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Commit 12943baa authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

vidjil.cpp: rename long options to --output-{,un}detected

parent da0a38e5
...@@ -547,7 +547,7 @@ int main (int argc, char **argv) ...@@ -547,7 +547,7 @@ 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)"; group = "Detailed output per read (generally not recommended, large files, but may be used for filtering, as in -uu -X 1000)";
bool output_segmented = false; bool output_segmented = false;
app.add_flag("--out-analyzed,-U", output_segmented, app.add_flag("--out-detected,-U", output_segmented,
"output reads with detected recombinations (in " SEGMENTED_FILENAME " file)") "output reads with detected recombinations (in " SEGMENTED_FILENAME " file)")
-> group(group); -> group(group);
...@@ -555,7 +555,7 @@ int main (int argc, char **argv) ...@@ -555,7 +555,7 @@ int main (int argc, char **argv)
bool output_unsegmented_detail = false; bool output_unsegmented_detail = false;
bool output_unsegmented_detail_full = false; bool output_unsegmented_detail_full = false;
app.add_flag_function("--out-unanalyzed,-u", [&](size_t n) { app.add_flag_function("--out-undetected,-u", [&](size_t n) {
output_unsegmented = (n >= 3); // -uuu output_unsegmented = (n >= 3); // -uuu
output_unsegmented_detail_full = (n >= 2); // -uu output_unsegmented_detail_full = (n >= 2); // -uu
output_unsegmented_detail = (n >= 1); // -u output_unsegmented_detail = (n >= 1); // -u
......
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