man/plotFeatures.Rd: Updated the documentation to be up-to-date with the main data structure

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
man/applyOnGroups.Rd: Added a manual

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
R/calculate_intensity.R: deprecated the applyOnBamFiles function

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
R/calculate_intensity.R: parseBamFiles now keep the reads densities before it removes the control in element bamFilesWithCTRL in group data structure

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

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
R/calculate_intensity.R: major changes in the removeControlsFromGroups that was bugged. The merge control is no longer working. Will be fixed in a future commit

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
R/calculate_intensity.R: corrected a bug that caused all the read for a feature to be ignored in the convertReadsToDensity function

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
R/calculate_intensity.R: Added some TODOs in binBootstrap function

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
R/calculate_intensity.R: changed the alpha value in plot.graphic function to make ribbons more visibles

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
Merge branch 'master' of https://github.com/adeschen/MetaFeatures
DESCRIPTION:correct A. Droit email. plotFeatures.Rd:adapt specie argument to new standard format (human, mouse).