modos.genomics.cram
===================

.. py:module:: modos.genomics.cram

.. autoapi-nested-parse::

   Utilities to interact with genomic intervals in CRAM files.



Functions
---------

.. autoapisummary::

   modos.genomics.cram.extract_metadata
   modos.genomics.cram.validate_cram_files
   modos.genomics.cram.create_sequence_id


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

.. py:function:: extract_metadata(instance, base_path)

   Extract metadata from the CRAM file header and
   convert specific attributes according to the modo schema.


.. py:function:: validate_cram_files(cram_path)

   Validate CRAM files using pysam.
   Checks if the file is sorted and has an index.


.. py:function:: create_sequence_id(name, sequence_md5)

   Helper function to create a unique id from a sequence name and md5 hash