Major feature release

Major feature release adding new output formats, cloud store support, a Python API, performance improvements and bug fixes.

New output formats:

• Add view-plink command for PLINK 1 binary output (.bed/.bim/.fam), following the semantics of plink2 --vcf X --make-bed. Use --no-bim/--no-fam to suppress sidecars.
• Add view-bgen command for Oxford BGEN output, streamed to stdout or written with .bgen.bgi/.sample sidecars (-o STEM). Supports haploid and mixed-ploidy data.

Cloud and remote storage:

• Read VCZ from cloud and remote stores via the optional [obstore] and [icechunk] extras; fsspec and HTTP stores are also supported.
• Add support for .vcz.zip files (#280).
• Support "proportional chunking" across arrays (#356).

Filtering and CLI:

• Support -R/--regions-file and -T/--targets-file (#268).
• Add -v/--types, -V/--exclude-types, -m/--min-alleles, and -M/--max-alleles to view and view-plink, matching bcftools view,
  along with a new N_ALT filter identifier.
• Add N_MISSING and F_MISSING filter variables
• Add --fill-tags to emulate bcftools +fill-tags
• Add --log-level and --log-file options; report throughput in MiB/s.

Data types:

• Add support for float16 and float64 data stored in Zarr (#413, #414).
• Add support for 64-bit integer POS and INFO/FORMAT fields.

Python API:

• Add a public Python API, documented under {ref}sec-python-api:
  • VczReader for variant data access, with sample selection by ID via set_samples(sample_ids, complement=, ignore_missing_samples=) (or by raw index via set_sample_indexes).
  • One-shot writers write_vcf / write_plink / write_bgen and streaming BedEncoder / BgenEncoder byte encoders.
  • Sidecar writers write_bim / write_fam / write_sample / write_bgi.
  • Click option bundles (ViewBgenOptions, ViewPlinkOptions, SelectionOptions, ZarrStoreOptions, ReaderOptions, LogOptions) and GroupedCommand for downstream CLI reuse.
  • Array-sentinel helpers is_missing / is_fill / trim_fill for interpreting missing and end-of-vector (fill) values in iterated arrays.

Platform and packaging:

• Add Windows support.
• Provide prebuilt wheels for Linux, macOS, and Windows (CPython 3.11-3.13).
• New required dependencies: pandas and humanfriendly; pyparsing>=3.1.0. Genomic-range operations now use ruranges_py on Python 3.12+ and pyranges on earlier versions.

Documentation:

• Add a documentation website covering installation, storage backends, the CLI, PLINK/BGEN output, and the Python API.

Deprecations:

• --zarr-backend-storage is deprecated in favour of --backend-storage; the old name still works and emits a warning.

Bug fixes:

• vcztools query silently truncated output on multi-chunk stores (#283)
• vcztools view crash on FILTER expressions on multi-chunk stores (#282)
• Incorrect output on vcztools query on FORMAT fields (#286, #287)
• Per-allele INFO field + -s crashes (#295)
• VCF header emitted even when filter expression is invalid (#221)
• Incorrect behaviour for bcftools query with FORMAT scoped filters and sample subsetting (#297)
• Incorrect output for filtering with missing Number=A INFO field + numeric (#299)
• Noise on stderr when performing arithmetic with missing values (#301)
• Null samples included in plink output (#310)
• Fill values handled incorrectly by query (#415)
• Crash evaluating non-scalar INFO field expressions (#435, #436)

Minor feature, maintenance and bugfix release.

Features:

• Add -N/--disable-automatic-newline option (#261)
• Support -S/--samples-file in query (#264)
• Ignore missing samples (#258)

Bug fixes:

• Fix region edge cases and improve test coverage (#262). Region queries or views were in some cases omitting variants that should have been returned.

Breaking:

• Require NumPy 2 (#249)
• Require Zarr Python version 3.1 or greater (#259)

Feature release

Improvements:

• Support filtering by FILTER (#217), CHROM (#223) and general string values (#220)
• Support regions (-r/-t), filter expressions (-i/-e) and samples (-s) in query command (#205)
• Various improvements to support VCZ datasets produced from tskit and plink files by bio2zarr.
• Use a fully dynamically generated header via vcf_meta_information attributes (#208). Requires vcf-zarr version >= 0.4 (bio2zarr >= 0.1.6) to fully recover the original header.
• Add --version (#197)

Breaking:

Update minimum Click version to 8.2.0 (#206)

Recommended bugfix release

Important bugfixes for filtering language and sample subsetting.

All users are recommended to upgrade ASAP.

Filtering mini-language

Clarify the implementation status of the filtering mini-lanuage in view/query. Version 0.0.1 contained several data-corrupting bugs, including incorrect missing data handling (#163), incorrect matching on FILTER (#164) and CHROM (#178) columns, and incorrect per-sample filtering in query (#179). These issues have been resolved by raising informative errors on aspects of the query language that are not implemented correctly.

The filtering mini-language now consists of arbitrary arithmetic expressions on 1-dimensional fields.

Sample subsetting

Add support for specifying samples via -s/-S options

Initial release

0.0.1

0.0.1

0.0.1a3

Alpha pre-release for testing

Alpha pre-release for testing

Early pre-release for testing.