use of htsjdk.samtools.fastq.FastqWriterFactory in project jvarkit by lindenb.
the class PadEmptyFastq method doWork.
@Override
public int doWork(final List<String> args) {
FastqWriter fqw = null;
try {
if (this.outFile == null) {
LOG.info("writing to stdout");
fqw = new BasicFastqWriter(stdout());
} else {
LOG.info("writing to " + this.outFile);
fqw = new FastqWriterFactory().newWriter(this.outFile);
}
if (args.isEmpty()) {
LOG.info("Reading from stdin");
FastqReader fqr = new FourLinesFastqReader(stdin());
copyTo(fqr, fqw);
fqr.close();
} else {
for (final String filename : args) {
LOG.info("Reading from " + filename);
FastqReader fqr = new FourLinesFastqReader(new File(filename));
copyTo(fqr, fqw);
fqr.close();
}
}
return 0;
} catch (final Exception err) {
LOG.error(err);
return -1;
} finally {
CloserUtil.close(fqw);
}
}
use of htsjdk.samtools.fastq.FastqWriterFactory in project gatk by broadinstitute.
the class SamToFastq method doWork.
@Override
protected Object doWork() {
IOUtil.assertFileIsReadable(INPUT);
final SamReader reader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(INPUT);
final Map<String, SAMRecord> firstSeenMates = new HashMap<>();
final FastqWriterFactory factory = new FastqWriterFactory();
factory.setCreateMd5(CREATE_MD5_FILE);
final Map<SAMReadGroupRecord, FastqWriters> writers = generateWriters(reader.getFileHeader().getReadGroups(), factory);
final ProgressLogger progress = new ProgressLogger(logger);
for (final SAMRecord currentRecord : reader) {
if (currentRecord.isSecondaryOrSupplementary() && !INCLUDE_NON_PRIMARY_ALIGNMENTS)
continue;
// Skip non-PF reads as necessary
if (currentRecord.getReadFailsVendorQualityCheckFlag() && !INCLUDE_NON_PF_READS)
continue;
final FastqWriters fq = writers.get(currentRecord.getReadGroup());
if (currentRecord.getReadPairedFlag()) {
final String currentReadName = currentRecord.getReadName();
final SAMRecord firstRecord = firstSeenMates.remove(currentReadName);
if (firstRecord == null) {
firstSeenMates.put(currentReadName, currentRecord);
} else {
assertPairedMates(firstRecord, currentRecord);
final SAMRecord read1 = currentRecord.getFirstOfPairFlag() ? currentRecord : firstRecord;
final SAMRecord read2 = currentRecord.getFirstOfPairFlag() ? firstRecord : currentRecord;
writeRecord(read1, 1, fq.getFirstOfPair(), READ1_TRIM, READ1_MAX_BASES_TO_WRITE);
final FastqWriter secondOfPairWriter = fq.getSecondOfPair();
if (secondOfPairWriter == null) {
throw new UserException("Input contains paired reads but no SECOND_END_FASTQ specified.");
}
writeRecord(read2, 2, secondOfPairWriter, READ2_TRIM, READ2_MAX_BASES_TO_WRITE);
}
} else {
writeRecord(currentRecord, null, fq.getUnpaired(), READ1_TRIM, READ1_MAX_BASES_TO_WRITE);
}
progress.record(currentRecord);
}
CloserUtil.close(reader);
// Close all the fastq writers being careful to close each one only once!
for (final FastqWriters writerMapping : new HashSet<>(writers.values())) {
writerMapping.closeAll();
}
if (!firstSeenMates.isEmpty()) {
SAMUtils.processValidationError(new SAMValidationError(SAMValidationError.Type.MATE_NOT_FOUND, "Found " + firstSeenMates.size() + " unpaired mates", null), VALIDATION_STRINGENCY);
}
return null;
}
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