From 3a04955a3085cd87bfec758eb144e78d5bf19b20 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 7 Sep 2011 14:01:42 -0400
Subject: [PATCH] We already had isPolymorphic and isMonomorphic in the
 VariantContext, but the implementation was incorrect for many edge cases
 (e.g. sites-only files, sites with samples who were no-called).  Fixing. 
 Moving on to VE now.

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

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 673fe4529..699133e38 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -983,7 +983,7 @@ public class VariantContext implements Feature { // to enable tribble intergrati
      * @return true if it's monomorphic
      */
     public boolean isMonomorphic() {
-        return ! isVariant() || getChromosomeCount(getReference()) == getChromosomeCount();
+        return ! isVariant() || (hasGenotypes() && getHomRefCount() + getNoCallCount() == getNSamples());
     }
 
     /**