Published November 18, 2025 | Version py-oxbow@v0.5.0
Software Open

abdenlab/oxbow: py-oxbow@v0.5.0

Creators

  • 1. marimo
  • 2. @aertslab

Description

New Features

CRAM support: Low-level PyCramScanner and high-level data source from_cram() for reading CRAM alignment files (#142)

  • Low-level scanner supports external reference FASTA files for reference-compressed CRAM, but not high-level data source yet
  • Genomic range queries using CRAI index files
  • Tag definition discovery and projection

Low-level Byte Range and Virtual Position Range scan methods for SAM, BAM, GTF, GFF, VCF, and BED formats (#143)

  • scan_byte_ranges(): Read specific byte ranges from uncompressed files
  • scan_virtual_ranges(): Read specific virtual position ranges from BGZF-compressed files

Bug fixes and maintenance

  • Made batch reader fragments pickleable (#124) and deterministically hashable (#122) for Dask.
  • Fixed numerous docstring inconsistencies
  • Updated Rust toolchain

Full Changelog: https://github.com/abdenlab/oxbow/compare/py-oxbow@v0.4.2...py-oxbow@v0.5.0

Files

abdenlab/oxbow-py-oxbow@v0.5.0.zip

Files (8.1 MB)

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Additional details

Related works

Is supplement to
Software: https://github.com/abdenlab/oxbow/tree/py-oxbow@v0.5.0 (URL)

Software

Repository URL
https://github.com/abdenlab/oxbow