This commit is focus on the performance of mpileup. By default, mpileup reads the whole reference chromosome regardless whether option -B is given. This means every mpileup command would read about 200MB of ref for a run. However, when option -B is given to mpielup, which indicates no need to realignment, it is not necessary to read the whole ref chr. My modification makes mpileup only read the ref bases of given region from ref file. And this results in about 100-times faster for a single process working on one region when option -B is given. Feel free to contact me: Kangbo Mo <kmo@student.unimelb.edu.au>, the university of Melbourne, Australia