ALLCools

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allc_to_region_count() missing 1 required positional argument: 'cmeta_path'

5

Hello, I recently noticed the function `allc_to_region_count()` in ALLCools 1.1.0 requires an additional argument 'cmeta_path' that is not described in the documentation, which subsequently causes an error when running `allcools...

rogadde

Fairly simple-bracketed TabixFile's initialization in a try/except IOError. If the default path doesn't exist, say, in a bucket that you don't have write access to, this enables allcools to handle...

theAeon

In rare cases, I find the ALLC files having the same cytosine position in more than one lines, which causes downstream errors during allc-to-bw. The picture is an example of...

Ren-L-H

Hello, I have recently started using allcools to analyze sample datasets from Scalebio. I am using a dataset from human PBMCs with 4426 cells. I am currently stuck on the...

sarangchafle

The call_dms function will raise an error of no file to open when some of the region chunks have empty enriched dms. It is suggested to add a check on...

juychen

updates: - https://github.com/psf/black → https://github.com/psf/black-pre-commit-mirror - [github.com/psf/black-pre-commit-mirror: 25.1.0 → 25.11.0](https://github.com/psf/black-pre-commit-mirror/compare/25.1.0...25.11.0) - [github.com/asottile/blacken-docs: 1.19.1 → 1.20.0](https://github.com/asottile/blacken-docs/compare/1.19.1...1.20.0) - [github.com/PyCQA/isort: 6.0.0 → 7.0.0](https://github.com/PyCQA/isort/compare/6.0.0...7.0.0) - [github.com/pre-commit/pre-commit-hooks: v5.0.0 → v6.0.0](https://github.com/pre-commit/pre-commit-hooks/compare/v5.0.0...v6.0.0) - [github.com/PyCQA/flake8: 7.1.2 → 7.3.0](https://github.com/PyCQA/flake8/compare/7.1.2...7.3.0)...

pre-commit-ci[bot]

Use Zarr library directly as a parallel write sink.

14

This eliminates the full readback of the zarr chunks that was done to merge the outputs of the parallel _write_single_zarr block and is saving me a significant amount of time...

theAeon