@Test public void testAsync() throws IOException { final SAMFileWriterFactory builder = new SAMFileWriterFactory(); final File outputFile = prepareOutputFile(BamFileIoUtils.BAM_FILE_EXTENSION); final SAMFileHeader header = new SAMFileHeader(); final SAMFileWriterFactory factory = createWriterFactoryWithOptions(header); final File referenceFile = new File(TEST_DATA_DIR, "hg19mini.fasta"); SAMFileWriter writer = builder.makeWriter(header, false, outputFile, referenceFile); Assert.assertEquals(writer instanceof AsyncSAMFileWriter, Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS, "testAsync default"); writer = builder.setUseAsyncIo(true).makeWriter(header, false, outputFile, referenceFile); Assert.assertTrue(writer instanceof AsyncSAMFileWriter, "testAsync option=set"); writer = builder.setUseAsyncIo(false).makeWriter(header, false, outputFile, referenceFile); Assert.assertFalse(writer instanceof AsyncSAMFileWriter, "testAsync option=unset"); } }
writerFactory.setUseAsyncIo(false); IntelDeflaterFactory intelDeflater = new IntelDeflaterFactory(); writerFactory.setDeflaterFactory(intelDeflater);
writerFactory.setUseAsyncIo(true); writerFactory.setAsyncOutputBufferSize(ASYNC_READ_CACHE_SIZE); writerFactory.setCreateIndex(shouldCreateIndex); } else { writerFactory.setUseAsyncIo(false);
writerFactory.setUseAsyncIo(true); writerFactory.setAsyncOutputBufferSize(1024 * 100); collate.writers[0] = writerFactory.makeBAMWriter(reader.getFileHeader(), false, file0);
samFileWriterFactory.setCreateIndex(false); samFileWriterFactory.setCreateMd5File(false); samFileWriterFactory.setUseAsyncIo(params.syncBamOutput);
final SAMFileWriterFactory samFileWriterFactory = new SAMFileWriterFactory(); if (USE_THREADING) { samFileWriterFactory.setUseAsyncIo(true);
final SAMFileWriterFactory samFileWriterFactory = new SAMFileWriterFactory(); if (USE_THREADING) { samFileWriterFactory.setUseAsyncIo(true);