Commits · 94cf78250b63800c4afff8fb4a8a23e9fef125fb · vidjil / vidjil

08 Aug, 2020 2 commits
- tests: json should parsing · 94cf7825
  Mathieu Giraud authored Aug 08, 2020
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see #3206
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  94cf7825
- should.py: update from upstream · 7e571312
  Mathieu Giraud authored Aug 07, 2020
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should@760fc37c, improve json parsing, improve and bikeshed outputs
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  7e571312
07 Aug, 2020 4 commits
- Merge branch 'feature-s/3830-calculer-l-index-de-morisita' into 'dev' · cab00d3a
  Mathieu Giraud authored Aug 07, 2020
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Resolve "Calculer l'index de Morisita."

Closes #3830

See merge request !465
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  cab00d3a
- fuse.py, remove useless string · 3f5b53c4
  flothoni authored Aug 07, 2020
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Link to #3830
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  3f5b53c4
- fuse; update overlaps index testing · dc031da7
  flothoni authored Aug 07, 2020
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Link to #3830
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  dc031da7
- tools/should.py: update from upstream · 532dbfa0
  Mathieu Giraud authored Aug 07, 2020
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should@3681b721, with json testing in nested lists
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  532dbfa0
04 Aug, 2020 1 commit
- fuse.py & test; Overlap is calculated if options is set · 12472d30
  flothoni authored Aug 04, 2020
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Update test to use this new parameter
Update test to use json values
Link to #3830"
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  12472d30
03 Aug, 2020 2 commits
- tools/test/overlap; update should test · a3d9af47
  flothoni authored Aug 03, 2020
  
  a3d9af47
- Merge branch 'dev' of gitlab.inria.fr:vidjil/vidjil into... · c978faaa
  flothoni authored Aug 03, 2020
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Merge branch 'dev' of gitlab.inria.fr:vidjil/vidjil into feature-s/3830-calculer-l-index-de-morisita
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  c978faaa
31 Jul, 2020 5 commits
- Merge branch 'feature-sc/do-not-deploy-prod-client' into 'dev' · 69922376
  Mikaël Salson authored Jul 31, 2020
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.gitlab-ci.yml: Prevent prod-client overwriting

See merge request !772
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  69922376
- Merge branch 'feature-c/4413-fix-a-bunch-of-non-blocking-js-error' into 'dev' · 6d919304
  Mikaël Salson authored Jul 31, 2020
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Feature c/4413 fix a bunch of non blocking js error

Closes #4413

See merge request !771
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  6d919304
- Merge branch 'feature-c/4443-url-erreur-clone_isvirtual' into 'dev' · aa20efdd
  Mathieu Giraud authored Jul 31, 2020
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Resolve "nouvelles URL, erreur de chargement"

Closes #4443

See merge request !776
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  aa20efdd
- test_url, add test on selection of clones by url · f8133d1f
  flothoni authored Jul 31, 2020
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Link to #4443
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  f8133d1f
- url.js, also select distribution clone · f771d865
  flothoni authored Jul 31, 2020
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Link to #4443
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  f771d865
30 Jul, 2020 13 commits
- Merge branch 'feature-a/3795-4387-out-vdjfa' into 'dev' · a8749f83
  Mikaël Salson authored Jul 30, 2020
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Feature a/3795 4387, --out-vdjfa

Closes #4387 and #3795

See merge request !775
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  a8749f83
- Merge branch 'feature-a/test-should-directives' into 'dev' · 24acd18e
  Mikaël Salson authored Jul 30, 2020
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update should.py, streamlined placement of directives, EXIT_CODEs

See merge request !669
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  24acd18e
- url.js; remove last call to a deleted function from clone.js · 8b204869
  flothoni authored Jul 30, 2020
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Remove call to isVirtual, deleted since distribution clone
Link to #4443
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  8b204869
- tests: update test, each command runs in a shell · d33b38f6
  Mathieu Giraud authored Jun 02, 2020
  
  d33b38f6
- tests: breaking change in should, put !REQUIRES before command · e4d1dca3
  Mathieu Giraud authored Jun 02, 2020
  
  e4d1dca3
- tests: breaking change in should, put !OUTPUT_FILE before commands · df4fa16b
  Mathieu Giraud authored Jul 30, 2020
  
  df4fa16b
- tests: hardcode 'defs.py.tmp' tempfile · 13f555e2
  Mathieu Giraud authored May 30, 2020
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./should does not remember variables now
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  13f555e2
- tests: breaking change in should, put !EXIT_CODE before commands · d793efe2
  Mathieu Giraud authored Apr 23, 2020
  
  d793efe2
- tools/should.py: update from upstream, 3.0.0 · 1c54c254
  Mathieu Giraud authored Apr 23, 2020
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should@c75648480, includes better handling of directives
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  1c54c254
- doc/vidjil-algo.md: move '.vdj.fa' to 'Auxiliary output files' and further updates · 56fb02a1
  Mathieu Giraud authored Jul 30, 2020
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vidjil-algo main outputs are .vidjil and .tsv files.
Closes #3795.
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  56fb02a1
- doc/vidjil-algo.md: document --out-vdjfa, deprecate .vdj.fa headers · dda559c7
  Mathieu Giraud authored Jul 28, 2020
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See #3795.
Closes #4387.
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  dda559c7
- tests: add and update · 090afd7f
  Mathieu Giraud authored Jul 28, 2020
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see #4425
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  090afd7f
- vidjil.cpp: remove .vdj.fa output, unless the new --out-vdjfa option · 3af4db23
  Mathieu Giraud authored Jul 28, 2020
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see #4387
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  3af4db23
28 Jul, 2020 13 commits
- Revert "main.js : comment unworking vmi code" · e8554e1d
  marc duez authored Jul 28, 2020
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This reverts commit 19471b9f.
-keep bug for fun.
-should be fixed by !624
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  e8554e1d
- Merge branch 'feature-a/4386-out-clone-files' into 'dev' · 9ad3f80f
  Mikaël Salson authored Jul 28, 2020
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Feature a/4386 --out-clone-files

Closes #4386

See merge request !773
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  9ad3f80f
- Morisita index; update function from fuse. · 4f23358a
  flothoni authored Jul 28, 2020
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* update tests
* Move results into 'overlaps' key in vidjil export
Link to #3830
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  4f23358a
- doc/vidjil-algo.md: --out-clone-files · 3dd35e59
  Mathieu Giraud authored Jul 28, 2020
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Closes #4386
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  3dd35e59
- tests: add and update · e3c149e8
  Mathieu Giraud authored Jul 28, 2020
```
see #4386
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  e3c149e8
- vidjil.cpp: --out-reads, bikeshed help message · 2d66798d
  Mathieu Giraud authored Jul 28, 2020
  
  2d66798d
- vidjil.cpp: --out-reads implies --out-clone-files · a659ccce
  Mathieu Giraud authored Jul 28, 2020
```
see #4386
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  a659ccce
- vidjil.cpp: seq/clone-*.fa output disabled by default, new advanced option --out-clone-files · fc0afd36
  Mathieu Giraud authored Jul 28, 2020
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see #4386
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  fc0afd36
- Merge branch... · c8f26ed9
  Mathieu Giraud authored Jul 28, 2020
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Merge branch 'feature-sc/2728-pouvoir-sauter-depuis-un-sample-a-ses-groupes-patient-run-set' into 'dev'

Resolve "Pouvoir sauter depuis un sample à ses groupes patient/run/set"

Closes #4220 and #2728

See merge request !635
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  c8f26ed9
- Merge branch 'feature-sc/cerbot-in-docker' into 'dev' · f5aab3ca
  Mathieu Giraud authored Jul 28, 2020
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Cerbot in docker

See merge request !770
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  f5aab3ca
- Apply 1 suggestion(s) to 1 file(s) · fc4fcfd3
  Mathieu Giraud authored Jul 28, 2020
  
  fc4fcfd3
- .gitlab-ci.yml: Prevent prod-client overwriting · 010f90a2
  Mikaël Salson authored Jul 28, 2020
```
See vdj#1093, #4418
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  010f90a2
- Merge branch 'feature-c/4375-pouvoir-cacher-les-clones-de-distribution' into 'dev' · 04a10603
  Mathieu Giraud authored Jul 28, 2020
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Resolve "Pouvoir cacher les clones de distribution"

Closes #4375

See merge request !755
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  04a10603