filtering by CTCF (or other featuers)

[gfudenberg]

for filtering by nearby features, current idea is to use 2x maximum padding as default.
Q: should this also be exposed as an extra number that can be provided in CLI

another Q is if all filtering functions can be refactored to
filter_by_table(sites, file_name, schema, exlude_bp, cols1, cols2, ...)

and if rmsk schema should go into bioframe

[PSmaruj]

I explored what are the differences between df length depending on the `exclude_window` For rmsk, I've chosen `exclude_window = flank_end` (so here, `30`) as default

For ctcf's - there's no difference:

So, I've chosen ctcf_exclude_window = 2 * flank_end (so here, 60) as default

[gfudenberg]

will also be able to modify filter_by_rmsk if we add the schema to bioframe

akita_utils/akita_utils/utils.py

Line 203 in 8cc84f4

def filter_by_rmsk(

bullet point one:
open2c/bioframe#123

[gfudenberg]

superseded by #47