annotation.R: keep only autosome and sexual chromosome from mouse

Signed-off-by: CharlesJB <Charles.Joly-Beauparlant@crchul.ulaval.ca>
calculate_intensity.R: Added Rsamtools library command in the correct function

Signed-off-by: CharlesJB <Charles.Joly-Beauparlant@crchul.ulaval.ca>
calculate_intensity.R: Removed useless comment

Signed-off-by: CharlesJB <Charles.Joly-Beauparlant@crchul.ulaval.ca>
calculate_intensity.R: Created a new function (convertReadsToPosVector) to simplify testing

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