Commit 0b25d667 authored by Mathieu Giraud's avatar Mathieu Giraud

vijil.cpp: CLI11, fix -uu and -uuu

add_flag_function() is called only once.
Bug found thanks to CI.
parent 59965130
Pipeline #28902 failed with stages
in 21 minutes and 21 seconds
......@@ -544,9 +544,9 @@ int main (int argc, char **argv)
-> group(group);
app.add_flag_function("-u", [&](size_t n) {
output_unsegmented = output_unsegmented_detail_full ; // -uuu
output_unsegmented_detail_full = output_unsegmented_detail; // -uu
output_unsegmented_detail = true; // -u
output_unsegmented = (n >= 3); // -uuu
output_unsegmented_detail_full = (n >= 2); // -uu
output_unsegmented_detail = (n >= 1); // -u
}, R"Z(
-u output unsegmented reads, gathered by unsegmentation cause, except for very short and 'too few V/J' reads (in *)Z" UNSEGMENTED_DETAIL_FILENAME R"Z( files)
-uu output unsegmented reads, gathered by unsegmentation cause, all reads (in *)Z" UNSEGMENTED_DETAIL_FILENAME R"Z( files) (use only for debug)
......
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