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vidjil
vidjil
Commits
e371b125
Commit
e371b125
authored
Feb 03, 2021
by
Mathieu Giraud
Browse files
vidjil-algo: release 2021.02
see
!884
parent
52fdaff2
Pipeline
#212436
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in 15 seconds
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algo/release
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e371b125
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algo/vidjil.cpp
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/*
This file is part of Vidjil-algo <http://www.vidjil.org>
Copyright (C) 2011-202
0
by VidjilNet consortium and Bonsai bioinformatics
Copyright (C) 2011-202
1
by VidjilNet consortium and Bonsai bioinformatics
at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
Contributors:
Mathieu Giraud <mathieu.giraud@vidjil.org>
...
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@@ -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) 2011-202
0
by the Vidjil team"
<<
endl
<<
"# Copyright (C) 2011-202
1
by the Vidjil team"
<<
endl
<<
"# Bonsai bioinformatics at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille"
<<
endl
<<
"# VidjilNet consortium"
<<
endl
<<
endl
...
...
doc/CHANGELOG
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e371b125
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
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doc/vidjil-algo.md
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e371b125
# vidjil-algo 202
0
.0
8
# vidjil-algo 202
1
.0
2
**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) 2011-202
0
by Bonsai bioinformatics
Copyright (C) 2011-202
1
by Bonsai bioinformatics
at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
and VidjilNet consortium.
contact@vidjil.org
...
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