API Reference
=============

This section documents the Malva Python API and the full algorithmic framework underlying index
construction and querying. The algorithmic documentation is intended to enable re-implementation
and reproducibility; the Python API exposes the components available via the open-source
distribution.

----

Algorithmic Framework
---------------------

The indexing and query algorithms are fully documented below, including data structures, pseudocode,
and default parameters.

.. toctree::
   :maxdepth: 2

   ../indexing_framework

----

Python Modules
--------------

The following modules are available in the open-source Python distribution:

.. toctree::
   :maxdepth: 4

   malva.indexes
   malva.fastq_processing
   malva.dbutils
   malva.spacemake
   malva.utils
