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52 lines
1.2 KiB
Julia
52 lines
1.2 KiB
Julia
module SequenceVariation
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"""
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Needs to be able to:
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* Given a sequence and a reference, create a `Haplotype` that unambiguously represents
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the sequence
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* Given a `Haplotype` and a new reference, translate the variant to the new reference.
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* Given a mutation and a reference and a sequence, determine if the sequence has that
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mutation
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TODO now:
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* Play around with some NGS results rel. to picked reference.
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* Is it easy to construct ref and variants? I.e. is API nice?
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* Is it nice and easy to check if a mut is present?
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*
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* Implement "reference switching".
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* Add tests
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"""
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using BioAlignments: BioAlignments, PairwiseAlignment, OP_SOFT_CLIP, sequence
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using BioGenerics: BioGenerics, leftposition, rightposition
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using BioSequences: BioSequences, BioSequence, NucleotideSeq, LongSequence, isgap
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using BioSymbols: BioSymbol
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export Deletion
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export Haplotype
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export Insertion
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export Substitution
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export Variation
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export altbases
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export mutation
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export reconstruct
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export refbases
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export reference
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export translate
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export variations
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const BA = BioAlignments
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const BS = BioSequences
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struct Unsafe end
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struct Inapplicable end
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include("Edit.jl")
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include("Haplotype.jl")
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include("Variation.jl")
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end # module
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