Feat/macs3/python style cython (1st)

[taoliu]

A first PR for rewriting cython code in pure python mode. Other changes:

* Features added

1) We extensively rewrote the `pyx` codes into `py` codes. In
another words, we now apply the 'pure python style' with PEP-484
type annotations to our previous Cython style codes. So that, the
source codes can be more compatible to Python programming tools
such as `flake8`. During rewritting, we cleaned the source codes
even more, and removed unnecessary dependencies during
compilation.

* Bug fixed

1) Fix issues in big-endian system in `Parser.py` codes. Enable
big-endian support in `BAM.py` codes for accessig certain
alignment records that overlap with givin genomic
coordinates using BAM/BAI files.

* Doc

1) Explanation on the filtering criteria on SAM/BAM/BAMPE files.