Bug: With a reasonnably large -r option (such as 2000), no representative is found.
This is because min_cover is larger than max_auditioned.

If -w is below the seed weight (hence the junction size), strange things may happen,
as for example a clone without representative.

Closes bug created by 59a1bcf6.

59a1bcf6 added some spurious output that breaks CGI.
Thanks to @mikael-s for pointing that out.

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

work with custom germline from vidjil.data

Kmer is used inside a IKmerStore<Kmer>, its constructor should thus accept
the (label, stand) parameters.

We had too few gcc warnings.

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

When exception is thrown from constructor, the destructor is not called

operator<< for Sequence already outputs one. No need to add another one

When the Sequence contains quality information, it outputs a FASTQ rather than a FASTA.
This may be useful is one day we output FASTQ information (we never know, isn't it?)

An exception can be caught while an exit can't. Thus we can test it.
Moreover some consistency is introduced: Fasta and OnlineFasta will
throw a invalid_argument in case of problem with the input file
(either in opening or parsing it).

Thanks to previous commit we can know catch those mistakes