VCF comparison remaining tasks

[GARRISON-2]

• Vamos ref comparisons issue
  • as of right now, Vamos levenshtein distances are going to contain more NAs because it is not able to pull the ref sequence
    ( it is not in the current vamos vcf file )
    - if the ref sequence is added to the vcf file, the script should automatically pull it and no changes should need to be made to the code
• Add command line capabilities for taking in the files
  - not necessary for script functionality, but would make it much easier to run multiple times in a row
• How are the off by 1 tools changing the ref
  - is it just a positional change or is the actual ref sequence being shortened or lengthened
• Check strdust reference sequences( The positions are correct, but I think the actual sequences are off by 1)
• On the analysis side of things test if running with trim_alleles = True will improve the longtr and strkit performance or not