Parsnp v2.0.0

What's Changed

• You can now pass a newline-separated file of paths to query sequences to -d in addition to directories and command-line lists.
• Adds --partition flag, which splits recruited genomes into partitions of size --partition-size (default 50).
• Adds --no-recruit option which skips the recruitment step, but still drops genomes if their size differs substantially from the reference.
• Fixes multiple bugs in the output:
  • Output can now be parsed by BioPython's AlignIO module with the "mauve" format
  • LCBs no longer overlap
  • Ambiguous base pairs and small contigs no longer lead to incorrect coordinates
  • VCF now contains the correct reference allele.
• FastANI now guarantees at least 100 segments (unless it requires a fragment length < 500)
• Adds --min-ref-cov option (default 90), which when used with --use-ani, removes query genomes that do not cover at least 90% of the reference.
• Output folder has been reorganized to separate logs and config files from the main output.