From cff645e98b9b3f21e5901e5415048c3816bf5986 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 9 Nov 2009 04:45:49 +0000
Subject: [PATCH] convenience method to deal with genotypes that are unsorted
 (e.g. CA vs. AC)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1997 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/utils/genotype/DiploidGenotype.java       | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java b/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java
index 9609af671..6c1102c9f 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/DiploidGenotype.java
@@ -61,4 +61,17 @@ public enum DiploidGenotype {
     public static DiploidGenotype createHomGenotype(char hom) {
         return DiploidGenotype.valueOf((String.valueOf(hom) + String.valueOf(hom)).toUpperCase());     
     }
+
+    /**
+     * get the genotype, given a string of 2 chars which may not necessarily be ordered correctly
+     * @param genotype the string representation
+     * @return the diploid genotype
+     */
+    public static DiploidGenotype unorderedValueOf(String genotype) {
+        if ( genotype == null || genotype.length() != 2 )
+            throw new IllegalArgumentException("Diploid genotypes are represented by 2 characters");
+        if ( genotype.charAt(0) > genotype.charAt(1) )
+            genotype = String.format("%c%c", genotype.charAt(1), genotype.charAt(0));
+        return valueOf(genotype);
+    }
 }
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