ENCODE Project Release - Apr 28th, 2017

Chiefly includes changes to BAM processing via Picard and how UMI samples are processed. Also consolidates single and paired end processing.

Release for the DCC ENCODE Project

filter_reads: Discard soft-clipped alignments

These alignments can have a negative effect on footprint calling, as
soft-clipping may move the called cut location slightly, so we discard
them. In testing, this filtered out only 0.01% of reads that would
otherwise pass quality controls.

Python2

This is the last commit for the Python2 version of the pipeline.