@@ -56,13 +56,13 @@ int main(int argc, char **argv) {
// Query options
query->add_option("--index,-i",index_file,"Basename of the index file (same value as the -b passed to the `index' command")->required();
CLI::Option*list=query->add_flag("--list,-l",do_list,"List the chromosomes stored in the index with their length");
CLI::Option*bed=query->add_option("--bed,-b",bed_file,"Create a bed file with the number of reads computed on the whole genome on "+std::to_string(window_size)+"-bp windows (see --range --bed-window for more customisation)");
CLI::Option*bed=query->add_option("--bed,-b",bed_file,"Create a BED file with the number of reads computed on the whole genome on "+std::to_string(window_size)+"-bp windows (see --range --bed-window for more customisation). We recall that in BED format positions start at 0, the start position is included and the end position is excluded");
query->add_option("--bed-window,-w",window_size,"Window size on which the number of reads is computed for the BED output")
},"Gives the number of reads overlapping the specified range (with the format: chr:start-pos, start and pos are included). When used with --bed computes the number of reads in each window in the specified range.");
},"Gives (in BED format) the number of reads overlapping the specified range (with the format: chr:start-pos, start and pos are included and start at 0). When used with --bed computes the number of reads in each window in the specified range.");
list->excludes(bed);
list->excludes(range_opt);
...
...
@@ -89,7 +89,7 @@ int main(int argc, char **argv) {