struct Record
	seq::Array{UInt8}
	name::String
	meta::String
end

A record obtained when parsing a single entry of a FASTA file.

struct Score <: AbstractArray{Float64,2}
	rows::Int
	cols::Int
	band::NamedTuple{(:lower, :upper)}
	data::Array{Float64}
	offset::Array{Int}
	starts::Array{Int}
	stops::Array{Int}
end

Store information about a banded pairwise alignment.

cost = (
	open   = -6.0,
	extend = -1.0,
	band   = (
		lower = Inf,
		upper = Inf,
	),
	gap    = k -> k == 0 ? 0 : cost.open + cost.extend*(k-1),
	match  = (c₁, c₂) -> 6.0*(c₁ == c₂) - 3.0,
)

cost are the default dynamic alignment parameters used.

align(seq₁::Array{UInt8}, seq₂::Array{UInt8}, cost::Score)

Perform a pairwise alignment using Needleman-Wunsch style dynamic programming between seq₁ and seq₂ given cost. The cost is defined by the Score structure.

cigar(seq₁::Array{UInt8}, seq₂::Array{UInt8})

Given two sequences, seq₁ and seq₂, perform a pairwise banded alignment and return the cigar string of alignment.

columns(s; nc=80)

Partition string s into an array of strings such that no string is longer than nc characters.

enforce_cutoff!(a::Alignment, χ)

Ensure that the alignment a does not have insertion or deletion segments larger than χ. Return the list of segments created by parsing the alignment such that all segments are larger than χ.

hamming_align(qry::Array{UInt8,1}, ref::Array{UInt8,1})

Perform a simple alignment of qry to ref by minimizing hamming distance. Useful for fast, approximate alignments of small sequences.

random_id(;len=10, alphabet=UInt8[])

Generate a random string of length len drawn from letters in alphabet.

read_fasta(io::IO)

Parse a FASTA file from IO stream io. Return an iterator over all records.

read_mmseqs2(io::IO)

Parse a simil-PAF file produced by mmseq2 from IO stream io. Return an iterator over all pairwise alignments.

read_paf(io::IO)

Parse a PAF file from IO stream io. Return an iterator over all pairwise alignments.

uncigar(cg::String)

Return an interator over intervals of alignment defined by cigar string cg.

write_fasta(io::IO, name, seq)

Output a single FASTA record with sequence seq and name name to IO stream io.

reverse_complement!(hit::Hit)

Reverse complement the qry of Hit in place.

reverse_complement(seq::Array{UInt8})

Return a newly allocated sequence array that is the reverse complement of seq.