Crate li_stephens

Crate li_stephens 

Source

Functionsยง

is_base
Quick helper function for testing whether or not a character is a valid base pair
li_stephens_probs
Calculates the liklihood of a given test sequence being generated from the same population that generated the given haplotypes and a rate for mutations and recombinations. The haplotypes and test sequence must be input as a vector of strings and a string respectively.
li_stephens_probs_matrix
Calculates the liklihood of a given test sequence being generated from the same population that generated the given haplotypes and a rate for mutations and recombinations. The haplotypes and test sequence must be input as a matrix of characters. The lenght of all the haplotypes and the test sequence must be the same and all characters in uppercase.