htsjdk.samtools.BAMIndexMetaData.getLastOffset java code examples

Common ways to obtain BAMIndexMetaData

private void myMethod () {
 BAMIndexMetaData b =new BAMIndexMetaData()
BAMIndexContent bAMIndexContent;bAMIndexContent.getMetaData()
List chunkList;new BAMIndexMetaData(chunkList)
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}

/**
 * Write the meta data represented by the chunkLists associated with bin MAX_BINS 37450
 *
 * @param metaData information describing numAligned records, numUnAligned, etc
 */
private void writeChunkMetaData(final int reference, final BAMIndexMetaData metaData) {
  final int nChunks = metaData == null ? 0 : 2;
  pw.print("  Ref " + reference + " bin 37450 has n_chunk= " + nChunks);
  if (nChunks == 0) {
    pw.println();
  } else {
    pw.println("     Chunk: " + //  c.toString() +
        " start: " + Long.toString(metaData.getFirstOffset(), 16) +
        " end: " + Long.toString(metaData.getLastOffset(), 16));
    pw.println("     Chunk: " + //  c.toString() +
        " start: " + Long.toString(metaData.getAlignedRecordCount(), 16) +
        " end: " + Long.toString(metaData.getUnalignedRecordCount(), 16));
  }
}

/**
 * Write the meta data represented by the chunkLists associated with bin MAX_BINS 37450
 *
 * @param metaData information describing numAligned records, numUnAligned, etc
 */
private void writeChunkMetaData(final int reference, final BAMIndexMetaData metaData) {
  final int nChunks = metaData == null ? 0 : 2;
  pw.print("  Ref " + reference + " bin 37450 has n_chunk= " + nChunks);
  if (nChunks == 0) {
    pw.println();
  } else {
    pw.println("     Chunk: " + //  c.toString() +
        " start: " + Long.toString(metaData.getFirstOffset(), 16) +
        " end: " + Long.toString(metaData.getLastOffset(), 16));
    pw.println("     Chunk: " + //  c.toString() +
        " start: " + Long.toString(metaData.getAlignedRecordCount(), 16) +
        " end: " + Long.toString(metaData.getUnalignedRecordCount(), 16));
  }
}

/**
 * Write the meta data represented by the chunkLists associated with bin MAX_BINS 37450
 *
 * @param metaData information describing numAligned records, numUnAligned, etc
 */
private void writeChunkMetaData(final int reference, final BAMIndexMetaData metaData) {
  final int nChunks = metaData == null ? 0 : 2;
  pw.print("  Ref " + reference + " bin 37450 has n_chunk= " + nChunks);
  if (nChunks == 0) {
    pw.println();
  } else {
    pw.println("     Chunk: " + //  c.toString() +
        " start: " + Long.toString(metaData.getFirstOffset(), 16) +
        " end: " + Long.toString(metaData.getLastOffset(), 16));
    pw.println("     Chunk: " + //  c.toString() +
        " start: " + Long.toString(metaData.getAlignedRecordCount(), 16) +
        " end: " + Long.toString(metaData.getUnalignedRecordCount(), 16));
  }
}

/**
 * Write the meta data represented by the chunkLists associated with bin MAX_BINS 37450
 *
 * @param metaData information describing numAligned records, numUnAligned, etc
 */
private void writeChunkMetaData(final BAMIndexMetaData metaData) {
  codec.writeInt(GenomicIndexUtil.MAX_BINS);
  final int nChunk = 2;
  codec.writeInt(nChunk);
  codec.writeLong(metaData.getFirstOffset());
  codec.writeLong(metaData.getLastOffset());
  codec.writeLong(metaData.getAlignedRecordCount());
  codec.writeLong(metaData.getUnalignedRecordCount());
}

/**
 * Write the meta data represented by the chunkLists associated with bin MAX_BINS 37450
 *
 * @param metaData information describing numAligned records, numUnAligned, etc
 */
private void writeChunkMetaData(final BAMIndexMetaData metaData) {
  codec.writeInt(GenomicIndexUtil.MAX_BINS);
  final int nChunk = 2;
  codec.writeInt(nChunk);
  codec.writeLong(metaData.getFirstOffset());
  codec.writeLong(metaData.getLastOffset());
  codec.writeLong(metaData.getAlignedRecordCount());
  codec.writeLong(metaData.getUnalignedRecordCount());
}

/**
 * Write the meta data represented by the chunkLists associated with bin MAX_BINS 37450
 *
 * @param metaData information describing numAligned records, numUnAligned, etc
 */
private void writeChunkMetaData(final BAMIndexMetaData metaData) {
  codec.writeInt(GenomicIndexUtil.MAX_BINS);
  final int nChunk = 2;
  codec.writeInt(nChunk);
  codec.writeLong(metaData.getFirstOffset());
  codec.writeLong(metaData.getLastOffset());
  codec.writeLong(metaData.getAlignedRecordCount());
  codec.writeLong(metaData.getUnalignedRecordCount());
}

/**
 * Write the meta data represented by the chunkLists associated with bin MAX_BINS 37450
 *
 * @param metaData information describing numAligned records, numUnAligned, etc
 */
private void writeChunkMetaData(final BAMIndexMetaData metaData) {
  codec.writeInt(GenomicIndexUtil.MAX_BINS);
  final int nChunk = 2;
  codec.writeInt(nChunk);
  codec.writeLong(metaData.getFirstOffset());
  codec.writeLong(metaData.getLastOffset());
  codec.writeLong(metaData.getAlignedRecordCount());
  codec.writeLong(metaData.getUnalignedRecordCount());
}

/**
 * Write the meta data represented by the chunkLists associated with bin MAX_BINS 37450
 *
 * @param metaData information describing numAligned records, numUnAligned, etc
 */
private void writeChunkMetaData(final BAMIndexMetaData metaData) {
  codec.writeInt(GenomicIndexUtil.MAX_BINS);
  final int nChunk = 2;
  codec.writeInt(nChunk);
  codec.writeLong(metaData.getFirstOffset());
  codec.writeLong(metaData.getLastOffset());
  codec.writeLong(metaData.getAlignedRecordCount());
  codec.writeLong(metaData.getUnalignedRecordCount());
}

Popular methods of BAMIndexMetaData

getAlignedRecordCount
getUnalignedRecordCount
getFirstOffset
getNoCoordinateRecordCount
newReference
Call for each new reference sequence encountered
recordMetaData
<init>
Constructor used when reading an index construct one instance for each index generated
getIndexStats
Prints meta-data statistics from BAM index (.bai) file Statistics include count of aligned and unali
incrementNoCoordinateRecordCount
Call whenever a reference with no coordinate information is encountered in the bam file
printIndexStats
Prints meta-data statistics from BAM index (.bai) file Statistics include count of aligned and unali
setNoCoordinateRecordCount
Set local variable. Normally noCoordinateRecord count accessed from AbstractBAMFileIndex when readin

setNoCoordinateRecordCount

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How to use getLastOffsetmethodin htsjdk.samtools.BAMIndexMetaData

Best Java code snippets using htsjdk.samtools.BAMIndexMetaData.getLastOffset (Showing top 8 results out of 315)

How to use
getLastOffset
method
in
htsjdk.samtools.BAMIndexMetaData