Will Rowe Hulk Versions Save

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 sketch subcommand:
  • 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 smash subcommand:
  • operates on JSON input
  • outputs matrix as csv
• replaced some unecessary features
  • the functionality of the print and distance subcommands is available in the smash subcommand

Minor bug fixes and improvements:

• adding buffered channels for read processing and hashing
• swapping countmin sketch parameters (back to epsilon and delta to offer more tuning)
• tweaking jump hash for counter placement in cms
• updating default settings to improve performance after the above changes

This release bumps HULK to a more stable version. Here are a summary of the main changes:

• swap uint64 encoding of k-mers to instead us ntHash (Go implementation)

• replace delta+epsilon values in CMS with a soft memory limit for the CMS structure

• use Jump hash adjusting/querying CMS counters

• also change the XORing of hash function so that the uint64 is split to 2 uint32s, with one of these being altered using the CMS depth iterator.

• allow FASTA input

• bug fixes (histosketch metadata, weighted jaccard similarity

First full release of HULK