Allowed pipeline (bias and train) to use defined +/- shifts

[PauBadiaM]

Current version (1.0.1) forces the pipeline (both bias and regular training) to always compute auto-shift detection.
Users might want to skip this step as in some corner cases the detection might fail even when there is no real shift. In my case for example it correctly finds a shift of +0/-0 in two of the three example motifs used, and in one it finds +1/-0, resulting in an error.
I've made bias and train correctly accept the parameters --plus-shift and --minus-shift which will be passed down to reads_to_bigwig.py