Commits · 6e9e9391cee8093e792a50ef0ef35b6ec1ebb022 · vidjil / vidjil

24 Jan, 2020 17 commits
- graph.js/css : update curves css · 6e9e9391
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
  
  6e9e9391
- scatterplot.js : store old_x/old_y positions before redraw · e4f42e5a
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
```
this was done by the move() function before but it has been replaced by a d3V5 forceX()/forceY()
```
  e4f42e5a
- scatterplot.js : add a small amount of randomness to the clone traget... · 321623ce
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
```
scatterplot.js : add a small amount of randomness to the clone traget positions to help the force simulation

clones can stack up vertically/horizontally without it
```
  321623ce
- scatterplot.js : adapt quadtree and collide() function for d3v5 focre simulation · f8261189
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
  
  f8261189
- scatterplot.js : add d3js V5 force simulation · 9b67795c
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
  
  9b67795c
- scatterplot.js : remove old d3jsV3 force simulation · 0d81cd02
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
  
  0d81cd02
- scatterplot.js : d3v5 drag function has changed · e95ca890
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
```
this is useless so currently disabled
```
  e95ca890
- scatterplot.js : smoothing++ · 8902397b
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
  
  8902397b
- numerical_axis.js : d3 scale.log function has been renamed in v5 · 81bcba36
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
  
  81bcba36
- model.js : d3 scale.log function has been renamed in v5 · d4fce2b0
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
  
  d4fce2b0
- graph.js : rewrite for d3v5 and misc · 338b3d51
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
  
  338b3d51
- graph.js : remove build_path_events() function, can be done safely during the update() · 9719b854
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
  
  9719b854
- graph.js : follow new d3js function names · a91a115c
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
  
  a91a115c
- graph.js : bugfix resolutioncurve can handle unusually low analyzed read · 0891daa4
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
```
resolutionCurve display was a mess for samples without reads or less than 5 reads
```
  0891daa4
- graph.js: put resolution curve on foreground · e5c9e333
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
  
  e5c9e333
- graph.js : use d3.lineGenerator for path · 2e7afc00
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
  
  2e7afc00
- add d3js version 5 library · c42c34ea
  marc authored Nov 27, 2019 and marc duez committed Jan 24, 2020
  
  c42c34ea
23 Jan, 2020 12 commits
- Merge branch 'bikeshed-message' into 'dev' · fe6f3fb5
  Mathieu Giraud authored Jan 23, 2020
```
vidjil.cpp: bikeshed help message

See merge request !592
```
  fe6f3fb5
- vidjil.cpp: bikeshed help message · cde5aca5
  Mathieu Giraud authored Jan 23, 2020
```
follows !589
```
  cde5aca5
- Merge branch 'feature-a/3861-no-output' into 'dev' · 49b8b832
  Mikaël Salson authored Jan 23, 2020
```
Feature a/3861 : options to limit output

Closes #3861

See merge request !589
```
  49b8b832
- Merge branch 'doc/airr-fuse' into 'dev' · 80ce835f
  Mikaël Salson authored Jan 23, 2020
```
Documentation on the AIRR .tsv import

See merge request !579
```
  80ce835f
- output.cpp: reindent · e86750d3
  Mikaël Salson authored Jan 23, 2020
  
  e86750d3
- Merge branch 'feature-a/4154-benchmark-current' into 'dev' · 5d9ab275
  Mikaël Salson authored Jan 23, 2020
```
Feature a/4154 : Benchmark also current HEAD

Closes #4154

See merge request !590
```
  5d9ab275
- .gitlab-ci.yml: benchmark also the current HEAD · 9a608613
  Mathieu Giraud authored Jan 23, 2020
```
Closes #4154
```
  9a608613
- benchmark-releases.py: -c, benchmark also the current HEAD · 64c78581
  Mathieu Giraud authored Jan 23, 2020
```
see #4154
```
  64c78581
- tests: add and update tests, --no-airr and --no-vidjil · 73066211
  Mathieu Giraud authored Jan 23, 2020
```
Closes #3861
```
  73066211
- vidjil.cpp: --no-airr · d8b4ad79
  Mathieu Giraud authored Jan 23, 2020
```
see #3861
```
  d8b4ad79
- vidjil.cpp: --no-vidjil · 828d7e09
  Mathieu Giraud authored Jan 23, 2020
```
see #3861
```
  828d7e09
- core/output.{h,cpp}: VidjilOuput, with_clones option · 39109911
  Mathieu Giraud authored Jan 23, 2020
```
see #3861
```
  39109911
22 Jan, 2020 11 commits
- Merge branch 'feature-a/3594-updated-evalue-computations-kmer-fine' into 'dev' · da83fb01
  Mathieu Giraud authored Jan 22, 2020
```
Update e-value multipliers and options

Closes #3594

See merge request !538
```
  da83fb01
- tools.md: typos, détails · 10dab250
  Mikaël Salson authored Jan 22, 2020
  
  10dab250
- 7038-long-deletions: Add quite some alternatives · d891b6dd
  Mikaël Salson authored Jan 22, 2020
```
As the deletions are large (both in V and J genes) many alternatives are possible
```
  d891b6dd
- Merge branch 'hotfix-c/segmenter_reset' into 'dev' · 4a8d91df
  Mikaël Salson authored Jan 22, 2020
```
segmenter.js : fix reset() + qunit tests

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

Closes #4148

See merge request !586
```
  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
```
See #4148.
```
  884d341c
- Merge branch 'feature-c/4100-analysis_load_of_segedited_clone' into 'dev' · cb748ee9
  Mathieu Giraud authored Jan 22, 2020
```
Resolve "Des données IMGt dans le fichier analysis bloquent la selection"

Closes #4100

See merge request !560
```
  cb748ee9
- test_cluster.rb; update test that not working with ff45 · 36ef820d
  flothoni authored Jan 22, 2020
```
Link to #4100
```
  36ef820d
- algo/Makefile: include 'doc/tools.md' in release · 37eebf5a
  Mathieu Giraud authored Jan 21, 2020
  
  37eebf5a
- doc/: AIRR import through fuse.py · ce6cb977
  Vidjil Team authored Jan 14, 2020 and Mathieu Giraud committed Jan 22, 2020
```
See #3673
by @flothoni and @magiraud
```
  ce6cb977