Commit ed8ef291 authored by Cyprien Borée's avatar Cyprien Borée

add -R option for alternative genes export

Now the option can be used with a number in order to export the alternative
genes into the json.

For more informations, see #1409.
parent 440f1e16
Pipeline #34197 passed with stages
in 51 minutes and 16 seconds
......@@ -17,4 +17,4 @@ $ Display advanced options
: custom Cost
$ Correct number of options
B48:^ -
B49:^ -
......@@ -477,7 +477,9 @@ int main (int argc, char **argv)
app.add_flag("-3,--cdr3", detect_CDR3, "CDR3/JUNCTION detection (requires gapped V/J germlines)")
-> group(group);
int alternative_genes = 0;
app.add_option("-R", alternative_genes, "export the N best genes into .vidjil file", true)
-> group(group) -> level();
// ----------------------------------------------------------------------------------------------------------------------
group = "Additional clustering (third pass, experimental)" ;
......@@ -1366,7 +1368,7 @@ int main (int argc, char **argv)
// FineSegmenter
size_t nb_fine_segmented = (size_t) max_clones; // When -1, it will become the max value.
nb_fine_segmented = MIN(nb_fine_segmented, sort_clones.size());
FineSegmenter seg(representative, segmented_germline, segment_cost, expected_value, nb_fine_segmented, kmer_threshold);
FineSegmenter seg(representative, segmented_germline, segment_cost, expected_value, nb_fine_segmented, kmer_threshold, alternative_genes);
if (segmented_germline->seg_method == SEG_METHOD_543)
seg.FineSegmentD(segmented_germline, several_D, expected_value_D, nb_fine_segmented);
......@@ -1587,7 +1589,7 @@ int main (int argc, char **argv)
KmerSegmenter *seg = kmseg.the_kseg ;
Germline *germline = seg->segmented_germline ;
FineSegmenter s(seq, germline, segment_cost, expected_value, nb_reads_for_evalue, kmer_threshold);
FineSegmenter s(seq, germline, segment_cost, expected_value, nb_reads_for_evalue, kmer_threshold, alternative_genes);
json json_clone;
json_clone["id"] = seq.label;
......
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