htsjdk.samtools.util.Log.debug()方法的使用及代码示例

x33g5p2x  于2022-01-24 转载在 其他  
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本文整理了Java中htsjdk.samtools.util.Log.debug()方法的一些代码示例，展示了Log.debug()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.debug()方法的具体详情如下：
包路径：htsjdk.samtools.util.Log
类名称：Log
方法名：debug

Log.debug介绍

[英]Logs a Throwable and optional message parts at level debug.
[中]在调试级别记录可丢弃和可选的消息部分。

代码示例

代码示例来源：origin: PapenfussLab/gridss

@Override
public void close() throws IOException {
  log.debug("close() called");
  if (reference != null) reference.close();
}

代码示例来源：origin: enasequence/cramtools

public boolean cleanUp() {
  log.debug("Cleaning up task ", fileNameBase);
  inProgressMarkerFile.delete();
  failedMarkerFile.delete();
  successMarkerFile.delete();
  outputFile.delete();
  errorFile.delete();
  if (outputFiles != null)
    for (File file : outputFiles)
      file.delete();
  return STATUS.NONE == status();
}

代码示例来源：origin: enasequence/cramtools

private OrderedByteArray flushStripe(ByteArrayOutputStream baos) throws InterruptedException, IOException {
    OrderedByteArray stripe = new OrderedByteArray();
    stripe.bytes = baos.toByteArray();
    log.debug(String.format("adding stripe: order=%d, ref=%d, records=%d, bytes=%d", order, refId, recordCounter,
        stripe.bytes.length));
    stripe.order = order++;
    baos.reset();
    recordCounter = 0;
    return stripe;
  }
}

代码示例来源：origin: PapenfussLab/gridss

private void syncEnsureNext() {
  while (!isClosed.get() && buffer.isEmpty()) {
    try {
      log.debug(String.format("%d alignments outstanding", outstandingReads.get()));
      Thread.sleep(POLL_INTERVAL);
    } catch (InterruptedException e) {
      log.warn(e);
      return;
    }
  }
}
/**

代码示例来源：origin: PapenfussLab/gridss

private void remove(VariantContextDirectedBreakpoint bp) {
  lookup.remove(bp);
  byQual.remove(bp);
  VariantContextDirectedBreakpoint mate = id.get(bp.getAttribute(VcfSvConstants.PARTNER_BREAKEND_ID_KEY));
  if (mate != null) {
    lookup.remove(mate);
    byQual.remove(mate);
  } else {
    log.debug(String.format("%s missing mate", bp.getID()));
  }
}
private void write(File output) throws IOException {

代码示例来源：origin: enasequence/cramtools

private static long seek(List<CramIndex.Entry> index, int seqId, int start, int end, SeekableStream cramStream)
    throws IOException {
  List<Entry> found = CramIndex.find(index, seqId, start, end - start + 1);
  if (found == null || found.size() == 0)
    return -1;
  cramStream.seek(found.get(0).containerStartOffset);
  log.debug("Found query at offset: " + found.get(0).containerStartOffset);
  return found.get(0).containerStartOffset;
}

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

/**
 * Prepare to compress at the given compression level
 * @param compressionLevel 1 <= compressionLevel <= 9
 * @param deflaterFactory custom factory to create deflaters (overrides the default)
 */
public BlockCompressedOutputStream(final Path path, final int compressionLevel, final DeflaterFactory deflaterFactory) {
  this.file = path;
  codec = new BinaryCodec(path, true);
  deflater = deflaterFactory.makeDeflater(compressionLevel, true);
  log.debug("Using deflater: " + deflater.getClass().getSimpleName());
}

代码示例来源：origin: samtools/htsjdk

/**
 * Prepare to compress at the given compression level
 * @param compressionLevel 1 <= compressionLevel <= 9
 * @param deflaterFactory custom factory to create deflaters (overrides the default)
 */
public BlockCompressedOutputStream(final Path path, final int compressionLevel, final DeflaterFactory deflaterFactory) {
  this.file = path;
  codec = new BinaryCodec(path, true);
  deflater = deflaterFactory.makeDeflater(compressionLevel, true);
  log.debug("Using deflater: " + deflater.getClass().getSimpleName());
}

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

private Alignment getCurrentAlignment() throws ErrorMsg {
  if (!isAligned) {
    throw new RuntimeException("Should be called for aligned records only");
  }
  if (alignmentIterator == null) {
    log.debug("Recovering SAM record after detaching from iterator. Alignment id: " + sraAlignmentId);
    if (sraAlignmentId == null) {
      throw new RuntimeException("Cannot recover SAM object after detaching from iterator: no alignment id");
    }
    alignmentIterator = getReadCollection().getAlignment(sraAlignmentId);
  }
  return alignmentIterator;
}

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

private ReadCollection getReadCollection() {
  if (run != null) {
    return run;
  }
  log.debug("Recovering SRA read collection. Accession: " + accession);
  try {
    return run = NGS.openReadCollection(accession.toString());
  } catch (ErrorMsg e) {
    throw new RuntimeException(e);
  }
}

代码示例来源：origin: samtools/htsjdk

private ReadCollection getReadCollection() {
  if (run != null) {
    return run;
  }
  log.debug("Recovering SRA read collection. Accession: " + accession);
  try {
    return run = NGS.openReadCollection(accession.toString());
  } catch (ErrorMsg e) {
    throw new RuntimeException(e);
  }
}

代码示例来源：origin: PapenfussLab/gridss

public static void ensureIndexed(File fa) throws IOException {
  try (ReferenceSequenceFile reference = ReferenceSequenceFileFactory.getReferenceSequenceFile(fa)) {
    if (!reference.isIndexed()) {
      String msg = String.format("Unable to find index for %1$s. Please run 'samtools faidx %1$s' or picard tools BuildBamIndex to generate an index file.", fa);
      log.error(msg);
      throw new IOException(msg);
    } else {
      log.debug(fa, " is indexed.");
    }
  }
}
public void ensureDictionariesMatch() throws IOException {

代码示例来源：origin: enasequence/cramtools

protected byte[] findBasesByMD5(String md5) throws MalformedURLException, IOException {
  for (PathPattern p : refPatterns) {
    String path = p.format(md5);
    byte[] data = loadFromPath(path, md5);
    if (data == null)
      continue;
    log.debug("Reference found at the location ", path);
    return data;
  }
  return null;
}

代码示例来源：origin: org.seqdoop/htsjdk

/**
 * Reads through the records in the provided SAM reader and uses their quality scores to sanity check the expected
 * quality passed in. If the expected quality format is sane we just hand this back otherwise we throw a
 * {@link SAMException}.
 */
public static FastqQualityFormat detect(final SAMFileReader reader, final FastqQualityFormat expectedQualityFormat) {
  //sanity check expectedQuality
  final QualityEncodingDetector detector = new QualityEncodingDetector();
  final long recordCount = detector.add(DEFAULT_MAX_RECORDS_TO_ITERATE, reader);
  log.debug(String.format("Read %s records from %s.", recordCount, reader));
  return detector.generateBestGuess(FileContext.SAM, expectedQualityFormat);
}

代码示例来源：origin: PapenfussLab/gridss

@Override
  public void close() {
    log.debug("Closing UntemplatedSequenceAnnotator");
    // TODO: close feeding thread more cleanly than just shutting down the process
    vcfStream.close();
    try {
      aligner.close();
    } catch (IOException e) {
      log.warn(e);
    }
  }
}

代码示例来源：origin: samtools/htsjdk

/**
 * Reads through the records in the provided SAM reader and uses their quality scores to sanity check the expected
 * quality passed in. If the expected quality format is sane we just hand this back otherwise we throw a
 * {@link SAMException}.
 */
public static FastqQualityFormat detect(final SamReader reader, final FastqQualityFormat expectedQualityFormat) {
  //sanity check expectedQuality
  final QualityEncodingDetector detector = new QualityEncodingDetector();
  final long recordCount = detector.add(DEFAULT_MAX_RECORDS_TO_ITERATE, reader.iterator());
  log.debug(String.format("Read %s records from %s.", recordCount, reader));
  return detector.generateBestGuess(FileContext.SAM, expectedQualityFormat);
}

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

/**
 * Reads through the records in the provided SAM reader and uses their quality scores to sanity check the expected
 * quality passed in. If the expected quality format is sane we just hand this back otherwise we throw a
 * {@link SAMException}.
 */
public static FastqQualityFormat detect(final SamReader reader, final FastqQualityFormat expectedQualityFormat) {
  //sanity check expectedQuality
  final QualityEncodingDetector detector = new QualityEncodingDetector();
  final long recordCount = detector.add(DEFAULT_MAX_RECORDS_TO_ITERATE, reader.iterator());
  log.debug(String.format("Read %s records from %s.", recordCount, reader));
  return detector.generateBestGuess(FileContext.SAM, expectedQualityFormat);
}

代码示例来源：origin: PapenfussLab/gridss

private void closeCurrentAssembler() {
  if (currentAssembler.getExportTracker() != null) {
    try {
      currentAssembler.getExportTracker().close();
    } catch (IOException e) {
      log.debug(e);
    }
  }
  currentAssembler = null;
}
private void ensureAssembler(boolean attemptRecovery) {

代码示例来源：origin: broadinstitute/picard

@Override
  public boolean apply(final VariantContext vc) {
    final boolean include = !intervalsOfInterestDetector.getOverlaps(new Interval(vc.getContig(), vc.getStart(), vc.getEnd())).isEmpty();
    if (!include) LOG.debug("Filtering variant at ", vc.getContig(), ":", vc.getStart(), "-", vc.getEnd());
    return include;
  }
}

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

@Override
  public boolean apply(final VariantContext vc) {
    final boolean include = !intervalsOfInterestDetector.getOverlaps(new Interval(vc.getContig(), vc.getStart(), vc.getEnd())).isEmpty();
    if (!include) LOG.debug("Filtering variant at ", vc.getContig(), ":", vc.getStart(), "-", vc.getEnd());
    return include;
  }
}

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