Bio.Sequence.HashWord

Documentation

data HashF k

This is a struct for containing a set of hashing functions

Constructors

HF

Fields

hash :: SeqData -> Offset -> Maybe k

calculates the hash at a given offset in the sequence

hashes :: SeqData -> [(k, Offset)]

calculate all hashes from a sequence, and their indices

ksort :: [k] -> [k]

for sorting hashes

genkeys :: HashF k -> HashF k

Adds a default hashes function to a HashF, when hash is defined.

contigous :: Integral k => Int -> HashF k

Contigous constructs an int/eger from a contigous k-word.

rcontig :: Integral k => Int -> HashF k

Like contigous, but returns the same hash for a word and its reverse complement.

compact :: SeqData -> [SeqData]

rcpacked :: Integral k => Int -> HashF k

Like rcontig, but ignoring monomers (i.e. arbitrarily long runs of a single nucelotide are treated the same a single nucleotide.

type Shape = String

gapped :: Integral k => Shape -> HashF k

isN :: Char -> Bool

n2k :: Integral k => Int -> SeqData -> k

n2i' :: Num a => a -> SeqData -> a

k2n :: Integral k => Int -> k -> SeqData

val :: Num t => Char -> t

unval :: Num a => a -> Char

complement :: Char -> Char