Commits · 225371943c48f921a8f52c14d4783a47aa45e518 · vidjil / vidjil

28 Dec, 2018 6 commits
- js/clone.js: getPrintableSize(), more robust · 22537194
  Mathieu Giraud authored Dec 28, 2018
  
  22537194
- js/{clone,segmenter}.js: display both raw and normalized reads on stats and export, when applicable · c104d5ac
  Mathieu Giraud authored Dec 28, 2018
```
see #3650
```
  c104d5ac
- js/clone.js: getPrintableSize() display both raw and normalized reads when applicable · e9ba8a2b
  Mathieu Giraud authored Dec 28, 2018
```
see #3650
```
  e9ba8a2b
- clone.js: getHtmlInfo(), display normalized_reads when applicable · 42aa9ea6
  Mathieu Giraud authored Dec 28, 2018
```
closes #3662
```
  42aa9ea6
- js/{model,clone}.js: clone.getRawReads(), bypass normalization · 8cce9045
  Mathieu Giraud authored Dec 28, 2018
```
see #3662 and #3650.
```
  8cce9045
- browser/index.html: put back normalization_list, but in devel mode · de61fc3f
  Mathieu Giraud authored Dec 28, 2018
```
See #3666.
```
  de61fc3f
27 Dec, 2018 18 commits
- Merge branch 'feature-c/3644-3645-normalization' into 'dev' · 58d7baf2
  Mathieu Giraud authored Dec 27, 2018
```
Refactor and extend normalization

See merge request !379
```
  58d7baf2
- tests: temporary comment a failing test · 56609a4c
  Mathieu Giraud authored Dec 27, 2018
  
  56609a4c
- js/clone.js: bikeshed icon for normalization · a9b32fa0
  Mathieu Giraud authored Dec 27, 2018
```
see #3663
```
  a9b32fa0
- browser/index.html: normalization, bikeshed menu elements · 976da3bd
  Mathieu Giraud authored Dec 27, 2018
```
see #3663.
```
  976da3bd
- tests: update · 3e5ee2c6
  Mathieu Giraud authored Dec 27, 2018
  
  3e5ee2c6
- js/clone.js: use m.normalize_reads()/m.normalize() when needed · 58075d6f
  Mathieu Giraud authored Dec 27, 2018
```
only clone.getReads() uses m.normalize_reads()

see #3645
```
  58075d6f
- js/model.js: model.normalize_reads() separated from model.normalize() · 086d168d
  Mathieu Giraud authored Dec 27, 2018
```
The former is on reads, the latter on ratios.
See #3644 and #3645.
```
  086d168d
- js/model.js: simplify m.normalize() · 7be1280e
  Mathieu Giraud authored Dec 27, 2018
  
  7be1280e
- js/model.js: NORM_EXTERNAL, round after division · 846b0abb
  Mathieu Giraud authored Dec 27, 2018
  
  846b0abb
- tests: update and add tests · 68ada44e
  Thonier Florian authored Dec 27, 2018
  
  68ada44e
- browser/index.html: normalization · da888a39
  Thonier Florian authored Dec 27, 2018
```
see #3644 and #3645
```
  da888a39
- js/model.js: at initialization, trigger NORM_EXTERNAL when needed · f37fb84f
  Thonier Florian authored Dec 27, 2018
```
see #3645
```
  f37fb84f
- js/clone.js: updateCloneTagIcon() · e324ed75
  Thonier Florian authored Dec 27, 2018
  
  e324ed75
- js/model.js: new normalization NORM_EXTERNAL · 74ccefcb
  Thonier Florian authored Dec 27, 2018
```
see #3645
```
  74ccefcb
- js/export.js, js/graph.js: use refactored m.normalize() · a79c3235
  Thonier Florian authored Dec 27, 2018
```
See #3644.
```
  a79c3235
- js/clone.js: use refactored m.normalize() · 997d754a
  Thonier Florian authored Dec 27, 2018
```
see #3644
```
  997d754a
- js/model.js: refactor normalization · 20599101
  Thonier Florian authored Dec 27, 2018
  
  20599101
- .gitignore: update · a2c6a194
  Thonier Florian authored Dec 27, 2018
  
  a2c6a194
12 Dec, 2018 4 commits
- Merge branch 'feature-g/3656-gitlab-deploy-germlines' into 'dev' · 3425e544
  Mathieu Giraud authored Dec 12, 2018
```
Add germline build and deploy on prod server

Closes #3656

See merge request !373
```
  3425e544
- .gitlab-ci.yml: bikeshed date format · 22eb9148
  Mathieu Giraud authored Dec 12, 2018
  
  22eb9148
- .gitlab-ci.yml: Add germline build and deploy on prod server · fcb2d6a2
  Vidjil Team authored Dec 12, 2018
```
Fixes #3656
```
  fcb2d6a2
- Merge branch 'feature-ga/3515-imgt-all' into 'dev' · 0e9493a7
  Mikaël Salson authored Dec 12, 2018
```
Feature ga/3515 imgt all

See merge request !372
```
  0e9493a7
06 Dec, 2018 4 commits
- tests: check in/outframe genes · 895c9480
  Mathieu Giraud authored Dec 06, 2018
```
See #3515.
```
  895c9480
- germline/split-from-imgt.py: get sequences from several files · ecbdbd2e
  Mathieu Giraud authored Dec 06, 2018
```
See #3515.
```
  ecbdbd2e
- germline/get-germline: gets from IMGT all genes, not only those inframe · 4bd2e72c
  Mathieu Giraud authored Dec 06, 2018
```
Note that we should also keep inframeP, which has gaps.
See #3515.
```
  4bd2e72c
- Merge branch 'feature-c/3641-more-space-for-rotated-labels' into 'dev' · 005d00b0
  Mikaël Salson authored Dec 06, 2018
```
js/scatterPlot.js: add 15px to the top margin when the labels are rotated

Closes #3641

See merge request !370
```
  005d00b0
04 Dec, 2018 7 commits
- Merge branch 'feature-ts/3585-fuse-keep-metadata' into 'dev' · d9f0b676
  Mikaël Salson authored Dec 04, 2018
```
Feature ts/3585 fuse keep metadata

Closes #3585

See merge request !371
```
  d9f0b676
- tools/fuse.py: keep all interesting clone metadata, even from non-topmost clones · 48ff68af
  Mathieu Giraud authored Dec 04, 2018
```
Closes #3585.
```
  48ff68af
- tests: update · c421fc67
  Mathieu Giraud authored Dec 04, 2018
  
  c421fc67
- tests: fuse should keep clone metadata from non-topmost clones · ec6d38c4
  Mathieu Giraud authored Dec 04, 2018
```
See #3585.
```
  ec6d38c4
- Merge branch 'feature-c/3642-div-data' into 'dev' · e830e520
  Mikaël Salson authored Dec 04, 2018
```
css: no border on 'data' div

See merge request !369
```
  e830e520
- css: no border for 'data' div · 92449186
  Mathieu Giraud authored Dec 04, 2018
```
See #3642.
```
  92449186
- js/scatterPlot.js: add 15px to the margin when the labels are rotated · 7100e81e
  Mathieu Giraud authored Dec 04, 2018
```
Close #3641.
```
  7100e81e
03 Dec, 2018 1 commit
- Merge branch 'feature-s/3638-no-chown-on-directories' into 'dev' · dac04142
  Mathieu Giraud authored Dec 03, 2018
```
Don't chown result/ and upload/

Closes #3638

See merge request !368
```
  dac04142