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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
This commit is contained in:
asivache 2010-11-01 20:53:51 +00:00
parent 2ac5e55130
commit fe3f78e1d3
1 changed files with 3 additions and 2 deletions
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5
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -254,11 +254,12 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
if ( nwayWriters.containsKey( rid ) ) if ( nwayWriters.containsKey( rid ) )
throw new StingException("nWayOut mode: Reader id for input sam file "+fName+" is already registered"); 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); SAMFileWriterImpl.setDefaultMaxRecordsInRam(MAX_RECORDS_IN_RAM);
SAMFileWriter sw = new SAMFileWriterFactory().makeSAMOrBAMWriter(setupHeader(getToolkit().getSAMFileHeader(rid)), SAMFileWriter sw = new SAMFileWriterFactory().makeSAMOrBAMWriter(setupHeader(getToolkit().getSAMFileHeader(rid)),
false,new File(prefix+N_WAY_OUT)); false,f);
try { try {
fw.append(prefix+N_WAY_OUT); fw.append(f.getAbsolutePath());
fw.append('\n'); fw.append('\n');
} catch (IOException e) { } 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. throw new StingException("I/O error: write failed for results.list file"); //To change body of catch statement use File | Settings | File Templates.