39 	SUBREADputs("  This program calculates the coverage of mapped reads at each location on");  in calcCount_usage()
40 	SUBREADputs("the reference genome. It generates a binary file for each chromosome by concate-");  in calcCount_usage()
41 	SUBREADputs("nating the coverage levels as 4-bytes integer numbers.");  in calcCount_usage()
42 	SUBREADputs("");  in calcCount_usage()
43 	SUBREADputs("Usage");  in calcCount_usage()
44 	SUBREADputs("");  in calcCount_usage()
45 	SUBREADputs("  ./coverageCount [options] -i <input_file> -o <output_prefix>");  in calcCount_usage()
46 	SUBREADputs("");  in calcCount_usage()
47 	SUBREADputs("Required arguments:");  in calcCount_usage()
48 	SUBREADputs("");  in calcCount_usage()
49 	SUBREADputs("  -i <string>  Name of input file in SAM or BAM format.");  in calcCount_usage()
50 	SUBREADputs("");  in calcCount_usage()
51 	SUBREADputs("  -o <string>  Prefix of the output files. Each output file contains Four-byte");  in calcCount_usage()
52 	SUBREADputs("               integer numbers");  in calcCount_usage()
53 	SUBREADputs("");  in calcCount_usage()
54 	SUBREADputs("Optional arguments:");  in calcCount_usage()
55 	SUBREADputs("");  in calcCount_usage()
56 	SUBREADputs("  -p           The input file contains paired-end reads.");  in calcCount_usage()
57 	SUBREADputs("");  in calcCount_usage()
58 	SUBREADputs("  --maxMOp <int> Maximum number of 'M' operations allowed in a CIGAR string.");  in calcCount_usage()
59 	SUBREADputs("               10 by default. Both 'X' and '=' are treated as 'M' and adjacent");  in calcCount_usage()
60 	SUBREADputs("               'M' operations are merged in the CIGAR string.");  in calcCount_usage()
61 	SUBREADputs("");  in calcCount_usage()