MACS v2.2.5

Python3 speed up

Features added

1. Github code only and Not included in MACS2 PyPI release New
   testing data for performance test. An subsampled ENCODE2 CTCF
   ChIP-seq dataset, including 5million ChIP reads and 5 million
   control reads, has been included in the test folder for testing
   CPU and memory usage (i.e. 5M test). Several related scripts ,
   including prockreport for output cpu memory usage, pyprofile
   and pyprofile_stat for debuging and profiling MACS2 codes, have
   been included.

2. Speed up pvalue-qvalue checkup (pqtable checkup) #335 #338.
   The old hashtable.pyx implementation copied from Pandas (very old
   version) doesn't work well in Python3+Cython. It slows down the
   pqtable checkup using the identical Cython codes as in
   v2.1.4. While running 5M test, the __getitem__ function in the
   hashtable.pyx took 3.5s with 37,382,037 calls in MACS2 v2.1.4, but
   148.6s with the same number of calls in MACS2 v2.2.4. As a
   consequence, the standard python dictionary implementation has
   replaced hashtable.pyx for pqtable checkup. Now MACS2 runs a bit
   faster than py2 version, but uses a bit more memory. In general,
   v2.2.5 can finish 5M reads test in 20% less time than MACS2
   v2.1.4, but use 15% more memory.

Bug fixed

1. More Python3 related fixes, e.g. the return value of keys from
   py3 dict. #333 #337

Note: The Github release package grows bigger since more testing
data have been included.