Documentation for the Code
**************************

.. automodule:: mirtop

bam
===

.. automodule:: mirtop.bam.bam
   :members:

.. automodule:: mirtop.bam.filter
   :members:


exporter
========

.. automodule:: mirtop.exporter.isomirs
   :members:

.. automodule:: mirtop.exporter.fasta
  :members:

.. automodule:: mirtop.exporter.vcf
   :members:


gff
===

.. automodule:: mirtop.gff.body
   :members:

.. automodule:: mirtop.gff.compare
   :members:

.. automodule:: mirtop.gff.header
   :members:

.. automodule:: mirtop.gff.merge
   :members:

.. automodule:: mirtop.gff.stats
   :members:

.. automodule:: mirtop.gff.update
  :members:

.. automodule:: mirtop.gff.validator
  :members:

importer
========

.. automodule:: mirtop.importer.isomirsea
   :members:

.. automodule:: mirtop.importer.prost
   :members:

.. automodule:: mirtop.importer.seqbuster
   :members:

.. automodule:: mirtop.importer.srnabench
   :members:

.. automodule:: mirtop.importer.optimir
  :members:

.. automodule:: mirtop.importer.manatee
  :members:

libs
====

.. automodule:: mirtop.libs.do
   :members:

.. automodule:: mirtop.libs.fastq
   :members:

.. automodule:: mirtop.libs.parse
   :members:

.. automodule:: mirtop.libs.utils
   :members:

mirna
=====

.. automodule:: mirtop.mirna.annotate
   :members:

.. automodule:: mirtop.mirna.fasta
   :members:

.. automodule:: mirtop.mirna.keys
   :members:

.. automodule:: mirtop.mirna.mapper
   :members:

.. automodule:: mirtop.mirna.realign
   :members:

.. automodule:: mirtop.mirna.snps
   :members:

classes
=======

.. autoclass:: mirtop.mirna.realign.hits
   :members:

.. autoclass:: mirtop.mirna.realign.isomir
   :members: