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This is a very rough method, but it already gives some hints of the germline used.

TODO: the list should not be hard-coded.

We want to have a command that browse a set of reads and predict the germlines used.
(Perhaps, in the future, some results of this scenario could be used as an input of the segment scenario ?)

No reason to have separate (hard-coded) constants for delta_max. Now we just have one.

Side effect: no 'clones.vdj.fa' and 'seq/*' files are produced.
The 'vidjil.data' file is still produced.

This is the main Vidjil output (as a fasta file): representatives of the clones, ready to be processed by other tools.
Until now, this output was on stdout and (partially) in out/seq/*

Vidjil should not be used to segment reads.

It could be nicer with python argparse :)

The threshold is a percentage, not a ratio.

Now that a representative is almost always found, it is better to limit short
examples to a small number of clones.

This enables to have representatives even when setting -R to very small values.
As a side effect, option -A should return representatives for every clone (-R is 1).

We have already MAX_CLONES limiting the default output.
In a typical MRD setup, the previous value of 0.1 was not meaningful.

This is really a debug option, because 'segmented.vdj.fa' is not a proper fasta file anymore.

We have to set k in a way that there is very few common k-mers between the V and J germline.
This depends on the system.

This is again a very bad idea. Only for short datasets.

It is a very bad idea, we should not let the user use that.

	* 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

	* Better heuristic, segments more reads (core/segment.cpp)
	* Better and faster selection of representative read (vidjil.cpp, core/read_chooser.cpp)
	* Better display of reason of non-segmenting reads
	* New normalization against a standard (-Z) (core/labels.cpp)
	* New experimental lazy_msa multiple aligner
	* New .json output
	* New unit tests
	* Bugs closed

	* New selection of representative read (core/read_chooser.cpp)
	* Faster spaced seed computation (core/tools.cpp)
	* New unit tests
	* Bugs closed

	* First public release