Commit c06c7fc2 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: --grep-reads combo

Bye-bye -FaW, see #3785.
parent d232fc28
......@@ -569,6 +569,20 @@ int main (int argc, char **argv)
bool __only_on_exit__clean_memory; // Do not use except on exit, see #3729
app.add_flag("--clean-memory", __only_on_exit__clean_memory, "clean memory on exit") -> group(group) -> level();
// ----------------------------------------------------------------------------------------------------------------------
group = "Presets";
app.add_option("--grep-reads",
[&only_labeled_windows,&windows_labels_explicit,&output_sequences_by_cluster](CLI::results_t res) {
only_labeled_windows = true;
windows_labels_explicit.push_back(res[0].c_str());
output_sequences_by_cluster = true;
return true;
},
"output, by clone, reads related to the given window sequence, even when they are below the thresholds"
PAD_HELP "(equivalent to --label SEQUENCE -label-filter --out-reads)")
-> group(group) -> level() -> set_type_name("SEQUENCE");
// ----------------------------------------------------------------------------------------------------------------------
group = "Help";
app.set_help_flag("--help,-h", "help")
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment