Commit fb6da11d authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: CLI11, replays back changed things when rebasing

parent b7d0bf8c
Pipeline #14484 failed with stages
in 5 minutes and 3 seconds
......@@ -383,7 +383,9 @@ int main (int argc, char **argv)
// if (advanced)
group = "Fine segmentation options (second pass)";
// << " -f <string> use custom Cost for fine segmenter : format \"match, subst, indels, homo, del_end\" (default "<<VDJ<<" )"<< endl
// << " -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();
......@@ -401,7 +403,7 @@ 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, homo, del_end\" (default "<<Cluster<<" )"<< endl
// << " -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);
group = "Limits to report a clone (or a window)";
......
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