agglovar.align.op
=================

.. py:module:: agglovar.align.op

.. autoapi-nested-parse::

   Constants and functions for working with alignment operations.

   Definitions in this subpackage are borrowed from
   `PAV 3+ <https://github.com/BeckLaboratory/pav>`__.



Attributes
----------

.. autoapisummary::

   agglovar.align.op.ADV_QRY_ARR
   agglovar.align.op.ADV_REF_ARR
   agglovar.align.op.ALIGN_SET
   agglovar.align.op.CIGAR_OP_SET
   agglovar.align.op.CLIP_SET
   agglovar.align.op.CONSUMES_QRY_ARR
   agglovar.align.op.CONSUMES_REF_ARR
   agglovar.align.op.D
   agglovar.align.op.EQ
   agglovar.align.op.EQX_SET
   agglovar.align.op.H
   agglovar.align.op.I
   agglovar.align.op.INT_STR_SET
   agglovar.align.op.M
   agglovar.align.op.N
   agglovar.align.op.OP_CHAR
   agglovar.align.op.OP_CHAR_FUNC
   agglovar.align.op.OP_CODE
   agglovar.align.op.P
   agglovar.align.op.S
   agglovar.align.op.VAR_ARR
   agglovar.align.op.X


Functions
---------

.. autoapisummary::

   agglovar.align.op.cigar_to_arr


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

.. py:function:: cigar_to_arr(cigar_str: str) -> numpy.ndarray

   Get a numpy array with two dimensions (dtype int).

   The first column is the operation codes, the second column is the operation lengths.

   :param cigar_str: CIGAR string.

   :returns: Array of operation codes and lengths (dtype int).

   :raises ValueError: If the CIGAR string is not properly formatted.


.. py:data:: ADV_QRY_ARR
   :type:  numpy.typing.NDArray[numpy.integer]

   Array of operation codes that advance the query position.


.. py:data:: ADV_REF_ARR
   :type:  numpy.typing.NDArray[numpy.integer]

   Array of operation codes that advance the reference position.


.. py:data:: ALIGN_SET
   :type:  frozenset[int]

   Set of alignment operation codes (match, sequence match, mismatch).


.. py:data:: CIGAR_OP_SET
   :type:  frozenset[str]

   Set of valid operation characters.


.. py:data:: CLIP_SET
   :type:  frozenset[int]

   Set of clipping operation codes (soft and hard clipping).


.. py:data:: CONSUMES_QRY_ARR
   :type:  numpy.typing.NDArray[numpy.integer]

   Array of operation codes that consume query bases.


.. py:data:: CONSUMES_REF_ARR
   :type:  numpy.typing.NDArray[numpy.integer]

   Array of operation codes that consume reference bases.


.. py:data:: D
   :type:  int
   :value: 2


   Deletion operation code.


.. py:data:: EQ
   :type:  int
   :value: 7


   Sequence match operation code.


.. py:data:: EQX_SET
   :type:  frozenset[int]

   Set of exact match/mismatch operation codes.


.. py:data:: H
   :type:  int
   :value: 5


   Hard clipping operation code.


.. py:data:: I
   :type:  int
   :value: 1


   Insertion operation code.


.. py:data:: INT_STR_SET
   :type:  frozenset[str]

   Set of valid integer character strings representing operation codes.


.. py:data:: M
   :type:  int
   :value: 0


   Match or mismatch operation code.


.. py:data:: N
   :type:  int
   :value: 3


   Skipped region operation code.


.. py:data:: OP_CHAR
   :type:  Mapping[int, str]

   Mapping from operation codes to their character representations.


.. py:data:: OP_CHAR_FUNC

   Vectorized function to convert operation codes to characters.


.. py:data:: OP_CODE
   :type:  Mapping[str, int]

   Mapping from CIGAR characters to operation codes.


.. py:data:: P
   :type:  int
   :value: 6


   Padding operation code.


.. py:data:: S
   :type:  int
   :value: 4


   Soft clipping operation code.


.. py:data:: VAR_ARR
   :type:  numpy.typing.NDArray[numpy.integer]

   Array of operation codes that introduce variation.


.. py:data:: X
   :type:  int
   :value: 8


   Sequence mismatch operation code.