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 2d9c7ce4 authored by Mathieu Giraud's avatar Mathieu Giraud

germline.cpp: build indexes for incomplete rearrangements

MultiGermline::build_incomplete_set() loads incomplete rearrangements into separate indexes.
This is temporary, one day we will parse germline.data, and gather several indexes into one.
parent d2f74a76
......@@ -166,6 +166,39 @@ void MultiGermline::build_default_set(string path)
}
void MultiGermline::build_incomplete_set(string path)
{
// Should parse 'data/germlines.data'
Germline *germline;
// DH-JH
germline = new Germline("IGH+", 'h', path + "/IGHD.fa", "", path + "/IGHJ.fa", -10, 20);
germline->new_index("######-######");
germlines.push_back(germline);
// DD2-DD3
germline = new Germline("TRD+", 'd', path + "/TRDD2-01.fa", "", path + "/TRDJ.fa", -10, 20);
germline->new_index("#####-#####");
germlines.push_back(germline);
germline = new Germline("TRD+", 'd', path + "/TRDV.fa", "", path + "/TRDD3-01.fa", -10, 20);
germline->new_index("#####-#####");
germlines.push_back(germline);
germline = new Germline("TRD+", 'd', path + "/TRDD2-01.fa", "", path + "/TRDD3-01.fa", -10, 20);
germline->new_index("#####-#####");
germlines.push_back(germline);
// IGK: KDE, INTRON
germline = new Germline("IGK", 'k', path + "/IGKV.fa", "", path + "/IGK-INTRON.fa", -10, 80);
germline->new_index("#####-#####");
germlines.push_back(germline);
germline = new Germline("IGK", 'k', path + "/IGK-KDE.fa", "", path + "/IGK-INTRON.fa", -10, 80);
germline->new_index("#####-#####");
germlines.push_back(germline);
}
void MultiGermline::load_standard_set(string path)
{
......
......@@ -86,6 +86,7 @@ class MultiGermline {
void insert(Germline *germline);
void build_default_set(string path);
void build_incomplete_set(string path);
void load_standard_set(string path);
void insert_in_one_index(IKmerStore<KmerAffect> *_index);
......
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