The Controller Module
---------------------

.. automodule:: camparee.camparee_controller
    :members:

Abstract Camparee Step
--------------------------------

.. automodule:: camparee.abstract_camparee_step
    :members:

Camparee Step Provider
--------------------------------

.. automodule:: camparee.camparee_step_provider
    :members:

The Expression Pipeline
-----------------------

.. automodule:: camparee.expression_pipeline
    :members:

Genome Alignment
----------------

.. automodule:: camparee.genome_alignment
    :members:

Indexing
--------

.. automodule:: camparee.run_pysam_index
    :members:

Variants Finding
----------------

.. automodule:: camparee.variants_finder
    :members:

Intron Quantification
---------------------

.. automodule:: camparee.intron_quant
    :members:

Variants Compilation
--------------------

.. automodule:: camparee.variants_compilation
    :members:

Gene Files Preparation
----------------------

.. automodule:: camparee.gene_files_preparation
    :members:

Beagle
------

.. automodule:: camparee.beagle
    :members:

Genome Builder
--------------

.. automodule:: camparee.genome_builder
    :members:

Annotation Updater
------------------

.. automodule:: camparee.update_annotation_for_genome
    :members:

Annotation Info
------------------

.. automodule:: camparee.annotation_info
    :members:


Transcriptome Preparation
-------------------------

.. automodule:: camparee.transcriptomes
    :members:

Allelic Imbalance Quantification
--------------------------------

.. automodule:: camparee.allelic_imbalance_quant
    :members:

Molecule Maker
--------------------------------

.. automodule:: camparee.molecule_maker
    :members:

Camparee Utils
--------------------------------

.. automodule:: camparee.camparee_utils
    :members: