From 835f1067d874d1d282f98d537268f16dbddca0bb Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 16 Apr 2009 18:41:39 +0000
Subject: [PATCH] added isHom() and isHet() queries to the Genotype interface
 (with the obvious meaning)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@452 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/gatk/refdata/Genotype.java  | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/Genotype.java b/java/src/org/broadinstitute/sting/gatk/refdata/Genotype.java
index aa4f30798..43780a1b2 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/Genotype.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/Genotype.java
@@ -106,6 +106,18 @@ public interface Genotype extends Comparable<ReferenceOrderedDatum> {
    * @return
    */
   boolean isBiallelic() ;
+  
+  /** Returns true if both observed alleles are the same (regardless of whether they are ref or alt)
+   *  
+   * @return
+   */
+  boolean isHom() ;
+
+  /** Returns true if observed alleles differ (regardless of whether they are ref or alt)
+   *  
+   * @return
+   */
+  boolean isHet() ;
 
   /** Returns reference (major) allele base for a SNP variant as a character; should throw IllegalStateException
      * if variant is not a SNP.