CAMPAREE API
============

The CAMPAREE Controller
-----------------------

.. automodule:: camparee.camparee_controller
    :members:

Expression Simulation Pipeline
------------------------------

.. automodule:: camparee.expression_pipeline
    :members:

Genome Alignment & BAM Indexing Steps
-------------------------------------

.. automodule:: camparee.genome_alignment
    :members:

Variant Finder Step
-------------------

.. automodule:: camparee.variants_finder
    :members:

Intron Quantification Step
--------------------------

.. automodule:: camparee.intron_quant
    :members:

Variant Compilation Step
------------------------

.. automodule:: camparee.variants_compilation
    :members:

Beagle Step
-----------

.. automodule:: camparee.beagle
    :members:

Genome Builder Step
-------------------

.. automodule:: camparee.genome_builder
    :members:

Update Annotation Step
----------------------

.. automodule:: camparee.update_annotation_for_genome
    :members:

Transcriptome FASTA Preparation Step
------------------------------------

.. automodule:: camparee.transcriptome_fasta_preparation
    :members:

Kallisto Index Generation & Quantification Steps
------------------------------------------------

.. automodule:: camparee.kallisto
    :members:

Bowtie2 Index Generation & Alignment Steps
------------------------------------------

.. automodule:: camparee.bowtie2
    :members:

Transcript Quantification Step
------------------------------

.. automodule:: camparee.transcript_gene_quant
    :members:

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

.. automodule:: camparee.allelic_imbalance_quant
    :members:

Molecule Maker Step
-------------------

.. automodule:: camparee.molecule_maker
    :members:

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

.. automodule:: camparee.annotation_info
    :members:

CAMPAREE Utils
--------------

.. automodule:: camparee.camparee_utils
    :members:

Abstract CAMPAREE Step
----------------------

.. automodule:: camparee.abstract_camparee_step
    :members:

CAMPAREE Step Provider
----------------------

.. automodule:: camparee.camparee_step_provider
    :members:

CAMPAREE Constants
------------------

.. automodule:: camparee.camparee_constants
    :members: