Commits · 8bc797d36b9f30cdd1c9af408406c5835e2adbf7 · vidjil / vidjil

19 Apr, 2019 4 commits
- tests: remove $VIDJIL_DEFAULT_OPTIONS when it is it in the first place · 8bc797d3
  Mathieu Giraud authored Apr 19, 2019
```
see #3762
```
  8bc797d3
- tests/should.cfg: no VIDJIL_DEFAULT_OPTIONS · 4b578d28
  Mathieu Giraud authored Apr 19, 2019
```
See #3762. We have --extra
```
  4b578d28
- tests: merging some related test files · dac8244f
  Mathieu Giraud authored Apr 18, 2019
  
  dac8244f
- tests: renaming some *.should files, remove duplicate file · 9d391a47
  Mathieu Giraud authored Apr 18, 2019
```
see #3206
```
  9d391a47
18 Apr, 2019 2 commits
- tests/Makefile: update · 6d491472
  Mathieu Giraud authored Apr 18, 2019
  
  6d491472
- algo/tests: rename *.should-get tests to *.should · ebb59d2f
  Mathieu Giraud authored Apr 18, 2019
```
see #3206
```
  ebb59d2f
09 Apr, 2019 1 commit
- Merge branch 'feature-s/3555-erreur-si-clones-null' into 'dev' · 2ddbea56
  Mathieu Giraud authored Apr 09, 2019
```
Resolve "Erreur si clones null dans un fichier vidjil côté serveur"

Closes #3555

See merge request !329
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  2ddbea56
04 Apr, 2019 10 commits
- Merge branch 'feature-a/dev' into 'dev' · 6bc84612
  Mathieu Giraud authored Apr 04, 2019
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Release 2019.04, doc, release

See merge request !462
```
  6bc84612
- algo/release, doc/vidjil-algo.md: release 2019.04 · ed3d3145
  Mathieu Giraud authored Apr 04, 2019
  
  ed3d3145
- Merge branch 'feature-a/dev' into 'dev' · 55235d47
  Mathieu Giraud authored Apr 04, 2019
```
Release 2019.04

See merge request !461
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  55235d47
- vidjil-algo: release 2019.04 · 06d9be90
  Mathieu Giraud authored Apr 04, 2019
```
see #3891
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  06d9be90
- vidjil-algo: prepare CHANGELOG for release 2019.04 · 23fcc9b0
  Mathieu Giraud authored Apr 04, 2019
```
see #3891
```
  23fcc9b0
- Merge branch 'feature-a/3414-output-equal-score-alternative-genes' into 'dev' · 46add06a
  Mathieu Giraud authored Apr 04, 2019
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Algo: output equal score alternative genes

Closes #3414

See merge request !459
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  46add06a
- segment.h: Update comment to show the correct order · 53162f32
  Mikaël Salson authored Apr 04, 2019
  
  53162f32
- segment.cpp: reindent · eb2714a5
  Mikaël Salson authored Apr 04, 2019
  
  eb2714a5
- segment.cpp: Also display alternative genes with the same score as the last one · 3d77f5a2
  Mikaël Salson authored Apr 04, 2019
```
Fix #3414
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  3d77f5a2
- alternative_genes.should-get: Cannot determine the third alternative gene · 0a23db36
  Mikaël Salson authored Apr 04, 2019
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IGHJ5*01 and IGHJ5*02 are equally good. Without #3414
we can have either sequences.

Alignment:
read             gactactggggccagggaaccctggtcaccgtctcctcag
IGHJ4*01   8     ..............A.........................
IGHJ4*02   8     ........................................
IGHJ4*02   8     ..............A..G......................
IGHJ5*01  11     ....C.........A.........................
IGHJ5*02  11     ...CC...................................
```
  0a23db36
03 Apr, 2019 4 commits
- Merge branch 'feature-a/dev' into 'dev' · 0e317911
  Mathieu Giraud authored Apr 04, 2019
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tests: this test can fail on some platforms

See merge request !458
```
  0e317911
- tests: this test can fail on some platforms · 10cf1300
  Mathieu Giraud authored Apr 04, 2019
```
See #3414 and 68b6ebcb.
```
  10cf1300
- Merge branch 'dev' of gitlab.inria.fr:vidjil/vidjil into feature-s/3555-erreur-si-clones-null · eedefd37
  Thonier Florian authored Apr 03, 2019
  
  eedefd37
- Merge branch... · 1fcf5a1c
  Mathieu Giraud authored Apr 03, 2019
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Merge branch 'feature-c/2041-l-alignement-multiple-plante-quand-la-premiere-sequence-est-retiree' into 'dev'

Resolve "L'alignement multiple plante quand la première séquence est retirée"

Closes #2041

See merge request !454
```
  1fcf5a1c
02 Apr, 2019 19 commits
- Merge branch 'feature-a/3839-config-labels' into 'dev' · 3be38c03
  Mikaël Salson authored Apr 02, 2019
```
--config, --labels-json

Closes #3839 and #3837

See merge request !456
```
  3be38c03
- tests: !NO_LAUNCHER · ca86677b
  Mathieu Giraud authored Apr 02, 2019
  
  ca86677b
- tests: update · b0afd492
  Mathieu Giraud authored Apr 02, 2019
```
Closes #3837, #3839.
```
  b0afd492
- vidjil.cpp: --labels-json · c17ed263
  Mathieu Giraud authored Apr 02, 2019
```
See #3839.
```
  c17ed263
- core/labels.{h,cpp}: load_into_map_from_json() · 2ff7f8d9
  Mathieu Giraud authored Apr 02, 2019
```
See #3839
```
  2ff7f8d9
- tests: add tests, dumping and reading labels with --label · 50fc5e97
  Mathieu Giraud authored Apr 02, 2019
```
Opens #3839.
```
  50fc5e97
- vidjil.cpp: --config · fd0f80df
  Mathieu Giraud authored Apr 02, 2019
```
See #3837.
```
  fd0f80df
- CLI11_json.cpp: reads config from "config" · db8d680f
  Mathieu Giraud authored Apr 02, 2019
```
see #3837.
```
  db8d680f
- vidjil.cpp: dump config into .vidjil · e0133fae
  Mathieu Giraud authored Apr 02, 2019
```
There is now some hack to get a json, it could be improved.
See #3837.
```
  e0133fae
- vidjil.cpp, lib/CLI11_json.hpp: include CLI11_json · 1fd605f6
  Mathieu Giraud authored Mar 21, 2019
  
  1fd605f6
- CLI11_json.cpp: include paths · 8bea162f
  Mathieu Giraud authored Mar 21, 2019
  
  8bea162f
- CLI11_json.cpp: no main() for us · 4bfc9912
  Mathieu Giraud authored Mar 21, 2019
  
  4bfc9912
- CLI11_json.cpp: ConfigJSON, from CLI11 examples · d2fd397d
  Mathieu Giraud authored Mar 21, 2019
```
https://github.com/CLIUtils/CLI11/commit/2ae5598d9570a
```
  d2fd397d
- tests: add tests, dumping and reading 'config' sections in .vidjil · a2901340
  Mathieu Giraud authored Apr 02, 2019
```
Opens #3837.
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  a2901340
- segmenter; jshint quality · 5e14efda
  Thonier Florian authored Apr 02, 2019
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link to #2041
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  5e14efda
- semgenter.js; at init, semgenter can haven't divParent listSeq present · fd278598
  Thonier Florian authored Apr 02, 2019
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In this case, ignore this function call (update_first_clone)
link to #2041
```
  fd278598
- segmenter & test: now first_clone cannot be setted as NaN value · 6f22700a
  Thonier Florian authored Apr 02, 2019
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link to #2041
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  6f22700a
- semgenter.js; minor typo · c9959e4b
  Thonier Florian authored Apr 02, 2019
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link to #2041
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  c9959e4b
- semgenter; default value of first_clone is -1 · 8865b8aa
  Thonier Florian authored Apr 02, 2019
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link to #2041
```
  8865b8aa