From ee8ed534e008d47fe8d449e35e2223df6b0aa7ac Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 23 Jul 2009 01:35:23 +0000
Subject: [PATCH] print full genotype for alt allele

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1297 348d0f76-0448-11de-a6fe-93d51630548a
---
 java/src/org/broadinstitute/sting/gatk/refdata/rodFLT.java     | 2 +-
 .../sting/playground/gatk/walkers/VennCallSetsWalker.java      | 3 +--
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/rodFLT.java b/java/src/org/broadinstitute/sting/gatk/refdata/rodFLT.java
index 82bb07cf3..6b6985570 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/rodFLT.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/rodFLT.java
@@ -52,7 +52,7 @@ public class rodFLT extends TabularROD implements SNPCallFromGenotypes {
         return (value > 0.0 ? value : 1.0);
     }
     public double getConsensusConfidence() { return -1; }
-    public List<String> getGenotype() throws IllegalStateException { throw new IllegalStateException(); }
+    public List<String> getGenotype() throws IllegalStateException { return Arrays.asList(getAltBasesFWD()); }
     public int getPloidy() throws IllegalStateException { return 2; }
     public boolean isBiallelic()   { return true; }
 
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 a68cade3b..4260cd063 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/VennCallSetsWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/VennCallSetsWalker.java
@@ -6,7 +6,6 @@ import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.RefWalker;
 import org.broadinstitute.sting.gatk.walkers.RMD;
 import org.broadinstitute.sting.gatk.walkers.Requires;
-import org.broadinstitute.sting.playground.utils.AlleleFrequencyEstimate;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 
@@ -83,7 +82,7 @@ public class VennCallSetsWalker extends RefWalker<Integer, Integer> {
             writer.println(variant.getLocation().getContig() + "\t"
                     + variant.getLocation().getStart() + "\t"
                     + variant.getRefSnpFWD() + "\t"
-                    + variant.getAltSnpFWD() + "\t"
+                    + variant.getGenotype().get(0) + "\t"
                     + variant.getMAF() + "\t0\t0\t0\t"
                     + variant.getVariationConfidence());
     }