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Hey, could windows labels (-l) be used for another thing ?

Doc updated accordingly.

This number is set by default to the max_auditioned sequences since we need that many sequences in maximum
(unless we want to see all the sequences).

core/windowExtractor.{cpp,h}, vidjil.cpp: option '-X' takes reads at regular intervals from the file

The first reads (now '-x') are sometimes different from the average reads.

With this debug option, all unsegmented reads of sufficient length will be kept,
with a fake window being their complete sequence.
These reads can then be seen in the browser.

This streamlines the different detailed outputs, requiring a new 'out_affects' attribute.

Now the MultiGermline contains only one germline.
The 'should' tests are still passing, but some unit tests are now broken.

	* 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