4817c8016a
feat: Add alignment(::Haplotype) function
2023-04-08 20:24:35 -05:00
95ef4fdc62
test: Add tests for cigar(::Haplotype)
2023-04-08 20:23:39 -05:00
719a123992
feat: Add cigar(::Haplotype) function
2023-04-08 20:23:34 -05:00
e84f765357
feat: Add _cigar_between(::Variation, ::Variation) function
...
Add a function that can calculate the matching bases between two
(non-matching) Variations and return a matching (M) CIGAR operation
2023-04-08 20:19:49 -05:00
c3a7788dbd
feat: Add _cigar(::Variation) function
...
Add a function that can convert the information contained in an
Insertion or a Deletion into a CIGAR operator.
2023-04-08 20:19:46 -05:00
011651857f
Bump version number in Project.toml to 0.2.2
2023-01-28 20:07:48 +00:00
4f39d9c822
Update CHANGELOG for v0.2.2
2023-01-28 20:07:48 +00:00
4f046fef9f
Update CHANGELOG
2023-01-28 19:57:10 +00:00
282050d442
Fix validation code for Haplotype
2023-01-28 19:57:10 +00:00
7bd39b1d54
Add tests for _is_valid(::Haplotype)
2023-01-28 19:57:10 +00:00
57ebe391bf
Fix tests for _is_valid(::Haplotype)
2023-01-28 19:57:10 +00:00
2a5a5389ec
Add tests for _is_valid(::Haplotype)
2023-01-28 19:57:10 +00:00
9776d5a31e
Bump version number in Project.toml to 0.2.1
2023-01-11 17:32:15 -06:00
d53acf0df9
Update CHANGELOG for v0.2.1
2023-01-11 17:32:15 -06:00
b7d4831cf2
Update CHANGELOG
2023-01-11 17:17:10 -06:00
2fa5782719
Add more informative errors to _is_valid
2023-01-11 17:17:10 -06:00
4e6c781c60
Update CHANGELOG
2023-01-11 15:01:43 -06:00
d0f55742d6
Add documentation for haplotype reference switching
2023-01-11 15:01:43 -06:00
ecaa995d2b
Update API documentation for different translate methods
2023-01-11 15:01:43 -06:00
6a4a39c859
Add tests for translate(::Haplotype)
2023-01-11 15:01:43 -06:00
a61a80d586
Add translate function for Haplotypes
2023-01-11 15:01:43 -06:00
e251b292a7
Fix tests for translate(::Variation)
2023-01-11 15:01:43 -06:00
239b366a1c
Add tests for translate(::Variation)
2023-01-11 15:01:43 -06:00
f38f0edb00
Bump version number to 0.2.0 in Project.toml
2023-01-10 12:29:04 -06:00
a437409afc
Update test information in READMEs
2023-01-10 12:29:04 -06:00
52d401d623
Update CHANGELOG for v0.2.0
2023-01-10 12:29:04 -06:00
381e4f9736
Add Zenodo badge
2023-01-10 18:12:03 +00:00
e621983dd5
Update CHANGELOG
2023-01-10 12:00:50 -06:00
c360caf9bd
Add tests for Variation sorting
2023-01-10 12:00:50 -06:00
0b2879b78c
Add isless function for Variation
2023-01-10 12:00:50 -06:00
6119368af3
Add tests for Edit sorting
2023-01-10 12:00:50 -06:00
860ce56b34
Add isless function for Edit
2023-01-10 12:00:50 -06:00
2ff4181dd8
Fix deletion equality function
...
Fixes: da2cbbd528
2023-01-10 11:41:08 -06:00
5bd939a15c
Update CHANGELOG
2023-01-10 11:22:06 -06:00
6c86782a2c
Update documentation to reflect new reconstruct syntax
2023-01-10 11:22:06 -06:00
b870007826
Add test for reconstruct function
2023-01-10 11:22:06 -06:00
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.
2023-01-10 11:22:06 -06:00
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.
2023-01-10 11:22:06 -06:00
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.
2023-01-05 11:58:29 -06:00
4e0d88039d
Update CHANGELOG
2023-01-05 11:58:29 -06:00
1384783fcc
Update documentation wording to reflect new type names
2023-01-05 11:58:29 -06:00
46c84b06bb
Rename variants.md to haplotypes.md
2023-01-05 11:58:29 -06:00
5839de3ce1
Rename Variant type to Haplotype
2023-01-05 11:58:29 -06:00
44aa41e628
Rename Variant.jl to Haplotype.jl
2023-01-05 11:58:29 -06:00
3ef4a92ba2
Update CHANGELOG
2023-01-04 11:56:45 -06:00
8ae09aa9a1
Add linting workflow for PRs
2023-01-04 11:56:45 -06:00
d29764d2bc
Apply Blue style to tests file
2023-01-04 11:56:45 -06:00
fb9ab68cca
Apply Blue style to docs file
2023-01-04 11:56:45 -06:00
cb53defe9a
Add Aqua tests
2023-01-04 11:56:45 -06:00
1942090cd6
Remove Windows and Mac CI tests
...
There is no platform-specific code in this package, so this just slows down
CI with no benefit
2023-01-04 11:56:45 -06:00
