Commits · release-2020.01 · vidjil / vidjil

24 Jan, 2020 3 commits
- vidjil-algo: release 2020.01 · a2af81a8
  Mathieu Giraud authored Jan 24, 2020
```
see #4035
```
  a2af81a8
- no-output.should: Add missing `$LAUNCHER` and `$EXTRA` · 4902c30e
  Mikaël Salson authored Jan 24, 2020 and Mathieu Giraud committed Jan 24, 2020
```
See !589
```
  4902c30e
- vidjil: pride, 2020, credits · 4fba0336
  Mathieu Giraud authored Jan 24, 2020
  
  4fba0336
23 Jan, 2020 14 commits
- algo/Makefile: 'doc/vidjil-format.md' and 'doc/should-vdj.md' in 'make release' · 5fc4d80a
  Mathieu Giraud authored Jan 23, 2020
  
  5fc4d80a
- vidjil-algo: prepare CHANGELOG for release 2019.12 · 9959fb40
  Mathieu Giraud authored Dec 17, 2019
```
See #4035
```
  9959fb40
- Merge branch 'bikeshed-message' into 'dev' · fe6f3fb5
  Mathieu Giraud authored Jan 23, 2020
```
vidjil.cpp: bikeshed help message

See merge request !592
```
  fe6f3fb5
- vidjil.cpp: bikeshed help message · cde5aca5
  Mathieu Giraud authored Jan 23, 2020
```
follows !589
```
  cde5aca5
- Merge branch 'feature-a/3861-no-output' into 'dev' · 49b8b832
  Mikaël Salson authored Jan 23, 2020
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Feature a/3861 : options to limit output

Closes #3861

See merge request !589
```
  49b8b832
- Merge branch 'doc/airr-fuse' into 'dev' · 80ce835f
  Mikaël Salson authored Jan 23, 2020
```
Documentation on the AIRR .tsv import

See merge request !579
```
  80ce835f
- output.cpp: reindent · e86750d3
  Mikaël Salson authored Jan 23, 2020
  
  e86750d3
- Merge branch 'feature-a/4154-benchmark-current' into 'dev' · 5d9ab275
  Mikaël Salson authored Jan 23, 2020
```
Feature a/4154 : Benchmark also current HEAD

Closes #4154

See merge request !590
```
  5d9ab275
- .gitlab-ci.yml: benchmark also the current HEAD · 9a608613
  Mathieu Giraud authored Jan 23, 2020
```
Closes #4154
```
  9a608613
- benchmark-releases.py: -c, benchmark also the current HEAD · 64c78581
  Mathieu Giraud authored Jan 23, 2020
```
see #4154
```
  64c78581
- tests: add and update tests, --no-airr and --no-vidjil · 73066211
  Mathieu Giraud authored Jan 23, 2020
```
Closes #3861
```
  73066211
- vidjil.cpp: --no-airr · d8b4ad79
  Mathieu Giraud authored Jan 23, 2020
```
see #3861
```
  d8b4ad79
- vidjil.cpp: --no-vidjil · 828d7e09
  Mathieu Giraud authored Jan 23, 2020
```
see #3861
```
  828d7e09
- core/output.{h,cpp}: VidjilOuput, with_clones option · 39109911
  Mathieu Giraud authored Jan 23, 2020
```
see #3861
```
  39109911
22 Jan, 2020 17 commits
- Merge branch 'feature-a/3594-updated-evalue-computations-kmer-fine' into 'dev' · da83fb01
  Mathieu Giraud authored Jan 22, 2020
```
Update e-value multipliers and options

Closes #3594

See merge request !538
```
  da83fb01
- tools.md: typos, détails · 10dab250
  Mikaël Salson authored Jan 22, 2020
  
  10dab250
- 7038-long-deletions: Add quite some alternatives · d891b6dd
  Mikaël Salson authored Jan 22, 2020
```
As the deletions are large (both in V and J genes) many alternatives are possible
```
  d891b6dd
- Merge branch 'hotfix-c/segmenter_reset' into 'dev' · 4a8d91df
  Mikaël Salson authored Jan 22, 2020
```
segmenter.js : fix reset() + qunit tests

See merge request !580
```
  4a8d91df
- Merge branch 'feature/4148-auto-build-doc-fix' into 'dev' · 5342619b
  Mikaël Salson authored Jan 22, 2020
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doc/.gitlab-ci.yml: launch docs jobs only on merge requests

Closes #4148

See merge request !586
```
  5342619b
- segmenter.js: factorize code · 779847be
  Mikaël Salson authored Jan 22, 2020
  
  779847be
- doc/.gitlab-ci.yml: launch docs jobs only on merge requests · 884d341c
  Mathieu Giraud authored Jan 22, 2020
```
See #4148.
```
  884d341c
- Merge branch 'feature-c/4100-analysis_load_of_segedited_clone' into 'dev' · cb748ee9
  Mathieu Giraud authored Jan 22, 2020
```
Resolve "Des données IMGt dans le fichier analysis bloquent la selection"

Closes #4100

See merge request !560
```
  cb748ee9
- test_cluster.rb; update test that not working with ff45 · 36ef820d
  flothoni authored Jan 22, 2020
```
Link to #4100
```
  36ef820d
- algo/Makefile: include 'doc/tools.md' in release · 37eebf5a
  Mathieu Giraud authored Jan 21, 2020
  
  37eebf5a
- doc/: AIRR import through fuse.py · ce6cb977
  Vidjil Team authored Jan 14, 2020 and Mathieu Giraud committed Jan 22, 2020
```
See #3673
by @flothoni and @magiraud
```
  ce6cb977
- Merge branch 'feature/4148-auto-build-doc' into 'dev' · 741e643d
  Mathieu Giraud authored Jan 22, 2020
```
.gitlab-ci.yml: Launch doc jobs when changes on doc

Closes #4148

See merge request !585
```
  741e643d
- .gitlab-ci.yml: Launch doc jobs when changes on doc · d0070f2b
  Mikaël Salson authored Jan 22, 2020
```
Fix #4148
```
  d0070f2b
- Merge branch 'doc/improve6' into 'dev' · 64adf9e4
  Mathieu Giraud authored Jan 22, 2020
```
doc: update should-vdj.md

See merge request !582
```
  64adf9e4
- doc/should-vdj.md: update · 4dbccff6
  Mathieu Giraud authored Jan 22, 2020
  
  4dbccff6
- doc/should-vdj.md: converted from should-vdj.org · 13501a70
  Mathieu Giraud authored Jan 21, 2020
```
see #4142
```
  13501a70
- doc/mkdocs-extra.css: bikeshed list styling · 3cbac074
  Mathieu Giraud authored Jan 22, 2020
  
  3cbac074
21 Jan, 2020 6 commits
- Merge branch 'doc/fix-doc' into 'dev' · 57d93bde
  Mikaël Salson authored Jan 21, 2020
```
server.md: fix poor ORG → MD conversion

See merge request !581
```
  57d93bde
- segmenter.js : fix reset() + qunit tests · 162f8806
  marc duez authored Jan 21, 2020
```
- reset() remove all content from segmenter
```
  162f8806
- test_cluster.rb; update test with a wait_while · 6b44e278
  flothoni authored Jan 21, 2020
```
Link to #4100
```
  6b44e278
- Merge branch 'feature-t/3673-import-tsv-airr-depuis-fuse-py' into 'dev' · 3eabc47b
  Mathieu Giraud authored Jan 21, 2020
```
Resolve "Import .tsv AIRR depuis fuse.py"

Closes #3673

See merge request !558
```
  3eabc47b
- fuse.py; update tests on AIRR use · bff5f722
  flothoni authored Jan 17, 2020 and Mathieu Giraud committed Jan 21, 2020
```
Link to #3673
```
  bff5f722
- fus.py; update tests · 7eaed0ca
  flothoni authored Jan 17, 2020 and Mathieu Giraud committed Jan 21, 2020
```
Link to #3673
```
  7eaed0ca