bugfixed indent problem in PAQR/scripts/deNovo-used-sites-and-usage-inference.single_distal_included.py

updated typos and git clone address in README;changed r-essentials for r-base3.3.2 in requirements_py3.txt

fixed small bug in create-coverage script: now, it is ensured that always a minimal coverage array with +1 at the first chromosome position is returned for each exon. Any chrom of the exon bed file should be in the pkl file

Updated KAPAC.R for detault values and removed file writing for k-mers with no counts (after filtering).