To create segment of genome for given windows and step size To convert input bam to bed file To count number of reads falls in the segments

Usage: gen_seg.py [options]

Options: -h, --help show this help message and exit -d FOLDER, --directory=FOLDER Path to directory that contains uniq.sorted bam files -g FILE, --genome-index=FILE Path to genome index -w INT, --window-size=INT Size of the window to use -s INT, --step-size=INT Base pairs to step before creating a new window -b FILE, --bedmap=FILE Path to bedmap bin -o STRING, --outfile=STRING Basename of the output file -p STRING, --isPair=STRING Reads are paired or not(yes = paired, no = single)