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Commit bcbc5043 authored by Mathieu Giraud's avatar Mathieu Giraud

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

Release 2021.02

Closes #4460

See merge request !884
parents a6c302c5 e371b125
Pipeline #212443 failed with stages
in 8 minutes and 37 seconds
......@@ -51,6 +51,7 @@ OnlineFasta::~OnlineFasta() {
void OnlineFasta::init() {
if (filename == STDIN_FILENAME) {
input = &cin;
input_allocated = false;
}
else if (! filename.empty()) {
input = new igzstream(filename.c_str());
......
!LAUNCH: cat ../should-vdj-tests/Demo-X5.should-vdj.fa | $LAUNCHER $VIDJIL_DIR/$EXEC --all -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG -
!LAUNCH: cat ../should-vdj-tests/Demo-X5.should-vdj.fa | $LAUNCHER $VIDJIL_DIR/$EXEC $EXTRA --all -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG -
$ Display message with the estimation of read number
1:reading from stdin, estimating 100 reads
......@@ -15,7 +15,7 @@ $ Detect and designate one read on TRG
# When --read-number gives a bad estimation, there is a warning
!LAUNCH: cat ../should-vdj-tests/Demo-X5.should-vdj.fa | $LAUNCHER $VIDJIL_DIR/$EXEC --read-number 1 --all -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG -
!LAUNCH: cat ../should-vdj-tests/Demo-X5.should-vdj.fa | $LAUNCHER $VIDJIL_DIR/$EXEC $EXTRA --read-number 1 --all -g $VIDJIL_DIR/germline/homo-sapiens.g:TRG -
$ Display message with the estimation of read number
1:reading from stdin, estimating 1 reads
......
/*
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
......
......@@ -981,13 +981,29 @@ class TestSuite():
continue
# Launch the command
test_lines, exit_test = self.launch([current_cmd], verbose, colorize)
self.one_test(exit_test, test_lines, verbose, colorize)
if not self.skip:
test_lines, exit_test = self.launch([current_cmd], verbose, colorize)
self.one_test(exit_test, test_lines, verbose, colorize)
self.cmds.append(current_cmd)
if not self.source:
# Regular testing, stdout added to 'current_test_lines'
current_test_lines += test_lines
self.test_lines += test_lines
else:
# !OUTPUT_FILE:, the content of the file overrides 'current_test_lines'
try:
with open(self.source) as f:
current_test_lines = f.readlines()
except OSError:
msg = self.source + ' not found'
self.skip_set(msg)
exit_test.status = Sta(S_FAILED)
exit_test.info += ' - ' + msg
current_test_lines = []
self.cmds.append(current_cmd)
current_cmd = ''
current_test_lines += test_lines
self.test_lines += test_lines
# end of loop on should_lines
......@@ -1040,7 +1056,7 @@ class TestSuite():
if verbose > 0:
self.print_stderr(colorize)
return open(self.source).readlines() if self.source else self.stdout, exit_test
return self.stdout, exit_test
......
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