pass partial numpy array to quick_pileup since that will mess up with pointers.
…kstemp(). Close file descriptors for temporary files after creating them with mkstemp() to avoid leaking file descriptors and running out of file descriptors or hitting the limit or the number of file descriptors that you are allowed to open, which can happen when you have a lot of chromosomes or scaffolds in your input files.
-O3 for compatibility.
2) pure C code files have first letter as 'c', such as cPosValCalculation.c/h/pxd; 3) subcommand files have been renamed as xxx_cmd.py such as callpeak_cmd.py. Optimization: now use pointer type to travel through the numpy arrays. Speed up to use about 1/2 time for pileup/p-value calculation and peak calling.
with flag 0x100 (secondary alignment) or with flag 0x800 (supplementary alignment).
sort right ends of BAMPE before passing values to it.
to minus strand. Note, this issue doesn't affect BAMPE module.
data, that will cause incorrect filtering of duplicated pairs and mess up coordinations.
previous change is unneccessary so I reverted it -- but still fixed a typo.