Commit fe6f5c6f authored by Cyprien Borée's avatar Cyprien Borée
Browse files

Avoid odd Sequence in vidjil.cpp

If seg.box_V has the same value as the ascii number of a Kmer ambiguous
or unknown it throws a segfault.
For now the case is controlled with a condition, however it needs to be fixed.

For more informations see #3224
parent b4670a6e
Pipeline #25602 failed with stages
in 13 minutes and 46 seconds
......@@ -1450,9 +1450,14 @@ 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)){
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(seg.box_V->ref_nb == 94){ // ascii value of kmer unknown : to fix
out_clone << filtered.read(seg.box_V->ref_nb + 1);
}else{
out_clone << filtered.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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