FIRST-MAPPING +

- First mapping pipeline script moved into the main script, ChimPipe.sh. Done to make easier to add
  new input arguments to the pipeline and to make it more compact.
- Replaced -e (exist) by -s (non zero value) in every check-point to check if each step run properly.
  Done since in some cases an error in a step can produce an empty file, not been detected in the check-point.
- Added autorship information and copyright to all the scripts.
- Replaced NONE by UNSTRANDED to specify that the library protocol is non strand specific. More intuitive.
MAKEFILE. Modified not to report no necessary information
CLEAN UP.

- Added a clean up step to delete intermediate files. By default is enabled,
  to disable it the user need to use the --no-cleanup flag.
- I still need to improve the way ChimPipe handle intermediate files.
It has to generate two additional folders to store first mapping and
unmapped files.
CLEAN UP. Modified Chimpipes script in order not to remove intermediate files
Merge branch 'master' of github.com:ChimPipe-pipeline/ChimPipe