLELE_STRING, true); } else if ( vcf.isDeletion() ) { int start = (int)(ref.getLocus().getStart() - ref.getWindow().getStart() + 1); int delLength = 0; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java index 730d57da4..f14c4e8c7 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java @@ -154,7 +154,8 @@ public class VariantEvalWalker extends RodWalker { public double minCompQualScore = NO_MIN_QUAL_SCORE; // Right now we will only be looking at SNPS - EnumSet ALLOW_VARIANT_CONTEXT_TYPES = EnumSet.of(VariantContext.Type.SNP, VariantContext.Type.NO_VARIATION); + // todo -- enable INDEL variant contexts, there's no reason not to but the integration tests need to be updated + EnumSet ALLOW_VARIANT_CONTEXT_TYPES = EnumSet.of(VariantContext.Type.SNP, VariantContext.Type.NO_VARIATION); //, VariantContext.Type.INDEL); @Argument(shortName="rsID", fullName="rsID", doc="If provided, list of rsID and build number for capping known snps by their build date", required=false) protected String rsIDFile = null;