fastaToJson.py : repair/update > python script, used to produce germline.js with fasta file from germline folder

work with custom germline from vidjil.data

TODO : change rbx /etc/nginx/sites-available/web2py config file manually

Note that germlines.data is not used now. It will change soon.

Corrects bug introduced by 59a1bcf6.

Dd2 and Dd3 may play interesting roles.

096ab901 unleashes the power of 1a05fe6a and 422964cc.

core/fasta.{h,cpp}: default constructor also takes extract_field and extract_separator, factorize constructors

Even if we start from an empty Fasta, we should remember these values.

The constructor now uses the add() method which, itself, relies on the >> operator which has been overloaded.
Unit tests added for the add() method.

C++ code should prefer cstdlib over stdlib.h

One could use constructor delegation for an even better factorisation but it
is C++11 only.

(Now only the last option of each is really stored and indexed, see 1a05fe6a.)

One may want to use several V (or D, or J) files for a unique germline, for example with TRDV + TRDD(D2).
(Now only the last file is really stored and indexed, but this will change soon.)