From e1e480a0b96d1a8715bbe339923a9de7cb832d12 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 30 Oct 2012 14:54:29 -0400
Subject: [PATCH] Bug fix: don't add no-call alleles to the list of ALT alleles
 being validated.

---
 .../sting/utils/variantcontext/VariantContext.java              | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
index b1aa4e759..27a5b0c24 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -1071,6 +1071,8 @@ public class VariantContext implements Feature { // to enable tribble integratio
             if ( g.isCalled() )
                 observedAlleles.addAll(g.getAlleles());
         }
+        if ( observedAlleles.contains(Allele.NO_CALL) )
+            observedAlleles.remove(Allele.NO_CALL);
 
         if ( reportedAlleles.size() != observedAlleles.size() )
             throw new TribbleException.InternalCodecException(String.format("one or more of the ALT allele(s) for the record at position %s:%d are not observed at all in the sample genotypes", getChr(), getStart()));