Commits · feature-a/4271-update-germlines · vidjil / vidjil

View open merge request

19 Jan, 2021 3 commits
- tests: IGHV3/OR16-7*03, another candidate · 971491c2
  Mathieu Giraud authored Jan 19, 2021
  
  971491c2
- tests: far better alignment with new gene IGHV3-41*01 · 297957bd
  Mathieu Giraud authored Jan 19, 2021
  
  297957bd
- tests: this sequence is still in BUG, but we should update it · 962dd2e5
  Mathieu Giraud authored Jan 18, 2021
  
  962dd2e5
15 Jan, 2021 2 commits
- tests/unit-tests/testFilter.cpp: filter should filter out most of the V genes... · 65dee58e
  Mathieu Giraud authored Jan 15, 2021
```
... but 10 is a good value :)
```
  65dee58e
- tests: update, IGHV4-4*03 has eight more nucleotides · f307a565
  Mathieu Giraud authored Jan 15, 2021
  
  f307a565
14 Jan, 2021 8 commits
- tests: update, more IGHV genes · 23a6e9c1
  Mathieu Giraud authored Jan 14, 2021
  
  23a6e9c1
- tests: update, TRGV10*02 has one more nucleotide · 0c817266
  Mathieu Giraud authored Jan 14, 2021
  
  0c817266
- tests: update, TRGJ1*02 has grown up · 970ee658
  Mathieu Giraud authored Jan 14, 2021
```
see #4640
```
  970ee658
- tests/unit-tests/testFilter.cpp: filter should filter out most of the V genes · c595cd7c
  Mathieu Giraud authored Jan 13, 2021
  
  c595cd7c
- tests: update · 8e4e4c13
  Mathieu Giraud authored Jan 13, 2021
  
  8e4e4c13
- tests: update, new germline urls · 27bd6370
  Mathieu Giraud authored Jan 13, 2021
  
  27bd6370
- tests: update · e40e3896
  Mathieu Giraud authored Jan 13, 2021
```
replay !374, but update with new values
```
  e40e3896
- germline_id, homo-sapiens.g: update germlines · 7b514225
  Mathieu Giraud authored Jan 13, 2021
```
see #4271
```
  7b514225
05 Jan, 2021 1 commit
- Merge branch 'feature-a/3569-airr-unproductivity-causes' into 'dev' · 15860a2c
  Mikaël Salson authored Jan 05, 2021
```
More AIRR fields, unproductivity causes

Closes #3569

See merge request !879
```
  15860a2c
04 Jan, 2021 3 commits
- Merge branch 'feature-c/skip-on-browser' into 'dev' · 3276b56d
  Thonier Florian authored Jan 04, 2021
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Further extract and use skip_on_browser

See merge request !878
```
  3276b56d
- Merge branch 'info/d3js' into 'dev' · 8d121bd1
  Mathieu Giraud authored Jan 04, 2021
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js/lib/info.txt: update info for d3js

Closes #4187

See merge request !880
```
  8d121bd1
- js/lib/info.txt: update info for d3js · 551f53e5
  Mathieu Giraud authored Jan 04, 2021
```
closes #4187
```
  551f53e5
31 Dec, 2020 4 commits
- doc/vidjil-algo.md: document AIRR fields 'vj_in_frame', 'stop_codon' · f2e35592
  Mathieu Giraud authored Dec 31, 2020
```
closes #3569
```
  f2e35592
- core/output.cpp: AIRR fields 'vj_in_frame', 'stop_codon' · 4f05481d
  Mathieu Giraud authored Dec 31, 2020
```
see #3569
```
  4f05481d
- core/output.cpp: extract constants AIRR_{FALSE,TRUE} · d1590646
  Mathieu Giraud authored Dec 31, 2020
  
  d1590646
- tests: tdd, AIRR fields 'vj_in_frame' and 'stop_codon' · 1ef91e19
  Mathieu Giraud authored Dec 31, 2020
```
see #3569
```
  1ef91e19
30 Dec, 2020 3 commits
- Merge branch 'feature-s/bikeshed-strings' into 'dev' · 0aa91600
  Mathieu Giraud authored Dec 30, 2020
```
views/*: bikeshedding, processes

Closes #4587

See merge request !863
```
  0aa91600
- browser_test.rb, tests: further extract and use skip_on_browser · b73da9f2
  Mathieu Giraud authored Dec 24, 2020
  
  b73da9f2
- Apply 1 suggestion(s) to 1 file(s) · baf43734
  Mathieu Giraud authored Dec 30, 2020
  
  baf43734
28 Dec, 2020 5 commits
- Merge branch 'feature-c/4014-clones-selectionnable-even-if-disable_new' into 'dev' · c23fd31a
  Mikaël Salson authored Dec 28, 2020
```
Resolve "clones virtuels: selectionnable même lorsqu'ils ne sont pas visibles" 2

Closes #4014

See merge request !862
```
  c23fd31a
- Merge branch 'feature-s/3001-anon-by-default' into 'dev' · c97212f7
  Mikaël Salson authored Dec 28, 2020
```
models/group.py: anon as a default permission for personal user groups

Closes #3001

See merge request !435
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  c97212f7
- Merge branch 'doc/4595-tests-tutorial-et-ff32' into 'dev' · b299de1c
  Mikaël Salson authored Dec 28, 2020
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Resolve "Tests tutorial et ff32, sauter quelques tests et enlever le allow:failure"

Closes #4595

See merge request !867
```
  b299de1c
- Merge branch 'feature-a/3569-more-airr-fields' into 'dev' · a6ef6d3a
  Mikaël Salson authored Dec 28, 2020
```
Feature a/3569 more AIRR fields

See merge request !715
```
  a6ef6d3a
- Merge branch 'feature-a/4599-unproductive-causes' into 'dev' · 7d09552a
  Mikaël Salson authored Dec 28, 2020
```
Unproductivity causes

Closes #4599

See merge request !860
```
  7d09552a
24 Dec, 2020 11 commits
- Merge branch 'feature-s/more_efficient_job_status' into 'dev' · 187ad4af
  Mathieu Giraud authored Dec 24, 2020
```
sample_set/index.html less queries for job status

See merge request !362
```
  187ad4af
- sample_set/index.html less queries for job status · 438c40cd
  Ryan Herbert authored Nov 21, 2018
```
Store the result of the querye for the job status to avoid performing it
twice. While this may have been optimised automatically by a web2py
cache or similar mechanism, I feel like the code produced is easier to
read/underestand.
```
  438c40cd
- Merge branch 'doc/update-2' into 'dev' · 791ab12c
  Mathieu Giraud authored Dec 24, 2020
```
doc/user.md: update

See merge request !868
```
  791ab12c
- views/*: partially revert previous commit · 2708a436
  Mathieu Giraud authored Dec 24, 2020
  
  2708a436
- tutorial: further skip two tests on ff32 · a765bf24
  Mathieu Giraud authored Dec 24, 2020
```
see #4595
```
  a765bf24
- browser_test.rb, tutorial: extract and factorize skip_on_browser() · 6cbb7dd8
  Mathieu Giraud authored Dec 24, 2020
  
  6cbb7dd8
- doc/tutorial tests; add a skip on some tests that fail for firefox 32 · 87b6f930
  flothoni authored Dec 09, 2020
```
Link to #4595
```
  87b6f930
- gitlab-ci.yml; remove large allow faillure on ff32-browser-tutorial pipeline · 21307a02
  flothoni authored Dec 09, 2020
```
Link to #4595
```
  21307a02
- doc/vidjil-algo.md: bikeshed help · 70872468
  Mathieu Giraud authored Dec 24, 2020
```
see #3569
```
  70872468
- update doc for AIRR output · 6fc8d39c
  flothoni authored Jun 10, 2020
```
Link to #3569
```
  6fc8d39c
- tests: tests on new AIRR fields · 9ed58a92
  Mathieu Giraud authored Jun 03, 2020
  
  9ed58a92