This pipeline doesn't use Stacks anymore, a replacement for stacks was implemented (still need to implemented process_radtags)
The python pipeline to be used with Stacks was moved to a legacy branch

For now, only implemented in loci_matrix, will be added to other components in the future. Eventually, there won't be a need for haplotypes file anymore

Moved file detection to parameters object. Streamlined function parameters, most things are stored in global parameters object

Tested quickly on frequencies, haplotypes, and heatmap

Statistics are now done in R when plotting the heatmap.
Test will be added again in this pipeline in a module to generate fasta file for significant sequences

First version of README
Added MIT License
Added install_packages.R script which installs packages required for visualization
Added examples directory with example plots