.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
.TH COVERAGECOUNT "1" "May 2018" "coverageCount 1.6.2+dfsg" "User Commands"
.SH NAME
coverageCount \- counting the coverage of mapped reads at each location on the entire reference genome
.SH DESCRIPTION
.PP
This program calculates the coverage of mapped reads at each location on
.PP
the reference genome. It generates a binary file for each chromosome by concatenating the coverage levels as 4\-bytes integer numbers.
.PP
.SH USAGE
.PP 
coverageCount [options] \fB\-i\fR <input_file> \fB\-o\fR <output_prefix>
.PP
Required arguments:
.TP
\fB\-i\fR <string>
Name of input file in SAM or BAM format.
.TP
\fB\-o\fR <string>
Prefix of the output files. Each output file contains Four\-byte
integer numbers
.PP
Optional arguments:
.TP
\fB\-p\fR
The input file contains paired\-end reads.
.HP
\fB\-\-maxMOp\fR <int> Maximum number of 'M' operations allowed in a CIGAR string.
.IP
10 by default. Both 'X' and '=' are treated as 'M' and adjacent
\&'M' operations are merged in the CIGAR string.