Sequences not found in any individual are an artefact of coverage filtering and are not relevant for other analyses

Added min coverage to process reads and implemented C-style file write (optimization still necessary)

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