Add code

.gitattributes

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+* text=auto

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/

COPYRIGHT.txt

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+This product includes third party software (“Third Party Programs”). Some of the Third Party Programs are available under open source 
+or free software licenses. The License Agreement accompanying the Licensed Software does not alter any rights or obligations you may 
+have under those open source or free software licenses.  The licenses that govern the terms and conditions of use of the Third Party 
+Programs included in the Licensed Software are provided in this file.  This document also contains copyright statements for the various 
+open source software components (or portions thereof) that are distributed with the Licensed Software.
+
+*************************************************************************************
+
+The following components are covered under the MIT license
+• six-1.12.0-py2.py3-none-any.whl Copyright 2010-2018 Benjamin Peterson
+• pysam-0.15.1-cp36-cp36m-manylinux1_x86_64.whl © 2009 Genome Research Ltd
+
+MIT License
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the 
+"Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, 
+distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject 
+to the following conditions:
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF 
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR
+ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH 
+THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+************************************************************************************
+
+The following components are covered under the BSD-3 license
+• statsmodels-0.9.0-cp36-cp36m-manylinux1_x86_64.whl © 2018 Josef Perktold, Skipper Seabold, Jonathan Taylor,  statsmodels-developers
+• numpy-1.16.3-cp36-cp36m-manylinux1_x86_64.whl "Copyright 2009 Free Software Foundation, Inc; Copyright 2007 Free Software Foundation, 
+Inc.; Copyright 1992-2013 The University of Tennessee and The University; Copyright 2002-2017 Free Software Foundation, Inc.; Copyright 
+2005-2019 NumPy Developers; Copyright 2006-2013 The University of Colorado Denver; Copyright 2000-2013 The University of California 
+Berkeley; and Copyright 2011-2014 The OpenBLAS Project"
+• scipy-1.2.1-cp36-cp36m-manylinux1_x86_64.whl "Copyright 2009 Free Software Foundation, Inc; Copyright 1984-1995 2000 by Stephen L; 
+Copyright 2007 Free Software Foundation, Inc; Copyright 1992-2013 The University of Tennessee and The University; Copyright 2003-2017 
+SciPy Developers; Copyright 2002-2017 Free Software Foundation, Inc; Copyright 2012 Massachusetts Institute of Technology; Copyright 
+2006-2013 The University of Colorado Denver; Copyright 2003-2009 The Regents of the University of California; Copyright 2000-2013 The
+University of California Berkeley; Copyright 2001-2002 Enthought, Inc; and Copyright 2011-2014 The OpenBLAS Project"		
+
+BSD-3 License
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions 
+are met: 
+* Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 
+* Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the 
+documentation and/or other materials provided with the distribution. 
+* Neither the name of the Copyright Holders nor the names of its contributors may be used to endorse or promote products derived from 
+this software without specific prior written permission. 
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT 
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE 
+COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
+BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER 
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN 
+ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 
+
+Code generated by the Protocol Buffer compiler is owned by the owner of the input file used when generating it.  This code is not 
+standalone and requires a support library to be linked with it.  This support library is itself covered by the above license.
+
+*************************************************************************************
+
+The following component is covered under the BSD-2 license
+• patsy-0.5.1-py2.py3-none-any.whl	© 2012 Patsy Developers	
+
+BSD-2 License
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions 
+are met:
+1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in 
+the documentation and/or other materials provided with the distribution.
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT 
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE 
+COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES 
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) 
+HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) 
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+**************************************************************************************************************************
+
+For the programs or components that are licensed under an open source license that gives you the right to receive the source code for 
+that binary, you can obtain a copy of the applicable source code on physical media by submitting a written request to:
+Illumina, Inc. 
+Attn: Legal Department
+5200 Illumina Way
+San Diego, CA 92122
+We may charge you a fee to cover the cost of physical media and processing. Your request must be sent (i) within three (3) years of 
+the date you received the Illumina product that included the component or binary file(s) that are the subject of your request.