Cnvpytor

What's new:
- Reduced Pytor file size by compressing the BAF likelihood matrix
- Option to avoid storing the full BAF likelihood matrix (-nolh), drastically reducing the final Pytor file size to less than 50 MB
- If the full BAF likelihood matrix is not stored in Pytor file, during -call step likelihood will be calculated during run time
- Introduced plotting parameter "lh_lite," used when the full BAF likelihood matrix is not present in the Pytor file
- Implemented log scale for Manhattan plot (126)
- Added plot RD difference/ratio between two samples (151)
- Updated the code for VCF output
- Included an error log for missing annotation links in reference genome settings
- Added matplotlib_use parameter to set the Matplotlib backend

Updates
1. Introduction of Semantic Versioning
2. Docs Update

Bug fixes
1. SNP count
2. 88

**CNVpytor:** a python extension of CNVnator

CNVpytor is a Python package and command line tool for CNV/CNA analysis from depth-of-coverage by mapped reads developed in Abyzov Lab, Mayo Clinic.