htsjdk.samtools.BAMIndexMetaData.getAlignedRecordCount 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());
}

  continue;
System.out.println("\tAligned= " + data[i].getAlignedRecordCount() +
    "\tUnaligned= " + data[i].getUnalignedRecordCount());

  continue;
System.out.println("\tAligned= " + data[i].getAlignedRecordCount() +
    "\tUnaligned= " + data[i].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());
}

count += meta.getAlignedRecordCount();

/**
 * 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());
}

public static long getAlignedReadCount(String bam) throws IOException{
  /*  ------------------------------------------------------ */
  /* This chunk prepares SamReader from local bam or URL bam */
  UrlValidator urlValidator = new UrlValidator();
  SamReaderFactory srf=SamReaderFactory.make();
  srf.validationStringency(ValidationStringency.SILENT);
  SamReader samReader;
  if(urlValidator.isValid(bam)){
    samReader = SamReaderFactory.makeDefault().open(
        SamInputResource.of(new URL(bam)).index(new URL(bam + ".bai"))
    );
  } else {
    samReader= srf.open(new File(bam));
  }
  /*  ------------------------------------------------------ */
  List<SAMSequenceRecord> sequences = samReader.getFileHeader().getSequenceDictionary().getSequences();
  long alnCount= 0;
  for(SAMSequenceRecord x : sequences){
    alnCount += samReader.indexing().getIndex().getMetaData(x.getSequenceIndex()).getAlignedRecordCount();
  }
  samReader.close();
  return alnCount;
}

final BAMIndexMetaData metaData_0 = index.getMetaData(0);
Assert.assertNotNull(metaData_0);
Assert.assertEquals(metaData_0.getAlignedRecordCount(), 1);
Assert.assertEquals(metaData_1.getAlignedRecordCount(), 3);
Assert.assertEquals(metaData_2.getAlignedRecordCount(), 2);

  continue;
System.out.println("\tAligned= " + data[i].getAlignedRecordCount() +
    "\tUnaligned= " + data[i].getUnalignedRecordCount());

  public static long countSamTotalRecord(final File samFile) {
    final SamReader reader = SamReaderFactory.make().open(samFile);
    assert reader.hasIndex();
    long total = 0;

    for (int i = 0; i < reader.getFileHeader().getSequenceDictionary().size(); i++) {
      total += reader.indexing().getIndex().getMetaData(i).getAlignedRecordCount();
      total += reader.indexing().getIndex().getMetaData(i).getUnalignedRecordCount();
    }
    return total;
  }
}

BAMIndexMetaData metaData = reader.indexing().getIndex().getMetaData(sequenceIndex);
Assert.assertEquals(EXPECTED_ALL_READS - EXPECTED_UNMAPPED_READS,
  metaData.getAlignedRecordCount());

Popular methods of BAMIndexMetaData

getUnalignedRecordCount
getFirstOffset
getLastOffset
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 getAlignedRecordCountmethodin htsjdk.samtools.BAMIndexMetaData

Best Java code snippets using htsjdk.samtools.BAMIndexMetaData.getAlignedRecordCount (Showing top 16 results out of 315)

How to use
getAlignedRecordCount
method
in
htsjdk.samtools.BAMIndexMetaData