Commit 9ac8c70b authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: CLI11, -u

parent 99edce38
......@@ -441,12 +441,16 @@ int main (int argc, char **argv)
group = "Detailed output per read (generally not recommended, large files, but may be used for filtering, as in -uu -X 1000)";
app.add_flag("-U", output_segmented, "output segmented reads (in " SEGMENTED_FILENAME " file)") -> group(group);
// << " -u output unsegmented reads, gathered by unsegmentation cause, except for very short and 'too few V/J' reads (in *" << UNSEGMENTED_DETAIL_FILENAME << " files)" << endl
// << " -uu output unsegmented reads, gathered by unsegmentation cause, all reads (in *" << UNSEGMENTED_DETAIL_FILENAME << " files) (use only for debug)" << endl
// << " -uuu output unsegmented reads, all reads, including a " << UNSEGMENTED_FILENAME << " file (use only for debug)" << endl
// output_unsegmented = output_unsegmented_detail_full ; // -uuu
// output_unsegmented_detail_full = output_unsegmented_detail; // -uu
// output_unsegmented_detail = true; // -u
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
}, 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)
-uuu output unsegmented reads, all reads, including a )Z" UNSEGMENTED_FILENAME R"Z( file (use only for debug)
)Z") -> group(group);
app.add_flag("-K", output_affects, "output detailed k-mer affectation on all reads (in " AFFECTS_FILENAME " file) (use only for debug, for example -KX 100)") -> group(group);
......
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