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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.

Previously, we have at many places things like "int *del_DD_left, int *DD_start, int *best_DD, int *DD_end, int *del_DD_right".
This was not so clean and error-prone. Now all these parameters are stored into a ‘AlignBox’ object.
This will lead to further simplifications of the code, better code maintenance, and allow some extensions.

We would like to call that on other places than between the V and the J.

This test is renamed 'testOverlap'.

We factorize some computations (seq_left, seq_right, seg_N).
This is the last commit of the day sponsored by the CERNA.

This enables in particular the analysis of +Vk/-Vk recombinations.
This commit is again sponsored by the CERNA.

As the KmerSegmenter is used in the FineSegmenter, a meaningful seed has to be choosen here.