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Update to BioAlignments v3

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This commit is contained in:
Thomas A. Christensen II 2022-11-19 15:32:40 -06:00
parent 4ab07c6857
commit a3cbfcaaee
Signed by: millironx
GPG key ID: 139C07724802BC5D
3 changed files with 328 additions and 368 deletions
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684
Manifest.toml
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File diff suppressed because it is too large Load diff

4
Project.toml
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@ -9,7 +9,6 @@ BioAlignments = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e"
BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea" BioGenerics = "47718e42-2ac5-11e9-14af-e5595289c2ea"
BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59" BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
BioServices = "a0d4ced5-b29c-5395-b614-ca030a679c4b" BioServices = "a0d4ced5-b29c-5395-b614-ca030a679c4b"
BioStructures = "de9282ab-8554-53be-b2d6-f6c222edabfc"
BioSymbols = "3c28c6f8-a34d-59c4-9654-267d177fcfa9" BioSymbols = "3c28c6f8-a34d-59c4-9654-267d177fcfa9"
BusinessDays = "4f18b42c-503e-5345-9536-bb0f25fc7038" BusinessDays = "4f18b42c-503e-5345-9536-bb0f25fc7038"
CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
@ -33,7 +32,6 @@ FASTX = "c2308a5c-f048-11e8-3e8a-31650f418d12"
Formatting = "59287772-0a20-5a39-b81b-1366585eb4c0" Formatting = "59287772-0a20-5a39-b81b-1366585eb4c0"
GFF3 = "af1dc308-cb6b-11e8-32f0-31192efa90f6" GFF3 = "af1dc308-cb6b-11e8-32f0-31192efa90f6"
GLM = "38e38edf-8417-5370-95a0-9cbb8c7f171a" GLM = "38e38edf-8417-5370-95a0-9cbb8c7f171a"
GenomeGraphs = "3aa97884-90e5-11e8-2134-af657ec4f203"
GenomicAnnotations = "4f8a0a0a-376d-5ac0-ab14-e88793df67f0" GenomicAnnotations = "4f8a0a0a-376d-5ac0-ab14-e88793df67f0"
GenomicFeatures = "899a7d2d-5c61-547b-bef9-6698a8d05446" GenomicFeatures = "899a7d2d-5c61-547b-bef9-6698a8d05446"
HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3" HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
@ -50,7 +48,6 @@ JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1"
JuliaWebAPI = "480116ec-64ea-5dec-baca-db6b11e96e37" JuliaWebAPI = "480116ec-64ea-5dec-baca-db6b11e96e37"
Kelpie = "1b112299-d6bc-44e2-912a-478f25731460" Kelpie = "1b112299-d6bc-44e2-912a-478f25731460"
KernelDensity = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b" KernelDensity = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b"
KmerAnalysis = "a20136b7-8e32-4c10-91d3-7060c0bd8ec7"
LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
Libz = "2ec943e9-cfe8-584d-b93d-64dcb6d567b7" Libz = "2ec943e9-cfe8-584d-b93d-64dcb6d567b7"
LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d" LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
@ -72,7 +69,6 @@ PopGen = "af524d12-c74b-11e9-22a8-3b091653023f"
PopGenCore = "45b36091-5ef7-4b08-b448-aaf24c763a14" PopGenCore = "45b36091-5ef7-4b08-b448-aaf24c763a14"
ProtoBuf = "3349acd9-ac6a-5e09-bcdb-63829b23a429" ProtoBuf = "3349acd9-ac6a-5e09-bcdb-63829b23a429"
QuantEcon = "fcd29c91-0bd7-5a09-975d-7ac3f643a60c" QuantEcon = "fcd29c91-0bd7-5a09-975d-7ac3f643a60c"
ReadDatastores = "70a005b8-9d8a-11e9-0d98-c909fa2e52d2"
Roots = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" Roots = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
SequenceVariation = "eef6e190-9969-4f06-a38f-35a110a8fdc8" SequenceVariation = "eef6e190-9969-4f06-a38f-35a110a8fdc8"
StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"

8
README.md
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@ -53,9 +53,9 @@ plus
- [x] [BioAlignments](https://github.com/MillironX/BioAlignments.jl) - [x] [BioAlignments](https://github.com/MillironX/BioAlignments.jl)
- [x] [BioSequences](https://github.com/BioJulia/BioSequences.jl) - [x] [BioSequences](https://github.com/BioJulia/BioSequences.jl)
- [x] [BioStructures](https://github.com/BioJulia/BioStructures.jl) - ~~[ ] [BioStructures](https://github.com/BioJulia/BioStructures.jl)~~ (Dependency mismatch with BioAlignments)
- [x] [BioSymbols](https://github.com/BioJulia/BioSymbols.jl) - [x] [BioSymbols](https://github.com/BioJulia/BioSymbols.jl)
- [x] [GenomeGraphs](https://github.com/BioJulia/GenomeGraphs.jl) - ~~[ ] [GenomeGraphs](https://github.com/BioJulia/GenomeGraphs.jl)~~ (Dependency mismatch with BioAlignments)
- [x] [IntervalTrees](https://github.com/BioJulia/IntervalTrees.jl) - [x] [IntervalTrees](https://github.com/BioJulia/IntervalTrees.jl)
- [x] [SubstitutionModels](https://github.com/BioJulia/SubstitutionModels.jl) - [x] [SubstitutionModels](https://github.com/BioJulia/SubstitutionModels.jl)
@ -76,7 +76,7 @@ plus
### Analyses ### Analyses
- [x] [KmerAnalysis](https://github.com/BioJulia/KmerAnalysis.jl) - ~~[ ] [KmerAnalysis](https://github.com/BioJulia/KmerAnalysis.jl)~~ (Dependency mismatch with BioAlignments)
- [x] [PopGen](https://github.com/BioJulia/PopGen.jl.git) - [x] [PopGen](https://github.com/BioJulia/PopGen.jl.git)
- [x] [SequenceVariation](https://BioJulia/SequenceVariation.jl) - [x] [SequenceVariation](https://BioJulia/SequenceVariation.jl)
@ -95,7 +95,7 @@ plus
### Data Storage and Retrieval ### Data Storage and Retrieval
- [x] [BioServices](https://github.com/BioJulia/BioServices.jl) - [x] [BioServices](https://github.com/BioJulia/BioServices.jl)
- [x] [ReadDatastores](https://github.com/BioJulia/ReadDatastores.jl) - ~~[ ] [ReadDatastores](https://github.com/BioJulia/ReadDatastores.jl)~~ (Dependency mismatch with BioAlignments)
[`JULIA_DEPOT_PATH`]: https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_DEPOT_PATH [`JULIA_DEPOT_PATH`]: https://docs.julialang.org/en/v1/manual/environment-variables/#JULIA_DEPOT_PATH
[biojulia]: https://biojulia.net [biojulia]: https://biojulia.net