call_erm41_lof_snps

cosmic_files::sequencing::erm41

Function call_erm41_lof_snps 

Source 
fn call_erm41_lof_snps(
    snps: &BTreeMap<usize, (u8, BTreeMap<u8, (String, Option<String>)>)>,
    ga: &GappedAlignment,
) -> Vec<Erm41LofCall>
Expand description

Maps each known loss-of-function SNP position to the base observed in the query sequence, adjusting for the alignment offset between reference and query coordinates.

snps maps each reference position to (wt_base, lof_alts), where lof_alts maps each loss-of-function alternate base to a (mutation_label, drug) pair.