[email protected]

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/[email protected]@v0.4.1

v0.4.0

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

[email protected]

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/[email protected]@v0.4.0

[email protected]

py-oxbow release candidate 2 with updated DataSource API

Full Changelog: https://github.com/abdenlab/oxbow/compare/[email protected]@v0.4.0rc2

v0.4.0-rc.1

Pre-release of crate with new streaming API.

[email protected]

Pre-release of py-oxbow with new streaming API and PyArrow interface.

v0.3.2

What's Changed

• chore: Update dependencies by @ghuls in #63
• feat: Use BufReader for reading BAM files with file-like objects by @pkerpedjiev in #68
• feat(py): Use BufReader for PyFileLikeObject with 1MB buffer by @manzt in #69
• feat(r): Update r-oxbow dependencies and replace deprecated APIs by @CGMossa in #66

New Contributors

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

Full Changelog: v0.3.1...v0.3.2

v0.3.1

What's Changed

• Simplify GFF/GTF reader types by @GarrettNg in #53
• Fastq file like objects and cleanup by @GarrettNg in #52

Full Changelog: v0.3.0...v0.3.1

v0.3.0

• New readers: BigBed, GFF, GTF
• File-like object support for readers
• BigWig zoom levels for bigwig reader
• Bam tags for bam reader
• Py-oxbow sphinx docs and tests

v0.2.0

New features (rust, python, r)

• Added genomic range query readers for indexed VCF, BCF, as well as FASTA and FASTQ
• Support for virtual position-based range queries for indexed BAM, VCF, BCF
• Virtual position-based partitioning from index files