agglovar.pairwise.base
======================

.. py:module:: agglovar.pairwise.base

.. autoapi-nested-parse::

   Base class for pairwise intersect strategies.

   Defines an interface and implements common functionality for pairwise intersect strategies.



Classes
-------

.. autoapisummary::

   agglovar.pairwise.base.PairwiseJoin


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

.. py:class:: PairwiseJoin(weight_strategy: agglovar.pairwise.weights.WeightStrategy = DEFAULT_WEIGHT_STRATEGY)

   Bases: :py:obj:`abc.ABC`


   Base class for pairwise intersection classes.


   .. py:method:: check_required_cols(df: polars.LazyFrame | polars.DataFrame | collections.abc.Iterable[str], raise_exception: bool = False) -> set[str]

      Check if a table has the expected columns.

      :param df: Table to check.
      :param raise_exception: If True, raise an exception if any expected columns are missing.

      :returns: A set of missing columns.

      :raises ValueError: If any expected columns are missing and `raise_exception` is True.



   .. py:method:: check_reserved_cols(df: polars.LazyFrame | polars.DataFrame | collections.abc.Iterable[str], raise_exception: bool = False) -> set[str]

      Check if a table has reserved columns.

      :param df: Table to check.
      :param raise_exception: If True, raise an exception if any reserved columns are found.

      :returns: A set of reserved columns found in the table.

      :raises ValueError: If any reserved columns are found and `raise_exception` is True.



   .. py:method:: join(df_a: polars.DataFrame | polars.LazyFrame, df_b: polars.DataFrame | polars.LazyFrame, retain_index: bool = False, temp_dir: bool | str | pathlib.Path = False) -> polars.LazyFrame

      Find all pairs of variants in two sources that meet a set of criteria.

      This is a convenience function that calls join_iter() and concatenates the results.

      :param df_a: Table A.
      :param df_b: Table B.
      :param retain_index: If True, do not drop an existing "_index" column in callset tables
          if they exist.
      :param temp_dir: See :meth:`join_iter`.

      :returns: A join table.



   .. py:method:: join_iter(df_a: polars.DataFrame | polars.LazyFrame, df_b: polars.DataFrame | polars.LazyFrame, retain_index: bool = False, temp_dir: bool | str | pathlib.Path = False) -> collections.abc.Iterator[polars.LazyFrame]
      :abstractmethod:


      Find all pairs of variants in two sources that meet a set of criteria.

      :param df_a: Source dataframe.
      :param df_b: Target dataframe.
      :param retain_index: If True, do not drop an existing "_index" column in callset tables
          if they exist.
      :param temp_dir: How to materialise the prepared tables before the chunked loop.
          ``False`` (default) collects both into memory; ``True`` writes them to the
          system temp directory as parquet files; a ``str``/``Path`` writes them to
          that directory. Temp files are always removed on exit.

      :yields: A LazyFrame for each chunk.



   .. py:property:: required_cols
      :type: set[str]

      :abstractmethod:


      The minimum set of columns that must be present in input tables.



   .. py:property:: reserved_cols
      :type: set[str]


      A set of columns that are reserved for internal use and must not be present in input tables.



   .. py:property:: weight_strategy
      :type: agglovar.pairwise.weights.WeightStrategy


      Weight strategy to use for this join.