calc.lib.score.scorepipeline
============================

.. py:module:: calc.lib.score.scorepipeline


Attributes
----------

.. autoapisummary::

   calc.lib.score.scorepipeline.logger


Classes
-------

.. autoapisummary::

   calc.lib.score.scorepipeline.ScorePipeline


Functions
---------

.. autoapisummary::

   calc.lib.score.scorepipeline.get_variants_from_zarr


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

.. py:class:: ScorePipeline(max_memory_gb: float, threads: int, out_dir: pgscatalog.calc.lib.types.Pathish, minimum_samples_for_impute: int = 50)

   .. py:method:: calculate_scores() -> None


   .. py:method:: export_full_match_log(out_directory: pgscatalog.calc.lib.types.Pathish) -> None


   .. py:method:: export_scores(out_path: pgscatalog.calc.lib.types.Pathish) -> None


   .. py:method:: export_summary_match_log(out_path: pgscatalog.calc.lib.types.Pathish) -> None


   .. py:method:: load_scores(scorefile_paths: pgscatalog.calc.lib.types.Pathish | pgscatalog.calc.lib.types.PathishList) -> None

      Copy scores processed with pgscatalog-format into a duckDB database table
      'scorevariants'



   .. py:method:: match_variants(match_ambiguous: bool = False, match_multiallelic: bool = False, min_overlap: float = 0.75) -> None


   .. py:property:: db_path
      :type: pathlib.Path



   .. py:property:: genotypes_root
      :type: zarr.Group



   .. py:property:: genotypes_root_path
      :type: str



   .. py:property:: out_dir
      :type: pathlib.Path



   .. py:property:: sampleset
      :type: str


      Read sampleset name from the zarr directory



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


      Get samplesets in the zarr store



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



.. py:function:: get_variants_from_zarr(group: zarr.Group) -> collections.abc.Generator[tuple[str, dict[str, numpy.typing.NDArrayLike]], None, None]

.. py:data:: logger