From 8f1cabd33dff321af4da2e691a2d7bcf40aa496c Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 26 May 2009 21:03:58 +0000
Subject: [PATCH] cmd line args changed - again; internally uses VariantType
 enum

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@818 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/MendelianInheritanceWalker.java     | 17 ++++++++---------
 1 file changed, 8 insertions(+), 9 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MendelianInheritanceWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MendelianInheritanceWalker.java
index 7ebda4fa1..5986499d9 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/MendelianInheritanceWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/MendelianInheritanceWalker.java
@@ -42,10 +42,11 @@ public class MendelianInheritanceWalker  extends RefWalker<TrioConcordanceRecord
 					      shortName="VT",
 					      doc="Assess concordance for the variants of the specified type, INDEL or POINT. If genotype track(s) provide both types, the requested one will be selected",
 					      required=true) 
-					      public GenotypeUtils.VariantType VARIANT_TYPE; 
+					      public String VTYPE_STR; 
 	
 	private static Logger logger = Logger.getLogger(MendelianInheritanceWalker.class);	
 	private final static String star = new String("*");
+	private GenotypeUtils.VariantType VARIANT_TYPE;
 	
 	@Override
 	public TrioConcordanceRecord map(RefMetaDataTracker rodData, char ref, LocusContext context) {
@@ -63,18 +64,16 @@ public class MendelianInheritanceWalker  extends RefWalker<TrioConcordanceRecord
 		return assessGenotypesInTrio(mom, dad, kid);
 	}
 	
-/*
- * 	@Override(non-Javadoc)
+
+/**	
+ * 	@Override
  * @see org.broadinstitute.sting.gatk.walkers.Walker#initialize()
- 
+ */
 	public void initialize() {
 		super.initialize();
-		if ( defCalls == null ) return;
-		defCalls = defCalls.toUpperCase();
-		if ( defCalls.equals("INDEL")) default_calls = 1;
-		else throw new StingException("POINT or BOTH default calls are not implemented yet");
+		VARIANT_TYPE = GenotypeUtils.VariantType.valueOf(VTYPE_STR.toUpperCase());
 	};
-*/	
+
 
 	/** Takes a single genotype object and returns properly filled new assessment object (covered/assessed/ref/variant set to 0/1 
 	 * according to what the genotype says)