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;
}
/**
* Asserts that files are readable and writable and then fires off an HsMetricsCalculator instance
* to do the real work.
*/
protected int doWork() {
IoUtil.assertFileIsReadable(getProbeIntervals());
IoUtil.assertFileIsReadable(TARGET_INTERVALS);
IoUtil.assertFileIsReadable(INPUT);
IoUtil.assertFileIsWritable(OUTPUT);
if (PER_TARGET_COVERAGE != null) IoUtil.assertFileIsWritable(PER_TARGET_COVERAGE);
final SAMFileReader samReader = new SAMFileReader(INPUT);
final File probeIntervals = getProbeIntervals();
// Validate that the targets and baits have the same references as the reads file
SequenceUtil.assertSequenceDictionariesEqual(
samReader.getFileHeader().getSequenceDictionary(),
IntervalList.fromFile(TARGET_INTERVALS).getHeader().getSequenceDictionary(),
INPUT,
TARGET_INTERVALS);
SequenceUtil.assertSequenceDictionariesEqual(
samReader.getFileHeader().getSequenceDictionary(),
IntervalList.fromFile(probeIntervals).getHeader().getSequenceDictionary(),
INPUT,
probeIntervals);
ReferenceSequenceFile ref = null;
if (REFERENCE_SEQUENCE != null) {
IoUtil.assertFileIsReadable(REFERENCE_SEQUENCE);
ref = ReferenceSequenceFileFactory.getReferenceSequenceFile(REFERENCE_SEQUENCE);
SequenceUtil.assertSequenceDictionariesEqual(
samReader.getFileHeader().getSequenceDictionary(),
ref.getSequenceDictionary(),
INPUT,
REFERENCE_SEQUENCE);
}
final TargetMetricsCollector collector =
makeCollector(
METRIC_ACCUMULATION_LEVEL,
samReader.getFileHeader().getReadGroups(),
ref,
PER_TARGET_COVERAGE,
TARGET_INTERVALS,
probeIntervals,
getProbeSetName());
// Add each record to the requested collectors
final Iterator<SAMRecord> records = samReader.iterator();
final ProgressLogger progress = new ProgressLogger(log);
while (records.hasNext()) {
final SAMRecord sam = records.next();
collector.acceptRecord(sam, null);
progress.record(sam);
}
// Write the output file
final MetricsFile<HsMetrics, Integer> metrics = getMetricsFile();
collector.finish();
collector.addAllLevelsToFile(metrics);
metrics.write(OUTPUT);
return 0;
}
