Maj terminée. Pour consulter la release notes associée voici le lien :
https://about.gitlab.com/releases/2021/07/07/critical-security-release-gitlab-14-0-4-released/

Commit 9e26c749 authored by Cyprien Borée's avatar Cyprien Borée
Browse files

replace sequence while calling filterBioReader

The filterBioReader method was not called with the correct parameter
causing an error in should-get/doc-examples.should-get test.
parent fe6f5c6f
Pipeline #25630 passed with stages
in 37 minutes and 59 seconds
......@@ -1449,14 +1449,12 @@ 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);
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{
Sequence s = seg.getSequence();
seqtype sq = s.sequence;
BioReader filtered = filterBioReaderWithACAutomaton(
segmented_germline->pair_automaton,
segmented_germline->rep_5, sq);
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) ;
......
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