Commit 9317d175 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: CLI11, -f and -C, with callback

parent 4a8d31e5
......@@ -412,9 +412,15 @@ int main (int argc, char **argv)
// if (advanced)
group = "Fine segmentation options (second pass)";
app.add_option("-f",
[&segment_cost](CLI::results_t res) {
segment_cost = strToCost(res[0].c_str(), VDJ);
return true;
},
"use custom Cost for fine segmenter : format \"match, subst, indels, del_end, homo\" (default DEFAULT_SEGMENT_COST )"
// TODO: description, default value
) -> group(group);
// << " -f <string> use custom Cost for fine segmenter : format \"match, subst, indels, del_end, homo\" (default "<< DEFAULT_SEGMENT_COST <<" )"<< endl
// case 'f'' segment_cost=strToCost(optarg, VDJ); break;
app.add_option("-E", expected_value_D, "maximal e-value for determining if a D segment can be trusted", true) -> group(group) -> level();
app.add_option("-Z", kmer_threshold, "typical number of V genes, selected by k-mer comparison, to compare to the read ('" NO_LIMIT "': all genes, default)", true) -> group(group)
......@@ -434,8 +440,15 @@ int main (int argc, char **argv)
app.add_option("-S", save_comp, "generate and save comparative matrix for clustering") -> group(group) -> level();
app.add_option("-L", load_comp, "load comparative matrix for clustering") -> group(group) -> level();
app.add_option("--forced-edges", forced_edges, "manual clustering -- a file used to force some specific edges") -> group(group) -> level();
// << " -C <string> use custom Cost for automatic clustering : format \"match, subst, indels, del_end, homo\" (default "<< DEFAULT_CLUSTER_COST <<" )"<< endl
// cluster_cost=strToCost(optarg, Cluster);
app.add_option("-C",
[&cluster_cost](CLI::results_t res) {
cluster_cost = strToCost(res[0].c_str(), Cluster);
return true;
},
"use custom Cost for automatic clustering : format \"match, subst, indels, del_end, homo\" (default DEFAULT_CLUSTER_COST )"
// TODO: description, default value
) -> group(group) -> level();
group = "Limits to report a clone (or a window)";
app.add_option("-r", min_reads_clone, "minimal number of reads supporting a clone", true) -> group(group);
......
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