Resolve "Implement null for normalized_reads"

Closes #3943

See merge request !485

If no read was segmented we may encounter an error in that case

Link to #3943

Link to #3943

IgReC replaces spaces with underscores

See merge request !496

Doing the opposite is not really satisfactory but, on the other hand, in such a case
we know the read name should contain spaces (because of the should-vdj format).

should-vdj-to-tap.py: --ignore_D option not working due to typo

Closes #3952

See merge request !494

Update repseq_vdj for mixcr

See merge request !495

doc/dev-{algo,client,server}.md: converted and split from dev.org

See merge request !491

Fixed and added some tests

Fix #3952

Feature t/3950 igrec parser

Closes #3950

See merge request !493

These *.py files should be moved to /tools

see #3950

Thanks to https://stackoverflow.com/a/8849771

should-vdj-to-tap.py: Wildcard must be at both places

See merge request !490

see #3932

pandoc --wrap=preserve --atx-headers -s -r org doc/dev.org -t gfm > doc/dev.md

Follows dbd61c55. Contrarily to the else case where the joker can
indifferently be placed before or after a term, it is not
the same when the term is a paranthesis expression.
Thus we need a joker both before and after to make sure we don't miss a case.

Alternative regex bug

Closes #3949

See merge request !489

We must allow anything *before* the alternative, not after (as in the else case)

Fix #3949

Link to #3943

Link to #3943

link to #3943

Docker : modify conf without rebuilding

Closes #3941

See merge request !486

This allows to modify the configurations without rebuilding the image

See #3941

link to #3943

This field should show a null value instead of 0 if not present
link to #3943

js/app.js: Load extra scripts depending on the administrator

Closes #3929

See merge request !481

Fix #3929

V-QUEST API change

Closes #3913

See merge request !472

Otherwise the ntseq is not given in the CSV file
See #3913

IMGT/V-QUEST now requires to have the common name of the species, not the latin one.
Thus we need a function to do the conversion.

See #3913

Those parameters are not useful anymore. They were used before #3913.

Some parameters were slightly different from what was expected.

See #3913