Commits · 5429d503b97025c349cb795cecd29c9cdb1bcc32 · vidjil / vidjil

22 Aug, 2019 1 commit
- algo/test/data; rename filename, add normalized reads fields · 5429d503
  Thonier Florian authored Aug 22, 2019
```
Link to #3944
```
  5429d503
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
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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
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  565babd4
24 May, 2019 2 commits
- Merge branch 'hotfix-s/880-download-results-permission' into 'dev' · c3117006
  Mathieu Giraud authored May 24, 2019
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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
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Fix vdj#880
```
  174379c4
23 May, 2019 6 commits
- Merge branch... · ee7e0c6d
  Mikaël Salson authored May 23, 2019
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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
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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 and Mathieu Giraud committed May 23, 2019
```
link to #3910
```
  5b626cc6
- split-from-imgt.py: add Gallus Gallus · af2af318
  Thonier Florian authored May 23, 2019 and Mathieu Giraud committed May 23, 2019
```
Link to #3910
```
  af2af318
- split-from-imgt.py; remove '<>' operand (available in python2) · 9d6b4e0d
  Thonier Florian authored May 23, 2019 and Mathieu Giraud committed May 23, 2019
```
link to #3910
```
  9d6b4e0d
22 May, 2019 3 commits
- Merge branch 'doc/2526-productivity' into 'dev' · eca7b0ac
  Mathieu Giraud authored May 22, 2019
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doc/vidjil-algo.md: productivity discordance + server

See merge request !475
```
  eca7b0ac
- doc/server.md: update again · aad0c6a2
  Mathieu Giraud authored May 22, 2019
  
  aad0c6a2
- doc/server.md: update, Docker for app, VidjilNet · d9a1036f
  Mathieu Giraud authored May 22, 2019
  
  d9a1036f
21 May, 2019 1 commit
- doc/vidjil-algo.md: productivity discordance · 703a4288
  Mathieu Giraud authored May 21, 2019
```
See #2526.
```
  703a4288
17 May, 2019 3 commits
- clone.js; add some descriptions · ea52b71f
  Thonier Florian authored May 17, 2019
```
link to #3488
```
  ea52b71f
- Merge branch 'feature-a/release' into 'dev' · 5f449d1a
  Mikaël Salson authored May 17, 2019
```
Release 2019.05

See merge request !473
```
  5f449d1a
- vidjil-algo: release 2019.05 · 9c0e51da
  Mathieu Giraud authored May 17, 2019
```
see #3914
```
  9c0e51da
16 May, 2019 7 commits
- vidjil-algo: prepare CHANGELOG for release 2019.05 · 7ad93fb1
  Mathieu Giraud authored May 16, 2019
```
see #3914
```
  7ad93fb1
- Merge branch 'feature-a/3866-random-sample-by-default' into 'dev' · 3139b094
  Mathieu Giraud authored May 16, 2019
```
core/representative.h, vidjil.cpp: RandomScore by default

See merge request !464
```
  3139b094
- consensus-random-read-choose.should: Update comments (default is not the same anymore) · 18565743
  Mikaël Salson authored May 16, 2019
  
  18565743
- analysis-S22.should: We cannot test exactly the representative found · a564ff7a
  Mikaël Salson authored May 16, 2019
```
It will depend on the order in which reads are coming when computing
the representative but this order is random. What is important is that
we find a representative of the correct length with the correct sequence
whatever the read name and read positions are.
```
  a564ff7a
- algo/tests/unit-tests: Use a deterministic scorer for the tests · 4f577854
  Mikaël Salson authored May 16, 2019 and Mathieu Giraud committed May 16, 2019
```
It is hard to predict the result is not totally deterministic
(as is the case with the RandomScorer, which is now by default,
whose results depend on the pseudo-random generator that may
differ depending on the OSes)

See #3866
```
  4f577854
- tests: update · 2b6236fb
  Mathieu Giraud authored May 16, 2019
```
see #3866
```
  2b6236fb
- core/representative.h, vidjil.cpp: RandomScore by default · a2898925
  Mathieu Giraud authored Apr 08, 2019
```
see #3866
```
  a2898925
15 May, 2019 4 commits
- test of clone, model and segmenter; update positons after fix of computeSegFeatureFromSeq fct · 7fab37d0
  Thonier Florian authored May 15, 2019
```
link to #3488
```
  7fab37d0
- clone.js; update computeSegFeatureFromSeq fct du to 1based fix · 54200a08
  Thonier Florian authored May 15, 2019
```
link to #3488
```
  54200a08
- clone_test; update tests with the bug fix on 1based positions · 198c3d20
  Thonier Florian authored May 15, 2019
```
link to #3488
```
  198c3d20
- clone.js, bug fix in getSegNtSequence (1based variation) · 09ec2c71
  Thonier Florian authored May 15, 2019
```
link to #3488
```
  09ec2c71
26 Apr, 2019 5 commits
- Merge branch 'feature-a/3206-rename-and-merge-should' into 'dev' · ed299a22
  Mikaël Salson authored Apr 26, 2019
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Feature a/3206 rename and merge should

Closes #3762

See merge request !467
```
  ed299a22
- Merge branch 'feature-a/some-optim' into 'dev' · 1973f7e8
  Mathieu Giraud authored Apr 26, 2019
```
Optimizations, including  e-value computations, max12

See merge request !468
```
  1973f7e8
- kmerstore.h: Precompute probability computations · eb8a268e
  Mikaël Salson authored Oct 18, 2018 and Mathieu Giraud committed Apr 26, 2019
```
Computing them for each read is time consuming.
But many of the are common (there are few different
index loads and the read length is small)
```
  eb8a268e
- automaton.hpp: Precompute the global index load · 2e5ca4cb
  Mikaël Salson authored Oct 18, 2018 and Mathieu Giraud committed Apr 26, 2019
```
This prevents from recomputing it each time
```
  2e5ca4cb
- segment.cpp: A KmerAffectAnalyser was already created · d3b4db3c
  Mikaël Salson authored Oct 18, 2018 and Mathieu Giraud committed Apr 26, 2019
  
  d3b4db3c