Bug fixes and improvements

• Projections onto all types of BED schemas now work correctly #148
• Updated noodles and arrow dependencies to latest versions #149

Full Changelog: v0.5.0...v0.5.1

Bug fixes and improvements

• 🎉 All Rust panics during batch scanning now propagate to Python as exceptions and are no longer fatal #146
• Projections onto all types of BED schemas now work correctly #148
• Updated noodles, arrow, pyo3, and pyo3-arrow dependencies to latest versions #149

Full Changelog: https://github.com/abdenlab/oxbow/compare/py-oxbow@v0.5.0...py-oxbow@v0.5.1

New Features

CRAM support: CramScanner for reading CRAM alignment files (#142)

• Support for external reference FASTA files for reference-compressed CRAM
• Genomic range queries using CRAI index files
• Tag definition discovery and projection

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

• Fixed numerous docstring inconsistencies
• Fixed repository URL in Cargo.toml
• Updated Rust toolchain

Full Changelog: v0.4.1...v0.5.0

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

What's Changed

• Run tests for all minor Python versions >3.8 by @conradbzura in #118
• docs: Remove theme version switcher by @nvictus in #119
• Moved version information to primary sidebar by @conradbzura in #120
• Add Datasource API unit tests by @ddehueck in #117
• Bump py-oxbow crate to v0.4.1 by @conradbzura in #121
• Bump pytest-manifest from 0.1 to 1.0 in /py-oxbow by @dependabot[bot] in #128
• Bump debugpy from 1.8.13 to 1.8.16 in /py-oxbow by @dependabot[bot] in #130
• Bump actions/download-artifact from 4 to 5 in the actions group by @dependabot[bot] in #131
• Bump the actions group across 1 directory with 2 updates by @dependabot[bot] in #134
• Bump actions/setup-python from 5 to 6 in the actions group by @dependabot[bot] in #135
• Bump debugpy from 1.8.16 to 1.8.17 in /py-oxbow by @dependabot[bot] in #136
• Fixed GFF end field builder by @conradbzura in #137

New Contributors

• @ddehueck made their first contribution in #117

Full Changelog: v0.4.0...v0.4.1

What's Changed

• Bump pytest-manifest from 0.1 to 1.0 in /py-oxbow by @dependabot[bot] in #128
• Bump debugpy from 1.8.13 to 1.8.16 in /py-oxbow by @dependabot[bot] in #130
• Bump actions/download-artifact from 4 to 5 in the actions group by @dependabot[bot] in #131
• Bump the actions group across 1 directory with 2 updates by @dependabot[bot] in #134
• Bump actions/setup-python from 5 to 6 in the actions group by @dependabot[bot] in #135
• Bump debugpy from 1.8.16 to 1.8.17 in /py-oxbow by @dependabot[bot] in #136
• Fixed GFF end field builder by @conradbzura in #137

Full Changelog: https://github.com/abdenlab/oxbow/compare/py-oxbow@v0.4.1...py-oxbow@v0.4.2

What's Changed

• Run tests for all minor Python versions >3.8 by @conradbzura in #118
• Remove theme version switcher from docs by @nvictus in #119
• Moved version information to primary sidebar by @conradbzura in #120
• Add Datasource API unit tests by @ddehueck in #117

New Contributors

• @ddehueck made their first contribution in #117

Full Changelog: https://github.com/abdenlab/oxbow/compare/py-oxbow@v0.4.0...py-oxbow@v0.4.1

This release is a complete refresh of the oxbow Rust crate with complete arrow-based data models for 11 file formats and support for column projection, complex fields, and genomic range querying via indexes. Each format is readable through a "scanner" struct that provides an iterator of arrow::record_batch::RecordBatch.

What's Changed

• New scanner interface for 11 formats:
  • FastaScanner, FastqScanner
  • SamScanner, BamScanner
  • VcfScanner, BcfScanner
  • GtfScanner, GffScanner
  • BedScanner
  • BigWigScanner, BigBedScanner as well as BBIZoomScanner for zoom levels

New Contributors

• @ghuls made their first contribution in #63
• @CGMossa made their first contribution in #66

Full Changelog: v0.3.2...v0.4.0

This release is a complete refresh of the oxbow Python package with a new streaming "data source" API.

It includes complete arrow-based data models for 11 file formats and support for column projection, complex fields, and genomic range querying via indexes. Each format is exposed as a high-level DataSource, providing convenient conversions into PyArrow, Pandas, Polars, DuckDB, and Dask data structures. There are also bindings to the lower-level "scanner" API of the oxbow Rust crate, as well as updated versions of the legacy read_* functions that return Arrow IPC.

Full Changelog: https://github.com/abdenlab/oxbow/compare/py-oxbow@v0.3.2...py-oxbow@v0.4.0

py-oxbow release candidate 2 with updated DataSource API

Full Changelog: https://github.com/abdenlab/oxbow/compare/py-oxbow@v0.4.0rc1...py-oxbow@v0.4.0rc2