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jeromekelleher merged 1 commit into from
Jun 8, 2026
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Final release prep for 0.2.0 #438

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17 changes: 9 additions & 8 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
# Changelog

## [0.2.0] - 2026-XX-XX
## [0.2.0] - 2026-06-08

New output formats:

Expand All @@ -14,20 +14,18 @@ New output formats:
Cloud and remote storage:

- Read VCZ from cloud and remote stores via the optional `[obstore]` and
`[icechunk]` extras (includes Azure); fsspec and HTTP stores are also
supported.
`[icechunk]` extras; fsspec and HTTP stores are also supported.
- Add support for `.vcz.zip` files (#280).
- Add `vcztools.open_zarr` for opening local, remote, and zipped stores.
- 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, e.g.
`-i 'F_MISSING < 0.05'`.
- Add `--fill-tags` to recompute `INFO/AC` and `INFO/AN`.
- 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:
Expand All @@ -41,7 +39,7 @@ 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_plink` / `write_bgen` and streaming
- 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`.
Expand All @@ -55,6 +53,9 @@ 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:

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