bedGraph2bigWig
===============

bedGraph2bigWig is a tool to convert bedgraph file format to bigwig file format. Two operation modes are available:

1) Multiple File Mode: Process batches of files specified in a manifest
2) Single File Mode: Convert individual bedgraph files

.. code-block:: sh
 
    Usage: bedGraph2bigWig [options] ...

Content
=======

.. contents:: 
    :local:

Required arguments
^^^^^^^^^^^^^^^^^^

``-s <species>``
  Supported species: hg38, hg19, or mm10. Selecting this option automatically loads the corresponding genomesizes file. If your species is not listed, manually provide these files via ``-g <genome_sizes>``. **[Default: None]**

``-g <genomesizes>``
  Required if ``-s`` is unspecified. Path to a genomesizes file (tab-delimited) listing chromosome lengths **[Default: None]**. Example::

    chr1  249250621
    ...

Multiple File Mode
""""""""""""""""""

``-f <file_list>``
  Tab-delimited file listing input/output pairs, required for batch mode **[Default: None]**. Example::

    /PATH/TO/example1.bedgraph       /PATH/TO/example1.bw
    /PATH/TO/example2.bedgraph       /PATH/TO/example2.bw
    ...

Single File Mode
""""""""""""""""

``-i <bedgraph>``
  Input bedGraph file, required for single mode. **[Default: None]**

``-o <outfile>``
  Output bigWig file, required for single mode. **[Default: None]**

Optional arguments
^^^^^^^^^^^^^^^^^^

``-p <nthreads>``
  Number of parallel processes. **[Default: 4]**

``-h``
  Show this help message and exit.

``-v``
  Show program's version number and exit.