From 1a92ee3593417941a31b32e60cb34796d9bd5d95 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Tue, 18 Oct 2011 10:57:02 -0400 Subject: [PATCH] No longer adds a binding of ID -> . when the ID field is dot in the VCF -- Really we should make ID a primary key in VariantContext. Putting it into the attributes is just annoying now --- .../sting/utils/codecs/vcf/AbstractVCFCodec.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java index c86b91b79..6b101ca74 100755 --- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java +++ b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java @@ -381,7 +381,8 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec, } } - attributes.put(VariantContext.ID_KEY, id); + if ( ! id.equals(VCFConstants.EMPTY_ID_FIELD) ) + attributes.put(VariantContext.ID_KEY, id); return attributes; }