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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

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.

When transferring information we may overwrite them. We need to take into
account the case where the destination state already has some information stored.

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.

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

test fuse; update a test on numbe rof clone,

See merge request !631

Update after add a clone in vidjil-format.md

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

Focus on clones in one sample (graph) + More sorting options (list)

Closes #3870 and #4104

See merge request !564

css; add a heigth rule for data table

See merge request !626

Resolve "Le top de fuse n'est pas bon"

Closes #4213

See merge request !623

Link to #4213

Link to #4211

Link to #4213

Tests algo avec docker

Closes #4203

See merge request !612

retrieve_patient_data.py: add original sequence filename in export

See merge request !622

Link to #3867

Files are required to submit new samples

Closes #3907

See merge request !613

Resolve "Documentation docker; dev en local"

Closes #4210

See merge request !619

Link to #4210

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

retrieve_patient_data.py: Script used to export some filtered patient data

See merge request !616

Because of issue in should.
See https://gitlab.bioinfo-diag.fr/vidjil/should/issues/47

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

See for instance vidjil/support/aphp#1

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).

See #3907

But this need to be updated (Javascript side) when switching configuration.

See #3907

doc: Wrong assertion on IMGT productivity computation

See merge request !611

See discussion in !520

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

Merge branch 'dev' of gitlab.inria.fr:vidjil/vidjil into feature-c/4181-des-clones-segedited-avec-de-nouvelles-germline-bloque-l-interface

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

Link to #4104

# Conflicts:
#   doc/.gitlab-ci.yml

doc/.gitlab-ci.yml: revert alltogether only:changes

See merge request !609