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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 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.

This further cleans the code and allows to output D1/D2 boxes as well.

One day, we may change '5del' and '3del' fields, their naming is not so consistent.

This was not used and not symmetrical.

Bug detected thanks to a full Valgrind.

Discussion with @mikael-s and @flothoni.

We now run another dynamic programming once the overlap was handled -- only
on the best reference sequence -- to check the actual e-value of the D segment.

We do not want to detect twice the same D gene.
Note that we do not currently forbid alleles of a same gene.

Discussion between @flothoni, @mikael-s, and @magiraud.

When a D has already been detected, we do not want to detect anything inside this D.
Before this commit, spurious D detections could happen in the EXTEND_D_ZONE.

Discussion between @flothoni, @mikael-s, and @magiraud.

When a D segment has been detected, we now try to detect an additional D between V/D or between D/J,
possibly detecting VDDJ (or even some VDDDJ) recombinations.

Note that this detection is not optimal. A chaining algorithm would be preferable here.
Moreover, statistics should be refined, as now the only filter is done before check_and_remove_overlap.

We need to store sequence_or_rc in the Segmenter.