modos.genomics.formats
======================

.. py:module:: modos.genomics.formats


Attributes
----------

.. autoapisummary::

   modos.genomics.formats.MAGIC_NUMBER


Classes
-------

.. autoapisummary::

   modos.genomics.formats.GenomicFileSuffix


Functions
---------

.. autoapisummary::

   modos.genomics.formats.read_pysam
   modos.genomics.formats.get_index
   modos.genomics.formats.is_encrypted
   modos.genomics.formats.add_suffix
   modos.genomics.formats.remove_suffix


Module Contents
---------------

.. py:data:: MAGIC_NUMBER
   :value: b'crypt4gh'


.. py:class:: GenomicFileSuffix

   Bases: :py:obj:`tuple`, :py:obj:`enum.Enum`


   Enumeration of all supported genomic file suffixes.


   .. py:attribute:: CRAM
      :value: ('.cram',)



   .. py:attribute:: BAM
      :value: ('.bam',)



   .. py:attribute:: SAM
      :value: ('.sam',)



   .. py:attribute:: VCF
      :value: ('.vcf', '.vcf.gz')



   .. py:attribute:: BCF
      :value: ('.bcf',)



   .. py:attribute:: FASTA
      :value: ('.fasta', '.fa')



   .. py:attribute:: FASTQ
      :value: ('.fastq', '.fq')



   .. py:method:: list_formats()
      :classmethod:



   .. py:method:: from_path(path)
      :classmethod:



   .. py:method:: get_index_suffix()

      Return the supported index suffix related to a genomic filetype



   .. py:method:: to_htsget_endpoint()

      Return the htsget endpoint for a genomic file type



.. py:function:: read_pysam(path, region = None, **kwargs)

   Automatically instantiate a pysam file object from input path and passes any additional kwarg to it.


.. py:function:: get_index(file_path)

.. py:function:: is_encrypted(file_path)

.. py:function:: add_suffix(file_path, suffix)

   Return the file path with specific suffix.


.. py:function:: remove_suffix(file_path, suffix)

   Return the file path without specific suffix.