millironx/SequenceVariation.jl
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Rename reconstruct! function to reconstruct

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The exclamation mark is conventionally used to mark mutating functions, but
reconstruct is no longer mutating, so change the notation.
This commit is contained in:
Thomas A. Christensen II 2023-01-05 12:32:54 -06:00
parent adbf0ce7f1
commit b80dd8c950
4 changed files with 6 additions and 6 deletions
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2
docs/src/api.md
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@ -21,7 +21,7 @@ Insertion
Haplotype Haplotype
reference(::Haplotype) reference(::Haplotype)
variations variations
reconstruct! reconstruct
``` ```
## Variations ## Variations

4
docs/src/haplotypes.md
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@ -31,11 +31,11 @@ bos_human_haplotype = Haplotype(bos_human_alignment)
If the alternate sequence of a haplotype is no longer available (as is often the If the alternate sequence of a haplotype is no longer available (as is often the
case when calling variants from alignment files), then the sequence can be case when calling variants from alignment files), then the sequence can be
retrieved using the [`reconstruct!`](@ref) function. retrieved using the [`reconstruct`](@ref) function.
```@repl call_variants ```@repl call_variants
human2 = copy(bovine); human2 = copy(bovine);
reconstruct!(human2, bos_human_haplotype) reconstruct(human2, bos_human_haplotype)
human2 == bovine human2 == bovine
human2 == human human2 == human
``` ```

4
src/Haplotype.jl
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@ -162,11 +162,11 @@ reference(h::Haplotype) = h.ref
Base.:(==)(x::Haplotype, y::Haplotype) = x.ref == y.ref && x.edits == y.edits Base.:(==)(x::Haplotype, y::Haplotype) = x.ref == y.ref && x.edits == y.edits
""" """
reconstruct!(h::Haplotype) reconstruct(h::Haplotype)
Apply the edits in `h` to the reference sequence of `h` and return the mutated sequence Apply the edits in `h` to the reference sequence of `h` and return the mutated sequence
""" """
function reconstruct!(h::Haplotype) function reconstruct(h::Haplotype)
len = length(reference(h)) + sum(edit -> _lendiff(edit), _edits(h)) len = length(reference(h)) + sum(edit -> _lendiff(edit), _edits(h))
seq = copy(reference(h)) seq = copy(reference(h))
resize!(seq, len % UInt) resize!(seq, len % UInt)

2
src/SequenceVariation.jl
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@ -32,7 +32,7 @@ export Substitution
export Variation export Variation
export altbases export altbases
export mutation export mutation
export reconstruct! export reconstruct
export refbases export refbases
export reference export reference
export translate export translate