private void createBAM(final List<GATKSAMRecord> reads) throws IOException {
testBAM = File.createTempFile("TraverseActiveRegionsUnitTest", ".bam");
testBAM.deleteOnExit();
SAMFileWriter out =
new SAMFileWriterFactory()
.setCreateIndex(true)
.makeBAMWriter(reads.get(0).getHeader(), true, testBAM);
for (GATKSAMRecord read : reads) {
out.addAlignment(read);
}
out.close();
new File(testBAM.getAbsolutePath().replace(".bam", ".bai")).deleteOnExit();
new File(testBAM.getAbsolutePath() + ".bai").deleteOnExit();
}
protected int doWork() {
IoUtil.assertFileIsReadable(INPUT);
IoUtil.assertFileIsWritable(OUTPUT);
final SAMFileReader in = new SAMFileReader(INPUT);
// create the read group we'll be using
final SAMReadGroupRecord rg = new SAMReadGroupRecord(RGID);
rg.setLibrary(RGLB);
rg.setPlatform(RGPL);
rg.setSample(RGSM);
rg.setPlatformUnit(RGPU);
if (RGCN != null) rg.setSequencingCenter(RGCN);
if (RGDS != null) rg.setDescription(RGDS);
if (RGDT != null) rg.setRunDate(RGDT);
log.info(
String.format(
"Created read group ID=%s PL=%s LB=%s SM=%s%n",
rg.getId(), rg.getPlatform(), rg.getLibrary(), rg.getSample()));
// create the new header and output file
final SAMFileHeader inHeader = in.getFileHeader();
final SAMFileHeader outHeader = inHeader.clone();
outHeader.setReadGroups(Arrays.asList(rg));
if (SORT_ORDER != null) outHeader.setSortOrder(SORT_ORDER);
final SAMFileWriter outWriter =
new SAMFileWriterFactory()
.makeSAMOrBAMWriter(
outHeader, outHeader.getSortOrder() == inHeader.getSortOrder(), OUTPUT);
final ProgressLogger progress = new ProgressLogger(log);
for (final SAMRecord read : in) {
read.setAttribute(SAMTag.RG.name(), RGID);
outWriter.addAlignment(read);
progress.record(read);
}
// cleanup
in.close();
outWriter.close();
return 0;
}
@Override
public void add(GATKSAMRecord read) {
bamWriter.addAlignment(read);
}
public void close() {
for (SAMFileWriter w : writerMap.values()) w.close();
}