Commits · b6fd59dab27fa3e8cd0171205ba5c1c5a526b933 · vidjil / vidjil

12 Jul, 2019 1 commit
- Merge branch 'feature-a/3952-ignore_D-bug' into 'dev' · b6fd59da
  Mathieu Giraud authored Jul 12, 2019
```
should-vdj-to-tap.py: --ignore_D option not working due to typo

Closes #3952

See merge request !494
```
  b6fd59da
11 Jul, 2019 7 commits
- Merge branch 'feature-a/update-repseq-vdj-for-mixcr' into 'dev' · 87dbfd0d
  Mathieu Giraud authored Jul 11, 2019
```
Update repseq_vdj for mixcr

See merge request !495
```
  87dbfd0d
- repseq_vdj.py: Get rid of spurious \n · d962a3e8
  Mikaël Salson authored Jul 10, 2019
  
  d962a3e8
- repseq_vdj.py: Check key existence as all may not be filled all the time · 65444d0b
  Mikaël Salson authored Jul 10, 2019
  
  65444d0b
- repseq_vdj.py: Field renaming for MiXCR · c65f84e5
  Mikaël Salson authored Jul 10, 2019
  
  c65f84e5
- Merge branch 'doc/split-dev-doc' into 'dev' · dc8209bd
  Mikaël Salson authored Jul 11, 2019
```
doc/dev-{algo,client,server}.md: converted and split from dev.org

See merge request !491
```
  dc8209bd
- should-vdj-to-tap.py: --ignore_D option not working due to typo · 3536be5e
  Mikaël Salson authored Jul 11, 2019
```
Fixed and added some tests

Fix #3952
```
  3536be5e
- Merge branch 'feature-t/3950-igrec-parser' into 'dev' · 50c032e4
  Mikaël Salson authored Jul 11, 2019
```
Feature t/3950 igrec parser

Closes #3950

See merge request !493
```
  50c032e4
10 Jul, 2019 11 commits
- repseq_vdj.py: actual IgReC output has also one locus field · 42dfd8c9
  Mathieu Giraud authored Jul 10, 2019
  
  42dfd8c9
- tools/tests/Makefile: doctests for repseq_vdj.py · a4366d74
  Mathieu Giraud authored Jul 10, 2019
```
These *.py files should be moved to /tools
```
  a4366d74
- repseq_vdj.py: IgReC_Result parser · 68d2334a
  Mathieu Giraud authored Jul 10, 2019
```
see #3950

Thanks to https://stackoverflow.com/a/8849771
```
  68d2334a
- Merge branch 'feature-a/correct-missing-wildcard-should-vdj-to-tap' into 'dev' · 9836a025
  Mathieu Giraud authored Jul 10, 2019
```
should-vdj-to-tap.py: Wildcard must be at both places

See merge request !490
```
  9836a025
- doc/dev-{algo,client,server}.md: converted and split from dev.org · fe70e5d0
  Mathieu Giraud authored Jul 10, 2019
```
see #3932

pandoc --wrap=preserve --atx-headers -s -r org doc/dev.org -t gfm > doc/dev.md
```
  fe70e5d0
- should-vdj-to-tap.py: Wildcard must be at both places · 0c421aa4
  Mikaël Salson authored Jul 10, 2019
```
Follows dbd61c55. Contrarily to the else case where the joker can
indifferently be placed before or after a term, it is not
the same when the term is a paranthesis expression.
Thus we need a joker both before and after to make sure we don't miss a case.
```
  0c421aa4
- Merge branch 'feature-a/3949-alternative-regex-bug' into 'dev' · 419bdf94
  Mathieu Giraud authored Jul 10, 2019
```
Alternative regex bug

Closes #3949

See merge request !489
```
  419bdf94
- should-vdj-to-tap.py: doctests · 276ff5e8
  Mikaël Salson authored Jul 10, 2019
  
  276ff5e8
- should-vdj-to-tap.py: Allow jokers · dbd61c55
  Mikaël Salson authored Jul 10, 2019
```
We must allow anything *before* the alternative, not after (as in the else case)
```
  dbd61c55
- should-vdj-to-tap.py: Remove suprious space · 2cd69443
  Mikaël Salson authored Jul 10, 2019
```
Fix #3949
```
  2cd69443
- bug-3949.should-vdj.fa: Example for #3949 · c0ce0020
  Mikaël Salson authored Jul 10, 2019
  
  c0ce0020
05 Jul, 2019 2 commits
- Merge branch 'feature-sc/3941-docker-modify-conf' into 'dev' · d6d3c13b
  Mikaël Salson authored Jul 05, 2019
```
Docker : modify conf without rebuilding

Closes #3941

See merge request !486
```
  d6d3c13b
- docker/vidjil-client/: Link to conf files rather than copy. · e51662ee
  Mikaël Salson authored Jul 04, 2019
```
This allows to modify the configurations without rebuilding the image

See #3941
```
  e51662ee
12 Jun, 2019 2 commits
- Merge branch 'feature-c/3929-addons' into 'dev' · bac84808
  Mathieu Giraud authored Jun 12, 2019
```
js/app.js: Load extra scripts depending on the administrator

Closes #3929

See merge request !481
```
  bac84808
- js/app.js: Load extra scripts depending on the administrator · 77f81d48
  Mikaël Salson authored Jun 12, 2019
```
Fix #3929
```
  77f81d48
03 Jun, 2019 8 commits
- Merge branch 'feature-c/3913-vquest-api-change' into 'dev' · ce69f30b
  Mikaël Salson authored Jun 03, 2019
```
V-QUEST API change

Closes #3913

See merge request !472
```
  ce69f30b
- test/functional/vidjil_browser.rb: Make sure the environment variable exists before accessing it · c3f93d8e
  Mikaël Salson authored Jun 03, 2019
  
  c3f93d8e
- crossDomain.js: Disable summary · f2b51b2c
  Mikaël Salson authored Jun 03, 2019
```
Otherwise the ntseq is not given in the CSV file
See #3913
```
  f2b51b2c
- tools.js: Function to get the common name of a species · a734fc73
  Mikaël Salson authored Jun 03, 2019
```
IMGT/V-QUEST now requires to have the common name of the species, not the latin one.
Thus we need a function to do the conversion.

See #3913
```
  a734fc73
- crossDomain.js: V-QUEST change: unnecessary parameters · 57402d95
  Mikaël Salson authored Jun 03, 2019
```
Those parameters are not useful anymore. They were used before #3913.
```
  57402d95
- crossDomain.js: V-QUEST form change · a7b0794b
  Mikaël Salson authored Jun 03, 2019
```
Some parameters were slightly different from what was expected.

See #3913
```
  a7b0794b
- imgt: change in V-QUEST URL · 73c5c4e7
  Mikaël Salson authored Jun 03, 2019
```
See #3913
```
  73c5c4e7
- browser/js: V-QUEST API change · 565babd4
  Mikaël Salson authored May 16, 2019
```
See #3913
```
  565babd4
24 May, 2019 2 commits
- Merge branch 'hotfix-s/880-download-results-permission' into 'dev' · c3117006
  Mathieu Giraud authored May 24, 2019
```
Check permissions before retrieving results

Closes vdj#880

See merge request !476
```
  c3117006
- sample_set.py: Check permissions before retrieving results · 174379c4
  Mikaël Salson authored May 24, 2019
```
Fix vdj#880
```
  174379c4
23 May, 2019 6 commits
- Merge branch... · ee7e0c6d
  Mikaël Salson authored May 23, 2019
```
Merge branch 'feature-c/3488-decalage-de-la-sequence-du-cdr3-et-de-la-jonction-dans-la-fenetre-info' into 'dev'

Resolve "Décalage de la séquence du CDR3 et de la jonction dans la fenêtre info"

Closes #3488

See merge request !471
```
  ee7e0c6d
- Merge branch 'feature-g/3910-avoir-des-germline-de-poulet' into 'dev' · e5952d44
  Mathieu Giraud authored May 23, 2019
```
Resolve "Avoir des germline de poulet"

Closes #3910

See merge request !470
```
  e5952d44
- germline, add a simple test on Gallus Gallus germline · f9b86544
  Mathieu Giraud authored May 23, 2019
```
link to #3910
```
  f9b86544
- germline, add Gallus Gallus germline *.g file · 5b626cc6
  Thonier Florian authored May 23, 2019
```
link to #3910
```
  5b626cc6
- split-from-imgt.py: add Gallus Gallus · af2af318
  Thonier Florian authored May 23, 2019
```
Link to #3910
```
  af2af318
- split-from-imgt.py; remove '<>' operand (available in python2) · 9d6b4e0d
  Thonier Florian authored May 23, 2019
```
link to #3910
```
  9d6b4e0d
22 May, 2019 1 commit
- Merge branch 'doc/2526-productivity' into 'dev' · eca7b0ac
  Mathieu Giraud authored May 22, 2019
```
doc/vidjil-algo.md: productivity discordance + server

See merge request !475
```
  eca7b0ac