API Reference

Substitution

Represents the presence of a T at a given position. The position is stored outside this struct.

Deletion

Represents the deletion of N symbols. The location of the deletion is stored outside this struct

Insertion{S <: BioSequence}

Represents the insertion of a S into a sequence. The location of the insertion is stored outside the struct.

Haplotype{S<:BioSequence,T<:BioSymbol}

A set of variations within a given sequence that are all found together. Depending on the field, it might also be referred to as a "genotype" or "strain."

Constructors

Haplotype(ref::S, edits::Vector{Edit{S,T}}) where {S<:BioSequence,T<:BioSymbol}
Haplotype(ref::S, vars::Vector{Variation{S,T}}) where {S<:BioSequence,T<:BioSymbol}
Haplotype(
    aln::PairwiseAlignment{T,T}
) where {T<:LongSequence{<:Union{BS.AminoAcidAlphabet,BS.NucleicAcidAlphabet}}}

When constructing a Haplotype from a vector of Edits or Variations, the edits are applied sequentially from first to last position, therefore the vector must always be sorted by position. These edits are sorted automatically if constructing from an alignment.

reference(h::Haplotype)

Gets the reference sequence of h.

variations(h::Haplotype{S,T}) where {S,T}

Converts the Edits of h into a vector of Variations.

reconstruct(h::Haplotype)

Apply the edits in h to the reference sequence of h and return the mutated sequence

translate(hap::Haplotype{S,T}, aln::PairwiseAlignment{S,S}) where {S,T}

Convert the variations in hap to a new reference sequence based upon aln. The alignment rules follow the conventions of translate(::Variation, PairwiseAlignment). Indels at the beginning or end may not be preserved. Returns a new Haplotype

Variation{S<:BioSequence,T<:BioSymbol}

A single change to a biological sequence. A general wrapper that can represent a sequence-specific Substitution, Deletion or Insertion. Variation is more robust than Edit, due to inclusion of the reference sequence and built-in validation.

Constructors

Variation(ref::S, e::Edit{S,T}) where {S<:BioSequence,T<:BioSymbol}
Variation(ref::S, edit::AbstractString) where {S<:BioSequence}

Generally speaking, the Edit constructor should be avoided to ensure corectness: use of variations(::Haplotype) is encouraged, instead.

Constructing a Variation from an AbstractString will parse the from edit using the following syntax:

• Substitution: "<REFBASE><POS><ALTBASE>", e.g. "G16C"
• Deletion: "Δ<STARTPOS>-<ENDPOS>", e.g. "Δ1-2"
• Insertion: "<POS><ALTBASES>", e.g. "11T"

reference(v::Variation)

Gets the reference sequence of v

mutation(v::Variation)

Gets the underlying Substitution, Insertion, or Deletion of v.

translate(var::Variation{S,T}, aln::PairwiseAlignment{S,S}) where {S,T}

Convert the difference in var to a new reference sequence based upon aln. aln is the alignment of the old reference (aln.b) and the new reference sequence (aln.seq). Returns the new Variation.

refbases(v::Variation)

Get the reference bases of v. Note that for deletions, refbases also returns the base before the deletion in accordance with the REF field of the VCF v4 specification.

altbases(v::Variation)

Get the alternate bases of v. Note that for insertions, altbases also returns the base before the insertion in accordance with the ALT field of the VCF v4 specification.

Edit{S <: BioSequence, T <: BioSymbol}

An edit of either Substitution{T}, Insertion{S} or Deletion at a position. If deletion: Deletion of length L at ref pos pos:pos+L-1 If insertion: Insertion of length L b/w ref pos pos:pos+1

_mutation(e::Edit)

Returns the underlying Substitution, Insertion, or Deletion of e.

_lendiff(edit::Edit)

Gets the number of bases that edit adds to the reference sequence

_edits(h::Haplotype)

Gets the Edits that comprise h

_is_valid(h::Haplotype{S,T}) where {S,T}

Validate h. h is invalid if any of its operations are out of bounds, or the same position is affected by multiple edits.

_edit(v::Variation)

Gets the underlying Edit of v

_is_valid(v::Variation)

Validate v. v is invalid if its opertation is out of bounds.