From 4366ce16e053b3c2bee717f659ff84b66afe7450 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 30 Jul 2009 14:53:27 +0000
Subject: [PATCH] Made sure all RODs have a (good) toString() method - and use
 it in the Venn walker. (thanks, Mark)

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1339 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../broadinstitute/sting/gatk/refdata/KGenomesSNPROD.java | 8 ++++++++
 .../broadinstitute/sting/gatk/refdata/SangerSNPROD.java   | 7 +++++++
 .../sting/playground/gatk/walkers/VennCallSetsWalker.java | 7 +------
 3 files changed, 16 insertions(+), 6 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/KGenomesSNPROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/KGenomesSNPROD.java
index 8672460e7..7fe6a39e5 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/KGenomesSNPROD.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/KGenomesSNPROD.java
@@ -50,4 +50,12 @@ public class KGenomesSNPROD extends TabularROD implements SNPCallFromGenotypes {
     public int nHomVarGenotypes()  { return -1; }
     public List<Genotype> getGenotypes() { return null; }
     public int length() { return 1; }
+
+    public String toString() {
+        StringBuffer sb = new StringBuffer();
+        sb.append(getLocation().getContig() + "\t" + getLocation().getStart() + "\t");
+        sb.append(getRefSnpFWD() + "\t" + getGenotype().get(0) + "\t");
+        sb.append(getMAF() + "\t0\t0\t0\t" + getVariationConfidence());
+        return sb.toString();
+    }
 }
\ No newline at end of file
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/SangerSNPROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/SangerSNPROD.java
index 05bacfab6..3e71e0457 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/SangerSNPROD.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/SangerSNPROD.java
@@ -39,4 +39,11 @@ public class SangerSNPROD extends TabularROD implements SNPCallFromGenotypes {
     public int nHetGenotypes()     { return -1; }
     public int nHomVarGenotypes()  { return -1; }
     public List<Genotype> getGenotypes() { return null; }
+
+    public String toString() {
+        StringBuffer sb = new StringBuffer();
+        sb.append(getLocation().getContig() + "\t" + getLocation().getStart() + "\t");
+        sb.append(getRefBasesFWD() + "\t" + getAltBasesFWD());
+        return sb.toString();
+    }
 }
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/VennCallSetsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/VennCallSetsWalker.java
index 4260cd063..e657f97b2 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/VennCallSetsWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/VennCallSetsWalker.java
@@ -79,12 +79,7 @@ public class VennCallSetsWalker extends RefWalker<Integer, Integer> {
 
     static void printVariant(PrintWriter writer, AllelicVariant variant) {
         if ( variant != null )
-            writer.println(variant.getLocation().getContig() + "\t"
-                    + variant.getLocation().getStart() + "\t"
-                    + variant.getRefSnpFWD() + "\t"
-                    + variant.getGenotype().get(0) + "\t"
-                    + variant.getMAF() + "\t0\t0\t0\t"
-                    + variant.getVariationConfidence());
+            writer.println(variant.toString());
     }
 
     /**