Commits · 1c8e1007cb5fd0269088c8040dca2029d65ecb0b · vidjil / vidjil

21 Jan, 2020 20 commits
- fuse airr; modify number of top given · 1c8e1007
  flothoni authored Dec 18, 2019 and Mathieu Giraud committed Jan 21, 2020
```
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
```
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
- fuse.py; refactor function load_airr · d379b7c3
  flothoni authored Dec 10, 2019 and Mathieu Giraud committed Jan 21, 2020
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Now each axe have it own declaration and is tested for presence or not inside the loaded airr file
Link to #3673
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  d379b7c3
- fuse.py; add airr axes name as use by mixcr · b5278b2e
  flothoni authored Dec 10, 2019 and Mathieu Giraud committed Jan 21, 2020
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mixcr don't use airr column names. So we need to make correlation between their names and airr names
Link to #3673
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  b5278b2e
- fuse.py; add function to use AIRR formated files. · 0b574ffe
  flothoni authored Dec 05, 2019 and Mathieu Giraud committed Jan 21, 2020
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Link to #3673
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  0b574ffe
- tools/test, add some airr ouput for testing · 8068fa3a
  flothoni authored Dec 04, 2019 and Mathieu Giraud committed Jan 21, 2020
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Link to #3673
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  8068fa3a
- Merge branch 'hotfix-c/segmenter_and_unconventional_clones' into 'dev' · 6c5a8810
  Mikaël Salson authored Jan 21, 2020
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segmenter.js: init segmenter without accessing clones content

Closes #4141 and #4140

See merge request !578
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  6c5a8810
- segmenter.js : don't build placeholder for clones that shouldn't be added to segmenter · 20a2af31
  marc duez authored Jan 21, 2020
  
  20a2af31
20 Jan, 2020 7 commits
- segmenter.js : excessive reset · 2bd92f0b
  marc duez authored Jan 20, 2020
  
  2bd92f0b
- segmenter.js: init segmenter without accessing clones content · e5dbc916
  marc duez authored Jan 20, 2020
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this should avoid problems related to clones with unexpected content (synthetic/virtual/distrib/...)
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  e5dbc916
- Merge branch 'feature-c/hotfix-align' into 'dev' · 624d1898
  Mikaël Salson authored Jan 20, 2020
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Feature c/hotfix align

See merge request !577
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  624d1898
- qunit: segmenter_test.js, fallback in case cgi_address is not set · c6545102
  marc duez authored Jan 20, 2020
  
  c6545102
- qunit: segmenter_test.js, use another set of data for test align · b3b8a581
  marc duez authored Jan 20, 2020
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to avoid breaking other tests
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  b3b8a581
- qunit: segmenter_test.js, test align() and resetAlign() functions · 7c065000
  marc duez authored Jan 20, 2020
  
  7c065000
- segmenter.js : fix align() and resetAlign() · 76433f43
  marc duez authored Jan 20, 2020
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was broken since indexedDom
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  76433f43
16 Jan, 2020 2 commits
- Merge branch 'doc/read-length' into 'dev' · cb586311
  Mathieu Giraud authored Jan 16, 2020
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doc/locus.md: considerations on the read length

Closes #4130

See merge request !576
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  cb586311
- doc/locus.md: considerations on the read length · 6276853e
  Mathieu Giraud authored Jan 16, 2020
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closes #4130
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  6276853e
15 Jan, 2020 3 commits
- Merge branch 'doc/library-preparation-sequencing' into 'dev' · 4c932600
  Mathieu Giraud authored Jan 15, 2020
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locus.md: link for validate-links.py

See merge request !574
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  4c932600
- locus.md: link for validate-links.py · 86cc9cb5
  Mathieu Giraud authored Jan 15, 2020
  
  86cc9cb5
- Merge branch 'doc/library-preparation-sequencing' into 'dev' · 3f599527
  Mathieu Giraud authored Jan 15, 2020
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Some documentation on library preparation and sequencing

See merge request !568
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  3f599527
14 Jan, 2020 8 commits
- doc/locus.md: fix links · 2bcf49f3
  Mathieu Giraud authored Jan 09, 2020
  
  2bcf49f3
- doc/locus.md: 1-step/2-steps · 1fa7fe67
  Mathieu Giraud authored Jan 10, 2020
  
  1fa7fe67
- doc/locus.md: details on capture and other strategies · 191c7f13
  Mathieu Giraud authored Jan 06, 2020
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thanks to @mikael-s
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  191c7f13
- doc/locus.md: not only ALL · 46140007
  Mathieu Giraud authored Jan 06, 2020
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thanks to @mikael-s
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  46140007
- locus.md: typos, détails · 1babc7f4
  Mikaël Salson authored Jan 06, 2020 and Mathieu Giraud committed Jan 14, 2020
  
  1babc7f4
- doc/*: links to library preparation and sequencing · ae5a9f5e
  Mathieu Giraud authored Dec 25, 2019
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vdj#945
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  ae5a9f5e
- doc/locus.md: library preparation and sequencing · 4fcfb973
  Mathieu Giraud authored Dec 25, 2019
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vdj#945
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  4fcfb973
- Merge branch 'doc/print-broken-urls' into 'dev' · ee1c8ac6
  Mathieu Giraud authored Jan 14, 2020
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tools/validate-links.py: display again failed url after the summary

See merge request !573
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  ee1c8ac6