Commit e371b125 authored by Mathieu Giraud's avatar Mathieu Giraud
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vidjil-algo: release 2021.02

see !884
parent 52fdaff2
Pipeline #212436 passed with stages
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/*
This file is part of Vidjil-algo <http://www.vidjil.org>
Copyright (C) 2011-2020 by VidjilNet consortium and Bonsai bioinformatics
Copyright (C) 2011-2021 by VidjilNet consortium and Bonsai bioinformatics
at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
Contributors:
Mathieu Giraud <mathieu.giraud@vidjil.org>
......@@ -205,7 +205,7 @@ string string_NO_LIMIT(string s)
int main (int argc, char **argv)
{
cout << "# " << PROGNAME << " -- V(D)J recombinations analysis <http://www.vidjil.org/>" << endl
<< "# Copyright (C) 2011-2020 by the Vidjil team" << endl
<< "# Copyright (C) 2011-2021 by the Vidjil team" << endl
<< "# Bonsai bioinformatics at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille" << endl
<< "# VidjilNet consortium" << endl
<< endl
......
This changelog concerns vijil-algo, the algorithmic part (C++) of the Vidjil platform.
2020-08-XX The Vidjil Team
2021-02-05 The Vidjil Team
* New report of unproductivity causes in 'seg.junction.unproductive' (core/segment.cpp) #4599
* New fields in AIRR .tsv output, 'vj_in_frame', 'stop_codon', '{v,j}_support', '{v,d,j,cdr3}_sequence_{start,end}' (core/output.cpp) #3569 #4643
* Ability to get the input reads from stdin with '-' (core/fasta.cpp) #4642
* New advanced option --read-number to override e-value multiplier, new warning W21 on doubtful multipliers (vidjil.cpp) !887
* New experimental option --show-junction, displaying germline genes on stdout (core/segment.cpp) !886
* Bugs closed (W61 warning check)
* New and updated documentation, including on input selection and on custom germline presets (-g)
* New and updated tests
2020-08-21 The Vidjil Team
* Cleaned output, no .vdj.fa and seq/clone-*.fa by default, new options --out-vdjfa and --out-clone-files #4386 #4387
Pipelines should not rely on the format of the headers in the .vdj.fa file, but rather parse the .vidjil file #3795
* Extended test and support to g++ 10.1, while reworking the documentation on supported compilers !733
......
# vidjil-algo 2020.08
# vidjil-algo 2021.02
**Command-line manual**
*The Vidjil team (Mathieu, Mikaël, Aurélien, Florian, Marc, Tatiana and Rayan)*
```
Vidjil -- High-throughput Analysis of V(D)J Immune Repertoire -- [[http://www.vidjil.org]]
Copyright (C) 2011-2020 by Bonsai bioinformatics
Copyright (C) 2011-2021 by Bonsai bioinformatics
at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
and VidjilNet consortium.
contact@vidjil.org
......
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