Resistance kmers

[ar0ch]

The following functionality needs to be added:

• Standardize naming scheme and file form for resistance kmer "db" file
• New section to configuration file for resistance kmer file
• Update config loading function for resistance kmer section
• Convert user input kmers to REGEX
• Add two-pass classification for read processor

[ar0ch]

#16 Tracking code additions

[ar0ch]

Proposed definition:

>header
NNNATGNNN

Where header is a heading matching the characterization column, N's are any base that get transformed into the REGEX [ATCG]{1} and ATG is the codon of interest. Multiple codons may be represented in the string, e.g. NNNGAANNNNNNATA