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This allows to remove any representative computation or fine segmenation with '-y 0' or '-z 0'.
Moreover, '-A' debug option now properly sets these two values.

Moreover, the argument 's' was not used

(Paris)

core/kmeraffect.{h,cpp}: remove 'kmer' argument to Kmer, KmerAffect and KmerStringAffect constructors

This argument was not used.
(Les Aubrais)

C++ polymorphism is awesome.
(Meung-sur-Loire)

AFFECT_AMBIGUOUS character is now '\1', in order to have a different value than AFFECT_UNKNOWN ('\0').

A IKmerStore maintains a list of labels that are used in the index.
This a step towards the removal of KmerStringAffect.

We can now create a Germline object without any index.

@duez worked a lot to implement the new .data format, described in doc/format-analysis.org
Behind, the access to the objects in the .js code have been streamlined.

Merge branch 'rework_data' of git+ssh://scm.gforge.inria.fr//gitroot//vidjil/vidjil into rework_data

- load cluster from data file
- detect missing windows

If there a '-g' option, we do not have to open default '-V'/'-D'/'-J' files.

This option is now undocumented, its use will change in a future release.

Reverts partially commit 9e7678b9.

This reverts commit 88044a01.
We do not want to chdir, the user may legitimately want to run vidjil from any directory.