R/calculate_intensity.R: Added prepareBamFile to plotFeatures

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
Removed R/annotation.R and R/annotation_WCE.R that were deprecated

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
R/calculate_intensity.R: modified the extractFeatures funtion in plotFeatures so it now returns a list of data.frame with group names as the name of each element in the list

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
R/calculate_intensity.R: debugged parseBamFiles function

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
R/calculate_intensity.R: Added parallel computing for critical steps

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