Simulation

struct Params
	N    :: Int
	L    :: Int
	σ    :: Int
	rate :: Rates
end

Store all parameters of a single recombinative Wright-Fisher model. N is the population size. L is the expected genome size of all descendants. σ is the variance of genome size of all descendants. rate is the various rate of evolutionary processes.

struct Rates
	snp :: Float64
	hgt :: Float64
	del :: Float64
	inv :: Float64
end

Store the rates of evolution of mutation snp, recombination hgt, deletion del, and inversion inv.

Sequence = Array{UInt64,1}

A bitpacked array of sequence state. Each UInt64 bits are interpreted as

30 bytes(ancestor) | 30 bytes (location) | 3 bytes (mutation) | 1 byte strand

delete!(s::Sequence, from::Int, to::Int)

Delete the interval from:to from sequence s.

insert!(acceptor::Sequence, donor::Sequence, at::Int)

Insert sequence donor into acceptor at locus at.

invert!(s::Sequence, from::Int, to::Int)

Replace the interval from:to of sequence s with its reverse complement.

model(param::Params)

Return an evolution function based upon parameters param.

mutate!(s::Sequence, at::Int)

Apply a random mutation to sequence s at locus at.

nucleotide(sequence::Array{Sequence}, ancestor::Array{Array{UInt8,1},1})

Generate the set of extant sequences from the ancestral mosiacs sequence and the original sequences ancestor.

pancontig!(s::Sequence, ancestor::Dict{Int,Array{Interval}})

Return the ancestral tiling imprinted upon Sequence s. Modifies ancestor in place.

pancontigs(s::Sequence)

Return the ancestral tiling imprinted upon a set of Sequences isolates.

run(evolve!::Function, time::Int, initial::Array{Array{UInt8,1},1}; graph=false)

The high level API of the module. Evolves a set of initial sequences initial for time generations using the one-step evolution function evolve! If graph is true, the function will return the pangraph associated to the ancestral tiling.