How to use

htsjdk.samtools.BAMIndexMetaData

constructor

  /**
   * Prints meta-data statistics from BAM index (.bai) file
   * Statistics include count of aligned and unaligned reads for each reference sequence
   * and a count of all records with no start coordinate
   */
  static public BAMIndexMetaData[] getIndexStats(final BAMFileReader bam) {

    AbstractBAMFileIndex index = (AbstractBAMFileIndex) bam.getIndex();
    // read through all the bins of every reference.
    int nRefs = index.getNumberOfReferences();
    BAMIndexMetaData[] result = new BAMIndexMetaData[nRefs == 0 ? 1 : nRefs];
    for (int i = 0; i < nRefs; i++) {
      result[i] = index.getMetaData(i);
    }

    if (result[0] == null) {
      result[0] = new BAMIndexMetaData();
    }
    final Long noCoordCount = index.getNoCoordinateCount();
    if (noCoordCount != null)  // null in old index files without metadata
      result[0].setNoCoordinateRecordCount(noCoordCount);

    return result;
  }
}

  /**
   * Prints meta-data statistics from BAM index (.bai) file
   * Statistics include count of aligned and unaligned reads for each reference sequence
   * and a count of all records with no start coordinate
   */
  static public BAMIndexMetaData[] getIndexStats(final BAMFileReader bam){

    AbstractBAMFileIndex index = (AbstractBAMFileIndex) bam.getIndex();
    // read through all the bins of every reference.
    int nRefs = index.getNumberOfReferences();
    BAMIndexMetaData[] result = new BAMIndexMetaData[nRefs == 0 ? 1 : nRefs];
    for (int i = 0; i < nRefs; i++) {
      result[i] = index.getMetaData(i);
    }

    if (result[0] == null){
      result[0] = new BAMIndexMetaData();
    }
    final Long noCoordCount = index.getNoCoordinateCount();
    if (noCoordCount != null)  // null in old index files without metadata
      result[0].setNoCoordinateRecordCount(noCoordCount);

    return result;
  }
}

  /**
   * Prints meta-data statistics from BAM index (.bai or .csi) file
   * Statistics include count of aligned and unaligned reads for each reference sequence
   * and a count of all records with no start coordinate
   */
  static public BAMIndexMetaData[] getIndexStats(final BAMFileReader bam) {

    AbstractBAMFileIndex index = (AbstractBAMFileIndex) bam.getIndex();
    // read through all the bins of every reference.
    int nRefs = index.getNumberOfReferences();
    BAMIndexMetaData[] result = new BAMIndexMetaData[nRefs == 0 ? 1 : nRefs];
    for (int i = 0; i < nRefs; i++) {
      result[i] = index.getMetaData(i);
    }

    if (result[0] == null) {
      result[0] = new BAMIndexMetaData();
    }
    final Long noCoordCount = index.getNoCoordinateCount();
    if (noCoordCount != null)  // null in old index files without metadata
      result[0].setNoCoordinateRecordCount(noCoordCount);

    return result;
  }
}

/**
 * Return meta data for the given reference including information about number of aligned, unaligned, and noCoordinate records
 *
 * @param reference the reference of interest
 * @return meta data for the reference
 */
@Override
public BAMIndexMetaData getMetaData(final int reference) {
  seek(4);
  final List<Chunk> metaDataChunks = new ArrayList<Chunk>();
  final int sequenceCount = readInteger();
  if (reference >= sequenceCount) {
    return null;
  }
  skipToSequence(reference);
  final int binCount = readInteger();
  for (int binNumber = 0; binNumber < binCount; binNumber++) {
    final int indexBin = readInteger();
    final int nChunks = readInteger();
    if (indexBin == GenomicIndexUtil.MAX_BINS) {
      readChunks(nChunks, metaDataChunks);
    } else {
      skipBytes(16 * nChunks);
    }
  }
  return new BAMIndexMetaData(metaDataChunks);
}

/**
 * Return meta data for the given reference including information about number of aligned, unaligned, and noCoordinate records
 *
 * @param reference the reference of interest
 * @return meta data for the reference
 */
public BAMIndexMetaData getMetaData(final int reference) {
  seek(4);
  final List<Chunk> metaDataChunks = new ArrayList<Chunk>();
  final int sequenceCount = readInteger();
  if (reference >= sequenceCount) {
    return null;
  }
  skipToSequence(reference);
  final int binCount = readInteger();
  for (int binNumber = 0; binNumber < binCount; binNumber++) {
    final int indexBin = readInteger();
    final int nChunks = readInteger();
    if (indexBin == GenomicIndexUtil.MAX_BINS) {
      for (int ci = 0; ci < nChunks; ci++) {
        final long chunkBegin = readLong();
        final long chunkEnd = readLong();
        metaDataChunks.add(new Chunk(chunkBegin, chunkEnd));
      }
    } else {
      skipBytes(16 * nChunks);
    }
  }
  return new BAMIndexMetaData(metaDataChunks);
}

return new BAMIndexMetaData(metaDataChunks);

return new BAMIndexContent(referenceSequence, bins, binCount - (metaDataSeen? 1 : 0), new BAMIndexMetaData(metaDataChunks), linearIndex);

return new BAMIndexContent(referenceSequence, bins, binCount - (metaDataSeen? 1 : 0), new BAMIndexMetaData(metaDataChunks), null);

return new BAMIndexContent(referenceSequence, bins, binCount - (metaDataSeen? 1 : 0), new BAMIndexMetaData(metaDataChunks), linearIndex);

return new BAMIndexContent(referenceSequence, bins, binCount - (metaDataSeen? 1 : 0), new BAMIndexMetaData(metaDataChunks), linearIndex);

/**
 * Return meta data for the given reference including information about number of aligned, unaligned, and noCoordinate records
 *
 * @param reference the reference of interest
 * @return meta data for the reference
 */
@Override
public BAMIndexMetaData getMetaData(final int reference) {
  if (metaDataPos > 0 && position() != metaDataPos) {
    seek(metaDataPos);
  }
  final List<Chunk> metaDataChunks = new ArrayList<Chunk>();
  final int sequenceCount = getNumberOfReferences();
  if (reference >= sequenceCount) {
    return null;
  }
  skipToSequence(reference);
  final int binCount = readInteger(); // n_bin
  for (int binNumber = 0; binNumber < binCount; binNumber++) {
    final int indexBin = readInteger(); // bin
    final long lOffset = readLong(); // loffset
    final int nChunks = readInteger(); // n_chunk
    if (indexBin == getMaxBins() + 1) {
      readChunks(nChunks, metaDataChunks);
    } else {
      skipBytes(BAMFileConstants.CSI_CHUNK_SIZE * nChunks);
    }
  }
  return new BAMIndexMetaData(metaDataChunks);
}