Filename changes
- renamed AMR marker list to AMR_genes_mutations_plasmids.csv
- renamed Genotype_specification.csv to GenoTyphi_specification.csv
Changes to AMR/plasmid marker probeset
- corrected OXA-7 to ampicillin resistance not ESBL
- added probes for carbapenemase genes
- added probes for plasmids IncX1, p0111
Changes to parse_typhi_mykrobe.py
- changed output column header from 'species' to 'serovar'
- changed drug column name from 'sulfamethoxazole' to 'trimethoprim-sulfamethoxazole'