Mise à jour terminée. Pour connaître les apports de la version 13.8.4 par rapport à notre ancienne version vous pouvez lire les "Release Notes" suivantes :
https://about.gitlab.com/releases/2021/02/11/security-release-gitlab-13-8-4-released/
https://about.gitlab.com/releases/2021/02/05/gitlab-13-8-3-released/

Commit 9a4f23cb authored by Mathieu Giraud's avatar Mathieu Giraud

core/segment.cpp: output germlines used when a read is segmented with MAX12

Sets code_short/info_extra in the FineSegmenter by running again a KmerSegmenter.
parent d278970d
......@@ -619,6 +619,7 @@ FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c)
because = NOT_PROCESSED ;
segmented_germline = germline ;
info_extra = "" ;
code_short = "" ;
label = seq.label ;
sequence = seq.sequence ;
Dend=0;
......@@ -631,7 +632,19 @@ FineSegmenter::FineSegmenter(Sequence seq, Germline *germline, Cost segment_c)
CDR3end = -1;
if (!germline->rep_5.size() || !germline->rep_3.size())
return ;
{
// We check whether this sequence is segmented with MAX12 (with default e-value parameters)
KmerSegmenter *kseg = new KmerSegmenter(seq, germline, THRESHOLD_NB_EXPECTED, 1);
if (kseg->isSegmented() && (!strcmp(germline->code.c_str(), PSEUDO_GERMLINE_MAX12)))
{
code_short = "Unexpected ";
code_short += kseg->before.toStringSigns() + germline->index->getLabel(kseg->before);
code_short += "/";
code_short += kseg->before.toStringSigns() + germline->index->getLabel(kseg->after);
info_extra += " " + kseg->before.toString() + "/" + kseg->after.toString() + " (" + code_short + ")";
}
return ;
}
// TODO: factoriser tout cela, peut-etre en lancant deux segmenteurs, un +, un -, puis un qui chapote
......
......@@ -1278,7 +1278,7 @@ int main (int argc, char **argv)
// From FineSegmenter
json_clone.add("sequence", seg.getSequence().sequence);
if (seg.isSegmented())
if (seg.code_short.length())
json_clone.add("name", seg.code_short);
seg.toJsonList(&json_seg);
......
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