From 107d5ff5fe9b532045d49d9d496c06aaadbc8533 Mon Sep 17 00:00:00 2001 From: Tom White Date: Wed, 2 Oct 2024 14:56:07 +0100 Subject: [PATCH] Update changelog --- docs/changelog.rst | 20 ++++++++++++-------- 1 file changed, 12 insertions(+), 8 deletions(-) diff --git a/docs/changelog.rst b/docs/changelog.rst index a5263767f..bfe91ee8a 100644 --- a/docs/changelog.rst +++ b/docs/changelog.rst @@ -14,8 +14,12 @@ New Features - Add 'matching' method to :func:`identity_by_state` function. (:user:`timothymillar`, :pr:`1229`, :issue:`1227`) -.. Breaking changes -.. ~~~~~~~~~~~~~~~~ +Breaking changes +~~~~~~~~~~~~~~~~ + +- Functions for reading and writing VCF were removed from sgkit, please use the `bio2zarr `_ + and `vcztools `_ packages instead. + (:user:`tomwhite`, :pr:`1264`) .. Deprecations .. ~~~~~~~~~~~~ @@ -147,22 +151,22 @@ New Features - Add :func:`sgkit.convert_call_to_index` method. (:user:`timothymillar`, :pr:`1050`, :issue:`1048`) -- Add ``read_chunk_length`` option to :func:`sgkit.io.vcf.vcf_to_zarr` and - :func:`sgkit.io.vcf.vcf_to_zarrs` functions. These are useful to reduce memory usage +- Add ``read_chunk_length`` option to ``sgkit.io.vcf.vcf_to_zarr`` and + ``sgkit.io.vcf.vcf_to_zarrs`` functions. These are useful to reduce memory usage with large sample counts or a large ``chunk_length``. (:user:`benjeffery`, :pr:`1044`, :issue:`1042`) -- Add ``retain_temp_files`` to :func:`sgkit.io.vcf.vcf_to_zarr` function. +- Add ``retain_temp_files`` to ``sgkit.io.vcf.vcf_to_zarr`` function. (:user:`benjeffery`, :pr:`1046`, :issue:`1036`) -- Add :func:`sgkit.io.vcf.read_vcf` convenience function. +- Add ``sgkit.io.vcf.read_vcf`` convenience function. (:user:`tomwhite`, :pr:`1052`, :issue:`1004`) - Add :func:`sgkit.hybrid_relationship`, :func:`sgkit.hybrid_inverse_relationship` and :func:`invert_relationship_matrix` methods. (:user:`timothymillar`, :pr:`1053`, :issue:`993`) -- Add :func:`sgkit.io.vcf.zarr_array_sizes` for determining array sizes for storage in Zarr. +- Add ``sgkit.io.vcf.zarr_array_sizes`` for determining array sizes for storage in Zarr. (:user:`tomwhite`, :pr:`1073`, :issue:`734`) - Add ``skipna`` option to :func:`genomic_relationship` function. @@ -174,7 +178,7 @@ New Features Breaking changes ~~~~~~~~~~~~~~~~ -- Generate VCF header by default when writing VCF using :func:`sgkit.io.vcf.write_vcf` or :func:`sgkit.io.vcf.zarr_to_vcf`. +- Generate VCF header by default when writing VCF using ``sgkit.io.vcf.write_vcf`` or ``sgkit.io.vcf.zarr_to_vcf``. Previously, the dataset had to contain a ``vcf_header`` attribute. (:user:`tomwhite`, :pr:`1021`, :issue:`1020`)