Module rrl

Structs§

ResistanceVariant 🔒
RrlSnpCall
RrlSusceptibilityCalls: All rrl susceptibility evidence for one sample, ready for UI display.

RRL_REFS 🔒: Parsed and substring-deduplicated rrl reference sequences, initialised once.
RRL_RESISTANCE_SNPS 🔒

call_rrl_snps 🔒
find_rrl_ntm_display_window 🔒: Locate the SNP site in a Sanger read and return the scan-coordinate window to display around it.
identify_sequence_rrl_ntm: Database was generated by filtering NCBI Nucleotide for Mycobacteriaceae[Organism] AND (23S ribosomal RNA[Title] OR rrl[Gene Name]) AND 1000:3200[SLEN] AND type_material[Filter] (via fetch_myco_sequences() in build.rs). Added to this database are the rrl sequences found in ntm-db (via extract_ntm_db_sequences() in build.rs).
is_susceptible_rrl: Returns Some(true) for wildtype (susceptible), Some(false) for a resistance-conferring mutation, and None when the call is undetermined.
is_susceptible_rrl_by_position: Returns susceptibility based on position 2058/2059 alone, without considering SNP calls.
is_susceptible_rrl_by_snp_calls: Returns Some(false) if any observed SNP base is a resistance-conferring alt, or None if no resistance alt is observed.
is_susceptible_rrl_by_snp_calls_rare: Returns Some(false) only when position 2058/2059 is wildtype (Some(true)) and a resistance-conferring SNP alt is observed elsewhere; otherwise returns None. This captures rare mutations where resistance is not due to 2058/2059.
parse_rrl_resistance_snps 🔒

RrlSnpMap 🔒: Maps a reference position to (wt_base, alts) where alts maps each resistance alt to (drugs, E.coli nomenclature).