Major upgrade

[Takadonet]

Changes:

• Adds ‘#N/A’ to the subtype column if no k-mers are found (#69)
• New QC check for missing nested k-mers leading to the final subtype call (#88)
  • ex. all subtypes is 2, 2.2.2, 2.2.2.2, QC will return that you are missing subtype 2.2
• New Feature: Degenerate Base Expansion for scheme k-mers using the IUPAC degenerate bases (#60)
  • ex. DAR = [‘AAA’, ‘AAG’, ‘GAA’, ‘GAG’, ‘TAA’, ‘TAG’]
• New Schemes:
  • Typhi
  • Typhimurium
  • Mycobacterium Tuberculosis
• Fixes:
  • Changed all mentions of ‘tile’ to ‘kmer’
  • Update enteritidis scheme to 1.0.7
  • Match positive k-mers first (#77)