SAMFileWriterFactory writerFactory = new SAMFileWriterFactory(); writerFactory.setUseAsyncIo(true); writerFactory.setAsyncOutputBufferSize(1024 * 100); collate.writers[0] = writerFactory.makeBAMWriter(reader.getFileHeader(), false, file0); collate.writers[1] = writerFactory.makeBAMWriter(reader.getFileHeader(), false, file1);
samFileWriterFactory.setAsyncOutputBufferSize(params.asyncBamBuffer); samFileWriterFactory.setCreateIndex(false); samFileWriterFactory.setCreateMd5File(false);
writerFactory.setAsyncOutputBufferSize(ASYNC_READ_CACHE_SIZE); writerFactory.setCreateIndex(shouldCreateIndex); } else {