Modules
=======

This section documents the Python modules in GRiD.

Command-Line Interface
----------------------

.. click:: grid.cli:cli
   :prog: grid
   :show-nested:

Module Documentation
--------------------

.. toctree::
   :maxdepth: 2
   :caption: Core Modules

   modules_dir/grid_core
   modules_dir/utilities_overview

.. toctree::
   :maxdepth: 2
   :caption: Utility Modules

   modules_dir/helper-functions
   modules_dir/count-reads
   modules_dir/mosdepth
   modules_dir/normalize-mosdepth
   modules_dir/find-neighbors
   modules_dir/lpa-realign
   modules_dir/compute-dipcn
   modules_dir/estimate-kiv

.. toctree::
   :maxdepth: 1
   :caption: Support Modules

   modules_dir/crai
   modules_dir/subset
   modules_dir/extract-reference