From b223b04331fa2e66bc084b2f0d58ee6120d6b83a Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 10 May 2010 14:51:18 +0000
Subject: [PATCH] Don't list '.' as an alternate allele, dummy!

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3337 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../playground/gatk/walkers/vcftools/VCFSubsetWalker.java     | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFSubsetWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFSubsetWalker.java
index 24a735422..58d678956 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFSubsetWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/vcftools/VCFSubsetWalker.java
@@ -125,7 +125,9 @@ public class VCFSubsetWalker extends RodWalker<ArrayList<VCFRecord>, VCFWriter>
 
         ArrayList<VCFGenotypeEncoding> genotypeEncodings = new ArrayList<VCFGenotypeEncoding>();
         for (VCFGenotypeEncoding allele : genotypeEncodingSet) {
-            genotypeEncodings.add(allele);
+            if (!allele.getBases().equalsIgnoreCase(".")) {
+                genotypeEncodings.add(allele);
+            }
         }
 
         VCFRecord subset = new VCFRecord(record.getReference(),