Commits · 6be9b9627caa365457cc4409ebba80963bc8b5f8 · vidjil / vidjil

22 Aug, 2019 9 commits
- fuse.py; minor renaming · 6be9b962
  Thonier Florian authored Aug 22, 2019
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Link to #3944
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  6be9b962
- tools/tests; add tests on distribution made by fuse · db7af3b5
  Thonier Florian authored Aug 22, 2019
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Link to #3944
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  db7af3b5
- fuse.py; add arguments to make distributions computing · 786e59fa
  Thonier Florian authored Aug 22, 2019
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One for compute distribution into a separtated file, another to put in directly into the fused file.
Link to #3944
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  786e59fa
- fuse; update doctests · 56c7aafe
  Thonier Florian authored Aug 22, 2019
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Link to #3944
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  56c7aafe
- fuse.py; add the list of distributions to compute · 676ab5bf
  Thonier Florian authored Aug 22, 2019
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Link to #3944
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  676ab5bf
- fuse.py; add function to compute the distributions · e99d0b77
  Thonier Florian authored Aug 22, 2019
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These functions allow to compute dirstibutions for each files, for each list of distribution in the list
Link to #3944
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  e99d0b77
- fuse.py; fix a bug in build_stats function · 5433b9b5
  Thonier Florian authored Aug 22, 2019
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Link to #3944
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  5433b9b5
- fuse.py; Add functions to clones to return axis values · 2df8292f
  Thonier Florian authored Aug 22, 2019
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Use for distributions
Link to #3944
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  2df8292f
- fuse.py; Add a clone for doctest · e975cf28
  Thonier Florian authored Aug 22, 2019
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Link to #3944
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  e975cf28
01 Apr, 2019 1 commit
- tools/should.py: update from upstream, 2.0.0 · 7bd5506d
  Mathieu Giraud authored Mar 30, 2019
  
  7bd5506d
27 Mar, 2019 1 commit
- tools/pear.py; invert the forward/reverse file keeped. · 74982253
  flothoni authored Mar 27, 2019
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Fix #3833
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  74982253
08 Mar, 2019 1 commit
- tools/tests/Makefile: launch should-vdj-to-tap.py tests · 0287283a
  Mathieu Giraud authored Mar 08, 2019
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should-vdj-to-tap.py could be moved to tools.
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  0287283a
28 Feb, 2019 1 commit
- tools/should.py: update from upstream · 4eb9e704
  Mathieu Giraud authored Feb 28, 2019
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should@28eaf5a6
see #3762
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  4eb9e704
12 Feb, 2019 1 commit
- tools/should.py: update from upstream · 2208ab8b
  Mikaël Salson authored Feb 12, 2019
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should@2a21dfd9
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  2208ab8b
15 Jan, 2019 2 commits
- fuse.py: --pre help · 22fe21d7
  Mathieu Giraud authored Jan 15, 2019
  
  22fe21d7
- defs.py: Specify the new variable for preprocess scripts · cbe07fac
  Mikaël Salson authored Jan 15, 2019
  
  cbe07fac
07 Jan, 2019 1 commit

fuse.py: pre-processing with --pre · 0cbc5c3d

Mikaël Salson authored Jan 07, 2019

- Define a function that could be used for post-processing
- Use defs.py to determine where the pre-process are stored
- Should tests

See #3647

0cbc5c3d

04 Dec, 2018 3 commits
- tools/fuse.py: keep all interesting clone metadata, even from non-topmost clones · 48ff68af
  Mathieu Giraud authored Dec 04, 2018
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Closes #3585.
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  48ff68af
- tests: update · c421fc67
  Mathieu Giraud authored Dec 04, 2018
  
  c421fc67
- tests: fuse should keep clone metadata from non-topmost clones · ec6d38c4
  Mathieu Giraud authored Dec 04, 2018
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See #3585.
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  ec6d38c4
30 Nov, 2018 1 commit
- fuse.py: pre-processing with --pre · 0ad34586
  Mathieu Giraud authored Nov 30, 2018
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See #3647.
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  0ad34586
23 Nov, 2018 1 commit
- tools/should.py: update from upstream · 336b8051
  Mathieu Giraud authored Nov 23, 2018
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should@8f711a78
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  336b8051
16 Oct, 2018 7 commits
- tools/pear_structured_log: add and update tests · a7042415
  Thonier Florian authored Oct 11, 2018 and Mathieu Giraud committed Oct 16, 2018
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link to #3054
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  a7042415
- tools/pear_structured_log; minor change in comment · c9d5d2d0
  Thonier Florian authored Oct 12, 2018 and Mathieu Giraud committed Oct 16, 2018
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link to 3054
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  c9d5d2d0
- pear_structured_log; return now percentage of reads merge/discarded/assembled · a424bef0
  Thonier Florian authored Oct 12, 2018 and Mathieu Giraud committed Oct 16, 2018
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link to #3054
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  a424bef0
- pear_structured_log; move some line outside of the for loop · 64e23fb6
  Thonier Florian authored Oct 11, 2018 and Mathieu Giraud committed Oct 16, 2018
  
  64e23fb6
- pear_structured_log; export now number value as int · b7238712
  Thonier Florian authored Oct 11, 2018 and Mathieu Giraud committed Oct 16, 2018
  
  b7238712
- pear log converter: rename file for more clarity · 572e1c05
  Thonier Florian authored Oct 11, 2018 and Mathieu Giraud committed Oct 16, 2018
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link to #3054
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  572e1c05
- pear_log_converter: add a scipt to convert pear log to json format · b0a89fd6
  flothoni authored Apr 27, 2018 and Mathieu Giraud committed Oct 16, 2018
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With this script, we have the possibility to get structured datas from the pear preprocess to use them into the server, for quality, warning, ...
link to #3054 #3049 #3154
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  b0a89fd6
15 Oct, 2018 1 commit

vidjil-to-fasta.py: Percentage on total of reads · 601f183b

Mikaël Salson authored Oct 15, 2018

This will allow to more reliably add percentages that otherwise would give
meaningless results.

In the test we now have 497 reads out of 786861.

601f183b

07 Aug, 2018 5 commits
- should.cfg: FUSE_OPTIONS is empty by default · 38ae3783
  Mathieu Giraud authored Aug 07, 2018
  
  38ae3783
- tools/should.py: update from upstream · 0656c910
  Mathieu Giraud authored Aug 07, 2018
  
  0656c910
- fuse.py, vidjilparser.py fix issue when no clones · 19d68ea9
  Ryan Herbert authored Aug 07, 2018
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allows vidjil files to contain no clones
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  19d68ea9
- tests: make should-ijson · 2276f061
  Mathieu Giraud authored Aug 07, 2018
  
  2276f061
- tests: add $FUSE_OPTIONS · 2613be29
  Mathieu Giraud authored Aug 07, 2018
  
  2613be29
26 Jul, 2018 1 commit
- browser,tools: Add percentages in CloneDB results · 850c746b
  Alexia Omietanski authored Jul 26, 2018 and Mikaël Salson committed Jul 26, 2018
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Fixes #2929
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  850c746b
18 Jul, 2018 4 commits
- fuse.py only import VidjilParser if used · 54aa32fe
  Ryan Herbert authored Jul 13, 2018 and Mikaël Salson committed Jul 18, 2018
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So that dependencies only need to be installed if VidjilParser is used.
Thanks @mikael-s :)
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  54aa32fe
- fuse.py use python3 shebang · b160d1c5
  Ryan Herbert authored Jun 13, 2018 and Mikaël Salson committed Jul 18, 2018
  
  b160d1c5
- vidjilparser.py use ijson yajl2_cffi backend · 5aa63668
  Ryan Herbert authored Jun 12, 2018 and Mikaël Salson committed Jul 18, 2018
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Being a fast parser allows us to gain a significant amount of time when
executing.
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  5aa63668
- fuse.py make ijson parser optional · 6c26c22e
  Ryan Herbert authored Jun 12, 2018 and Mikaël Salson committed Jul 18, 2018
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Restore old functionality and make new functionality optional.
Due to the amount of time it takes to run the vidjilparser we may need
to decide between speed and memory efficiency

See #3234
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  6c26c22e