ok here's what i am doing.
I am using 8052 derivative micro controller.
I am driving the stepper motor by the use of the sequence 12,6,3,9.The pin 3.2 has been made an input pin for receving the reflection from the reflective tapes.once the signal is receieved i send the step data at this point to the pc.Then the no. of transitions are checked it is 2 for one target and 6 for the other target.i will have to do similar thing for the anticlockwise direction and at no point the stepper motor stop stop rotating and also it shld keep counting the no. of steps.