Commit e371b125 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

vidjil-algo: release 2021.02

see !884
parent 52fdaff2
Pipeline #212436 passed with stages
in 15 seconds
/* /*
This file is part of Vidjil-algo <http://www.vidjil.org> 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 at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
Contributors: Contributors:
Mathieu Giraud <mathieu.giraud@vidjil.org> Mathieu Giraud <mathieu.giraud@vidjil.org>
...@@ -205,7 +205,7 @@ string string_NO_LIMIT(string s) ...@@ -205,7 +205,7 @@ string string_NO_LIMIT(string s)
int main (int argc, char **argv) int main (int argc, char **argv)
{ {
cout << "# " << PROGNAME << " -- V(D)J recombinations analysis <http://www.vidjil.org/>" << endl 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 << "# Bonsai bioinformatics at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille" << endl
<< "# VidjilNet consortium" << endl << "# VidjilNet consortium" << endl
<< endl << endl
......
This changelog concerns vijil-algo, the algorithmic part (C++) of the Vidjil platform. 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 * 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 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 * 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** **Command-line manual**
*The Vidjil team (Mathieu, Mikaël, Aurélien, Florian, Marc, Tatiana and Rayan)* *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]] 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 at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
and VidjilNet consortium. and VidjilNet consortium.
contact@vidjil.org contact@vidjil.org
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment