From d6277b70d8e860ac4ef37d7438687480e79eb111 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 24 Apr 2012 11:32:28 -0400
Subject: [PATCH] Forgot to consider the optimized case in hasAllele

---
 .../sting/utils/variantcontext/VariantContext.java  | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

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 a7956ec2d..39b351e50 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -593,25 +593,26 @@ public class VariantContext implements Feature { // to enable tribble intergrati
      * @return True if this context contains Allele allele, or false otherwise
      */
     public boolean hasAllele(final Allele allele) {
-        return hasAllele(allele, false, getAlleles());
+        return hasAllele(allele, false, true);
     }
 
     public boolean hasAllele(final Allele allele, final boolean ignoreRefState) {
-        return hasAllele(allele, ignoreRefState, getAlleles());
+        return hasAllele(allele, ignoreRefState, true);
     }
 
     public boolean hasAlternateAllele(final Allele allele) {
-        return hasAllele(allele, false, getAlternateAlleles());
+        return hasAllele(allele, false, false);
     }
 
     public boolean hasAlternateAllele(final Allele allele, final boolean ignoreRefState) {
-        return hasAllele(allele, ignoreRefState, getAlternateAlleles());
+        return hasAllele(allele, ignoreRefState, false);
     }
 
-    private boolean hasAllele(final Allele allele, final boolean ignoreRefState, final List<Allele> allelesToConsider) {
-        if ( allele == REF || allele == ALT ) // optimization for cached cases
+    private boolean hasAllele(final Allele allele, final boolean ignoreRefState, final boolean considerRefAllele) {
+        if ( (considerRefAllele && allele == REF) || allele == ALT ) // optimization for cached cases
             return true;
 
+        final List<Allele> allelesToConsider = considerRefAllele ? getAlleles() : getAlternateAlleles();
         for ( Allele a : allelesToConsider ) {
             if ( a.equals(allele, ignoreRefState) )
                 return true;