Commit 3a944f57 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: CLI11, -s, with callback

See #3292.
parent 300525b4
......@@ -353,8 +353,6 @@ int main (int argc, char **argv)
/*
<< " (use either -s or -k option, but not both)" << endl
<< " (all these options, except -w, are overriden when using -g)" << endl
<< " -s <string> spaced seed used for the V/J affectation" << endl
<< " (default: #####-#####, ######-######, #######-#######, depends on germline)" << endl
*/
#endif
......@@ -374,13 +372,18 @@ int main (int argc, char **argv)
app.add_option("-t", trim_sequences, // trim_sequences_changed = true
"trim V and J genes (resp. 5' and 3' regions) to keep at most <int> nt (0: no trim)") -> group(group);
app.add_option("-s",
[&](CLI::results_t res) {
seed = res[0] ;
options_s_k++ ;
seed_changed = true;
return true;
},
"spaced seeds used for the V/J affectation (default: depends on germline)"
) -> group(group) -> level();
/*
case 's':
#ifndef NO_SPACED_SEEDS
seed = string(optarg);
seed_changed = true;
options_s_k++ ;
#else
#ifdef NO_SPACED_SEEDS
cerr << "To enable the option -s, please compile without NO_SPACED_SEEDS" << endl;
#endif
*/
......
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