diff --git a/CHANGELOG.md b/CHANGELOG.md index bc260de..d6414c9 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,6 @@ # Changelog -## [0.2.0] - 2026-XX-XX +## [0.2.0] - 2026-06-08 New output formats: @@ -14,10 +14,9 @@ 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: @@ -25,9 +24,8 @@ Filtering and CLI: - 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: @@ -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`. @@ -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: