modos.genomics.c4gh
===================

.. py:module:: modos.genomics.c4gh

.. autoapi-nested-parse::

   crypt4gh implementation

   Crypt4gh allows envelop encryption of genomic files. See [1]_ for more details.

   Here we use the crypt4gh python [2]_ implementation to allow de/encryption of genomic files within modos.

   .. rubric:: References

   .. [1] https://samtools.github.io/hts-specs/crypt4gh.pdf
   .. [2] https://github.com/EGA-archive/crypt4gh



Functions
---------

.. autoapisummary::

   modos.genomics.c4gh.get_secret_key
   modos.genomics.c4gh.get_keys
   modos.genomics.c4gh.encrypt_file
   modos.genomics.c4gh.decrypt_file


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

.. py:function:: get_secret_key(seckey_path = None, passphrase = None)

   Get the secret key for encryption/decryption.
   If no secret key path is provided a new secret key will be generated automatically.
   This can be used to allow authicated encryption without prior key generation.

   :param seckey_path: Path to the secret key.
   :param passphrase: Passphrase for the secret key.


.. py:function:: get_keys(recipient_pubkeys, seckey)

   Retrieves recipient public keys and builds a collection of "key tuples".

   :param recipient_pubkeys: Path to the recipient public key, or list of paths if multiple recipients.
   :param seckey: Secret key of the sender.

   :returns: Set of key triplets, one for each recipient.
   :rtype: {(method, seckey, recipient_pubkey)}


.. py:function:: encrypt_file(recipient_pubkeys, infile, outfile, seckey_path = None, passphrase = None)

   Encrypt a file using the crypt4gh algorithm (authenticated encryption).


.. py:function:: decrypt_file(seckey_path, infile, outfile, sender_pubkey = None, passphrase = None)