From fe3f78e1d3f5f3586d058ec1b812c29cb85b91e5 Mon Sep 17 00:00:00 2001
From: asivache <asivache@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 1 Nov 2010 20:53:51 +0000
Subject: [PATCH] make it full (absolute) path for the file names recorded in
 results.list

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4608 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/indels/IndelRealigner.java            | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index 0b656d9da..72136dd3a 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -254,11 +254,12 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
                 if ( nwayWriters.containsKey( rid ) )
                     throw new StingException("nWayOut mode: Reader id for input sam file "+fName+" is already registered");
 
+                File f = new File(prefix+N_WAY_OUT);
                 SAMFileWriterImpl.setDefaultMaxRecordsInRam(MAX_RECORDS_IN_RAM);
                 SAMFileWriter sw = new SAMFileWriterFactory().makeSAMOrBAMWriter(setupHeader(getToolkit().getSAMFileHeader(rid)),
-                        false,new File(prefix+N_WAY_OUT));
+                        false,f);
                 try {
-                    fw.append(prefix+N_WAY_OUT);
+                    fw.append(f.getAbsolutePath());
                     fw.append('\n');
                 } catch (IOException e) {
                     throw new StingException("I/O error: write failed for results.list file");  //To change body of catch statement use File | Settings | File Templates.