BGSpiegl/GCparagon: v0.5.5-beta

Intended for the purpose of SW publication. Includes additional code and plots for target output checking for the processing of 4 WGS samples deposited at the European Genome-Phenome Archive (EGA): https://ega-archive.org/studies/EGAS00001006963 Newest version on this branch can also be cloned using "git clone --branch including_EGAS00001006963_results --single-branch https://github.com/BGSpiegl/GCparagon.git" includes;

main code including setup.py
YAML file for easy conda software environment creation
2bit reference genome download script
exclusion-masked regions processing
preselection of genomic intervals
target output files for preset computation
computation of GC content reference distribution based on fragment length distribution
improvements over 0.5.4:
   + improved alignment filter now does not depend on "aligned in proper pair" flag
   + new validation includes benchmark with Griffin results
   + more customization options on the commandline (also Griffin rare fragment rejection behaviour can be imitated)
   + several smaller bug fixes