public static SamReader getSamReader(String filename) { return SamReaderFactory.make() .validationStringency(ValidationStringency.SILENT) .samRecordFactory(DefaultSAMRecordFactory.getInstance()) .open(new File(filename)); }
@Test(dataProvider = "variousFormatReaderTestCases") public void samRecordFactoryTest(final String inputFile) throws IOException { final File input = new File(TEST_DATA_DIR, inputFile); final SAMRecordFactoryTester factory = new SAMRecordFactoryTester(); int i = 0; try(final SamReader reader = SamReaderFactory.makeDefault().samRecordFactory(factory).open(input)){ for (final SAMRecord rec : reader) { ++i; } } Assert.assertTrue(i > 0); if (inputFile.endsWith(".sam") || inputFile.endsWith(".sam.gz")) { Assert.assertEquals(factory.samRecordsCreated, i); } else if (inputFile.endsWith(".bam")) { Assert.assertEquals(factory.bamRecordsCreated, i); } }
@Test(dataProvider = "variousFormatReaderTestCases") public void samRecordFactoryTest(final String inputFile) throws IOException { final File input = new File(TEST_DATA_DIR, inputFile); final SAMRecordFactoryTester recordFactory = new SAMRecordFactoryTester(); final SamReaderFactory readerFactory = SamReaderFactory.makeDefault().samRecordFactory(recordFactory); final SamReader reader = readerFactory.open(input); int i = 0; for (final SAMRecord ignored : reader) { ++i; } reader.close(); Assert.assertTrue(i > 0); if (inputFile.endsWith(".sam") || inputFile.endsWith(".sam.gz")) { Assert.assertEquals(recordFactory.samRecordsCreated, i); } else if (inputFile.endsWith(".bam")) { Assert.assertEquals(recordFactory.bamRecordsCreated, i); } }
.enable(SamReaderFactory.Option.DONT_MEMORY_MAP_INDEX) .validationStringency(ValidationStringency.SILENT) .samRecordFactory(DefaultSAMRecordFactory.getInstance()) .open(new File("/my.bam"));
.enable(SamReaderFactory.Option.DONT_MEMORY_MAP_INDEX) .validationStringency(ValidationStringency.SILENT) .samRecordFactory(DefaultSAMRecordFactory.getInstance()) .open(new File("/my.bam"));
.enable(SamReaderFactory.Option.DONT_MEMORY_MAP_INDEX) .validationStringency(ValidationStringency.SILENT) .samRecordFactory(DefaultSAMRecordFactory.getInstance()) .open(new File("/my.bam"));