From 542af6402e9ea00bc98a10c996bae47740ba63d7 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 9 Sep 2009 19:21:53 +0000
Subject: [PATCH] output correct format for Sequenom SNPs

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1567 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
index eaae05c6b..078b16a5a 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceWalker.java
@@ -66,7 +66,7 @@ public class FastaAlternateReferenceWalker extends FastaReferenceWalker {
                 return new Pair<GenomeLoc, String>(context.getLocation(), (SEQUENOM ? refBase.concat("[-/"+variant.getAltBasesFWD()+"]") : refBase.concat(variant.getAltBasesFWD())));
             } else if ( variant.isSNP() ) {
                 basesSeen++;
-                return new Pair<GenomeLoc, String>(context.getLocation(), (rod.getName().startsWith("snpmask") ? "N" : variant.getAltBasesFWD()));
+                return new Pair<GenomeLoc, String>(context.getLocation(), (rod.getName().startsWith("snpmask") ? "N" : ("[" + refBase + "/" + variant.getAltBasesFWD() + "]")));
             }
         }