Commit 59965130 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

vidjil.cpp: some options are advanced

parent aa899d80
Pipeline #28899 failed with stages
in 12 minutes and 50 seconds
...@@ -387,7 +387,7 @@ int main (int argc, char **argv) ...@@ -387,7 +387,7 @@ int main (int argc, char **argv)
return worked; return worked;
}, },
"k-mer size used for the V/J affectation (default: 10, 12, 13, depends on germline)") "k-mer size used for the V/J affectation (default: 10, 12, 13, depends on germline)")
-> group(group) -> set_type_name("INT"); -> group(group) -> level() -> set_type_name("INT");
#ifndef NO_SPACED_SEEDS #ifndef NO_SPACED_SEEDS
...@@ -395,11 +395,11 @@ int main (int argc, char **argv) ...@@ -395,11 +395,11 @@ int main (int argc, char **argv)
#endif #endif
app.add_option("-w", wmer_size, app.add_option("-w", wmer_size,
"w-mer size used for the length of the extracted window ('" NO_LIMIT "': use all the read, no window clustering)") "w-mer size used for the length of the extracted window ('" NO_LIMIT "': use all the read, no window clustering)")
-> group(group) -> transform(string_NO_LIMIT); -> group(group) -> level() -> transform(string_NO_LIMIT);
app.add_option("-e", expected_value, app.add_option("-e", expected_value,
"maximal e-value for determining if a V-J segmentation can be trusted", true) "maximal e-value for determining if a V-J segmentation can be trusted", true)
-> group(group) -> transform(string_NO_LIMIT); -> group(group) -> level() -> transform(string_NO_LIMIT);
app.add_option("-t", app.add_option("-t",
[&](CLI::results_t res) { [&](CLI::results_t res) {
...@@ -409,7 +409,7 @@ int main (int argc, char **argv) ...@@ -409,7 +409,7 @@ int main (int argc, char **argv)
}, },
// trim_sequences, // trim_sequences,
"trim V and J genes (resp. 5' and 3' regions) to keep at most <INT> nt (0: no trim)") "trim V and J genes (resp. 5' and 3' regions) to keep at most <INT> nt (0: no trim)")
-> group(group) -> set_type_name("INT"); -> group(group) -> level() -> set_type_name("INT");
app.add_option("-s", app.add_option("-s",
[&](CLI::results_t res) { [&](CLI::results_t res) {
...@@ -450,9 +450,9 @@ int main (int argc, char **argv) ...@@ -450,9 +450,9 @@ int main (int argc, char **argv)
// ---------------------------------------------------------------------------------------------------------------------- // ----------------------------------------------------------------------------------------------------------------------
group = "Labeled sequences (windows related to these sequences will be kept even if -r/--ratio thresholds are not reached)"; group = "Labeled sequences (windows related to these sequences will be kept even if -r/--ratio thresholds are not reached)";
app.add_option("-W", windows_labels_explicit, "label the given sequence(s)") -> group(group) -> set_type_name("SEQUENCE"); app.add_option("-W", windows_labels_explicit, "label the given sequence(s)") -> group(group) -> level() -> set_type_name("SEQUENCE");
app.add_option("-l", windows_labels_file, "label a set of sequences given in <file>") -> group(group) -> set_type_name("FILE"); app.add_option("-l", windows_labels_file, "label a set of sequences given in <file>") -> group(group) -> level() -> set_type_name("FILE");
app.add_flag("-F", only_labeled_windows, "filter -- keep only the windows related to the labeled sequences") -> group(group); app.add_flag("-F", only_labeled_windows, "filter -- keep only the windows related to the labeled sequences") -> group(group) -> level();
// ---------------------------------------------------------------------------------------------------------------------- // ----------------------------------------------------------------------------------------------------------------------
......
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