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Closes #3837, #3839.

See #3839.

See #3839

Opens #3839.

See #3837.

see #3837.

There is now some hack to get a json, it could be improved.
See #3837.

https://github.com/CLIUtils/CLI11/commit/2ae5598d9570a

Opens #3837.

Resolve "Lien vers le gitlab dans le menu help"

Closes #3820

See merge request !443

Feature at/update-should

See merge request !455

link to #3820

Following should#43, we cannot anymore use 'B' here.

Feature a/fix min cover representative

See merge request !448

Correct upload menu

Closes #3805

See merge request !452

In such a case we are clicking on the clone.
If the mouse is not on hovering the clone there is no reason for its name
to appear in the infoline. And the hovering is already tested.

Resolve "Clone en R2 perdu en R1+R2 (+R2)"

Closes #3879 and #3833

See merge request !453

Fix #3833

This requires to reorder elements in the HTML.
Thus they are now in a 'natural' order (ie. in the same order
as displayed). We use flex to make them appear contiguously the
ones after the other. Thus we don't need anymore float: right
apart from the #menu_right_part that was added.

Fix #3805

Following the fix on min_cover_representative.
The representative on small datasets may be longer.

Thus we need to update those. There also some side effects:
- V genes are less ambiguous (hence less warnings)
- Consensus is longer (hence less warnings too)
- Positions changes of end of V, J, CDR3…

Checks previous commit

min_cover_representative should be seen as a strict minimum on the number of reads
that can support a representative sequence.
The purpose is to avoid a too low ABSOLUTE number of reads to define a representative.
For the relative number, it is ratio_representative's role.

Before, if we specified -r 100 we needed to have 100 corresponding
k-mers which is very strict when a clone has just slightly more than
100 reads

Update CLI11

See merge request !445

Update tutorial

See merge request !447