cooltools
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cooltools stats CLI
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