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update json output for 2014.10.10 format

Conflicts:
	server/fuse.py

These programs are not used anymore (and mostly do not compile...)

.travis.yml/Makefile: better 'make unit_coveralls' rule to upload to coveralls.io, runs tests only once

Note that only the results of unit tests are uploaded, and not the results of should_get tests.

Mikaël Salson authored Oct 03, 2014 and Vidjil Team committed Oct 10, 2014

Placing options at the end allows to override default options.
On the contrary if options are placed at the beginning we have no way
to modify default behaviour.

The default command is now '-c clones'. The 'out/clones.vdj.fa' now contains:
 - clones with their representative (or even with fine segmentation) (controled with '-y'/'-z' options)
 - but also all other clones (as soon as they pass the '-r'/'-%' thresholds)

Vidjil can now be easily used as 'filter' to shrink a read dataset to this 'out/clones.vdj.fa' file.

The '-z' option is clearer now: maximal number of clones with a FineSegmenation

Detailed help is now in doc/algo.org.

(and we should decide whether .data should be output on '-c windows')

Runs windowsStorage->keepInterestingWindows even in the case of CMD_WINDOWS.

clones become clusters ( now stored as array instead of object)
split move to clone.js
use reads object from data file
auto detect germline
and more ...

Otherwise cobertura is not able to display the corresponding source files, it is unable to find them.