Functions
--------------
+-------------------------------------------------+-----------------------+-------------------------------------+--------------------------------------------------------------------------------------------------------------------------------+
| function                                        | type                  | input files                         | main output file(s)                                                                                                            |
+=================================================+=======================+=====================================+============================================+===================================================================================+
|:doc:`qc_report`                                 | QC                    | 1 or more BAM                       | summary report with figures & table for read length, mapping quality, basecall quality, etc.                                   |
+-------------------------------------------------+-----------------------+-------------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`plot_browser`                              | visualization         | 1 or more BAM                       | single-molecule browser as html or pdf; aggregate browser plots and coverage                                                   |
+-------------------------------------------------+-----------------------+-------------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`plot_enrichment`                           | visualization         | 1 or more BAM, 1 or more BED        | barplot of fraction modified bases within region(s) defined by BED(s)                                                          |
+-------------------------------------------------+-----------------------+-------------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`plot_enrichment_profile`                   | visualization         | 1 or more BAM, 1 or more BED        | profile, single molecule plots, base abundance; option to overlay if input multiple BAM/BED                                    |
+-------------------------------------------------+-----------------------+-------------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+
|:doc:`parse_bam`                                 | data formatting       | 1 BAM                               | sql database (to allow for custom visualization)                                                                               |
+-------------------------------------------------+-----------------------+-------------------------------------+--------------------------------------------+-----------------------------------------------------------------------------------+

.. toctree::
   :maxdepth: 2
   :hidden:
   
   qc_report
   plot_browser
   plot_enrichment
   plot_enrichment_profile
   parse_bam