Automatic filter of ENCODE blacklist

[marziacremona]

I think it would be great to add an automatic filtering of known artifacts, such as the ones present in ENCODE blacklists.

Functional genomics experiments based on next-gen sequencing (e.g. ChIP-seq, MNase-seq, DNase-seq, FAIRE-seq) that measure biochemical activity of various elements in the genome often produce artifact signal in certain regions of the genome. It is important to keep track of and filter artifact regions that tend to show artificially high signal (excessive unstructured anomalous reads mapping).

MSPC could have an additional argument (say, --blacklist ) so that the user can decide not to filter anything (--blacklist none), or to filter out every peak overlapping the ENCODE blacklist corresponding to the genome of reference (--blacklist hg19, --blacklist GRCh38 and so on. The complete list of available blacklists can be found here).