Commits · 828d7e093bdff6f9b4676fb19e2adcd097256cd8 · vidjil / vidjil

23 Jan, 2020 2 commits
- vidjil.cpp: --no-vidjil · 828d7e09
  Mathieu Giraud authored Jan 23, 2020
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see #3861
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  828d7e09
- core/output.{h,cpp}: VidjilOuput, with_clones option · 39109911
  Mathieu Giraud authored Jan 23, 2020
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see #3861
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  39109911
22 Jan, 2020 14 commits
- Merge branch 'feature-a/3594-updated-evalue-computations-kmer-fine' into 'dev' · da83fb01
  Mathieu Giraud authored Jan 22, 2020
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Update e-value multipliers and options

Closes #3594

See merge request !538
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  da83fb01
- 7038-long-deletions: Add quite some alternatives · d891b6dd
  Mikaël Salson authored Jan 22, 2020
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As the deletions are large (both in V and J genes) many alternatives are possible
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  d891b6dd
- Merge branch 'hotfix-c/segmenter_reset' into 'dev' · 4a8d91df
  Mikaël Salson authored Jan 22, 2020
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segmenter.js : fix reset() + qunit tests

See merge request !580
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  4a8d91df
- Merge branch 'feature/4148-auto-build-doc-fix' into 'dev' · 5342619b
  Mikaël Salson authored Jan 22, 2020
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doc/.gitlab-ci.yml: launch docs jobs only on merge requests

Closes #4148

See merge request !586
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  5342619b
- segmenter.js: factorize code · 779847be
  Mikaël Salson authored Jan 22, 2020
  
  779847be
- doc/.gitlab-ci.yml: launch docs jobs only on merge requests · 884d341c
  Mathieu Giraud authored Jan 22, 2020
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See #4148.
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  884d341c
- Merge branch 'feature-c/4100-analysis_load_of_segedited_clone' into 'dev' · cb748ee9
  Mathieu Giraud authored Jan 22, 2020
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Resolve "Des données IMGt dans le fichier analysis bloquent la selection"

Closes #4100

See merge request !560
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  cb748ee9
- test_cluster.rb; update test that not working with ff45 · 36ef820d
  flothoni authored Jan 22, 2020
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Link to #4100
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  36ef820d
- Merge branch 'feature/4148-auto-build-doc' into 'dev' · 741e643d
  Mathieu Giraud authored Jan 22, 2020
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.gitlab-ci.yml: Launch doc jobs when changes on doc

Closes #4148

See merge request !585
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  741e643d
- .gitlab-ci.yml: Launch doc jobs when changes on doc · d0070f2b
  Mikaël Salson authored Jan 22, 2020
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Fix #4148
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  d0070f2b
- Merge branch 'doc/improve6' into 'dev' · 64adf9e4
  Mathieu Giraud authored Jan 22, 2020
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doc: update should-vdj.md

See merge request !582
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  64adf9e4
- doc/should-vdj.md: update · 4dbccff6
  Mathieu Giraud authored Jan 22, 2020
  
  4dbccff6
- doc/should-vdj.md: converted from should-vdj.org · 13501a70
  Mathieu Giraud authored Jan 21, 2020
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see #4142
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  13501a70
- doc/mkdocs-extra.css: bikeshed list styling · 3cbac074
  Mathieu Giraud authored Jan 22, 2020
  
  3cbac074
21 Jan, 2020 24 commits
- Merge branch 'doc/fix-doc' into 'dev' · 57d93bde
  Mikaël Salson authored Jan 21, 2020
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server.md: fix poor ORG → MD conversion

See merge request !581
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  57d93bde
- segmenter.js : fix reset() + qunit tests · 162f8806
  marc duez authored Jan 21, 2020
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- reset() remove all content from segmenter
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  162f8806
- test_cluster.rb; update test with a wait_while · 6b44e278
  flothoni authored Jan 21, 2020
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Link to #4100
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  6b44e278
- Merge branch 'feature-t/3673-import-tsv-airr-depuis-fuse-py' into 'dev' · 3eabc47b
  Mathieu Giraud authored Jan 21, 2020
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Resolve "Import .tsv AIRR depuis fuse.py"

Closes #3673

See merge request !558
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  3eabc47b
- fuse.py; update tests on AIRR use · bff5f722
  flothoni authored Jan 17, 2020 and Mathieu Giraud committed Jan 21, 2020
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Link to #3673
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  bff5f722
- fus.py; update tests · 7eaed0ca
  flothoni authored Jan 17, 2020 and Mathieu Giraud committed Jan 21, 2020
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Link to #3673
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  7eaed0ca
- fuse.py; now, airr value are converted (int, bool) if needed · f3b53f37
  flothoni authored Jan 17, 2020 and Mathieu Giraud committed Jan 21, 2020
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Some software don't give correct bool value and should be converted
Link to #3673
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  f3b53f37
- fuse.py; minor change in comments · 56f7c89a
  flothoni authored Jan 14, 2020 and Mathieu Giraud committed Jan 21, 2020
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Link to #3673
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  56f7c89a
- fuse.py: some comments · f2b05710
  Mathieu Giraud authored Jan 14, 2020
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together with @flothoni
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  f2b05710
- fuse.py; remove bypass on unsegmented row and add cdr1 for exemple · 3a47872b
  flothoni authored Dec 18, 2019 and Mathieu Giraud committed Jan 21, 2020
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CDR1 value are given in imgt files and have a start/stop couple of data. This is translate in the vidjil file
Link to #3673
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  3a47872b
- fuse airr; modify number of top given · 1c8e1007
  flothoni authored Dec 18, 2019 and Mathieu Giraud committed Jan 21, 2020
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All clones, segmented or not, should be output in output vidjil file
Also add control on number of cdr1 present
Link to #3673
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  1c8e1007
- fuse; AIRR import; fix error with python2 · bbc96d37
  flothoni authored Dec 16, 2019 and Mathieu Giraud committed Jan 21, 2020
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Should is lunched with python2 on gitlab side.
Key could be in different order
Link to #3673
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  bbc96d37
- fuse test, mjnor fix · 5e50899b
  flothoni authored Dec 16, 2019 and Mathieu Giraud committed Jan 21, 2020
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Link to #3673
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  5e50899b
- fuse; AIRR import; give an undefined values if no germline given · 0fd472a7
  flothoni authored Dec 16, 2019 and Mathieu Giraud committed Jan 21, 2020
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Link to #3673
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  0fd472a7
- fuse; AIRR import; add warnings usage (as define by vidjil) · ab6e080e
  flothoni authored Dec 16, 2019 and Mathieu Giraud committed Jan 21, 2020
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Link to #3673
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  ab6e080e
- fuse; AIRR import; minor bug fix · 50802d71
  flothoni authored Dec 16, 2019 and Mathieu Giraud committed Jan 21, 2020
  
  50802d71
- fuse; AIRR import; better naming · 2c4e10e0
  flothoni authored Dec 16, 2019 and Mathieu Giraud committed Jan 21, 2020
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Link to #3673
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  2c4e10e0
- fuse.py; AIRR import; add cleaning step to erase supplmentary data · a013beff
  flothoni authored Dec 16, 2019 and Mathieu Giraud committed Jan 21, 2020
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Link to #3673
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  a013beff
- fuse.p, AIRR import; add control on id of clone to avoid duplicate · 4d130682
  flothoni authored Dec 16, 2019 and Mathieu Giraud committed Jan 21, 2020
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Link to #3673
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  4d130682
- AIRR import; add should-get tests · bbc562c8
  flothoni authored Dec 16, 2019 and Mathieu Giraud committed Jan 21, 2020
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Add test for igBlast, miXcr, Vquest and Vidjil
Link to #3673
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  bbc562c8
- test tools: add dat for test (AIRR import) · e2cb35dd
  flothoni authored Dec 16, 2019 and Mathieu Giraud committed Jan 21, 2020
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Link to #3673
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  e2cb35dd
- fuse.py; add some data for tests · 6963e1a6
  flothoni authored Dec 10, 2019 and Mathieu Giraud committed Jan 21, 2020
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of load_airr function
Link to #3673
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  6963e1a6
- fuse.py; add some tests on load airr function · 5d7c8aa5
  flothoni authored Dec 10, 2019 and Mathieu Giraud committed Jan 21, 2020
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Link to #3673
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  5d7c8aa5
- fuse.py, function load_airr; don't add empty values · 3818fd17
  flothoni authored Dec 10, 2019 and Mathieu Giraud committed Jan 21, 2020
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If a clone have no value for a column, don't add an empty value in clone data; Link to #3673
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  3818fd17