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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

link to #3910

Link to #3910

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.

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

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)

This prevents from recomputing it each time

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

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

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