Fast way to get number of aligned reads in indexed CRAM file.

[dariober]

With this method I can quickly get the total number of aligned reads in an indexed bam file by querying the index.

However, with CRAM input, it returns 0. Is there a way to quickly get the total number of reads in a CRAM without iterating through each record?

This is with htsjdk 4.3.0

  public static long getAlignedReadCount(String bam) throws IOException {
    SamReaderFactory srf = SamReaderFactory.make();
    srf.validationStringency(ValidationStringency.SILENT);
    SamReader samReader;
    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;
  }