calc.lib.cache.targetvariants
=============================

.. py:module:: calc.lib.cache.targetvariants

.. autoapi-nested-parse::

   Provides the TargetVariants class for representing hard-called genotypes and variants

   This module defines a lightweight container of variant information, including:

   - chromosome name
   - chromosome position
   - reference allele
   - alternate allele

   Genotypes are stored in numpy unsigned 8-bit integer arrays (values between 0 - 255).
   Valid genotype values include 0, 1, and a sentinel value to represent missing data.

   The class exposes accessors for:

   - genotypes: a 3D numpy array of shape (n_variants, n_samples, ploidy)
   - samples: a list of sample identifiers
   - variant_df: a polars dataframe which contains variant metadata

   The module depends on:

   - numpy for genotype matrix ops
   - polars for building variant metadata tables quickly



Attributes
----------

.. autoapisummary::

   calc.lib.cache.targetvariants.logger


Classes
-------

.. autoapisummary::

   calc.lib.cache.targetvariants.TargetVariants


Functions
---------

.. autoapisummary::

   calc.lib.cache.targetvariants.add_missing_positions_to_lists


Module Contents
---------------

.. py:class:: TargetVariants(chr_name: list[str], pos: list[int], refs: list[str | None], alts: list[list[str] | None], gts: list[numpy.typing.NDArray[numpy.uint8]], samples: list[str], target_path: pgscatalog.calc.lib.types.Pathish, sampleset: str)

   .. py:method:: write_zarr(zarr_group: zarr.Group) -> None

      Write TargetVariants to a zarr group

      Sample IDs, variant metadata, and a genotype array is written to the zarr group

      The group must be at a file level in the hierarchy



   .. py:property:: genotypes
      :type: numpy.typing.NDArray[numpy.uint8]



   .. py:property:: samples
      :type: list[str]



   .. py:property:: variant_ids
      :type: list[str]



   .. py:property:: variant_metadata
      :type: calc.lib.cache.zarrmodels.ZarrVariantMetadata


      Convert variant metadata to a dict



.. py:function:: add_missing_positions_to_lists(*, chroms: list[str], positions: list[int], ref_alleles: list[str | None], alt_alleles: list[list[str] | None], hard_calls: list[numpy.typing.NDArray[numpy.uint8]], scoring_file_regions: list[tuple[str, int]], seen_positions: set[tuple[str, int]], n_samples: int) -> None

   Mutates lists in place!


.. py:data:: logger