public FastqWriter newWriter(final File out) { final FastqWriter writer = new BasicFastqWriter(out, createMd5); if (useAsyncIo) { return new AsyncFastqWriter(writer, AsyncFastqWriter.DEFAULT_QUEUE_SIZE); } else { return writer; } } }
public FastqWriter newWriter(final File out) { final FastqWriter writer = new BasicFastqWriter(out, createMd5); if (useAsyncIo) { return new AsyncFastqWriter(writer, AsyncFastqWriter.DEFAULT_QUEUE_SIZE); } else { return writer; } } }
public FastqWriter newWriter(final File out) { final FastqWriter writer = new BasicFastqWriter(out, createMd5); if (useAsyncIo) { return new AsyncFastqWriter(writer, AsyncFastqWriter.DEFAULT_QUEUE_SIZE); } else { return writer; } } }
protected int createSupplementaryAlignmentFastq(File input, File fq, boolean isRecursive) throws IOException { int recordsWritten = 0; try (SamReader reader = readerFactory.open(input)) { try (AsyncBufferedIterator<SAMRecord> bufferedIt = new AsyncBufferedIterator<>(reader.iterator(), input.getName())) { try (FastqWriter writer = new AsyncFastqWriter(new NonFlushingBasicFastqWriter(fq), AsyncFastqWriter.DEFAULT_QUEUE_SIZE)) { SplitReadFastqExtractionIterator fastqit = new SplitReadFastqExtractionIterator( bufferedIt, isRecursive, minSoftClipLength, minSoftClipQuality, !isRecursive && isProcessSecondaryAlignments(), isRealignExistingSplitReads(), isRealignEntireRecord(), eidgen); while (fastqit.hasNext()) { writer.write(fastqit.next()); recordsWritten++; } } } } return recordsWritten; } public boolean isRealignExistingSplitReads() {