- 24 Mar, 2020 6 commits
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Mikaël Salson authored
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Mikaël Salson authored
In Aho-Corasick automaton we know the affect once we traversed the sequence. However for backward-compatibility reasons with k-mer indexes we need to move those affects so that they correspond to the start of the sequence. However for an Unknown Affect, it is hard to tell where we should put it as the affect is unknown. If we see that we will overwrite an existing affect, we try another position. This solves some cases in #4225
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Mikaël Salson authored
This is an arbitrary choice but when building the final automaton we may add information from previous states in the current state (so information from shorter seeds). We prefer to keep the longest one.
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Mikaël Salson authored
When transferring information we may overwrite them. We need to take into account the case where the destination state already has some information stored.
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Mikaël Salson authored
That wasn't a bug (as a null info has a 0-length). But I prefer preventing an overwriting of an actual result with an empty result.
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Mikaël Salson authored
When finalising the automaton we can define new final states that actually are a “copy” of another final state. In such a case we also need to copy the Info that are in that former final state. Added a test to check that. The test uses a IGKJ sequence: thus all the kmers should be +k or (potentially undetermined). Fix #4225
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- 19 Mar, 2020 2 commits
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Mathieu Giraud authored
test fuse; update a test on numbe rof clone, See merge request !631
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flothoni authored
Update after add a clone in vidjil-format.md
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- 18 Mar, 2020 2 commits
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Mikaël Salson authored
Merge branch 'feature-c/4211-gethtmlinfo-adapter-pour-clones-de-distributions-representative-sequence' into 'dev' Resolve "getHTMLinfo : adapter pour clones de distributions, representative sequence" Closes #4211 See merge request !625
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Mathieu Giraud authored
Focus on clones in one sample (graph) + More sorting options (list) Closes #3870 and #4104 See merge request !564
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- 17 Mar, 2020 1 commit
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Mathieu Giraud authored
css; add a heigth rule for data table See merge request !626
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- 16 Mar, 2020 1 commit
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Mathieu Giraud authored
Resolve "Le top de fuse n'est pas bon" Closes #4213 See merge request !623
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- 12 Mar, 2020 1 commit
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- 11 Mar, 2020 1 commit
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- 10 Mar, 2020 2 commits
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Thonier Florian authored
Link to #4213
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Mathieu Giraud authored
Tests algo avec docker Closes #4203 See merge request !612
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- 09 Mar, 2020 6 commits
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Mikaël Salson authored
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Mikaël Salson authored
retrieve_patient_data.py: add original sequence filename in export See merge request !622
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Mikaël Salson authored
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Mathieu Giraud authored
Files are required to submit new samples Closes #3907 See merge request !613
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Mathieu Giraud authored
Resolve "Documentation docker; dev en local" Closes #4210 See merge request !619
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- 06 Mar, 2020 1 commit
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- 04 Mar, 2020 1 commit
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Mikaël Salson authored
As the parameter is a reference, it may cause some problems if it is optimized out at some point (or something else, I won't pretend mastering compiler optimizations). Instead we pass a variable in parameter and instead of an empty string we give a string whose length is the same as the affectation string. This was causing issues with clang-4.0 and clang-6.0. See !612
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- 03 Mar, 2020 5 commits
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Mikaël Salson authored
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Mikaël Salson authored
retrieve_patient_data.py: Script used to export some filtered patient data See merge request !616
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Mikaël Salson authored
Because of issue in should. See https://gitlab.bioinfo-diag.fr/vidjil/should/issues/47
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Mikaël Salson authored
We have a docker image for gcc, fine (apart from apt-get that doesn't work with gcc:4.8 image). For clang we don't have a ready to use image so we need to install it by hand. Fix #4203
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Mikaël Salson authored
See for instance vidjil/support/aphp#1
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- 02 Mar, 2020 3 commits
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Mikaël Salson authored
We don't want to allow launching an analysis while one of the file is still uploading (which is the case with a pre-process with two files). Thus to be able to launch a process we expect either to have no pre-process or to have one but already finished. We allow to launch a process even if the pre-process failed to prevent the user from being blocked (he/she can still analyse the R1 file).
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Mikaël Salson authored
See #3907
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Mikaël Salson authored
But this need to be updated (Javascript side) when switching configuration. See #3907
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- 26 Feb, 2020 2 commits
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Mikaël Salson authored
doc: Wrong assertion on IMGT productivity computation See merge request !611
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Mikaël Salson authored
See discussion in !520
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- 25 Feb, 2020 1 commit
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Mathieu Giraud authored
Merge branch 'feature-c/4181-des-clones-segedited-avec-de-nouvelles-germline-bloque-l-interface' into 'dev' Resolve "Des clones segedited avec de nouvelles germline bloque l'interface" Closes #4181 See merge request !602
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- 24 Feb, 2020 3 commits
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flothoni authored
Merge branch 'dev' of gitlab.inria.fr:vidjil/vidjil into feature-c/4181-des-clones-segedited-avec-de-nouvelles-germline-bloque-l-interface
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flothoni authored
Merge branch 'feature-c/4104-n-afficher-dans-le-graph-que-les-clones-du-sample-courant' of gitlab.inria.fr:vidjil/vidjil into feature-c/4104-n-afficher-dans-le-graph-que-les-clones-du-sample-courant
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- 21 Feb, 2020 2 commits
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Thonier Florian authored
# Conflicts: # doc/.gitlab-ci.yml
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Mathieu Giraud authored
doc/.gitlab-ci.yml: revert alltogether only:changes See merge request !609
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