vidjil merge requestshttps://gitlab.inria.fr/vidjil/vidjil/-/merge_requests2021-04-08T16:06:18+02:00https://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/478Resolve "Avoir des germline de poulet"2021-04-08T16:06:18+02:00Thonier FlorianResolve "Avoir des germline de poulet"Closes #3910Closes #3910Algo 2021.04https://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/885Update germlines to 2021-01-212022-05-23T10:09:32+02:00Mathieu GiraudUpdate germlines to 2021-01-21Closes #4271.
Quasi au-dessus de !839/!892 (en tout cas en prenant les germlines 2021-01-21 générés par !892).
Rend obsolète !374.Closes #4271.
Quasi au-dessus de !839/!892 (en tout cas en prenant les germlines 2021-01-21 générés par !892).
Rend obsolète !374.Algo 2021.04Mikaël SalsonMikaël Salsonhttps://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/947No more -3 option2021-04-19T18:39:59+02:00Mathieu GiraudNo more -3 optionThe CDR3 analysis is fast and robust. We now launch it for all clones under the `--max-designations` threshold.
Close #4758.The CDR3 analysis is fast and robust. We now launch it for all clones under the `--max-designations` threshold.
Close #4758.Algo 2021.04Mikaël SalsonMikaël Salsonhttps://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/945doc: (un)productivity estimation, static binaries, other fixes/updates2021-04-27T09:02:52+02:00Mathieu Girauddoc: (un)productivity estimation, static binaries, other fixes/updatesCloses #4755, #4759 (and #1720)Closes #4755, #4759 (and #1720)Algo 2021.04Mikaël SalsonMikaël Salsonhttps://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/939Release 2021.042022-02-19T20:00:15+01:00Mathieu GiraudRelease 2021.04
## Before the release
### Documentation
* [x] New features are described in `doc/vidjil-algo.md`
* [x] Breaking changes (and needed configuration changes) are understood
On the `feature-a/release` branch, the last commit is the rele...
## Before the release
### Documentation
* [x] New features are described in `doc/vidjil-algo.md`
* [x] Breaking changes (and needed configuration changes) are understood
On the `feature-a/release` branch, the last commit is the release commit updating the three following files:
* [x] CHANGELOG
* [x] `doc/vidjil-algo.md` with the proper release tag
* [x] `algo/release` with the proper release tag
### Pipelines
https://gitlab.inria.fr/vidjil/vidjil/-/pipelines/242713
(if tests passed on different pipelines, indicate below the relevant pipelines)
Usual tests should pass, but also:
* [x] ~~prepare_release~~ #4109
* [x] valgrind_unit
* [x] valgrind_functional : voir ci-dessous, ok modulo #4706
* [x] multiple_tests
Benchmarks
* [ ] almost no change...
* [x] ... or significant changes are understood
Profiling
* cpu: PointerACAutomaton.getResults, ~37% ?
* mem: PointerACAutomaton.insert, ~73% ?
* [ ] almost no change...
* [x] ... or significant changes are understood
## The release, publish, tag and push
* [x] merge this MR to *master* and tag: `git tag release-20XX-XX`
* [x] push: `git push origin master release-20XX-XX`
* [x] mirror to GH: `git push github master release-20XX.XX`
* [x] deploy to vidjil.org/releases and app.vidjil.org: click on `copy_release` (there may be changes to CD...)
* [x] deploy the doc: click on `deploy_doc`
After these steps, we merge back the release in `dev`:
* [x] merge this MR to dev
## After the release: deploy
* [x] Click `deploy_release_prod` in the `deploy_prod` stage, deploying the release on `vidjil-algo-next` on the public server
* [x] Open a new internal issue with the `Deploy (vidjil-algo)` template : vdj#1238
* [ ] Possibly fix things in `merge_request_templates/Release (vidjil-algo).md` on a new MRAlgo 2021.04https://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/935Make IGH clones without a {WP}GxG pattern unproductive2021-04-14T17:49:49+02:00Mathieu GiraudMake IGH clones without a {WP}GxG pattern unproductiveClose #4701Close #4701Algo 2021.04Mikaël SalsonMikaël Salsonhttps://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/932fix typos, show D seeds, bikeshed .affects2021-04-23T06:24:15+02:00Mathieu Giraudfix typos, show D seeds, bikeshed .affectsVarious small fixes/bikeshedding on output.
Close #4338 and #4727.Various small fixes/bikeshedding on output.
Close #4338 and #4727.Algo 2021.04Mikaël SalsonMikaël Salsonhttps://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/916--gz outputs .fa.gz files, --filter-reads outputs .fa{,.gz} files2021-02-17T21:02:03+01:00Mathieu Giraud--gz outputs .fa.gz files, --filter-reads outputs .fa{,.gz} filesAu-dessus de !906.Au-dessus de !906.Algo 2021.04Mikaël SalsonMikaël Salsonhttps://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/915Doc: post-sequencer workflow, filtering reads2021-03-17T15:46:46+01:00Mathieu GiraudDoc: post-sequencer workflow, filtering reads
Préparé avec @flothoni.
Je me suis permis d'ajouter un paragraphe sur les formats de fichiers.
On pourrait aussi avoir un jour des considérations sur la qualité.
Préparé avec @flothoni.
Je me suis permis d'ajouter un paragraphe sur les formats de fichiers.
On pourrait aussi avoir un jour des considérations sur la qualité.Algo 2021.04Mikaël SalsonMikaël Salsonhttps://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/912doc/releases.md: release cycle2021-02-15T14:38:12+01:00Mathieu Girauddoc/releases.md: release cycleCloses vdj#1173Closes vdj#1173Algo 2021.04Mikaël SalsonMikaël Salsonhttps://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/906Preset --filter-reads2021-03-17T15:46:46+01:00Mathieu GiraudPreset --filter-readsCloses #4681Closes #4681Algo 2021.04Mikaël SalsonMikaël Salsonhttps://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/89260 bp up/down-stream2021-04-23T06:29:02+02:00Mathieu Giraud60 bp up/down-streamAu-dessus de !891.Au-dessus de !891.Algo 2021.04Mikaël SalsonMikaël Salsonhttps://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/891Tuning germline up/downstreams2021-07-14T17:06:09+02:00Mathieu GiraudTuning germline up/downstreamsFollowing !606, we need some tunings to use the updated germlines (!885).
Closes #4656 and #4647.Following !606, we need some tunings to use the updated germlines (!885).
Closes #4656 and #4647.Algo 2021.04Mikaël SalsonMikaël Salsonhttps://gitlab.inria.fr/vidjil/vidjil/-/merge_requests/724vidjil.cpp: smaller -y export2021-04-14T17:02:48+02:00Mathieu Giraudvidjil.cpp: smaller -y export
Juste un essai pour #4036 / #4250 :
```
{
"_average_read_length": [
333.6000061035156
],
"germline": "IGH",
"id": "AAAAAAGCAAAACTGGGGCCCCAGCGGGCGGGTATGGGACGTCTGGGGGC",
"reads": [
5
...
Juste un essai pour #4036 / #4250 :
```
{
"_average_read_length": [
333.6000061035156
],
"germline": "IGH",
"id": "AAAAAAGCAAAACTGGGGCCCCAGCGGGCGGGTATGGGACGTCTGGGGGC",
"reads": [
5
],
"seg_stat": {
"3": 5
},
"top": 16601
},
```
Pas de surprises, sur `./vidjil-algo -g germline/homo-sapiens.g -y all -z 0 demo/LIL-L3-0.fastq.gz` (le .gz fait 308 M) :
- `.vidjil`, dev: **29M**
- `.vidjil`, cette MR, mais on garde les séquences et pas `average_read_length`: **7,2M**
- `.vidjil`, cette MR: **4,5M** (ping #4334 qui devient non négligeable)
- Est-ce que les champs présents avec cette MR suffisent vraiment à faire le ~"server-fuse" pour calculer les distributions actuelles `-d lenSeqAverage` ? @flothoni ?
- Les tests ne vont pas passer car on perd beaucoup d'informations avec ce `-y` allégé. Et un `-y all` traditionnel est toujours intéressant dans certains cas...
- Par compatibilité, garder le `-y` actuel, et faire un `-Y` (ou autre, `-W` ?) et on ferait plutôt `-Y all -z 100` en prod... ?
- Ou bien finalement non, on allège le `-y` actuel, et on met une option type `--output-more-details` ?
- Effet collatéral: on sort moins de données, y compris dans le AIRR.
- Mais si `sequence` n'est plus obligatoire, #4317 ?
- Pourrait-on même ne pas lancer ~"cpp-representative" ?Algo 2021.04Mikaël SalsonMikaël Salson