Commit e01870a4 authored by Cyprien Borée's avatar Cyprien Borée
Browse files

fix functional test: should-get/stanford-detailed

The algorithm output some sequences belonging to the original germline
bioreader even though we use the filtered one.
Thus, the test couldn't pass. It is fixed now.
parent 5ddf8895
Pipeline #25572 failed with stages
in 15 minutes and 24 seconds
......@@ -1448,8 +1448,11 @@ int main (int argc, char **argv)
}
// Output best V, (D) and J germlines to CLONE_FILENAME-*
if ((segmented_germline->seg_method == SEG_METHOD_53) || (segmented_germline->seg_method == SEG_METHOD_543))
out_clone << segmented_germline->rep_5.read(seg.box_V->ref_nb) ;
if ((segmented_germline->seg_method == SEG_METHOD_53) || (segmented_germline->seg_method == SEG_METHOD_543)){
BioReader filtered = filterBioReaderWithACAutomaton(segmented_germline->pair_automaton,segmented_germline->rep_5,representative.sequence);
out_clone << filtered.read(seg.box_V->ref_nb);
}
//out_clone << segmented_germline->rep_5.read(seg.box_V->ref_nb) ;
if ((segmented_germline->seg_method == SEG_METHOD_543) || (segmented_germline->seg_method == SEG_METHOD_ONE))
out_clone << segmented_germline->rep_4.read(seg.box_D->ref_nb) ;
if ((segmented_germline->seg_method == SEG_METHOD_53) || (segmented_germline->seg_method == SEG_METHOD_543))
......
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