Ilya Flyamer
Ilya Flyamer
This would allow one to more fairly sample libraries in cases of divergence in very short range contact frequency (very typical, and accounts for a large % of total contacts)....
I think the logic here is wrong, compared to cooler: https://github.com/open2c/cooltools/blob/6fd5aea56e8a9e55b8917f5104a18ae219347e4e/cooltools/api/snipping.py#L428 in case of the end not falling exactly on the bin edge, it should include the rightmost partially covered...
Explain the problem and show how to manually invert weights
Some tools lack the `-o` option in CLI. In some cases using `>` (which creates the output file immediately, even if the command fails) interferes with snakemake, which uses presence...
Scaling without a view was broken! Docs said it would use the chromsizes from the header, but there was no code that was doing it...
We should create them... From highest priority to lowest: - [ ] io/header: https://github.com/open2c/pairtools/blob/master/pairtools/lib/headerops.py - [ ] scaling: https://github.com/open2c/pairtools/blob/master/pairtools/lib/scaling.py - [ ] stats: https://github.com/open2c/pairtools/blob/master/pairtools/lib/stats.py
As suggested by @gfudenberg , let's add convergence point of the four orientations to stats!
Discussion to address https://github.com/mirnylab/distiller-nf/issues/96. Since there is `pairsamtools restrict`, we can use that as a starting point for adding fragment-level stats. But after some thinking, it seems more complicated to...
If you have any other columns in the bedframe that might contain NaNs (bins from a cooler...), they will be also dropped - not what I expected. https://github.com/open2c/bioframe/blob/f0682ff0eb11ed707019cbd50bfa76fce01d2c17/bioframe/ops.py#L1886
In light of Anton's PR, just want to start a discussion about future possible functions for 2D interval operations for a later release. 1. I think we decided on Slack...