BioSequences.jl patch

# Create a 4 bit DNA/RNA sequence from a 2 bit DNA/RNA sequence, and vice-versa.
function BioSequence{DNAAlphabet{N}}(seq::BioSequence{DNAAlphabet{M}}) where {N<:Int,M<:Int}
    @assert N == 4 && M == 2
    newseq = BioSequence{DNAAlphabet{4}}(length(seq))
    for (i, x) in enumerate(seq)
        unsafe_setindex!(newseq, x, i)
    end
    return newseq
end
function BioSequence{DNAAlphabet{M}}(seq::BioSequence{DNAAlphabet{N}}) where {N<:Int, M<:Int}
    @assert N == 4 && M == 2
    newseq = BioSequence{DNAAlphabet{2}}(length(seq))
    for (i, x) in enumerate(seq)
        unsafe_setindex!(newseq, x, i)
    end
    return newseq
end
function BioSequence{RNAAlphabet{N}}(seq::BioSequence{RNAAlphabet{M}}) where {N<:Int, M<:Int}
    @assert N == 4 && M == 2
    newseq = BioSequence{RNAAlphabet{4}}(length(seq))
    for (i, x) in enumerate(seq)
        unsafe_setindex!(newseq, x, i)
    end
    return newseq
end
function BioSequence{RNAAlphabet{M}}(seq::BioSequence{RNAAlphabet{N}}) where {N<:Int, M<:Int}
    @assert N == 4 && M == 2
    newseq = BioSequence{RNAAlphabet{2}}(length(seq))
    for (i, x) in enumerate(seq)
        unsafe_setindex!(newseq, x, i)
    end
    return newseq
end

function BioSequence{DNAAlphabet{M}}(seq::BioSequence{RNAAlphabet{M}}) where M<:Int
    @assert M == 2
    newseq = BioSequence{DNAAlphabet{2}}(seq.data, seq.part, true)
    seq.shared = true
    return newseq
end
function BioSequence{RNAAlphabet{M}}(seq::BioSequence{DNAAlphabet{M}}) where M<:Int
    @assert M == 2
    newseq = BioSequence{RNAAlphabet{2}}(seq.data, seq.part, true)
    seq.shared = true
    return newseq
end
function BioSequence{DNAAlphabet{N}}(seq::BioSequence{RNAAlphabet{N}}) where N<:Int
    @assert N == 4
    newseq = BioSequence{DNAAlphabet{4}}(seq.data, seq.part, true)
    seq.shared = true
    return newseq
end
function BioSequence{RNAAlphabet{N}}(seq::BioSequence{DNAAlphabet{N}}) where N<:Int
    @assert N == 4
    newseq = BioSequence{RNAAlphabet{4}}(seq.data, seq.part, true)
    seq.shared = true
    return newseq
end

function Base.repeat(chunk::BioSequence{A}, n::Integer) where {A<:Alphabet}
    seq = BioSequence{A}(length(chunk) * n)
    offset = 1
    for _ in 1:n
        copyto!(seq, offset, chunk, 1)
        offset += length(chunk)
    end
    return seq
end