Commits · 64adf9e4952426819240ab05bef588f16850ebca · vidjil / vidjil

22 Jan, 2020 4 commits
- Merge branch 'doc/improve6' into 'dev' · 64adf9e4
  Mathieu Giraud authored Jan 22, 2020
```
doc: update should-vdj.md

See merge request !582
```
  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
```
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 28 commits
- Merge branch 'doc/fix-doc' into 'dev' · 57d93bde
  Mikaël Salson authored Jan 21, 2020
```
server.md: fix poor ORG → MD conversion

See merge request !581
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  57d93bde
- Merge branch 'feature-t/3673-import-tsv-airr-depuis-fuse-py' into 'dev' · 3eabc47b
  Mathieu Giraud authored Jan 21, 2020
```
Resolve "Import .tsv AIRR depuis fuse.py"

Closes #3673

See merge request !558
```
  3eabc47b
- fuse.py; update tests on AIRR use · bff5f722
  flothoni authored Jan 17, 2020 and Mathieu Giraud committed Jan 21, 2020
```
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
```
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
```
  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
```
  bbc96d37
- fuse test, mjnor fix · 5e50899b
  flothoni authored Dec 16, 2019 and Mathieu Giraud committed Jan 21, 2020
```
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
```
Link to #3673
```
  0fd472a7
- fuse; AIRR import; add warnings usage (as define by vidjil) · ab6e080e
  flothoni authored Dec 16, 2019 and Mathieu Giraud committed Jan 21, 2020
```
Link to #3673
```
  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
```
  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
```
Link to #3673
```
  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
```
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
```
  bbc562c8
- test tools: add dat for test (AIRR import) · e2cb35dd
  flothoni authored Dec 16, 2019 and Mathieu Giraud committed Jan 21, 2020
```
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
```
  6963e1a6
- fuse.py; add some tests on load airr function · 5d7c8aa5
  flothoni authored Dec 10, 2019 and Mathieu Giraud committed Jan 21, 2020
```
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
```
  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
```
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
```
  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 8 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
- server.md: fix poor ORG → MD conversion · 971bc23b
  Mikaël Salson authored Jan 20, 2020
  
  971bc23b
- 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
```
  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
```
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
```
was broken since indexedDom
```
  76433f43