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SliceBams now handles properly the case where multiple read groups clash in the input BAM files 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6012 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-06-17 20:19:19 +00:00
parent 03a0185566
commit 1afd24c831
1 changed files with 5 additions and 11 deletions
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16
java/src/org/broadinstitute/sting/playground/tools/SliceBams.java
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@ -42,6 +42,7 @@ import org.broadinstitute.sting.utils.text.XReadLines;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.concurrent.ArrayBlockingQueue;
import java.util.concurrent.BlockingQueue;
@ -96,7 +97,7 @@ public class SliceBams extends CommandLineProgram {
* @return
*/
private SAMFileWriter createOutputBAM(List<File> inputBAMs) {
SAMFileHeader header = null;
Collection<SAMFileHeader> headers = new ArrayList<SAMFileHeader>();
log.info("Reading headers");
int fileCounter = 1;
@ -105,19 +106,12 @@ public class SliceBams extends CommandLineProgram {
final SAMFileReader inReader = new SAMFileReader(inFile, null); // null because we don't want it to look for the index
final SAMFileHeader inHeader = inReader.getFileHeader();
log.info(" Reading header from file " + inFile + " " + fileCounter++ + " of " + inputBAMs.size());
if (header == null) {
header = inHeader;
}
else {
for ( SAMReadGroupRecord rg : inHeader.getReadGroups() )
header.addReadGroup(rg);
}
headers.add(inHeader);
inReader.close();
}
SAMFileWriter out = new SAMFileWriterFactory().makeSAMOrBAMWriter(header, false, OUTPUT);
final SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(SAMFileHeader.SortOrder.coordinate, headers, true);
SAMFileWriter out = new SAMFileWriterFactory().makeSAMOrBAMWriter(headerMerger.getMergedHeader(), false, OUTPUT);
return new SimplifyingSAMFileWriter(out);
}