Feature c/3325 display codons

Closes #3325

See merge request !296

Close #3325.

See #3325.
Could be improved, there are string manipulations here.

See #3485. Same technique than in 8af03769.

See #3325.

(could be later bikesheded)

Resolve "Extraire/tester isProductive/referencePhase dans clone.js"

Closes #3483

See merge request !295

This is a bit tricky, we should warn coders properly.
And we test that this is actually the case.

See c3bbaf4c

See #3483

Feature c/2056 display synonymous mutations

Closes #2056

See merge request !232

See !232 (comment 121298).

Mikaël Salson authored Jul 05, 2018 and Mathieu Giraud committed Sep 26, 2018

As get_codons may return codons with gaps inside, testing for the codon length is not enough
we must first clean the codons by removing the common gaps.
However the codons must not be cleaned to early so that positions are properly counted.

See #2056

Mikaël Salson authored Jul 05, 2018 and Mathieu Giraud committed Sep 26, 2018

Make sure they are handled correctly

Mikaël Salson authored Jul 05, 2018 and Mathieu Giraud committed Sep 26, 2018

Otherwise it induces unvoluntary frameshifts.  Therefore the total number of
characters returned in both lists must be equal and must also be equal to the
number of characters in the original sequences.

See #2056

Mikaël Salson authored Jul 04, 2018 and Mathieu Giraud committed Sep 26, 2018

A whole border is just a test. To be modified.

See #2056

Mikaël Salson authored Jul 04, 2018 and Mathieu Giraud committed Sep 26, 2018

Now spanify_mutation just do some display and doesn't
compute anything (basic) anymore.

We use get_mutations to be able to know where the mutations are.

Fix #2056

Mikaël Salson authored Jul 04, 2018 and Mathieu Giraud committed Sep 26, 2018

Those two functions are useful to detect synonymous mutations.
We also have fallbacks in case we don't want to split the
sequence in codons.

See #2056

Display CDR3 in production

Closes #3330

See merge request !294

Merge branch 'doc/3175-documenter-le-processus-de-a-a-z-pour-deployer-sur-un-serveur-sous-docker' into 'dev'

Improve Docker and server documentation (server.org/md)

See merge request !285

Mikaël Salson authored Sep 26, 2018 and Mathieu Giraud committed Sep 26, 2018

Replays 2a263ddf.

Ryan Herbert authored Sep 26, 2018 and Mathieu Giraud committed Sep 26, 2018

For deploying images to a server that does not have access to internet
or hub.docker.com

Replays 9a6421a9.