本文整理了Java中htsjdk.samtools.util.Log.info()方法的一些代码示例，展示了Log.info()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.info()方法的具体详情如下：
包路径：htsjdk.samtools.util.Log
类名称：Log
方法名：info

Log.info介绍

[英]Logs a Throwable and optional message parts at level info.
[中]记录信息级别的可丢弃和可选消息部分。

代码示例

代码示例来源：origin: com.github.samtools/htsjdk

@Override
  protected void log(final String... message) {
    log.info((Object[])message);
  }
}

代码示例来源：origin: samtools/htsjdk

/** ReaderImplementation */
@Override
void enableFileSource(final SamReader reader, final boolean enabled) {
  log.info("enableFileSource is not supported");
}

代码示例来源：origin: com.github.samtools/htsjdk

/** ReaderImplementation */
@Override
void enableFileSource(final SamReader reader, final boolean enabled) {
  log.info("enableFileSource is not supported");
}

代码示例来源：origin: broadinstitute/picard

@Override
  public void run() {
    log.info("Before explicit GC, Runtime.totalMemory()=" + Runtime.getRuntime().totalMemory());
    System.gc();
    System.runFinalization();
    log.info("After explicit GC, Runtime.totalMemory()=" + Runtime.getRuntime().totalMemory());
  }
};

代码示例来源：origin: com.github.broadinstitute/picard

@Override
  public void run() {
    log.info("Before explicit GC, Runtime.totalMemory()=" + Runtime.getRuntime().totalMemory());
    System.gc();
    System.runFinalization();
    log.info("After explicit GC, Runtime.totalMemory()=" + Runtime.getRuntime().totalMemory());
  }
};

代码示例来源：origin: broadinstitute/picard

/**
 * Print out some quick JVM memory stats.
 */
private void reportMemoryStats(final String stage) {
  System.gc();
  final Runtime runtime = Runtime.getRuntime();
  log.info(stage + " freeMemory: " + runtime.freeMemory() + "; totalMemory: " + runtime.totalMemory() +
      "; maxMemory: " + runtime.maxMemory());
}

代码示例来源：origin: samtools/htsjdk

private static void printConfigurationInfo() throws IOException {
    log.info("Executing as " +
        System.getProperty("user.name") + '@' + InetAddress.getLocalHost().getHostName() +
        " on " + System.getProperty("os.name") + ' ' + System.getProperty("os.version") +
        ' ' + System.getProperty("os.arch") + "; " + System.getProperty("java.vm.name") +
        ' ' + System.getProperty("java.runtime.version"));

    final List<String> list = Defaults.allDefaults().entrySet().stream().map(e -> e.getKey() + ':' + e.getValue()).collect(Collectors.toList());
    log.info(String.join(" ", list));
  }
}

代码示例来源：origin: com.github.samtools/htsjdk

private static void printConfigurationInfo() throws IOException {
    log.info("Executing as " +
        System.getProperty("user.name") + '@' + InetAddress.getLocalHost().getHostName() +
        " on " + System.getProperty("os.name") + ' ' + System.getProperty("os.version") +
        ' ' + System.getProperty("os.arch") + "; " + System.getProperty("java.vm.name") +
        ' ' + System.getProperty("java.runtime.version"));

    final List<String> list = Defaults.allDefaults().entrySet().stream().map(e -> e.getKey() + ':' + e.getValue()).collect(Collectors.toList());
    log.info(String.join(" ", list));
  }
}

代码示例来源：origin: broadinstitute/picard

private static File writeMetrics(final MetricsFile<MetricBase, Comparable<?>> metricsFile, final File outputDirectory,
                 final String outputPrefix, final String outputExtension) {
  final File outputFile = new File(outputDirectory, String.format("%s.%s", outputPrefix, outputExtension));
  LOG.info(String.format("Writing %s lane metrics to %s ...", metricsFile.getMetrics().size(), outputFile));
  metricsFile.write(outputFile);
  return outputFile;
}

代码示例来源：origin: broadinstitute/picard

public void logMemoryStats(final Log log) {
  System.gc();
  final Runtime runtime = Runtime.getRuntime();
  log.info("freeMemory: " + runtime.freeMemory() +
      "; totalMemory: " + runtime.totalMemory() +
      "; maxMemory: " + runtime.maxMemory() +
      "; output buffer size: " + outputBuffer.size() +
      "; duplicate queue size: " + toMarkQueue.size()
  );
}

代码示例来源：origin: broadinstitute/picard

public static void awaitThreadPoolTermination(final String executorName, final ThreadPoolExecutor executorService,
                         final Duration timeBetweenChecks) {
    try {
      while (!executorService.awaitTermination(timeBetweenChecks.getSeconds(), TimeUnit.SECONDS)) {
        log.info(String.format("%s waiting for job completion. Finished jobs - %d : Running jobs - %d : Queued jobs  - %d",
            executorName, executorService.getCompletedTaskCount(), executorService.getActiveCount(),
            executorService.getQueue().size()));
      }
    } catch (final InterruptedException e) {
      log.error("Interrupted exception caught: ", e);
    }
  }
}

代码示例来源：origin: com.github.broadinstitute/picard

public void logMemoryStats(final Log log) {
  System.gc();
  final Runtime runtime = Runtime.getRuntime();
  log.info("freeMemory: " + runtime.freeMemory() +
      "; totalMemory: " + runtime.totalMemory() +
      "; maxMemory: " + runtime.maxMemory() +
      "; output buffer size: " + outputBuffer.size() +
      "; duplicate queue size: " + toMarkQueue.size()
  );
}

代码示例来源：origin: broadinstitute/picard

private Set<String> makeContextStrings(final int contextSize) {
  final Set<String> contexts = new HashSet<>();
  for (final byte[] kmer : SequenceUtil.generateAllKmers(2 * contextSize + 1)) {
    if (kmer[contextSize] == 'C') {
      contexts.add(StringUtil.bytesToString(kmer));
    }
  }
  log.info("Generated " + contexts.size() + " context strings.");
  return contexts;
}

代码示例来源：origin: broadinstitute/picard

/**
   * Helper function to print out a sequence dictionary
   */
  private void printDictionary(String name, SAMSequenceDictionary dict) {
    log.info(name);
    for (final SAMSequenceRecord contig : dict.getSequences()) {
      log.info("  SN=%s LN=%d%n", contig.getSequenceName(), contig.getSequenceLength());
    }
  }
}

代码示例来源：origin: PapenfussLab/gridss

private void readAllAlignments(final SamReaderFactory readerFactory) {
  SamReader fromExternalProgram = readerFactory.open(SamInputResource.of(aligner.getInputStream()));
  SAMRecordIterator it = fromExternalProgram.iterator();
  while (it.hasNext()) {
    SAMRecord r = it.next();
    buffer.add(r);
    outstandingReads.decrementAndGet();
  }
  log.info(String.format("Reader thread complete. %s reads in output buffer", buffer.size()));
}
/**

代码示例来源：origin: broadinstitute/picard

/**
 * Add record if it is primary or optionally secondary.
 */
private void addIfNotFiltered(final Sink out, final SAMRecord rec) {
  if (includeSecondaryAlignments || !rec.getNotPrimaryAlignmentFlag()) {
    out.add(rec);
    if (this.progress.record(rec) && crossSpeciesReads > 0) {
      log.info(String.format("%d Reads have been unmapped due to being suspected of being Cross-species contamination.", crossSpeciesReads));
    }
  }
}

代码示例来源：origin: com.github.broadinstitute/picard

/**
 * Add record if it is primary or optionally secondary.
 */
private void addIfNotFiltered(final Sink out, final SAMRecord rec) {
  if (includeSecondaryAlignments || !rec.getNotPrimaryAlignmentFlag()) {
    out.add(rec);
    if (this.progress.record(rec) && crossSpeciesReads > 0) {
      log.info(String.format("%d Reads have been unmapped due to being suspected of being Cross-species contamination.", crossSpeciesReads));
    }
  }
}

代码示例来源：origin: PapenfussLab/gridss

private void write(File output) throws IOException {
  log.info("Writing simplified variant calls to " + output.getName() + ". Only use this output if your pipeline is unable to process variants in VCF breakend notation.");
  File working = FileSystemContext.getWorkingFileFor(output);
  VariantContextWriter vcfWriter = processContext.getVariantContextWriter(working, true);
  Collections.sort(outputBuffer, IdsvVariantContext.ByLocationStart);
  for (IdsvVariantContext v : outputBuffer) {
    vcfWriter.add(v);
  }
  CloserUtil.close(vcfWriter);
  FileHelper.move(working, output, true);
}
private void load(File breakendCalls) {

代码示例来源：origin: PapenfussLab/gridss

@Override
  public int doWork(ExecutorService threadpool) throws IOException, InterruptedException, ExecutionException {
    IOUtil.assertFileIsWritable(OUTPUT_VCF);
    VariantCaller caller = new VariantCaller(getContext(), getSamEvidenceSources(), getAssemblySource());
    caller.callBreakends(OUTPUT_VCF, threadpool);
    log.info("Raw variant calls written to " + OUTPUT_VCF);
    return 0;
  }
}

代码示例来源：origin: enasequence/cramtools

CramToBam_OBA_Function(CramHeader header, ReferenceSource referenceSource) {
  this.header = header;
  parser = new ContainerParser(header.getSamFileHeader());
  f = new Cram2SamRecordFactory(header.getSamFileHeader());
  codec = new BAMRecordCodec(header.getSamFileHeader());
  n = new CramNormalizer(header.getSamFileHeader(), referenceSource);
  log.info("converter created");
}