@BeforeClass public void initClass() { Log.setGlobalLogLevel(LogLevel.ERROR); }
@BeforeClass public void initClass() { Log.setGlobalLogLevel(LogLevel.ERROR); }
@BeforeClass public void initClass() { Log.setGlobalLogLevel(Log.LogLevel.ERROR); }
public static void main(String[] args) throws Exception { Params params = new Params(); JCommander jc = new JCommander(params); try { jc.parse(args); } catch (Exception e) { System.out.println("Failed to parse parameteres, detailed message below: "); System.out.println(e.getMessage()); System.out.println(); System.out.println("See usage: -h"); System.exit(1); } if (args.length == 0 || params.help) { printUsage(jc); System.exit(1); } Log.setGlobalLogLevel(params.logLevel); dist(params.inputFile, (byte) (0xFF & params.defaultQualityScore)); }
Log.setGlobalLogLevel(htsjdkLevel);
public static void main(String[] args) throws IOException, IllegalArgumentException, IllegalAccessException { Log.setGlobalLogLevel(LogLevel.INFO); File cramFile = new File(args[0]); InputStream is = new BufferedInputStream(new FileInputStream(cramFile)); CramHeader header = CramIO.readCramHeader(is); Container c = null; while ((c = ContainerIO.readContainer(header.getVersion(), is)) != null && !c.isEOF()) { for (Slice slice : c.slices) { if (slice.sequenceId == Slice.MULTI_REFERENCE) { System.out.println("Read feature B detected."); System.exit(1); } } } } }
@BeforeTest public void beforeTest() { Log.setGlobalLogLevel(Log.LogLevel.ERROR); }
@BeforeTest public void beforeTest() { Log.setGlobalLogLevel(Log.LogLevel.ERROR); }
Log.setGlobalLogLevel(params.logLevel);
public static void main(String[] args) throws IOException, IllegalArgumentException, IllegalAccessException { Log.setGlobalLogLevel(LogLevel.INFO); File cramFile = new File(args[0]); InputStream is = new BufferedInputStream(new FileInputStream(cramFile));
public static void main(String[] args) throws IOException { Log.setGlobalLogLevel(LogLevel.INFO); File bamFile = new File(args[0]); File outCramFile = new File(args[1]); ReferenceSource source = new ReferenceSource(new File(args[2])); int maxThreads = Integer.valueOf(args[3]); BAMFileReader reader = new BAMFileReader(bamFile, null, false, false, ValidationStringency.SILENT, new DefaultSAMRecordFactory()); OutputStream os = new FileOutputStream(outCramFile); CRAMFileWriter writer = new CRAMFileWriter(os, source, reader.getFileHeader(), outCramFile.getName(), maxThreads); CloseableIterator<SAMRecord> iterator = reader.getIterator(); while (iterator.hasNext()) { SAMRecord record = iterator.next(); writer.addAlignment(record); } writer.close(); reader.close(); }
@Test public void testLogToFile() throws IOException { final File logFile = File.createTempFile(getClass().getSimpleName(), ".tmp"); logFile.deleteOnExit(); final Log.LogLevel originalLogLevel = Log.getGlobalLogLevel(); final PrintStream originalStream = Log.getGlobalPrintStream(); try (final PrintStream stream = new PrintStream(new FileOutputStream(logFile.getPath(), true))) { Log.setGlobalPrintStream(stream); Log.setGlobalLogLevel(Log.LogLevel.DEBUG); final String words = "Hello World"; log.info(words); final List<String> list = Files.readAllLines(logFile.toPath()); Assert.assertEquals(Log.getGlobalLogLevel(), Log.LogLevel.DEBUG); Assert.assertEquals(list.size(), 1); Assert.assertTrue(list.get(0).contains(words)); } finally { Log.setGlobalLogLevel(originalLogLevel); Log.setGlobalPrintStream(originalStream); } } }
Log.setGlobalLogLevel(Log.LogLevel.INFO);
System.setProperty("reference", params.referenceFasta.getAbsolutePath()); Log.setGlobalLogLevel(params.logLevel);
jc.parse(args); Log.setGlobalLogLevel(params.logLevel);
Log.setGlobalLogLevel(params.logLevel);
@BeforeTest public void prepare() throws IOException { Log.setGlobalLogLevel(Log.LogLevel.ERROR); source = new ReferenceSource(new FakeReferenceSequenceFile(SamReaderFactory.makeDefault().getFileHeader(BAM_FILE).getSequenceDictionary().getSequences())); cramBytes = cramFromBAM(BAM_FILE, source); cramFile = File.createTempFile(BAM_FILE.getName(), ".cram") ; cramFile.deleteOnExit(); indexFile = new File (cramFile.getAbsolutePath() + ".bai"); indexFile.deleteOnExit(); FileOutputStream fos = new FileOutputStream(cramFile); fos.write(cramBytes); fos.close(); CRAMBAIIndexer.createIndex(new SeekableFileStream(cramFile), indexFile, null, ValidationStringency.STRICT); baiBytes = readFile(indexFile); }
Log.setGlobalLogLevel(params.logLevel);
@BeforeTest public void prepare() throws IOException { Log.setGlobalLogLevel(Log.LogLevel.ERROR); source = new ReferenceSource(new FakeReferenceSequenceFile( SamReaderFactory.makeDefault().getFileHeader(BAM_FILE).getSequenceDictionary().getSequences())); tmpCramFile = File.createTempFile(BAM_FILE.getName(), ".cram") ; tmpCramFile.deleteOnExit(); tmpCraiFile = new File (tmpCramFile.getAbsolutePath() + ".crai"); tmpCraiFile.deleteOnExit(); cramBytes = cramFromBAM(BAM_FILE, source); FileOutputStream fos = new FileOutputStream(tmpCramFile); fos.write(cramBytes); fos.close(); FileOutputStream fios = new FileOutputStream(tmpCraiFile); CRAMCRAIIndexer.writeIndex(new SeekableFileStream(tmpCramFile), fios); craiBytes = readFile(tmpCraiFile); }
@BeforeTest public void beforeTest() throws Exception { Log.setGlobalLogLevel(Log.LogLevel.ERROR);