195 	SUBREADputs("");  in propMapped_usage()
196 	SUBREADputs("  Calculate the proportion of mapped reads/fragments.");  in propMapped_usage()
197 	SUBREADputs("");  in propMapped_usage()
198 	SUBREADputs("Usage:");  in propMapped_usage()
199 	SUBREADputs("");  in propMapped_usage()
200 	SUBREADputs("  ./prommapped [options] -i <file>");  in propMapped_usage()
201 	SUBREADputs("");  in propMapped_usage()
202 	SUBREADputs("Required arguments:");  in propMapped_usage()
203 	SUBREADputs("");  in propMapped_usage()
204 	SUBREADputs("  -i <string>  An input file containing read mapping results. Both SAM or BAM");  in propMapped_usage()
205 	SUBREADputs("               formats are supported.");  in propMapped_usage()
206 	SUBREADputs("");  in propMapped_usage()
207 	SUBREADputs("Optional arguments:");  in propMapped_usage()
208 	SUBREADputs("");  in propMapped_usage()
209 	SUBREADputs("  -o <string>  Name of output file including mapping statistics.");  in propMapped_usage()
210 	SUBREADputs("");  in propMapped_usage()
211 	SUBREADputs("  -f           If specified, fragments (read pairs) will be counted instead of");  in propMapped_usage()
212 	SUBREADputs("               individual reads. This option is only applicable for paired-end");  in propMapped_usage()
213 	SUBREADputs("               reads.");  in propMapped_usage()
214 	SUBREADputs("");  in propMapped_usage()
215 	SUBREADputs("  -p           If specified, only properly paired reads will be counted. This");  in propMapped_usage()
216 	SUBREADputs("               option is only applicable for paired-end reads.");  in propMapped_usage()
217 	SUBREADputs("");  in propMapped_usage()