@benedictpaten Unfortunately this isn't the functionality you wanted in that it does not use the index, rather it requires a scan of the whole file.
So you have the choice of
taffy stats -s : use the index to quickly get list of reference contig names and their (estimated) lengths
taffy stats -b : print out a bed of all reference intervals (but requires a full scan).
Putting the intervals themselves in the index requires a fairly major refactor (more than I'd initially thought)-- certainly possible, but not something I want to tackle this week if I can avoid it.
@benedictpaten Unfortunately this isn't the functionality you wanted in that it does not use the index, rather it requires a scan of the whole file.
So you have the choice of
taffy stats -s: use the index to quickly get list of reference contig names and their (estimated) lengthstaffy stats -b: print out a bed of all reference intervals (but requires a full scan).Putting the intervals themselves in the index requires a fairly major refactor (more than I'd initially thought)-- certainly possible, but not something I want to tackle this week if I can avoid it.