本文整理了Java中htsjdk.samtools.util.Log.setGlobalLogLevel()方法的一些代码示例，展示了Log.setGlobalLogLevel()的具体用法。这些代码示例主要来源于Github/Stackoverflow/Maven等平台，是从一些精选项目中提取出来的代码，具有较强的参考意义，能在一定程度帮忙到你。Log.setGlobalLogLevel()方法的具体详情如下：
包路径：htsjdk.samtools.util.Log
类名称：Log
方法名：setGlobalLogLevel

Log.setGlobalLogLevel介绍

[英]Set the log level.
[中]设置日志级别。

代码示例

代码示例来源：origin: samtools/htsjdk

@BeforeClass
public void initClass() {
  Log.setGlobalLogLevel(LogLevel.ERROR);
}

代码示例来源：origin: samtools/htsjdk

@BeforeClass
public void initClass() {
  Log.setGlobalLogLevel(LogLevel.ERROR);
}

代码示例来源：origin: samtools/htsjdk

@BeforeClass
public void initClass() {
  Log.setGlobalLogLevel(Log.LogLevel.ERROR);
}

代码示例来源：origin: enasequence/cramtools

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));
}

代码示例来源：origin: broadgsa/gatk

Log.setGlobalLogLevel(htsjdkLevel);

代码示例来源：origin: enasequence/cramtools

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);
        }
      }
    }
  }
}

代码示例来源：origin: samtools/htsjdk

@BeforeTest
public void beforeTest() {
  Log.setGlobalLogLevel(Log.LogLevel.ERROR);
}

代码示例来源：origin: samtools/htsjdk

@BeforeTest
public void beforeTest() {
  Log.setGlobalLogLevel(Log.LogLevel.ERROR);
}

代码示例来源：origin: enasequence/cramtools

Log.setGlobalLogLevel(params.logLevel);

代码示例来源：origin: enasequence/cramtools

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));

代码示例来源：origin: enasequence/cramtools

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();
}

代码示例来源：origin: samtools/htsjdk

@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);
    }
  }
}

代码示例来源：origin: enasequence/cramtools

Log.setGlobalLogLevel(Log.LogLevel.INFO);

代码示例来源：origin: enasequence/cramtools

System.setProperty("reference", params.referenceFasta.getAbsolutePath());
Log.setGlobalLogLevel(params.logLevel);

代码示例来源：origin: enasequence/cramtools

jc.parse(args);
Log.setGlobalLogLevel(params.logLevel);

代码示例来源：origin: enasequence/cramtools

Log.setGlobalLogLevel(params.logLevel);

代码示例来源：origin: samtools/htsjdk

@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);
}

代码示例来源：origin: enasequence/cramtools

Log.setGlobalLogLevel(params.logLevel);

代码示例来源：origin: samtools/htsjdk

@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);
}

代码示例来源：origin: samtools/htsjdk

@BeforeTest
public void beforeTest() throws Exception {
  Log.setGlobalLogLevel(Log.LogLevel.ERROR);