Some allocations were not properly free-ed.
Spotted by Valgrind.

See #3031

We now have an abstract class to deal with biological sequence files. This
will allow to more easily manage different file types.

This commit only reorganizes the code so that we will be able to add a BAM
reader easily. Functionnally the code should be equivalent to its previous
version.

Some functions that were not used have been removed.

The operator>> has been removed as it was only used in unit testing. This
operator is not convenient as having the filename may be useful to reopen the
file or to know its extension, to guess the filetype.

See #2016

A temporary file is created in CGI mode to store the FASTA on which we compute
the similarity matrix

Even if the CGI fails for an unknown reason we still have the content type, which should
satisty the web server

I thought mkstemp would do that by itself. While it may seem not very satistfactory to hardcode
the path, /tmp is POSIX.

Closes bug created by 59a1bcf6.

C++ code should prefer cstdlib over stdlib.h

No need to specify a hard-coded value for the number of sequences.
Fasta object knows how many sequences there are.

	* browser/ : D3.js/javascript-based V(D)J recombination browser
	* server/fuse.py : script to combine data from several points

	* Refactored main vidjil.cpp (core/windows.cpp, core/windowExtractor.cpp)
	* Removed unused html output
	* Better json output (core/json.cpp)
	* Updated main stdout, with representative sequence for each clone
	* Updated parameters for FineSegmenter (delta_max) and dynprog (substition cost)
	* Bugs closed