Thomas A. Christensen II
282050d442
Fix validation code for `Haplotype`
1 year ago
Thomas A. Christensen II
57ebe391bf
Fix tests for _is_valid(::Haplotype)
1 year ago
Thomas A. Christensen II
2fa5782719
Add more informative errors to `_is_valid`
1 year ago
Thomas A. Christensen II
a61a80d586
Add translate function for Haplotypes
1 year ago
Thomas A. Christensen II
e251b292a7
Fix tests for `translate(::Variation)`
1 year ago
Thomas A. Christensen II
0b2879b78c
Add `isless` function for `Variation`
1 year ago
Thomas A. Christensen II
860ce56b34
Add `isless` function for `Edit`
1 year ago
Thomas A. Christensen II
2ff4181dd8
Fix deletion equality function
...
Fixes: da2cbbd528
1 year ago
Thomas A. Christensen II
b80dd8c950
Rename reconstruct! function to reconstruct
...
The exclamation mark is conventionally used to mark mutating functions, but
reconstruct is no longer mutating, so change the notation.
1 year ago
Thomas A. Christensen II
adbf0ce7f1
Refactor `reconstruct!` to use the built-in reference sequence
...
reconstruct! previously allow changing of _any_ sequence to match a
haplotype, with no check to see if that sequence is compatible with the
reference sequence the haplotype is based on. Change that to only allow
reconstructing sequences from the reference sequence itself, making this a
non-mutating function.
1 year ago
Thomas A. Christensen II
8a71715cd9
Change `v::Haplotype` function arguments to `h::Haplotype`
...
`v` made sense for a `Variant`, but doesn't for a `Haplotype`, so pretty
things up.
1 year ago
Thomas A. Christensen II
1384783fcc
Update documentation wording to reflect new type names
1 year ago
Thomas A. Christensen II
5839de3ce1
Rename `Variant` type to `Haplotype`
1 year ago
Thomas A. Christensen II
44aa41e628
Rename Variant.jl to Haplotype.jl
1 year ago
Thomas A. Christensen II
2a7d61e43d
Add docstrings for Variation functions
1 year ago
Thomas A. Christensen II
673481b40f
Add docstring for Variation
1 year ago
Thomas A. Christensen II
ea25ab87dc
Add docstrings for Variant methods
1 year ago
Thomas A. Christensen II
f49220782b
Add docstring for Variant
1 year ago
Thomas A. Christensen II
f1baf27865
Add docstring for `lendiff(::Edit)`
1 year ago
Thomas A. Christensen II
82ba838614
Add docstring for `mutation(::Edit)`
1 year ago
Thomas A. Christensen II
1f2b116518
Mark is_valid(::Variation) as private function
1 year ago
Thomas A. Christensen II
386acba8ab
Mark `edits(::Variant)` as private API
1 year ago
Thomas A. Christensen II
a573693737
Mark `edit(::Variation)` as private function
1 year ago
Thomas A. Christensen II
2f4f5fb5ae
Mark `is_valid(::Variant)` as private function
1 year ago
Thomas A. Christensen II
2719c438f3
Mark `lendiff(::Edit)` as private API
1 year ago
Thomas A. Christensen II
e8457e4241
Mark `mutation(::Edit)` as private API
1 year ago
Thomas A. Christensen II
cb1c429610
Update getter usage in translate function
1 year ago
Thomas A. Christensen II
ef4460bbbf
Replace field accession with getter function usage
1 year ago
Thomas A. Christensen II
dd405c5f4b
Refactor _lendiff to use multiple dispatch
1 year ago
Thomas A. Christensen II
cab3029bc6
Refactor Edit length to use dispatch instead of type checking
1 year ago
Thomas A. Christensen II
22d460b15a
Remove unused argument names from base getters for edits
1 year ago
Thomas A. Christensen II
da2cbbd528
Add equals functionality to Deletion
1 year ago
Thomas A. Christensen II
f08d6eb991
Add length method for Substitution
1 year ago
Thomas A. Christensen II
3b2730b5c1
Add export for translate and reconstruct!
1 year ago
Thomas A. Christensen II
25c63906dc
Move exports to top of file
...
Per Blue style, exports should be one per line, and appear immediately
after using statements. Reorganize module file to comply
1 year ago
Thomas A. Christensen II
9f9d0899bd
Move Insertion-related code to edits/Insertion.jl
1 year ago
Thomas A. Christensen II
b36ab69c72
Move Deletion-related code to edits/Deletion.jl
1 year ago
Thomas A. Christensen II
ba9f0e8fb1
Move Substitution-related code to edits/Substitution.jl
1 year ago
Thomas A. Christensen II
8c2dd271f3
Move Variation-related code to Variation.jl
1 year ago
Thomas A. Christensen II
37965ac7eb
Move Variant-related code to Variant.jl
1 year ago
Thomas A. Christensen II
3f631ace8f
Move Edit-related code to Edit.jl
1 year ago
Thomas A. Christensen II
fb5b7dfacf
Remove commented-out code
1 year ago
Thomas A. Christensen II
128a5445ad
Switch alignment validation to after edit construction
1 year ago
Thomas A. Christensen II
f9058c5cb3
Update ranges to allow end position insertions
1 year ago
Thomas A. Christensen II
5be4dce200
Add check for soft clips when construction Variants from alignment
1 year ago
Thomas A. Christensen II
d8435be115
Add Variation-level validation for Variants
...
Testing indicates that some Variants (particularly those with insertions
and/or clips at the send of the query sequence) will validate fine as a
Variant, but will fail validation as a Variation. This problem is
particularly annoying when constructing Variants in the REPL, as the
creation will complete successfully, but the show of the Variant will
error out. To fix this, leverage the existing validation of Variation to
check each Edit within a Variant upon construction.
1 year ago
Thomas A. Christensen II
91c3acc85e
Add equality function for Variant
1 year ago
Thomas A. Christensen II
3b33c85d00
Add type parameterization to variations getter
...
I have encountered some cases where having a non-parameterized vector can
crash a downstream process. I don't yet know how to make a MWE of that, but
adding type parameters fixes my problem, and doesn't break any tests here.
2 years ago
Thomas A. Christensen II
f7278bd7d7
Remove unused AminoAcidSeq reference
2 years ago
Thomas A. Christensen II
1bbb85153c
Add constructor for Variant based on Variations
...
A Variant is a collection of Variations, right? Unfortunately there was no
way to convert a collection of Variations into a Variant, so I added one.
2 years ago
