A cartridge assembly that comprises a housing, including a flow cell chamber to receive a flow cell, and a well plate having liquid wells to receive desired amounts of liquids. The well plate includes a valve station, a pump station and a fluidics analysis station, and channels associated therewith. A pump assembly to manage fluid flow through the channels between the pump station and the fluidics analysis station. A rotary valve assembly that includes a rotor shaft and rotor valve positioned to rotate about a rotational axis and to selectively couple the wells to the pump station. The rotor shaft includes a dual spline configuration at the distal end thereof. The dual spline configuration has first and second sets of splines. The first set of splines forms a drive interface and the second set of splines forms a position encoding interface.