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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.

A collection of sequences on all locus, gathered from other files.

This somewhat restores a test removed in 0ae4e1e6.

tests/should-vdj-to-tap.py: option '-D', ignore gene/allele names for D genes in .should-vdj patterns

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.