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Since the 2015.07 release, many changes improved the V(D)J designation (core/segment.cpp,
in particular c5c781ec, 77af56b8, 185c3bd9, 60a15629), and this is now better tested
(.should-vdj.fa tests, with new curated sequences and an improved test mechanism).

This was a bug hidden since the first release of Vidjil.
It is now corrected, and the test added in 002adbd2 is now passing.

Our current Jenkins builds are broken on FreeBSD and Fedora.

This test was not passing 10 days ago, before the work on close V-J xxx

When entering mnaually curated sequences, this is faster than launching
a full 'make shouldlocus_and_vdj' (which further recompiles everything).

Generate all possible recombinations and add the possibility to have
random number of insertions and deletions at the junctions (following a
Gaussian law) and add the possiblity to have mutation in the sequences.

We don't want to re-generate the recombinations each time we launch the
process. It would certainly be convenient to have the recombinations
generated when the files do not exist. But I didn't succeed to specify a
joker in the dependance list.

Random recombinations with random deletions and insertions at the
junction and mismatches in the sequence (1%)

add 6 errors :
 - 2 double DD
 - 3 ambigous
 - 1 real error (the TRB error)

Now the locus is handled by should-vdj-to-tap.py,
but these sequences are too short to be properly segmented.

Handle '[xxx]' locus information.

Completes a36f0231.

The actual command line is stored in the .log file.