AMRFinderPlus v3.8.28

AMRFinderPlus v3.8.28 has several changes, new features requested by users, and some optimization of the handling of certain edge cases.

• amrfinder -u option no longer overwrites databases if they already exist.
  New --force_update option will still overwrite the database as the old -u
  option did. (#16)
• New --protein_output and --nucleotide_output options will produce FASTA files
  containing the sequence of AMRFinderPlus hits
• --mutation_all output has been streamlined and some bugs have been fixed
• New --name option will prepend a "Name" field to every row of the
  AMRFinderPlus report (#25)
• Fusion genes are now reported with both element symbols separated by a '/' on
  both lines of the report. E.g., aac(6')-Ie/aph(2'')-If2
• For HMM-only hits (have HMM in the method column which means they do not have
  BLAST results that meet cutoff) BLAST statistics will now be reported
  if any alignment at that location was made.
• When in COMBINED (nucleotide + protein) mode and when an "INTERNAL_STOP" is detected
  at a locus that also has a protein, the protein result will be reported with
  Method of INTERNAL_STOP (Previously the nucleotide result was reported. This
  would affect the identity, length, and coverage statistics AMRFinderPlus reports.)
• Improved handling of partial alignments for point-mutation detection, including
  prioritization of translated matches (POINTX) when the protein match identifies fewer
  known SNPs.
• Incorrect amino acids inferred by protein annotations extended in the 5' (N-terminal)
  direction because correct annotations start with alternative start codons will
  no longer count as mismatches.
• Small improvements in performance.