From 9b7512fd94f532d18b6793d2c81b03c2a306656c Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 25 Aug 2011 22:42:14 -0400 Subject: [PATCH] Just because there's a ref base doesn't mean the VC needs to be padded --- .../sting/gatk/walkers/variantutils/VariantsToTable.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java index 7d0b4c3d4..0cf425e6f 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java @@ -271,7 +271,7 @@ public class VariantsToTable extends RodWalker { getters.put("REF", new Getter() { public String get(VariantContext vc) { String x = ""; - if ( vc.hasReferenceBaseForIndel() ) { + if ( vc.hasReferenceBaseForIndel() && !vc.isSNP() ) { Byte refByte = vc.getReferenceBaseForIndel(); x=x+new String(new byte[]{refByte}); } @@ -283,7 +283,7 @@ public class VariantsToTable extends RodWalker { StringBuilder x = new StringBuilder(); int n = vc.getAlternateAlleles().size(); if ( n == 0 ) return "."; - if ( vc.hasReferenceBaseForIndel() ) { + if ( vc.hasReferenceBaseForIndel() && !vc.isSNP() ) { Byte refByte = vc.getReferenceBaseForIndel(); x.append(new String(new byte[]{refByte})); }