Commits · 5e9ddebd0d465b8361b0092642e41afe4d267daa · vidjil / vidjil

02 Dec, 2014 1 commit
- fuse.py / browser : small fix for clntab file · 5e9ddebd
  Marc Duez authored Dec 02, 2014
  
  5e9ddebd
27 Nov, 2014 2 commits
- latex.py: display clones in a LaTeX table · 37656f88
  Mathieu Giraud authored Nov 27, 2014 and Vidjil Team committed Nov 27, 2014
  
  37656f88
- latex.py: output clones in a LaTeX table · 1910a774
  Mathieu Giraud authored Nov 27, 2014
  
  1910a774
13 Nov, 2014 5 commits
- fuse.py, ListWindows.load(): optional verbose argument · 08835262
  Mathieu Giraud authored Nov 13, 2014 and Vidjil Team committed Nov 13, 2014
  
  08835262
- fuse.py: ignore non-list values in concatenate_with_padding() · 44a98b8d
  Mathieu Giraud authored Nov 13, 2014 and Vidjil Team committed Nov 13, 2014
```
This was introduced by b9cd02c4, but removed with b9cd02c4. This prevents fuse.py from halting
if unknown non-list fields are present.

I am not sure that this is useful (and here it's somewhat different: such values are ignored).
We need more unit and functional tests on fuse.py !
```
  44a98b8d
- fuse.py: Windows.__add__() also uses concatenate_with_padding() · e9aac210
  Mathieu Giraud authored Nov 13, 2014 and Vidjil Team committed Nov 13, 2014
```
0ee4e4e9 forgot this one
```
  e9aac210
- fuse.py: --multi option is deprecated · 24ac221f
  Mathieu Giraud authored Nov 13, 2014 and Vidjil Team committed Nov 13, 2014
```
Multiple germlines are correctly handled by the regular fuse.py.
```
  24ac221f
- fuse.py: add "vidjil_json_version" to fields that should not be concatened · b2bf072a
  Mathieu Giraud authored Nov 13, 2014 and Vidjil Team committed Nov 13, 2014
  
  b2bf072a
07 Nov, 2014 1 commit
- fuse.py : handle germlines field / debug clntab / remove list trick · b9cd02c4
  Marc Duez authored Nov 07, 2014
  
  b9cd02c4
04 Nov, 2014 1 commit
- fuse.py : save fuse timestamp · 1b0e3356
  Marc Duez authored Nov 04, 2014
  
  1b0e3356
22 Oct, 2014 3 commits
- model.js : debug loadAnalysis url · 43824d40
  Marc Duez authored Oct 22, 2014
```
replace .vidjil with .analysis only for extension
```
  43824d40
- model.js : debug parsejson from url · 61fab8f7
  Marc Duez authored Oct 22, 2014
  
  61fab8f7
- fuse.py, format-analysis.org: the format is now 2014.10 · b83d868c
  Mathieu Giraud authored Oct 22, 2014
  
  b83d868c
19 Oct, 2014 4 commits
- fuse.py: repair unit tests · a0b8881c
  Mathieu Giraud authored Oct 18, 2014
  
  a0b8881c
- fuse.py: Samples, Readme, __str__ method · 68b38522
  Mathieu Giraud authored Oct 18, 2014
  
  68b38522
- fuse.py: ListWindows, __iter__/__getitem__/__len__ methods · 466fbeba
  Mathieu Giraud authored Oct 17, 2014
  
  466fbeba
- fuse.py: factorize concatenate_with_padding() function · 0ee4e4e9
  Mathieu Giraud authored Oct 17, 2014
  
  0ee4e4e9
14 Oct, 2014 1 commit
- fuse.py : debug samples · f641d7be
  Marc Duez authored Oct 14, 2014
  
  f641d7be
13 Oct, 2014 1 commit
- fuse.py : handle 10.10.2014 data format · 5b7b5264
  Marc Duez authored Oct 13, 2014
  
  5b7b5264
10 Oct, 2014 1 commit
- browser.js : use segmentation info · abbd7983
  Marc Duez authored Oct 10, 2014
  
  abbd7983
09 Oct, 2014 1 commit
- fuse.py : debug system_segmented field · 8b11e1f3
  Marc Duez authored Oct 09, 2014
  
  8b11e1f3
26 Sep, 2014 1 commit
- fuse.py : better fuse for multi-system · a9e0e89c
  Marc Duez authored Sep 26, 2014
```
debug: original name order
```
  a9e0e89c
23 Sep, 2014 1 commit
- fuse.py: user help · d256bad6
  Mathieu Giraud authored Sep 23, 2014
  
  d256bad6
18 Sep, 2014 2 commits
- fuse.py : change filter again · 9ab655a8
  Marc Duez authored Sep 18, 2014
  
  9ab655a8
- fuse.py : improve filtering · 3b3d0d53
  Marc Duez authored Sep 18, 2014
  
  3b3d0d53
16 Sep, 2014 4 commits
- fuse.py : pre-filtering · 61139b3f
  Marc Duez authored Sep 15, 2014
  
  61139b3f
- fuse.py: debug clntab · a058233c
  Marc Duez authored Sep 15, 2014
  
  a058233c
- fuse.py : mute synthetic clones · 7e762d66
  Marc Duez authored Sep 15, 2014
  
  7e762d66
- fuse.py : handle samples field · cdd64ca6
  Marc Duez authored Sep 15, 2014
  
  cdd64ca6
15 Sep, 2014 4 commits
- fuse.py : pre-filtering · 9d195ef0
  Marc Duez authored Sep 15, 2014
  
  9d195ef0
- fuse.py: debug clntab · 782749cf
  Marc Duez authored Sep 15, 2014
  
  782749cf
- fuse.py : mute synthetic clones · 71a6b438
  Marc Duez authored Sep 15, 2014
  
  71a6b438
- fuse.py : handle samples field · a32cd3b5
  Marc Duez authored Sep 15, 2014
  
  a32cd3b5
09 Sep, 2014 1 commit
- fuse.py: orders 'systems_segmented' according to GERMLINES_ORDER · 686bf290
  Mathieu Giraud authored Sep 09, 2014
  
  686bf290
05 Sep, 2014 4 commits
- fuse.py: allow germline code with 4 letters (DHJH) · 8772aa38
  Mathieu Giraud authored Sep 05, 2014 and Vidjil Team committed Sep 05, 2014
  
  8772aa38
- fuse.py: rename --merge option to --multi · 09f7183c
  Mathieu Giraud authored Sep 05, 2014 and Vidjil Team committed Sep 05, 2014
```
--merge was confusing, this option is meant to merge several .data files with multiple germlines
(note that it works only with one sample)
```
  09f7183c
- fuse.py: --merge works again · 3d381981
  Mathieu Giraud authored Sep 05, 2014 and Vidjil Team committed Sep 05, 2014
```
Corrects bug introduced by 92519fc9
```
  3d381981
- fuse.py : build stats about reads distribution / mute "others" artificial clones · 49046ca6
  Marc Duez authored Sep 05, 2014
```
TODO : auto-compute others clones with javascript
```
  49046ca6
02 Sep, 2014 1 commit
- merge · c77282ab
  Marc Duez authored Sep 01, 2014
  
  c77282ab
28 Aug, 2014 1 commit
- fuse.py: remove unnecessary debug output · 20b95a6c
  Mathieu Giraud authored Aug 28, 2014
  
  20b95a6c