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vidjil
vidjil
Commit 6fc60d59 authored by Mathieu Giraud's avatar Mathieu Giraud
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vidjil.cpp: update following CLI11 update

parent b7d5f688
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Showing with 22 additions and 22 deletions
algo/vidjil.cpp
View file @ 6fc60d59
......@@ -167,7 +167,7 @@ inline std::string failure_message_doc(const CLI::App *app, const CLI::Error &e)
std::string header = ERROR_STRING + std::string(e.what()) + "\n";
header += "For more information, ";
if(app->get_help_ptr() != nullptr)
header += "run with " + app->get_help_ptr()->single_name() + " or ";
header += "run with " + app->get_help_ptr()->get_name() + " or ";
header += "see " DOCUMENTATION ".\n";
return header;
}
......@@ -224,7 +224,7 @@ int main (int argc, char **argv)
#endif
CLI::App app{"# vidjil-algo -- V(D)J recombinations analysis", argv[0]};
app.set_failure_message(failure_message_doc);
app.failure_message(failure_message_doc);
//$$ options: defaults
float ratio_representative = DEFAULT_RATIO_REPRESENTATIVE;
......@@ -242,7 +242,7 @@ int main (int argc, char **argv)
- BAM (.bam)
Paired-end reads should be merged before given as an input to vidjil-algo.
)Z")
-> required() -> set_type_name("");
-> required() -> type_name("");
// ----------------------------------------------------------------------------------------------------------------------
......@@ -254,14 +254,14 @@ int main (int argc, char **argv)
"\n \t\t" COMMAND_WINDOWS " \t locus detection, window extraction"
"\n \t\t" COMMAND_SEGMENT " \t detailed V(D)J designation, without prior clustering (not as efficient)"
"\n \t\t" COMMAND_GERMLINES " \t statistics on k-mers in different germlines")
-> group(group) -> set_type_name("COMMAND");
-> group(group) -> type_name("COMMAND");
// ----------------------------------------------------------------------------------------------------------------------
group = "Input" ;
string read_header_separator = DEFAULT_READ_HEADER_SEPARATOR ;
app.add_option("--header-sep", read_header_separator, "separator for headers in the reads file", false)
-> group(group) -> level() -> set_type_name("CHAR='" DEFAULT_READ_HEADER_SEPARATOR "'");
-> group(group) -> level() -> type_name("CHAR='" DEFAULT_READ_HEADER_SEPARATOR "'");
int max_reads_processed = NO_LIMIT_VALUE;
int max_reads_processed_sample = NO_LIMIT_VALUE;
......@@ -287,7 +287,7 @@ int main (int argc, char **argv)
-g PATH
multiple locus/germlines, shortcut for '-g PATH/)Z" DEFAULT_MULTI_GERMLINE_FILE R"Z(',
processes human TRA, TRB, TRG, TRD, IGH, IGK and IGL locus, possibly with incomplete/unusal recombinations)Z")
-> group(group) -> set_type_name("GERMLINES");
-> group(group) -> type_name("GERMLINES");
vector <string> v_reps_V ;
vector <string> v_reps_D ;
......@@ -295,16 +295,16 @@ int main (int argc, char **argv)
app.add_option("-V", v_reps_V,
"custom V germline multi-fasta file(s)")
-> group(group) -> set_type_name("FILE");
-> group(group) -> type_name("FILE");
app.add_option("-D", v_reps_D,
"custom D germline multi-fasta file(s), analyze into V(D)J components")
-> group(group) -> set_type_name("FILE");
-> group(group) -> type_name("FILE");
app.add_option("-J", v_reps_J,
"custom V germline multi-fasta file(s)")
-> group(group) -> set_type_name("FILE");
-> group(group) -> type_name("FILE");
bool multi_germline_unexpected_recombinations_12 = false;
......@@ -339,7 +339,7 @@ int main (int argc, char **argv)
return worked;
},
"k-mer size used for the V/J affectation (default: 10, 12, 13, depends on germline)")
-> group(group) -> level() -> set_type_name("INT");
-> group(group) -> level() -> type_name("INT");
int wmer_size = DEFAULT_W ;
app.add_option("--window,-w", wmer_size,
......@@ -362,7 +362,7 @@ int main (int argc, char **argv)
},
// trim_sequences,
"trim V and J genes (resp. 5' and 3' regions) to keep at most <INT> nt (0: no trim)")
-> group(group) -> level() -> set_type_name("INT");
-> group(group) -> level() -> type_name("INT");
app.add_option("--seed,-s",
[&](CLI::results_t res) {
......@@ -374,7 +374,7 @@ int main (int argc, char **argv)
"seed, possibly spaced, used for the V/J affectation (default: depends on germline), given either explicitely or by an alias"
PAD_HELP + string_of_map(seedMap, " ")
)
-> group(group) -> level() -> set_type_name("SEED=" DEFAULT_SEED);
-> group(group) -> level() -> type_name("SEED=" DEFAULT_SEED);
// ----------------------------------------------------------------------------------------------------------------------
......@@ -408,8 +408,8 @@ int main (int argc, char **argv)
vector <string> windows_labels_explicit ;
string windows_labels_file = "" ;
app.add_option("--label", windows_labels_explicit, "label the given sequence(s)") -> group(group) -> level() -> set_type_name("SEQUENCE");
app.add_option("--label-file", windows_labels_file, "label a set of sequences given in <file>") -> group(group) -> level() -> set_type_name("FILE");
app.add_option("--label", windows_labels_explicit, "label the given sequence(s)") -> group(group) -> level() -> type_name("SEQUENCE");
app.add_option("--label-file", windows_labels_file, "label a set of sequences given in <file>") -> group(group) -> level() -> type_name("FILE");
bool only_labeled_windows = false ;
app.add_flag("--label-filter", only_labeled_windows, "filter -- keep only the windows related to the labeled sequences") -> group(group) -> level();
......@@ -441,7 +441,7 @@ int main (int argc, char **argv)
// TODO: return false on bad input
},
"maximal number of clones to be analyzed with a full V(D)J designation ('" NO_LIMIT "': no limit, do not use)")
-> group(group) -> set_type_name("INT=" + string_of_int(max_clones));
-> group(group) -> type_name("INT=" + string_of_int(max_clones));
app.add_flag_function("--all", [&](size_t n) {
UNUSED(n);
......@@ -474,7 +474,7 @@ int main (int argc, char **argv)
return true;
},
"use custom Cost for clone analysis: format \"match, subst, indels, del_end, homo\" (default " + string_of_cost(DEFAULT_SEGMENT_COST) + ")")
-> group(group) -> level() -> set_type_name("COST");
-> group(group) -> level() -> type_name("COST");
double expected_value_D = THRESHOLD_NB_EXPECTED_D;
app.add_option("--analysis-e-value-D,-E", expected_value_D,
......@@ -510,7 +510,7 @@ int main (int argc, char **argv)
app.add_flag("--cluster-load-matrix", load_comp, "load comparative matrix for clustering") -> group(group) -> level();
string forced_edges = "" ;
app.add_option("--cluster-forced-edges", forced_edges, "manual clustering -- a file used to force some specific edges") -> group(group) -> level() -> set_type_name("FILE");
app.add_option("--cluster-forced-edges", forced_edges, "manual clustering -- a file used to force some specific edges") -> group(group) -> level() -> type_name("FILE");
Cost cluster_cost = DEFAULT_CLUSTER_COST ;
app.add_option("--cluster-cost",
......@@ -519,7 +519,7 @@ int main (int argc, char **argv)
return true;
},
"use custom Cost for automatic clustering : format \"match, subst, indels, del_end, homo\" (default " + string_of_cost(DEFAULT_CLUSTER_COST) + ")")
-> group(group) -> level() -> set_type_name("COST");
-> group(group) -> level() -> type_name("COST");
// ----------------------------------------------------------------------------------------------------------------------
......@@ -559,8 +559,8 @@ int main (int argc, char **argv)
string out_dir = DEFAULT_OUT_DIR;
string f_basename = "";
app.add_option("--dir,-o", out_dir, "output directory", true) -> group(group) -> set_type_name("PATH");
app.add_option("--base,-b", f_basename, "output basename (by default basename of the input file)") -> group(group) -> set_type_name("STRING");
app.add_option("--dir,-o", out_dir, "output directory", true) -> group(group) -> type_name("PATH");
app.add_option("--base,-b", f_basename, "output basename (by default basename of the input file)") -> group(group) -> type_name("STRING");
int verbose = 0 ;
......@@ -581,7 +581,7 @@ int main (int argc, char **argv)
},
"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(group) -> level() -> type_name("SEQUENCE");
// ----------------------------------------------------------------------------------------------------------------------
group = "Help";
......@@ -606,7 +606,7 @@ int main (int argc, char **argv)
DEPRECATED("-l", "'-l' is deprecated, please use '--label'");
// ----------------------------------------------------------------------------------------------------------------------
app.set_footer(usage_examples(argv[0]));
app.footer(usage_examples(argv[0]));
//$$ options: parsing
CLI11_PARSE(app, argc, argv);
......
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