refactoring of the ragout_coords2camsa_points script:
refactoring of the ragout_coords2camsa_points script:

* now a pipeline support the output of multiple genomes at the same time (previously only a single "reference" genome assembly was output)
* removed the silent_block_skip flag and corresponding check in the program. Can be added back if enough interest would be shown
* fixed the description text
* made [no-] option possible for duplications / indels filtration
* made duplication filtration enabled by default
* made indel filtration disabled by default

compbiol/CAMSA,compbiol/CAMSA,compbiol/CAMSA,compbiol/CAMSA