genesis v0.33.0

Notable changes

• sequence
  • Add k-mer classes and functions
    • Extraction from sequences and strings
    • Scanning microvariant neighborhood
    • Minimal canonical encoding functionality
    • Helper functions for canonical k-mers
  • Add setting for Fasta Reader to not validate labels
  • Allow empty sequences in Fastx Input View Stream
• taxonomy
  • Change Taxon ID to uint instead of string
  • Refactor Taxonomy for simplicity and speed
  • Refactor NCBI taxonomy reader to improve speed and memory
  • Add Accession Lookup table class
  • Add Taxon Kmer Data class
  • Add Taxonomy kmer grouping functions
  • Add Taxonomy Json Reader and Writer
• utils
  • Bitvector
    • Refactor Bitvector to use more free functions
    • Add functions offering different lengths policies
    • Add find first and last bit set functions
    • Add Jaccard similarity functions
    • Add Bitvector serialization functionality
  • Add hierarchical agglomerative clustering functionality
  • Add Bitpacked Vector class
  • Add Concurrent Vector Guard class
  • Add Shannon entropy function
  • Extend median and quartiles functions to other numerical types
  • Refactor serialization functionality for simplicity
  • Add Thread Local Cache helper class
  • Add exception handler callback to Thread Pool
  • Refine Thread Pool timed wait functions
• CMake and build
  • Fix compatibility issues with C++17 and later
  • Add auto-detection of C++ standard to CMake
  • Activate automatic AVX detection in CMake
  • Deprecate MacOS 12 in GitHub Actions CI

Bug fixes

• Fix several issues with different compilers in CI
• Fix exception handling bug in Thread Pool
• Fix numerical epsilon for SVG color bar
• Fix nan lengths in Jplace Writer
• Fix taxonomy data check functions
• Fix taxonomy preorder iterator reference bugs
• Fix edge case in Newick Reader