Commit 75d83be3 authored by Mathieu Giraud's avatar Mathieu Giraud

vidjil.cpp: CLI11, -Z

parent 88753b38
......@@ -111,6 +111,8 @@ enum { CMD_WINDOWS, CMD_CLONES, CMD_SEGMENT, CMD_GERMLINES } ;
#define DEFAULT_MAX_AUDITIONED 2000
#define DEFAULT_RATIO_REPRESENTATIVE 0.5
#define DEFAULT_KMER_THRESHOLD NO_LIMIT_VALUE
#define DEFAULT_EPSILON 0
#define DEFAULT_MINPTS 10
......@@ -284,6 +286,8 @@ int main (int argc, char **argv)
json jsonLevenshtein;
bool jsonLevenshteinComputed = false ;
int kmer_threshold = DEFAULT_KMER_THRESHOLD;
//$$ options: definition wiht CLI11
string group = "";
......@@ -390,6 +394,10 @@ int main (int argc, char **argv)
// << " -f <string> use custom Cost for fine segmenter : format \"match, subst, indels, del_end, homo\" (default "<< DEFAULT_SEGMENT_COST <<" )"<< endl
// case 'f'' segment_cost=strToCost(optarg, VDJ); break;
app.add_option("-E", expected_value_D, "maximal e-value for determining if a D segment can be trusted", true) -> group(group) -> level();
app.add_option("-Z", kmer_threshold, "typical number of V genes, selected by k-mer comparison, to compare to the read ('" NO_LIMIT "': all genes, default)", true) -> group(group) -> level() -> set_type_name("NB");
// atoi_NO_LIMIT(optarg);
group = "Clone analysis (second pass)";
app.add_flag("-3,--cdr3", detect_CDR3, "CDR3/JUNCTION detection (requires gapped V/J germlines)") -> group(group);
......
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