@Override public void setProgressLogger(final ProgressLoggerInterface logger) { dest.setProgressLogger(logger); } }
@Override public void setProgressLogger(final ProgressLoggerInterface logger) { writer.setProgressLogger(logger); } }
@Override public void setProgressLogger(final ProgressLoggerInterface progress) { this.underlyingWriter.setProgressLogger(progress); }
@Override public void setProgressLogger(final ProgressLoggerInterface progress) { this.underlyingWriter.setProgressLogger(progress); }
@Override public void setProgressLogger(final ProgressLoggerInterface progress) { this.underlyingWriter.setProgressLogger(progress); }
@Override public void setProgressLogger(final ProgressLoggerInterface logger) { for (final SAMFileWriter writer: writerMap.values()) { writer.setProgressLogger(logger); } } }
protected int doWork() { IOUtil.assertFileIsReadable(INPUT); IOUtil.assertFileIsWritable(OUTPUT); final SamReader reader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(INPUT); if (reader.getFileHeader().getSortOrder() != SAMFileHeader.SortOrder.coordinate) { throw new SAMException("Input must be coordinate-sorted for this program to run. Found: " + reader.getFileHeader().getSortOrder()); } final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(reader.getFileHeader(), true, OUTPUT); writer.setProgressLogger( new ProgressLogger(log, (int) 1e7, "Wrote", "records")); final ReferenceSequenceFileWalker refSeqWalker = new ReferenceSequenceFileWalker(REFERENCE_SEQUENCE); StreamSupport.stream(reader.spliterator(), false) .peek(rec -> fixRecord(rec, refSeqWalker)) .forEach(writer::addAlignment); CloserUtil.close(reader); writer.close(); return 0; }
protected int doWork() { IOUtil.assertFileIsReadable(INPUT); IOUtil.assertFileIsWritable(OUTPUT); final SamReader reader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(INPUT); if (reader.getFileHeader().getSortOrder() != SAMFileHeader.SortOrder.coordinate) { throw new SAMException("Input must be coordinate-sorted for this program to run. Found: " + reader.getFileHeader().getSortOrder()); } final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(reader.getFileHeader(), true, OUTPUT); writer.setProgressLogger( new ProgressLogger(log, (int) 1e7, "Wrote", "records")); final ReferenceSequenceFileWalker refSeqWalker = new ReferenceSequenceFileWalker(REFERENCE_SEQUENCE); StreamSupport.stream(reader.spliterator(), false) .peek(rec -> fixRecord(rec, refSeqWalker)) .forEach(writer::addAlignment); CloserUtil.close(reader); writer.close(); return 0; }
@Override protected int doWork() { try (final SamReader reader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(IOUtil.getPath(INPUT)); final SAMFileWriter writer = new SAMFileWriterFactory().makeWriter(reader.getFileHeader(), true, IOUtil.getPath(OUTPUT), REFERENCE_SEQUENCE)) { writer.setProgressLogger( new ProgressLogger(log, (int) 1e7, "Wrote", "records")); final OverlapDetector overlapDetector = getOverlapDetectorFromIntervalListFile(INTERVAL_LIST, 0, 0); for (final SAMRecord rec : reader) { if (overlapDetector == null || overlapDetector.overlapsAny(rec)) { setOATag(rec); } writer.addAlignment(rec); } } catch (IOException e) { log.error(e); return 1; } return 0; }
writer.setProgressLogger(new ProgressLogger(log, 10000000)); try (CloseableIterator<SAMRecord> wit = collection.iterator()) { @SuppressWarnings("resource") // bad eclipse warning
@Override protected int doWork() { try (final SamReader reader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(IOUtil.getPath(INPUT)); final SAMFileWriter writer = new SAMFileWriterFactory().makeWriter(reader.getFileHeader(), true, IOUtil.getPath(OUTPUT), REFERENCE_SEQUENCE)) { writer.setProgressLogger( new ProgressLogger(log, (int) 1e7, "Wrote", "records")); final OverlapDetector overlapDetector = getOverlapDetectorFromIntervalListFile(INTERVAL_LIST, 0, 0); for (final SAMRecord rec : reader) { if (overlapDetector == null || overlapDetector.overlapsAny(rec)) { setOATag(rec); } writer.addAlignment(rec); } } catch (IOException e) { log.error(e); return 1; } return 0; }
protected int doWork() { IOUtil.assertFileIsReadable(INPUT); IOUtil.assertFileIsWritable(OUTPUT); final SamReader reader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(INPUT); ; reader.getFileHeader().setSortOrder(SORT_ORDER.getSortOrder()); final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(reader.getFileHeader(), false, OUTPUT); writer.setProgressLogger( new ProgressLogger(log, (int) 1e7, "Wrote", "records from a sorting collection")); final ProgressLogger progress = new ProgressLogger(log, (int) 1e7, "Read"); for (final SAMRecord rec : reader) { writer.addAlignment(rec); progress.record(rec); } log.info("Finished reading inputs, merging and writing to output now."); CloserUtil.close(reader); writer.close(); return 0; } }
protected int doWork() { IOUtil.assertFileIsReadable(INPUT); IOUtil.assertFileIsWritable(OUTPUT); final SamReader reader = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).open(INPUT); ; reader.getFileHeader().setSortOrder(SORT_ORDER.getSortOrder()); final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(reader.getFileHeader(), false, OUTPUT); writer.setProgressLogger( new ProgressLogger(log, (int) 1e7, "Wrote", "records from a sorting collection")); final ProgressLogger progress = new ProgressLogger(log, (int) 1e7, "Read"); for (final SAMRecord rec : reader) { writer.addAlignment(rec); progress.record(rec); } log.info("Finished reading inputs, merging and writing to output now."); CloserUtil.close(reader); writer.close(); return 0; } }
header.setSortOrder(this.sortOrder); final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(header, true, this.targetBamFile); writer.setProgressLogger(new ProgressLogger(log, (int) 1e7, "Wrote", "records to output in queryname order")); sink = new Sink(writer); header.setSortOrder(this.sortOrder); final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(header, true, this.targetBamFile); writer.setProgressLogger(new ProgressLogger(log, (int) 1e7, "Wrote", "records from a sorting collection")); final ProgressLogger finalProgress = new ProgressLogger(log, 10000000, "Written in coordinate order to output", "records");
header.setSortOrder(this.sortOrder); final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(header, true, this.targetBamFile); writer.setProgressLogger(new ProgressLogger(log, (int) 1e7, "Wrote", "records to output in queryname order")); sink = new Sink(writer); header.setSortOrder(this.sortOrder); final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(header, true, this.targetBamFile); writer.setProgressLogger(new ProgressLogger(log, (int) 1e7, "Wrote", "records from a sorting collection")); final ProgressLogger finalProgress = new ProgressLogger(log, 10000000, "Written in coordinate order to output", "records");