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Bug detected thanks to a full Valgrind.

This is the only test checking the raw json output.

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.

Launching vidjil with '-d' now enables to detect some recombinations with several D.
The method is not optimal (see 41d08568), but should anyway recognize most VDDJ recombinations.
This was developed and discussed by @flothoni, @mikael-s, and @magiraud.

These mixed TRA/TRD VDDJ sequences should be further studied.

Back in april 2013, when @mikael-s designed this simulated sequence,
he premonitorily included a borderline case of a VDDJ recombination.
There are here 6-7 nucleotides exactly conserved for the second D.

The second D has 20 nucleotides that are exactly conserved.

We are confident enough to use '-d' on our should-vdj tests.

VDDJ segmentation is still somewhat experimental.
Moreover, it will have someday some consequence on the json output, that are not always desirable.
We prefer thus to keep this optional.

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.

Due to germline update (cf. 526beeb8)

With all locus analyzed, the -z 100 option gives a better description of the lympohcyte population.
Note that the FineSegmenter is more than two times faster than in the 2015.10 release.

Changes in IGHV:
1. Three new genes (IGHV3-23D*02, IGHV3-30-5*01 and
   IGHV3-30-5*02). Welcome on board.
2. One gene deleted (IGHV4-28*05). You left us too early,
   we had good time together…
3. One gene (IGHV3-30-3*01) increased by two nucleotides. Congratulations!

Functionality changes in two genes in IGLV (IGLV10-54*03) and TRAV
(TRAV11*01).

We don't know yet the meaning of this letter. Depending on this answer
we may add some processing

For consistency reason we need to specify what rule creates the data files.

We need to store sequence_or_rc in the Segmenter.