Class BAMIndexMetaData


  • public class BAMIndexMetaData
    extends Object
    Metadata about the bam index contained within the bam index. One instance created per index file.
    • Method Detail

      • getAlignedRecordCount

        public int getAlignedRecordCount()
        Returns:
        the count of aligned records associated with this reference
      • getUnalignedRecordCount

        public int getUnalignedRecordCount()
        Returns:
        the count of unaligned records associated with this reference
      • printIndexStats

        public static void printIndexStats​(File inputBamFile)
        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
      • getIndexStats

        public static BAMIndexMetaData[] getIndexStats​(BAMFileReader bam)
        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