To make output better organized

[fanggang]

Better to organize output in a three-layer hierarchy:

Layer 1 named by genome reference

Layer 2 named by motif_pos_SMsn_x or motif_pos_SMp_x where x is additional parameter information to differentiate among runs with different settings.

Layer 3 named by contig names and contig size. Remove '|' from HGAP output