From 2ddbdee3bcd930f7b7221c5b8340c7ad6d1bf662 Mon Sep 17 00:00:00 2001
From: Guillermo del Angel <delangel@broadinstitute.org>
Date: Sun, 3 Jun 2012 08:38:38 -0400
Subject: [PATCH] Fixed broken VariantEval stratifications VariantType and
 IndelSize - integration tests to follow

---
 .../gatk/walkers/varianteval/stratifications/IndelSize.java | 4 ++++
 .../walkers/varianteval/stratifications/VariantType.java    | 6 ++++--
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java
index 01b10c502..089351eaa 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java
@@ -47,4 +47,8 @@ public class IndelSize extends VariantStratifier {
 
         return Collections.emptyList();
     }
+    @Override
+    public String getFormat() {
+        return "%d";
+    }
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java
index a9be7c3c0..09b89386f 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java
@@ -38,10 +38,12 @@ import java.util.List;
 public class VariantType extends VariantStratifier {
     @Override
     public void initialize() {
-        states.addAll(Arrays.asList(VariantContext.Type.values()));
+        for (VariantContext.Type t : VariantContext.Type.values())
+            states.add(t.toString());
     }
 
     public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
-        return eval == null ? Collections.emptyList() : Collections.singletonList((Object)eval.getType());
+        return eval == null ? Collections.emptyList() : Collections.singletonList((Object)eval.getType().toString());
     }
+
 }