AstrobioMike/bit: v1.13.10

Changed

• bit-get-cov-stats
  • the --include-non-primary flag now in addition to calculation percent ID including supplemental and secondary alignments also runs mosdepth with --flag 1540
• bit-dl-ncbi-assemblies
  • in python now instead of bash (i hope this doesn't hinder performance too much...)
  • default concurrent downloads is 10 now instead of 1
  • default format is fasta now instead of gbk
  • downloads only happen in http now, no more ftp, so the -P flag to specify http has been removed
  • added optional output dir
• no longer keeping stubs in scripts/, instead keeping a ton of entry points in pyproject.toml
• bit-filter-seqs-by-length renamed to bit-filter-fasta-by-length to be more specific (prior still retained for now)

Full Changelog: https://github.com/AstrobioMike/bit/compare/v1.13.9...v1.13.10