GitLab

The recommended option is now '-g germline/homo-sapiens.g'.

Defers to core/germline.cpp the possible failure in opening the file.
Completes the previous commit to fix #2134.

We now recognize only exact matches. See #2134.

See #1233

Germlines are now on the www for consistency.

When using custome germlines the
this.m.germlineList.list[system]['recombinations'] was not defined and generated an error that prevented the loading of the germlines.

Fix vidjil/vdj#334

Completes #1987 and #2132.

Fixes #2132.

See #2132.

HTML entities end with a ;

Feature/species

Closes #1987

See merge request !4

The .g files will be now referred as "germline/homo-sapiens.g", instead of
the longer and redundant "germline/homo-sapiens.germline".
This will improve readability at several places, and is
far more meaningful than the previous "germline/germlines.data".

Fixes #1987.

See #1987.

See #1987.

See #1987.

As the pre-process name can be quite long, we first show the status
otherwise it could be hidden.

We must show that we can click on the preprocess to have further informations.

Refining productivity computation. In-frames stop codons will be detected.
However if a sequence goes until the stop codon, it is normal to have an
in-frame stop codon. But our sequence (usually?) don't go after the J gene.

See #1824

When JUNCTIONstart or JUNCTIONend equaled 0, their values
were not modified. But the CDR3/Junction are output in the JSON
as long as the values of the variables are >= 0 (maybe this
should also have been modified). Therefore we could have weird results
with JUNCTIONstart=0 and JUNCTIONend=40.

Tests added.