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Add Project.toml #31

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Apr 16, 2023
Merged

Add Project.toml #31

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7b7fa34
Add Project.toml
rasmushenningsson Aug 18, 2020
06cf100
Compat fixes
rasmushenningsson Sep 11, 2020
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4 changes: 4 additions & 0 deletions .gitignore
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@@ -1 +1,5 @@
.DS_Store
*.jl.*.cov
*.jl.cov
*.jl.mem
Manifest.toml
2 changes: 1 addition & 1 deletion .travis.yml
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Expand Up @@ -3,8 +3,8 @@ os:
- linux
- osx
julia:
- 0.7
- 1.0
- 1.5
- nightly
notifications:
email:
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -5,6 +5,8 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).

## [Unreleased]
### Added
- :arrow_up: Added Project.toml

## [0.4.0] - 2018-11-22
### Added
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32 changes: 32 additions & 0 deletions Project.toml
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@@ -0,0 +1,32 @@
name = "GeneticVariation"
uuid = "9bc6ac9d-e6b2-5f70-b0a8-242a01662520"
authors = ["Ben J. Ward <benjward@protonmail.com>"]
version = "0.4.1"

[deps]
Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
BGZFStreams = "28d598bf-9b8f-59f1-b38c-5a06b4a0f5e6"
BioCore = "37cfa864-2cd6-5c12-ad9e-b6597d696c81"
BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
BufferedStreams = "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d"
Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
IntervalTrees = "524e6230-43b7-53ae-be76-1e9e4d08d11b"
Twiddle = "7200193e-83a8-5a55-b20d-5d36d44a0795"

[compat]
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How sure about these compat bounds are you? I suppose we can just set the bounds to current versions, and then test and relax things if anyone complains.

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I've checked and relaxed the compat bounds.
The biggest issue is incompatibility with BioSequences v2. But that requires larger changes and I think that's better to solve in another release. (And a better approach might be to split out a VCF.jl from this package that will simplify the compatibility situation.)

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Yeah, fixing that seems outside the scope of this PR.

Automa = "0.7, 0.8"
BGZFStreams = "0.3"
BioCore = "2.0.5"
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What's going on here? According to SemVer, this should be the same as 2.0, shouldn't it?

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No, BioCore has some changes (bug fixes?) that we need. The tests won't pass unless we require at least v2.0.5.

BioSequences = "1"
BufferedStreams = "1"
Combinatorics = "0.7"
IntervalTrees = "1"
Twiddle = "1.1"
julia = "1"

[extras]
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"

[targets]
test = ["Test", "YAML"]
9 changes: 0 additions & 9 deletions REQUIRE
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3 changes: 2 additions & 1 deletion appveyor.yml
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@@ -1,6 +1,7 @@
environment:
matrix:
- julia_version: 1
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If we're going to say it's compatible with 1.0, I think we should test on 1.0.

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Agreed!

- julia_version: 1.0
- julia_version: 1.5
- julia_version: nightly

platform:
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6 changes: 2 additions & 4 deletions src/GeneticVariation.jl
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Expand Up @@ -73,11 +73,9 @@ import IntervalTrees: Interval, IntervalValue
import Twiddle:
enumerate_nibbles,
nibble_mask,
count_zero_nibbles,
count_0000_nibbles,
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lol

count_nonzero_nibbles,
count_one_nibbles,
count_zero_bitpairs,
count_nonzero_bitpairs
count_1111_nibbles

include("vcf/vcf.jl")
include("bcf/bcf.jl")
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6 changes: 3 additions & 3 deletions src/site_counting.jl
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Expand Up @@ -77,16 +77,16 @@ for A in (DNAAlphabet, RNAAlphabet)
@inline function bp_chunk_count(::Type{Mutated}, ::Type{$A{4}}, a::UInt64, b::UInt64)
m = nibble_mask(Certain, a, b)
d = (a ⊻ b) & m
return count_nonzero_nibbles(d), count_one_nibbles(m)
return count_nonzero_nibbles(d), count_1111_nibbles(m)
end

# TODO Finish transitions and transversions
# Transition
@inline function bp_chunk_count(::Type{Transition}, ::Type{$A{4}}, a::UInt64, b::UInt64)
m = nibble_mask(Certain, a, b)
d = (a ⊻ b) & m
remcount = count_zero_nibbles(d) # Count of the identical nucleotides.
tve = count_one_nibbles(nibble_mask(0x9999999999999999, d)) # Count the 1001 transversion edge case.
remcount = count_0000_nibbles(d) # Count of the identical nucleotides.
tve = count_1111_nibbles(nibble_mask(0x9999999999999999, d)) # Count the 1001 transversion edge case.
d &= (d >> 1)
d &= 0x7777777777777777
tvc = count_ones(d)
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