From ec774f62be0d7f0f29c07be3de8056877a7102c4 Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 6 Jan 2010 14:53:24 +0000
Subject: [PATCH] Some checking to protect the BasicGenotype

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2509 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/utils/genotype/BasicGenotype.java               | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/utils/genotype/BasicGenotype.java b/java/src/org/broadinstitute/sting/utils/genotype/BasicGenotype.java
index df6025729..cfe7f94b6 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/BasicGenotype.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/BasicGenotype.java
@@ -1,6 +1,8 @@
 package org.broadinstitute.sting.utils.genotype;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.StingException;
 
 import java.util.List;
 
@@ -38,6 +40,12 @@ public class BasicGenotype implements Genotype {
      */
     public BasicGenotype(GenomeLoc location, String genotype, char ref, double negLog10PError) {
         mNegLog10PError = negLog10PError;
+
+        for ( char base : genotype.toCharArray() ) {
+            if (! ( BaseUtils.isRegularBase(base) || BaseUtils.isNBase((byte)base) ) )
+                throw new StingException(String.format("Unexpected base in Genotype at %s: '%s'", location, genotype));
+        }
+
         mGenotype = genotype;
         mLocation = location;
         mRef = ref;