enhance mpileup performance when -B is given

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.