empty splitread writes
added mate tracker for 2-size pairs
splitread writing works
added bam types
added bam types
lowq and split work up to correctness
write splitread is plugged into parser
new args added to parser
arg parser works w map
range check works
cutoff range check works
basic runs
min pct aligned used but not threaded all the way
minpct aligned passes
min aligned pct now goes to library as well
duplicate is now a type
ignore and platform thread through
lori translation works
lori translation works
rori installed