This is a complete re-implementation of HULK. The change log states the main changes:
- fully re-written codebase
- I've aimed for it to be largely backwards compatible with previous releases
- fully open-sourced!
- MIT license (OSI approved)
- algorithm changes
- underlying histogram is now based on minimizer frequencies
- count-min sketch for k-mer frequencies is now replaced with a fixed-size array and a jump-hash for minimizer placement
- changes to the
sketchsubcommand:- sketches saved to JSON by default (ala sourmash)
- histosketch count-min sketch is no longer configurable by the user (this was Epsilon and Delta)
- spectrum size is determined based on k-mer size
- minCount for k-mer frequencies is removed
- changes to the
smashsubcommand:- operates on JSON input
- outputs matrix as csv
- replaced some unecessary features
- the functionality of the
printanddistancesubcommands is available in thesmashsubcommand
- the functionality of the