vidjil-algo: release 2021.02

see !884

algo/release

-2020.08
+2021.02

algo/vidjil.cpp

 /*
   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

doc/CHANGELOG

 
 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

doc/vidjil-algo.md

-# 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