R/calculate_intensity.R: Changed the mergeMatrix function to fit with new data structure

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

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
R/calculate_intensity.R: Updated the parseBamFiles documentation

Signed-off-by: Charles Joly Beauparlant <Charles.Joly-Beauparlant@crchul.ulaval.ca>
R/calculate_intensity.R: relaxed the params validation in extractReadsInRegions

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