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src/analysis/roimethstat.cpp: using the raw mode for help messages to…
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… display more information about the output
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andrewdavidsmith committed Jun 9, 2024
1 parent 5721bad commit e4812fe
Showing 1 changed file with 10 additions and 14 deletions.
24 changes: 10 additions & 14 deletions src/analysis/roimethstat.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -172,8 +172,10 @@ is_sorted_within_chrom(const vector<MSite> &sites) {
};
auto a = cbegin(sites);
while (a != cend(sites)) {
const auto b = find_if(a, cend(sites),
[a](const MSite &s) { return s.chrom != a->chrom; });
const auto a_chrom = a->chrom;
const auto b = find_if(a, cend(sites), [&a_chrom](const MSite &s) {
return s.chrom != a_chrom;
});
if (!is_sorted(a, b, pos_cmp)) return false;
a = b;
}
Expand Down Expand Up @@ -306,12 +308,10 @@ get_bed_columns(const string &regions_file) {
int
main_roimethstat(int argc, const char **argv) {
try {
// ADS: this information should be somehow presented to the user
// when the tool is run without arguments.
static const string description = R"""(
Compute average site methylation levels in each interval from a given
set of genomic intervals
set of genomic intervals. The 5th column (the "score" column in BED
format) is determined by the '-l' or '-level' argument.
Columns (beyond the first 6) in the BED format output:
(7) weighted mean methylation
Expand All @@ -321,7 +321,6 @@ Columns (beyond the first 6) in the BED format output:
(11) number of sites covered at least once
(12) number of observations in reads indicating methylation
(13) total number of observations from reads in the region
)""";

static const string default_name_prefix = "X";
Expand All @@ -337,10 +336,7 @@ Columns (beyond the first 6) in the BED format output:
string outfile;

/****************** COMMAND LINE OPTIONS ********************/
OptionParser opt_parse(strip_path(argv[0]),
"Compute average site "
"methylation levels in each interval from "
"a given set of genomic intervals",
OptionParser opt_parse(strip_path(argv[0]), description,
"<intervals-bed> <methylation-file>");
opt_parse.set_show_defaults();
opt_parse.add_opt("output", 'o', "Name of output file (default: stdout)",
Expand All @@ -360,12 +356,12 @@ Columns (beyond the first 6) in the BED format output:
vector<string> leftover_args;
opt_parse.parse(argc, argv, leftover_args);
if (argc == 1 || opt_parse.help_requested()) {
cerr << opt_parse.help_message() << endl
<< opt_parse.about_message() << endl;
cerr << opt_parse.help_message()
<< opt_parse.about_message_raw() << endl;
return EXIT_SUCCESS;
}
if (opt_parse.about_requested()) {
cerr << opt_parse.about_message() << endl;
cerr << opt_parse.about_message_raw() << endl;
return EXIT_SUCCESS;
}
if (opt_parse.option_missing()) {
Expand Down

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