Hashfast

[edawson]

This branch brings lots of improvements:

• Improved MKMH minhash library

  Unit Tests Most commonly-used functions now inlined expanded use of lookup tables expanded use of references/pointers over pass-by-value. Refactors HASHTCounter and improves filtering kmers by frequency.

• Addition of kseq_reader library

  buffered FASTQ/FASTA reading Allows Openmp task parallelism + lower RAM usage when done right (at the cost of some speed)

• Improvements to rkmh

  25-50% improvement in speed (basic stream usage up to 2X faster)
  Safer (thanks to mkmh improvements) Reduced RAM usage Crushes some major bugs and memleaks

• Additional documentation

  Readme improvements examples via testing in mkmh Slightly cleaner, better-commented code in places paper directory for JOSS-style writeup Additional test data