added ENCODE ENCFF159KBI.gtf annotations (use --species GRCh38_v29e)

update installation in

from setup.py to pip install

add myself to help message

update readme.md

updated readsToWiggle to count regions deleted in a read as a mapped …

…location.

allowed soft-clipping in mapped read cigar string

first commit of parse clip analysis

fixed bug when superlocal flag isn't enabled

significantly spead up count total reads function

putting stable version on pypi