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Update changelog
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tomwhite committed Oct 2, 2024
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Showing 1 changed file with 12 additions and 8 deletions.
20 changes: 12 additions & 8 deletions docs/changelog.rst
Original file line number Diff line number Diff line change
Expand Up @@ -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 <https://github.com/sgkit-dev/bio2zarr>`_
and `vcztools <https://github.com/sgkit-dev/vcztools>`_ packages instead.
(:user:`tomwhite`, :pr:`1264`)

.. Deprecations
.. ~~~~~~~~~~~~
Expand Down Expand Up @@ -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.
Expand All @@ -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`)

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