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Merge branch 'feature-c/3488-decalage-de-la-sequence-du-cdr3-et-de-la-jonction-dans-la-fenetre-info' into 'dev'

Resolve "Décalage de la séquence du CDR3 et de la jonction dans la fenêtre info"

Closes #3488

See merge request !471

Resolve "Avoir des germline de poulet"

Closes #3910

See merge request !470

link to #3910

Thonier Florian authored May 23, 2019 and Mathieu Giraud committed May 23, 2019

link to #3910

Thonier Florian authored May 23, 2019 and Mathieu Giraud committed May 23, 2019

Link to #3910

Thonier Florian authored May 23, 2019 and Mathieu Giraud committed May 23, 2019

link to #3910

doc/vidjil-algo.md: productivity discordance + server

See merge request !475

See #2526.

link to #3488

Release 2019.05

See merge request !473

see #3914

see #3914

core/representative.h, vidjil.cpp: RandomScore by default

See merge request !464

It will depend on the order in which reads are coming when computing
the representative but this order is random. What is important is that
we find a representative of the correct length with the correct sequence
whatever the read name and read positions are.

Mikaël Salson authored May 16, 2019 and Mathieu Giraud committed May 16, 2019

It is hard to predict the result is not totally deterministic
(as is the case with the RandomScorer, which is now by default,
whose results depend on the pseudo-random generator that may
differ depending on the OSes)

See #3866

see #3866

see #3866

link to #3488

link to #3488

link to #3488

link to #3488

Feature a/3206 rename and merge should

Closes #3762

See merge request !467

Optimizations, including  e-value computations, max12

See merge request !468

Mikaël Salson authored Oct 18, 2018 and Mathieu Giraud committed Apr 26, 2019

Computing them for each read is time consuming.
But many of the are common (there are few different
index loads and the read length is small)

Mikaël Salson authored Oct 18, 2018 and Mathieu Giraud committed Apr 26, 2019

This prevents from recomputing it each time

Mikaël Salson authored Oct 19, 2018 and Mathieu Giraud committed Apr 26, 2019

This is needed now that we use an unordered_map with a KmerAffect (see
previous commit) as explained here:
https://stackoverflow.com/questions/17016175/c-unordered-map-using-a-custom-class-type-as-the-key

Mikaël Salson authored Oct 18, 2018 and Mathieu Giraud committed Apr 26, 2019

max12() actually didn't require a CountKmerAffectAnalyser.
The CountKmerAffectAnalyser builds a data structure to improve
KmerAffect counting at any position. But this was not needed for the max12() function

Mikaël Salson authored Oct 18, 2018 and Mathieu Giraud committed Apr 26, 2019

We absolutely don't need to call getDistinctAffectations to destroy the objects

Closes #3762.

see #3762

see #3762

See #3762. We have --extra

see #3206