Commits · 75a201e355cfa4732190c31a9eda5cfa882f0d21 · vidjil / vidjil

10 Jul, 2018 23 commits
- split-from-imgt.py: reorder, always retrieve gene_data before genome_data · 75a201e3
  Mathieu Giraud authored Apr 20, 2018
```
See #3009.
```
  75a201e3
- ncbi.py, split-from-imgt.py: move 'additional_length' to ncbi.get_gene_sequence() · ccd58bb6
  Mathieu Giraud authored Apr 20, 2018
  
  ccd58bb6
- ncbi.py, split-from-imgt.py: be more robust on non-found genes · 2ad7d54d
  Mathieu Giraud authored Apr 20, 2018
  
  2ad7d54d
- split-from-imgt.py: when gene_id is found, extract from chromosome rather than gene · 91adbc24
  Mathieu Giraud authored Apr 20, 2018
```
Closes #3009 ? To be verified.
```
  91adbc24
- split-from-imgt.py: reindent · eca46b8c
  Mathieu Giraud authored Apr 20, 2018
  
  eca46b8c
- split-from-imgt.py: propagate gene_list and call it inside retrieve_genes() · 326e3378
  Mathieu Giraud authored Apr 20, 2018
```
See #3009.
```
  326e3378
- split-from-imgt.py: __main__() · aedb69a5
  Mathieu Giraud authored Apr 20, 2018
  
  aedb69a5
- split-from-imgt.py: IMGTGENEDBGeneList() · c5d65caa
  Mathieu Giraud authored Apr 20, 2018
```
See #3009.
```
  c5d65caa
- ncbi.py: comment · c1f2fbe0
  Mathieu Giraud authored Apr 06, 2018
  
  c1f2fbe0
- ncbi.py: get_gene_position(), from eutils API · dad1bca1
  Mathieu Giraud authored Apr 06, 2018
  
  dad1bca1
- ncbi.py: extract and refactor from split-from-imgt.py and get-CD.py · ab308abe
  Mathieu Giraud authored Apr 06, 2018
  
  ab308abe
- get-germline, split-from-imgt.py: retrieve also IMGTGENEDB-GeneList and use stored files · 2771e711
  Mathieu Giraud authored Apr 06, 2018
```
See #3009
```
  2771e711
- Merge branch 'feature-a/3347-max-clones' into 'dev' · 65a03851
  Mikaël Salson authored Jul 10, 2018
```
Feature a/3347 max clones

Closes #3347

See merge request !238
```
  65a03851
- Merge branch 'feature-a/3307-json-fwd' into 'dev' · 6da11427
  Mikaël Salson authored Jul 10, 2018
```
Feature a/3307 json fwd

Closes #3307

See merge request !229
```
  6da11427
- core/filter.{h,cpp}: move typedef in .h · bc08111a
  Mathieu Giraud authored Jul 10, 2018
  
  bc08111a
- tests: update · 23a47b92
  Mathieu Giraud authored Jul 10, 2018
  
  23a47b92
- Merge branch 'feature-a/3293-seeds' into 'dev' · 5a25394d
  Mikaël Salson authored Jul 10, 2018
```
Feature a/3293 seeds

Closes #3293

See merge request !226
```
  5a25394d
- tests: update · 8b1b7c74
  Mathieu Giraud authored Jun 26, 2018
```
Close #3307.
```
  8b1b7c74
- core/*.{h,cpp}: speed up build time · 4d7f1a27
  Mathieu Giraud authored Jun 26, 2018
```
Use lib/json.hpp only when needed, and use lib/json_fwd.h elsewhere.
Yield a 40% speedup in build time on at least one platform.

See #3307.
```
  4d7f1a27
- lib/json_fwd.hpp: from upstream · eb0f52de
  Mathieu Giraud authored Jun 26, 2018
```
See #3307 and next commit.
```
  eb0f52de
- vidjil.cpp: --max-clones, limit clones both on stdout and on json output · bd85dcd0
  Mathieu Giraud authored Jul 10, 2018
```
Closes #3347.
See also #3302.
```
  bd85dcd0
- core/windows.{h,cpp}: sortedWindowsToJson() can stop after a maximal number of clones · d9ddc010
  Mathieu Giraud authored Jul 10, 2018
```
See #3347.
```
  d9ddc010
- tdd: --max-clones · 5c54f210
  Mathieu Giraud authored Jul 10, 2018
```
Opens #3347.
```
  5c54f210
06 Jul, 2018 2 commits
- Merge branch 'feature-a/3346--debug-filter-with-kmer-info' into 'dev' · 5d2c0f4d
  Mathieu Giraud authored Jul 06, 2018
```
Display the number of k-mer for each genes if debug_filter is defined

Closes #3346

See merge request !236
```
  5d2c0f4d
- Display the number of k-mer for each genes if debug_filter is defined · ab4e65b9
  Cyprien Borée authored Jul 06, 2018
```
For more informations see #3346.
```
  ab4e65b9
05 Jul, 2018 15 commits
- algo/vidjil.cpp: show -Z statistics only with -v · 055851f2
  Mathieu Giraud authored Jul 05, 2018
```
See #3259.
```
  055851f2
- Revert ".gitlab-ci.yml: move coverage analysis to the end, set it manual" · cc1e303c
  Mikaël Salson authored Jul 05, 2018
```
Reverts commit c0d14efb.
We don't need this extreme solution: coverage can be quick if not computing
branch coverage.
```
  cc1e303c
- algo/Makefile: Coverage without branching · 3ae1c307
  Mikaël Salson authored Jul 05, 2018
```
Coverage is now much quicker. The additional time for coverage over all the
jobs is about 3 min.

Fixes #3339
```
  3ae1c307
- tests: three mutations makes it difficult to recognize a V · 76e8be96
  Mathieu Giraud authored Jun 18, 2018
```
Perversely chosen mutations may fool our best heuristics.
See #3297 and #3298.
```
  76e8be96
- Merge branch 'feature-a/3339-coverage-stage' into 'dev' · 2c19fe92
  Mathieu Giraud authored Jul 05, 2018
```
.gitlab-ci.yml: move coverage analysis to the end, set it manual

See merge request !233
```
  2c19fe92
- .gitlab-ci.yml: move coverage analysis to the end, set it manual · c0d14efb
  Mathieu Giraud authored Jul 05, 2018
```
See #3339. We want to have first fast tests.
Once we will have #3340, we will run again always this stage.
```
  c0d14efb
- germline/homo-sapiens.g: seed is now called '9c' · d289f5b4
  Mathieu Giraud authored Jul 05, 2018
  
  d289f5b4
- vidjil.cpp: bikeshed -s help message · f9ea53dd
  Mathieu Giraud authored Jul 05, 2018
  
  f9ea53dd
- core/tools.cpp: throw an exception when the seed is unknown · d3ddd510
  Mathieu Giraud authored Jul 05, 2018
  
  d3ddd510
- core/tools.{h,cpp}: const · f10e2458
  Mathieu Giraud authored Jun 27, 2018
  
  f10e2458
- tests: add test · 86b13819
  Mathieu Giraud authored Jun 18, 2018
```
See #3293.
```
  86b13819
- algo/vidjil.cpp: -s help, show seedMap · cbac8704
  Mathieu Giraud authored Jun 18, 2018
```
See #3293.
```
  cbac8704
- core/germline.cpp: init(), calls expand_seed() when necessary · 85a73fb9
  Mathieu Giraud authored Jun 17, 2018
```
See #3293.
```
  85a73fb9
- core/tools.{h,cpp}: expand_seed(), and redefine DEFAULT_SEED · db5ebbc7
  Mathieu Giraud authored Jun 27, 2018
```
See #3293.
```
  db5ebbc7
- core/tools.{h,cpp}: string_of_map() · 3dbb2099
  Mathieu Giraud authored Jun 18, 2018
  
  3dbb2099