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In n-way-out mode, added printing names of all the output files into 'results.list' file 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4606 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2010-11-01 20:37:38 +00:00
parent 64599d1074
commit 0e6dd38936
1 changed files with 22 additions and 2 deletions
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24
java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -54,6 +54,7 @@ import org.broadinstitute.sting.utils.collections.Pair;
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
import java.util.*;
/**
@ -132,10 +133,11 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
@Hidden
@Argument(fullName="nWayOut", shortName="nWayOut", required=false,
doc="In this mode, there will be one output file for each input (-I) bam file. Reads from all input files "+
"will be realigned together, but then each read wiil be saved in the output file corresponding to "+
"will be realigned together, but then each read will be saved in the output file corresponding to "+
"the input file the read came from. The names of the output bam files will be constructed by "+
"stripping extensions (\".bam\" or \".sam\") from the input file names and pasting the value "+
"of -nWayOut argument to the result.")
"of -nWayOut argument to the result. The names of all output files will be also saved in a "+
"separate results.list file")
protected String N_WAY_OUT = null;
@ -228,6 +230,13 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
if ( writer != null ) throw new UserException.BadInput("-nWayOut and -o arguments are mutually exclusive");
FileWriter fw;
try {
fw = new FileWriter("results.list");
} catch (IOException e) {
throw new StingException("O/O error: Failed to create results.list file");
}
nwayWriters = new HashMap<SAMReaderID,SAMFileWriter>();
for ( SAMReaderID rid : getToolkit().getDataSource().getReaderIDs() ) {
@ -248,9 +257,20 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
SAMFileWriterImpl.setDefaultMaxRecordsInRam(MAX_RECORDS_IN_RAM);
SAMFileWriter sw = new SAMFileWriterFactory().makeSAMOrBAMWriter(setupHeader(getToolkit().getSAMFileHeader(rid)),
false,new File(prefix+N_WAY_OUT));
try {
fw.append(prefix+N_WAY_OUT);
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.
}
nwayWriters.put(rid,sw);
}
try {
fw.close();
} catch (IOException e) {
throw new StingException("I/O error: failed to close results.list file"); //To change body of catch statement use File | Settings | File Templates.
}
}