Snaf

. expose add_coord_frequency_table to snaf namespace

---------------------------

This is a release since the paper's original resubmission, in the past year, we added a ton of new features, main changes are briefly summarized below:

. differential gene analysis, differential splicing analysis, gene enrichment analysis
. hla coverage analysis, for each pHLA, what percentage of the population it can cover (benefit)
. enhanced and more flexible control database, adding two normal cohorts by default, and allowing user to add customized
. improved algorithms for MLE tumor specificity score, and external BayesTS score (https://github.com/frankligy/BayesTS)
. improved output for both T and B antigens
. fix multiple bugs

----------------------------

Adding New functionalities:

. report B and T antigen in a more readable format
. allow users to add all info to the frequency table at once
. add long_read mode for B antigen when inferring full-length isoform and update the B viewer codebase as well

----------------------------

Fixed multiple bugs:

. scratch folder cleaning issue and multiprocessing conflist issues resolved
. tumor_specificity issue resolved
. fix docstring displacement
. In test folder, contain a complete testing case.

----------------------------

Fixed two bugs:

--------------------------
I started this project since ``Feb 2020`` during my second rotation in Dr. Nathan Salomonis Lab, The initial code base can be seen from the first GitHub
repository listed below. The neoantigen has been used in a few manuscript and ongoing project, in which I rename it as ``AltNeo-BT``, the codebase can be
seen from the second GitHub repository.

* `NeoAntigenWorkflow <https://github.com/frankligy/NeoAntigenWorkflow/commit/8aa37114b47513496e0fe14f15155f2bdd159e5d>`_
* `AltNeo-BT <https://github.com/frankligy/AltNeo-BT>`_