Commits · 10547fe6edc2803a8a51ea2c861c44bcf57fd313 · vidjil / vidjil

22 Apr, 2020 1 commit
- vidjil.cpp: correct output messages with or without --no-vidjil · ecb92708
  Mathieu Giraud authored Apr 22, 2020
```
fixes 828d7e09
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  ecb92708
26 Mar, 2020 1 commit
- algo: Use different seed for V, D and J · c788e295
  Mikaël Salson authored Mar 25, 2020
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Fix #3954
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  c788e295
23 Jan, 2020 3 commits
- vidjil.cpp: bikeshed help message · cde5aca5
  Mathieu Giraud authored Jan 23, 2020
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follows !589
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  cde5aca5
- vidjil.cpp: --no-airr · d8b4ad79
  Mathieu Giraud authored Jan 23, 2020
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see #3861
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  d8b4ad79
- vidjil.cpp: --no-vidjil · 828d7e09
  Mathieu Giraud authored Jan 23, 2020
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see #3861
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  828d7e09
17 Dec, 2019 3 commits
- vidjil.cpp: typo in warning string · c3bdead8
  Mathieu Giraud authored Dec 15, 2019
  
  c3bdead8
- vidjil.cpp: move '-e' in relevant section, make it a non-advanced option · 30c4dd1d
  Mathieu Giraud authored Nov 14, 2019
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See #3594.
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  30c4dd1d
- vidjil.cpp: Updated e-value corrections for multiple testing with FineSegmenter · 3e406c5a
  Vidjil Team authored Oct 11, 2019 and Mathieu Giraud committed Dec 17, 2019
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See #3594. '-e' is now the global e-value configuration.
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  3e406c5a
06 Nov, 2019 1 commit
- algo/vidjil.cpp: progress bar for clones beyond the clones displayed on stdout · d9a141b3
  Mathieu Giraud authored Nov 05, 2019
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Closes #3302, opens #4031.
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  d9a141b3
05 Nov, 2019 1 commit
- algo/vidjil.cpp: no more than a few clones on stdout, unless -v · 5eb2d955
  Mathieu Giraud authored Nov 05, 2019
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stdout is not our main output.
See #3302.
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  5eb2d955
24 Sep, 2019 1 commit
- vidjil.cpp: --c designations outputs the read name in 'name' in .vidjil · cbfff9d5
  Mathieu Giraud authored Sep 24, 2019
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Follows 6bd291b0.
See !457 and #3890
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  cbfff9d5
16 May, 2019 1 commit
- core/representative.h, vidjil.cpp: RandomScore by default · a2898925
  Mathieu Giraud authored Apr 08, 2019
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see #3866
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  a2898925
02 Apr, 2019 4 commits
- vidjil.cpp: --labels-json · c17ed263
  Mathieu Giraud authored Apr 02, 2019
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See #3839.
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  c17ed263
- vidjil.cpp: --config · fd0f80df
  Mathieu Giraud authored Apr 02, 2019
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See #3837.
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  fd0f80df
- vidjil.cpp: dump config into .vidjil · e0133fae
  Mathieu Giraud authored Apr 02, 2019
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There is now some hack to get a json, it could be improved.
See #3837.
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  e0133fae
- vidjil.cpp, lib/CLI11_json.hpp: include CLI11_json · 1fd605f6
  Mathieu Giraud authored Mar 21, 2019
  
  1fd605f6
22 Mar, 2019 1 commit

vidjil.cpp: Fix definition of min_cover_representative · 5c9296f9

Mikaël Salson authored Mar 21, 2019

min_cover_representative should be seen as a strict minimum on the number of reads
that can support a representative sequence.
The purpose is to avoid a too low ABSOLUTE number of reads to define a representative.
For the relative number, it is ratio_representative's role.

Before, if we specified -r 100 we needed to have 100 corresponding
k-mers which is very strict when a clone has just slightly more than
100 reads

5c9296f9

21 Mar, 2019 2 commits
- vidjil.cpp: bikeshed help strings from vidjil.cpp rather than in lib/CLI11.hpp · 1fa65b5c
  Mathieu Giraud authored Mar 20, 2019
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Better than what was done in 5359314cb.
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  1fa65b5c
- vidjil.cpp: update following CLI11 update · 6fc60d59
  Mathieu Giraud authored Mar 21, 2019
  
  6fc60d59
12 Mar, 2019 1 commit
- vidjil-algo: pride, 2019, VidjilNet · 162d49cb
  Mathieu Giraud authored Mar 12, 2019
  
  162d49cb
11 Mar, 2019 2 commits
- vidjil.cpp: --grep-reads combo · c06c7fc2
  Mathieu Giraud authored Mar 11, 2019
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Bye-bye -FaW, see #3785.
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  c06c7fc2
- vidjil.cpp: --all help message, typo, more positive message · 27686080
  Mathieu Giraud authored Mar 08, 2019
  
  27686080
08 Mar, 2019 3 commits
- vidjil.cpp: show hint on some deprecated options · 34b97c50
  Mathieu Giraud authored Mar 08, 2019
```
See #3295.
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  34b97c50
- vidjil.cpp: --label · da844b3c
  Mathieu Giraud authored Mar 08, 2019
  
  da844b3c
- vidjil.cpp: bikeshed option names and help messages · c7c56f21
  Vidjil Team authored Mar 08, 2019 and Mathieu Giraud committed Mar 08, 2019
```
Following passionate discussions (!245) :
 - add many long option names, using updated terms
 - deprecate 11 short options, including many rare options coming form ancient times
 - reorder options and bikeshed some help texts

See #3295.
```
  c7c56f21
06 Mar, 2019 5 commits
- vidjil.cpp: use CLI11::ConstructionError() when relevant · 7364857c
  Mathieu Giraud authored Mar 06, 2019
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Add display the error message improved in the previous commit.

see #3775
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  7364857c
- vidjil.cpp: better CLI11 error messages, using ERROR_STRING and DOCUMENTATION · cc587fc6
  Mathieu Giraud authored Mar 06, 2019
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define and use failure_message_doc(), taking inspiration from FailureMessage::simple()

see #3775
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  cc587fc6
- vidjil.cpp: deprecation error on '-c segment' · 339c7789
  Mathieu Giraud authored Mar 06, 2019
```
See #3772.
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  339c7789
- algo/vidjil.cpp: CMD_SEGMENT is now '-c designations', more balanced help and warn messages · 2a098ac3
  Mathieu Giraud authored Mar 06, 2019
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See #3772.
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  2a098ac3
- vidjil.cpp: define and use DOCUMENTATION · ee010248
  Mathieu Giraud authored Mar 06, 2019
  
  ee010248
05 Mar, 2019 4 commits
- vidjil.cpp: Use pointer to define the readScorer · 40e75d6e
  Mikaël Salson authored Mar 05, 2019
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A reference cannot be redefined in C++.
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  40e75d6e
- algo/vidjil.cpp: advanced option + bikeshed text · 72fee6c7
  Mathieu Giraud authored Mar 05, 2019 and Mikaël Salson committed Mar 05, 2019
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see #3764.
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  72fee6c7
- vidjil.cpp: Define option to use random sample for representative computation · 107407b2
  Mikaël Salson authored Mar 05, 2019
  
  107407b2
- algo/: Use the same scorer for read filtering and representative computation · a6383d82
  Mikaël Salson authored Mar 05, 2019
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This was put in two different places and could lead to inconsistencies. Now the
reads are necessarily selected in the same way.
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  a6383d82
04 Mar, 2019 1 commit
- vidjil.cpp: Don't use exit() · 8a216586
  Mikaël Salson authored Mar 04, 2019
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See 1a7bb7f8 for reason why.

Fix (in part?) #3771
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  8a216586
28 Feb, 2019 3 commits
- vidjil.cpp: --plain-index, option name and help · b8fae1c9
  Mathieu Giraud authored Feb 12, 2019
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Completes ac562c7e. See #2556.
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  b8fae1c9
- vidjil.cpp: Use Aho-Corasick as default index · d7a38755
  Mikaël Salson authored Jul 07, 2017 and Mathieu Giraud committed Feb 28, 2019
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This index was made to be used.
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  d7a38755
- vidjil.cpp: --clean-memory · ae8269a0
  Mathieu Giraud authored Feb 12, 2019
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See #3729.
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  ae8269a0
26 Nov, 2018 1 commit
- vidjil.cpp: Don't use a pointer for output · 894bb14a
  Mikaël Salson authored Nov 23, 2018 and Mathieu Giraud committed Nov 26, 2018
```
This avoids some issue with memory leak when leaving main earlier than expected.

See #3571
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  894bb14a
26 Oct, 2018 1 commit
- vidjil.cpp, doc/vidjil-algo.md: pride, VidjilNet · b118541a
  Mathieu Giraud authored Oct 26, 2018
  
  b118541a