"maximal e-value for determining if a V-J segmentation can be trusted",true)->group(group);
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)")->group(group)->transform(string_NO_LIMIT);
app.add_option("-e",expected_value,
"maximal e-value for determining if a V-J segmentation can be trusted",true)->group(group)->transform(string_NO_LIMIT);
"trim V and J genes (resp. 5' and 3' regions) to keep at most <int> nt (0: no trim)")->group(group);
...
...
@@ -396,9 +406,8 @@ int main (int argc, char **argv)
// 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);
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)