Commit 48bf444e authored by Mathieu Giraud's avatar Mathieu Giraud

Merge branch 'feature-a/release' into 'dev'

Release 2020.01

See merge request !563
parents fe6f3fb5 a2af81a8
Pipeline #116246 passed with stages
in 52 minutes and 18 seconds
......@@ -278,7 +278,7 @@ RELEASE_TOOLS = $(wildcard ../tools/*.py)
RELEASE_MAKE = ../tools/tests/Makefile ../doc/Makefile
RELEASE_TESTS = ../doc/vidjil-format.md $(wildcard ../doc/analysis-example.vidjil) $(wildcard ../tools/tests/*.should_get) ../tools/should.py ../tools/diff_json.sh ../demo/get-sequences ../demo/Demo-X5.fa ../demo/Makefile
RELEASE_GERMLINES = ../germline/Makefile ../germline/germline_id ../germline/get-saved-germline ../germline/get-germline ../germline/split-from-imgt.py $(wildcard ../germline/*.g) ../germline/revcomp-fasta.py ../germline/fasta.py ../germline/homo-sapiens/IKZF*fa ../germline/homo-sapiens/ERG*fa
RELEASE_HELP = ../doc/vidjil-algo.md ../doc/locus.md ../doc/tools.md ../doc/should-vdj.org ../doc/quality.md ../doc/credits.md ../doc/CHANGELOG ../doc/LICENSE ../README.md ../INSTALL.md
RELEASE_HELP = ../doc/vidjil-algo.md ../doc/locus.md ../doc/tools.md ../doc/vidjil-format.md ../doc/should-vdj.md ../doc/quality.md ../doc/credits.md ../doc/CHANGELOG ../doc/LICENSE ../README.md ../INSTALL.md
RELEASE_FILES = $(RELEASE_TOOLS) $(RELEASE_TESTS) $(RELEASE_MAKE) $(RELEASE_GERMLINES) $(RELEASE_HELP)
......
/*
This file is part of Vidjil <http://www.vidjil.org>
Copyright (C) 2011-2019 by VidjilNet consortium and Bonsai bioinformatics
Copyright (C) 2011-2020 by VidjilNet consortium and Bonsai bioinformatics
at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
Contributors:
Mathieu Giraud <mathieu.giraud@vidjil.org>
......
/*
This file is part of Vidjil <http://www.vidjil.org>
Copyright (C) 2011-2019 by VidjilNet consortium and Bonsai bioinformatics
Copyright (C) 2011-2020 by VidjilNet consortium and Bonsai bioinformatics
at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
Contributors:
Mathieu Giraud <mathieu.giraud@vidjil.org>
......
/*
This file is part of Vidjil <http://www.vidjil.org>
Copyright (C) 2011-2019 by VidjilNet consortium and Bonsai bioinformatics
Copyright (C) 2011-2020 by VidjilNet consortium and Bonsai bioinformatics
at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
Contributors:
Mathieu Giraud <mathieu.giraud@vidjil.org>
......
/*
This file is part of Vidjil <http://www.vidjil.org>
Copyright (C) 2011-2019 by VidjilNet consortium and Bonsai bioinformatics
Copyright (C) 2011-2020 by VidjilNet consortium and Bonsai bioinformatics
at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
Contributors:
Mathieu Giraud <mathieu.giraud@vidjil.org>
......
/*
This file is part of Vidjil <http://www.vidjil.org>
Copyright (C) 2011-2019 by VidjilNet consortium and Bonsai bioinformatics
Copyright (C) 2011-2020 by VidjilNet consortium and Bonsai bioinformatics
at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
Contributors:
Mathieu Giraud <mathieu.giraud@vidjil.org>
......
/*
This file is part of Vidjil <http://www.vidjil.org>
Copyright (C) 2011-2019 by VidjilNet consortium and Bonsai bioinformatics
Copyright (C) 2011-2020 by VidjilNet consortium and Bonsai bioinformatics
at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
Contributors:
Mathieu Giraud <mathieu.giraud@vidjil.org>
......
/*
This file is part of Vidjil <http://www.vidjil.org>
Copyright (C) 2011-2019 by VidjilNet consortium and Bonsai bioinformatics
Copyright (C) 2011-2020 by VidjilNet consortium and Bonsai bioinformatics
at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
Contributors:
Mathieu Giraud <mathieu.giraud@vidjil.org>
......
/*
This file is part of Vidjil <http://www.vidjil.org>
Copyright (C) 2011-2019 by VidjilNet consortium and Bonsai bioinformatics
Copyright (C) 2011-2020 by VidjilNet consortium and Bonsai bioinformatics
at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
Contributors:
Mathieu Giraud <mathieu.giraud@vidjil.org>
......
/*
This file is part of Vidjil <http://www.vidjil.org>
Copyright (C) 2011-2019 by VidjilNet consortium and Bonsai bioinformatics
Copyright (C) 2011-2020 by VidjilNet consortium and Bonsai bioinformatics
at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
Contributors:
Mathieu Giraud <mathieu.giraud@vidjil.org>
......
/*
This file is part of Vidjil <http://www.vidjil.org>
Copyright (C) 2011-2019 by VidjilNet consortium and Bonsai bioinformatics
Copyright (C) 2011-2020 by VidjilNet consortium and Bonsai bioinformatics
at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
Contributors:
Mathieu Giraud <mathieu.giraud@vidjil.org>
......
/*
This file is part of Vidjil <http://www.vidjil.org>
Copyright (C) 2011-2019 by VidjilNet consortium and Bonsai bioinformatics
Copyright (C) 2011-2020 by VidjilNet consortium and Bonsai bioinformatics
at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lille
Contributors:
Mathieu Giraud <mathieu.giraud@vidjil.org>
......
......@@ -9,12 +9,12 @@ $ There are no clones in the .vidjil
0:"id"
!LAUNCH: rm out/Stanford_S22.tsv ; $VIDJIL_DIR/$EXEC -z 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta > /dev/null ; touch out/Stanford_S22.tsv ; cat out/Stanford_S22.tsv
!LAUNCH: rm out/Stanford_S22.tsv ; $LAUNCHER $VIDJIL_DIR/$EXEC $EXTRA -z 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta > /dev/null ; touch out/Stanford_S22.tsv ; cat out/Stanford_S22.tsv
$ The AIRR .tsv file has four lines
4:
!LAUNCH: rm out/Stanford_S22.tsv ; $VIDJIL_DIR/$EXEC --no-airr -z 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta > /dev/null ; touch out/Stanford_S22.tsv ; cat out/Stanford_S22.tsv
!LAUNCH: rm out/Stanford_S22.tsv ; $LAUNCHER $VIDJIL_DIR/$EXEC $EXTRA --no-airr -z 0 -g $VIDJIL_DIR/germline/homo-sapiens.g:IGH $VIDJIL_DATA/Stanford_S22.fasta > /dev/null ; touch out/Stanford_S22.tsv ; cat out/Stanford_S22.tsv
$ No AIRR .tsv file
0:
\ No newline at end of file
This changelog concerns vijil-algo, the algorithmic part (C++) of the Vidjil platform.
2020-01-24 The Vidjil Team
* Improved e-value estimation, -e is now the global e-value, new advanced option --e-value-kmer
Sequences on larger datasets will now be better analyzed #3594 !538
* Added 'seg.cdr3.seq' output with nucleotide sequence #4017
* Improved 'name' output on sequences not fully analyzed with '-c designations' #3890
* Limit on 50 clones on stdout, as the main output is the .vidjil file #3302 !530
* New --no-vidjil and --no-airr advanced options to control the output #3861
* Extended and updated documentation, including on library preparation and sequencing and on quality
* New and updated tests
2019-05-17 The Vidjil Team
* Better method to build consensus sequences used by default, old behaviour with --consensus-on-longest-sequences #3866
* Optimized analyses with pre-computations, including for e-value estimation !468
......
# Credits
Vidjil is an open-source platform for the analysis of high-throughput sequencing data from lymphocytes, developed and maintained by
the [Bonsai bioinformatics lab](http://cristal.univ-lille.fr/bonsai) at CRIStAL (UMR CNRS 9189, Université Lille) and Inria Lillendation
the [Bonsai bioinformatics lab](http://cristal.univ-lille.fr/bonsai) at CRIStAL (UMR CNRS 9189, Université Lille)
and the [VidjilNet consortium](http://www.vidjil.net) at Inria.
Contact: [Mathieu Giraud and Mikaël Salson](mailto:contact@vidjil.org)
## Vidjil core development
- Mathieu Giraud, 2011-2019
- Mikaël Salson, 2011-2019
- Marc Duez, 2012-2016
- Mathieu Giraud, 2011-2020
- Mikaël Salson, 2011-2020
- Marc Duez, 2012-2016, 2019-2020
- Tatiana Rocher, 2014-2017
- Florian Thonier, 2015-2019
- Ryan Herbert, 2015-2018
- Florian Thonier, 2015-2020
- Ryan Herbert, 2015-2020
- Aurélien Béliard, 2016-2017
## Other contributors
......@@ -65,7 +65,7 @@ The development of Vidjil is funded by:
- SIRIC ONCOLille (Grant INCa-DGOS-Inserm 6041), 2014-2017
- Inria Lille, 2015-2018
- InCA, 2016-2019
- VidjilNet consortium at Inria, 2018-
- VidjilNet consortium at Inria, 2018-2020
## References
......
# vidjil-algo 2019.05
# vidjil-algo 2020.01
**Command-line manual**
*The Vidjil team (Mathieu, Mikaël, Aurélien, Florian, Marc, Tatiana and Rayan)*
......
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