NAME

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

DESCRIPTION

       coverageCount Version 1.5.0-p1

              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:

       --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.

       coverageCount Version 1.5.0-p1

              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:

       --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.

coverageCount 1.5.0-p1+dfsg-2                     January 2016                                  COVERAGECOUNT(1)