R/calculate_intensity.R: Changed the data structure returned by the prepareGroups function.

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
R/calculate_intensity.R: parseBam now produce the output in the correct format

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
R/calculate_intensity.R: Changed the parseBam function to make it more generic
R/calculate_intensity.R: Added documentation to parseBamFiles and parseBamFile functions

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
R/calculate_intensity.R: corrected a bug introduced in f2957536639fef00ea3648a1d79b649641420215

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>