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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.

The Sequence structure has now an additional field.

The gapped sequences should be all aligned. One may want to remember a specific position.

(n * n) may be too large for an int when (n) is large.

The problem detected in 0eccf628 is now corrected.

Fixes a bug introduced in 90b8bb4e

The germline package has now a correct germline.js.

There are minor differences in the IMGT header of some sequences.
There is still something happening on IGHD_upstream.