From 7b7fa346fd94d9cfced5d55f06786a355a940315 Mon Sep 17 00:00:00 2001 From: Rasmus Henningsson Date: Tue, 18 Aug 2020 17:05:22 +0200 Subject: [PATCH 1/2] Add Project.toml Also fixed deprecation warnings. --- .gitignore | 4 ++++ .travis.yml | 2 +- CHANGELOG.md | 2 ++ Project.toml | 32 ++++++++++++++++++++++++++++++++ REQUIRE | 9 --------- appveyor.yml | 2 +- src/GeneticVariation.jl | 6 ++---- src/site_counting.jl | 6 +++--- 8 files changed, 45 insertions(+), 18 deletions(-) create mode 100644 Project.toml delete mode 100644 REQUIRE diff --git a/.gitignore b/.gitignore index e43b0f9..463c3e1 100644 --- a/.gitignore +++ b/.gitignore @@ -1 +1,5 @@ .DS_Store +*.jl.*.cov +*.jl.cov +*.jl.mem +Manifest.toml diff --git a/.travis.yml b/.travis.yml index 866cb45..f894d36 100644 --- a/.travis.yml +++ b/.travis.yml @@ -3,8 +3,8 @@ os: - linux - osx julia: - - 0.7 - 1.0 + - 1.5 - nightly notifications: email: diff --git a/CHANGELOG.md b/CHANGELOG.md index e54898d..3253f39 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -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 diff --git a/Project.toml b/Project.toml new file mode 100644 index 0000000..4edeecb --- /dev/null +++ b/Project.toml @@ -0,0 +1,32 @@ +name = "GeneticVariation" +uuid = "9bc6ac9d-e6b2-5f70-b0a8-242a01662520" +authors = ["Ben J. Ward "] +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] +Automa = "0.8" +BGZFStreams = "0.3" +BioCore = "2.0.5" +BioSequences = "1.1" +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"] diff --git a/REQUIRE b/REQUIRE deleted file mode 100644 index 9dfcb72..0000000 --- a/REQUIRE +++ /dev/null @@ -1,9 +0,0 @@ -julia 0.7 -Automa 0.7 -BGZFStreams -BioCore 2.0.5 -BioSequences 0.8.0 -BufferedStreams -Combinatorics -Twiddle -IntervalTrees 1.0.0 diff --git a/appveyor.yml b/appveyor.yml index 7bde269..5448ed6 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -1,6 +1,6 @@ environment: matrix: - - julia_version: 1 + - julia_version: 1.5 - julia_version: nightly platform: diff --git a/src/GeneticVariation.jl b/src/GeneticVariation.jl index 5f3e480..df9be5c 100644 --- a/src/GeneticVariation.jl +++ b/src/GeneticVariation.jl @@ -73,11 +73,9 @@ import IntervalTrees: Interval, IntervalValue import Twiddle: enumerate_nibbles, nibble_mask, - count_zero_nibbles, + count_0000_nibbles, count_nonzero_nibbles, - count_one_nibbles, - count_zero_bitpairs, - count_nonzero_bitpairs + count_1111_nibbles include("vcf/vcf.jl") include("bcf/bcf.jl") diff --git a/src/site_counting.jl b/src/site_counting.jl index 5e4de1b..7ca61d7 100644 --- a/src/site_counting.jl +++ b/src/site_counting.jl @@ -77,7 +77,7 @@ for A in (DNAAlphabet, RNAAlphabet) @inline function bp_chunk_count(::Type{Mutated}, ::Type{$A{4}}, a::UInt64, b::UInt64) m = nibble_mask(Certain, a, b) d = (a ⊻ b) & m - return count_nonzero_nibbles(d), count_one_nibbles(m) + return count_nonzero_nibbles(d), count_1111_nibbles(m) end # TODO Finish transitions and transversions @@ -85,8 +85,8 @@ for A in (DNAAlphabet, RNAAlphabet) @inline function bp_chunk_count(::Type{Transition}, ::Type{$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) From 06cf1001642be35e8e05a7831de33893390e6803 Mon Sep 17 00:00:00 2001 From: Rasmus Henningsson Date: Fri, 11 Sep 2020 17:17:59 +0200 Subject: [PATCH 2/2] Compat fixes --- Project.toml | 6 +++--- appveyor.yml | 1 + 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/Project.toml b/Project.toml index 4edeecb..a39fa9c 100644 --- a/Project.toml +++ b/Project.toml @@ -14,10 +14,10 @@ IntervalTrees = "524e6230-43b7-53ae-be76-1e9e4d08d11b" Twiddle = "7200193e-83a8-5a55-b20d-5d36d44a0795" [compat] -Automa = "0.8" +Automa = "0.7, 0.8" BGZFStreams = "0.3" BioCore = "2.0.5" -BioSequences = "1.1" +BioSequences = "1" BufferedStreams = "1" Combinatorics = "0.7" IntervalTrees = "1" @@ -29,4 +29,4 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" [targets] -test = ["Test","YAML"] +test = ["Test", "YAML"] diff --git a/appveyor.yml b/appveyor.yml index 5448ed6..04163aa 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -1,5 +1,6 @@ environment: matrix: + - julia_version: 1.0 - julia_version: 1.5 - julia_version: nightly