VariationInfo

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

Represents statistics associated with a SequenceVariation.Variation within an aligned sequencing read.

Fields

• variation::Variation{S,T}: The Variation this object represents
• readpos::Float64: The location where variation occurs within a sequencing read
• quality::Float64: The phred-scaled basecall quality of variation
• Strand::GenomicFeatures.Strand: Which strand variation appears on

quality(vi::VariationInfo) -> Float64

Gets the phred-scaled basecall quality of variation(vi) within a sequencing read

readpos(vi::VariationInfo) -> Float64

Gets the position of variation(vi) within a sequencing read

strand(vi::VariationInfo) -> GenomicFeatures.Strand

Gets the strand that variation(vi) appears on

variation(vi::VariationInfo) -> SequenceVariation.Variation

Gets the Variation of a VariationInfo

variationinfos(
    query::Union{SAM.Record,BAM.Record}, reference::NucleotideSeq
) -> Vector{VariationInfo}
variationinfos(
    query::Union{AbstractString,AbstractPath},
    reference::Union{AbstractString,AbstractPath}
) -> Vector{VariationInfo}

Calls Variations based on the alignments in query against reference, and returns every variation call found within query as a Vector{VariationInfo}