NAME

       coverageCount  -  counting  the  coverage  of  mapped reads at each location on the entire
       reference genome

DESCRIPTION

       This program calculates the coverage of mapped reads at each location on

       the reference genome. It generates a binary file for each chromosome by concatenating  the
       coverage levels as 4-bytes integer numbers.

USAGE

       coverageCount [options] -i <input_file> -o <output_prefix>

       Required arguments:

       -i <string>
              Name of input file in SAM or BAM format.

       -o <string>
              Prefix of the output files. Each output file contains Four-byte integer numbers

       Optional arguments:

       -p     The input file contains paired-end reads.

       --maxMOp <int> Maximum number of 'M' operations allowed in a CIGAR string.

              10  by default. Both 'X' and '=' are treated as 'M' and adjacent 'M' operations are
              merged in the CIGAR string.