agglovar.merge.base
===================

.. py:module:: agglovar.merge.base

.. autoapi-nested-parse::

   Base class for callset intersects.



Attributes
----------

.. autoapisummary::

   agglovar.merge.base.CallsetDefType


Classes
-------

.. autoapisummary::

   agglovar.merge.base.MergeBase


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

.. py:class:: MergeBase

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


   Base class for callset intersects.


   .. py:method:: __call__(callsets: collections.abc.Iterable[CallsetDefType], retain_index: bool = False, pre_filter: Optional[collections.abc.Iterable[polars.Expr]] = None, temp_dir: bool | str | pathlib.Path = False) -> polars.LazyFrame
      :abstractmethod:


      Intersect callsets.

      :param callsets: Callsets to intersect.
      :param retain_index: If `True`, do not drop an existing "_index" column if it exists.
      :param pre_filter: If set, filter each table with these expressions. Filter is applied
          last (after "_index" is set).
      :param temp_dir: How the underlying pairwise intersect materialises prepared tables before
          its chunked loop. ``False`` (default) keeps tables in memory; ``True`` writes them to
          the system temp directory as parquet; a ``str``/``Path`` writes them to that directory.
          Temp files are always removed on exit.

      :return: A merged callset table.



   .. py:method:: get_intersect_tuples(callsets: collections.abc.Iterable[CallsetDefType], retain_index: bool = False, pre_filter: Optional[collections.abc.Iterable[polars.Expr] | polars.Expr] = None) -> list[tuple[polars.LazyFrame, str, int]]
      :staticmethod:


      Transform input arguments to a list of tuples with set fields.

      Each returned tuple has three fields:

          1. A lazy frame
          2. A name for the source
          3. An index for the source (0 for the first, increments by 1)

      If a source name is given, the given name is used. If it is not, then a default name is
      generated using the source index.

      Lazy frames are transformed to add an index ("_index" column) and to enusre a variant ID
      is present ("id" column) and that all non-null values are filled in.

      :param callsets: Callsets parameter. May be an iterable of DataFrames, LazyFrames, or
          tuples of (DataFrame, name).
      :param retain_index: If `True`, do not drop an existing "_index" column if it exists.
      :param pre_filter: If set, filter each table with these expressions. Filter is applied
          last (after "_index" is set).

      :return: A list of tuples where each tuple element represents one input source.



.. py:type:: CallsetDefType
   :canonical: pl.DataFrame | pl.LazyFrame | Iterable[pl.DataFrame | pl.LazyFrame | str]


   Alias for acceptable types.