
This set of changes will bring about the following:
    - the removal of self alignments, which are probably mostly unnecessary and expensive, saving around 25% in alignment time
    - the ability to plug either minimap2 or lastz for alignment, in the future it should be easy to add others
    - the ability to align a set of phased genomes to a reference, with an outgroup (proto-pangenome pipeline)
    - the addition of chaining to better determine synteny in complex regions


:::::Other todos::::

Minimap2 script (develop script to run minimap2 to align closely related genomic sequences)

Convert Cactus to use PAF [DONE]

Write a PAF library [DONE]

Write tests [PARTIALLY DONE]

Get a dotplot working [DONE]

