Many people are used to have the full JUNCTION, including Cys104 and Phe118/Trp118.
We thus output both 'cdr3' and 'junction' fields in the json output.

We compute CDR3startJfull directly from JUNCTIONend.

This solves the problem identified in 0aae0cf8.

Will be used to test CDR3/JUNCTION detection.

All full codons aligned with the J germline gene are translated according to this frame.

Finally Vidjil learns the genetic code.

This was realized after prototyping and tests by @flothoni.
As in IMGT/JunctionAnalysis, the detection relies on the positions of Cys104 and Phe118/Trp118.
The detection is here in O(n), taking advantage of the already aligned V and J segments.

The current implementation will not give a precise positions when there are insertions or deletions
between Cys104 and the end of the V segment  (or between the start of J segment and Phe118/Trp118).
This could be improved by backtracking the DP matrix.

There are currently no gapped J sequences distributed by IMGT.
We create these sequences aligned on the Phe118/Trp118.

The Sequence structure has now an additional field.