Increase default flank length from 20 to 100
Add script with code to run primer3 and do digital digests
Change way enzymes are formatted in caps marker hash
Define design_primers and get_snp_positions subs
Skip markers w/o good primers
Define digest_amplicons & get_fragment_lengths subs
Add TODOs
Refactor design_primers sub
Write primer and digest info to file
Fix multi_cut logic
Sort chromosomes when writing primer file
Add TODOs
Run all calls to primer3 in one step (fails because 'Argument list too long')
Write primer3 parameters and run primer3 using the parameters file (1.5x as fast)
Add verbose mode
Remove completed TODOs
Add CAPS marker counter
Gitignore output files and repro-archive
Add TODOs
Fix bug: CAPS markers based on presence of restriction site in id1 genotype only