From 124ef6c4834d8a948629291762b7f9d7d9696d50 Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Fri, 2 Sep 2011 21:12:28 -0400 Subject: [PATCH] MISSING_VALUE now gets defaultValue in getAttribute functions --- .../sting/utils/variantcontext/InferredGeneticContext.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/InferredGeneticContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/InferredGeneticContext.java index 4266fb4b5..bf16cd1cf 100755 --- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/InferredGeneticContext.java +++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/InferredGeneticContext.java @@ -1,6 +1,8 @@ package org.broadinstitute.sting.utils.variantcontext; +import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants; + import java.util.*; @@ -213,7 +215,7 @@ public final class InferredGeneticContext { public int getAttributeAsInt(String key, int defaultValue) { Object x = getAttribute(key); - if ( x == null ) return defaultValue; + if ( x == null || x == VCFConstants.MISSING_VALUE_v4 ) return defaultValue; if ( x instanceof Integer ) return (Integer)x; return Integer.valueOf((String)x); // throws an exception if this isn't a string }