cooltools stats CLI

[agalitsyna]

build stats CLI that will report pairtools-like stats:

• nnz per region (cis); per pair of regions ("trans"); in total
• fraction of contacts per region; per pair of regions ("trans"); in total
• distance decay: % of contacts by distance ranges
• cis2trans, cis and trans per region and in total

I put "trans" in quotation marks because it can be in cis (in terms of chromosomes) but between different regions.
User can provide a single region to get its properties of only this one.

Suggested API:

cooltools stats input.cool --view regions.txt --nproc 10

Additional options:

--chrom-subset
--yaml/--no-yaml

Maybe also:

• --cis2trans-only
• --nnz-only
• --decay-only
• --fraction-only
• --cis-only to remove the stats between regions (may reduce computations)
• --trans-only to calculate only trans stats and ignore all the cis ones

[Phlya]

Implementation idea: go through pixel chunks and collect stats per chunk - perhaps some code from PairCounter in pairtools can be reused!