From 74ad0081630ab7b58bb3e97d77d853fd0da2e388 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 24 Apr 2012 11:07:46 -0400
Subject: [PATCH] Adding VariantContext.hasAlternateAllele functionality

---
 .../utils/variantcontext/VariantContext.java  | 20 +++++++++++++++----
 1 file changed, 16 insertions(+), 4 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 5d2444b8d..a7956ec2d 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -592,15 +592,27 @@ public class VariantContext implements Feature { // to enable tribble intergrati
     /**
      * @return True if this context contains Allele allele, or false otherwise
      */
-    public boolean hasAllele(Allele allele) {
-        return hasAllele(allele, false);
+    public boolean hasAllele(final Allele allele) {
+        return hasAllele(allele, false, getAlleles());
     }
 
-    public boolean hasAllele(Allele allele, boolean ignoreRefState) {
+    public boolean hasAllele(final Allele allele, final boolean ignoreRefState) {
+        return hasAllele(allele, ignoreRefState, getAlleles());
+    }
+
+    public boolean hasAlternateAllele(final Allele allele) {
+        return hasAllele(allele, false, getAlternateAlleles());
+    }
+
+    public boolean hasAlternateAllele(final Allele allele, final boolean ignoreRefState) {
+        return hasAllele(allele, ignoreRefState, getAlternateAlleles());
+    }
+
+    private boolean hasAllele(final Allele allele, final boolean ignoreRefState, final List<Allele> allelesToConsider) {
         if ( allele == REF || allele == ALT ) // optimization for cached cases
             return true;
 
-        for ( Allele a : getAlleles() ) {
+        for ( Allele a : allelesToConsider ) {
             if ( a.equals(allele, ignoreRefState) )
                 return true;
         }