v1.2.4

Major Updates

• Parallelized batch mode for the extract module (#25, #32)
  • Allows running extract on a directory of FASTA files (*.fa, *.fna, *.fasta).
  • See the tutorial or run extract -h for details.
• New website
  • Now mobile-friendly and served over HTTPS (finally! 😅).

Bug Fixes

• File deletion failures now raise a warning instead of stopping the process (#21).
• Added directory write-permission checks for outputs and temporary files (#22).

v1.2.3

Major updates

• bioconda support - #16, thanks to @aaronmussig
• Added convertdb module - #17
  • Basically convert module backwards; reverts mmseqs database to CDS FASTA file
• Added -self flag to calculate module - #18
  • Explicitly indicates self batch comparison, in which -i and -j inputs are identical
  • Skips redundant comparisons and assumes self-comparsion to be 100% AAI
  • Improves calculation throughput by slightly more than factor of 2
• Fixed logical flaw around average calculations with custom identity value given - #19

Minor updates

• Added -u option to cluster module, which substitutes leaf labels to UIDs
• Temp directory can be now customized using -tmp option in most of the modules
• extract and convert modules now add ezaai_ prefix to the CDS fasta headers to evade mmseqs header parser
• Compilable maven settings
• Help text formatting

v1.2.2

• Parallelize prodigal with ufasta
• More sensitive binary check
• Minor fixes

v1.2.1

• Auto checks dependent binaries
  • makeblastdb binary is now customizable
  • Adjusted option flags for binary paths
• Fail-safe on zero division
• Process builder stabilization
• Minor fixes

v1.2

• Stand-alone update: Reduced binary size from ~40MB to ~773kB
• License update
• Minor bug fixes