Merge branch 'release/v0.2.5'

.github/workflows/CompatHelper.yml

@@ -2,37 +2,16 @@ name: CompatHelper
 
 on:
   schedule:
-    - cron: '00 * * * *'
+    - cron: '0 0 * * *'
 
 jobs:
   CompatHelper:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        julia-version: [1.3.0]
-        julia-arch: [x86]
-        os: [ubuntu-latest]
+    runs-on: ubuntu-latest
     steps:
-      - uses: julia-actions/setup-julia@latest
-        with:
-          version: ${{ matrix.julia-version }}
       - name: Add CompatHelper
-        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
-      - name: CompatHelper.main
+        run: julia --color=yes -e 'using Pkg; Pkg.add("CompatHelper")'
+      - name: Run CompatHelper
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: julia -e '
-                using CompatHelper, Pkg;
-                my_registries = [
-                    Pkg.RegistrySpec(
-                        name = "BioJuliaRegistry",
-                        uuid = "ccbd2cc2-2954-11e9-1ccf-f3e7900901ca",
-                        url = "https://github.com/BioJulia/BioJuliaRegistry.git"
-                    ),
-                    Pkg.RegistrySpec(
-                        name = "General",
-                        uuid = "23338594-aafe-5451-b93e-139f81909106",
-                        url = "https://github.com/JuliaRegistries/General.git"
-                    )
-                ];
-                CompatHelper.main(; registries = my_registries, master_branch = "master");'
+          COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}
+        run: julia --color=yes -e 'using CompatHelper; CompatHelper.main(master_branch = "master")'

.github/workflows/Documentation.yml

@@ -1,34 +1,26 @@
-name: Documentation
+name: Build Documentation
 
 on:
-    push:
-        branches:
-            - 'master'
-            - 'develop'
-            - 'release/.*'
-        tags: '*'
-    pull_request:
+  push:
+    branches:
+      - master
+      - develop
+      - release/*
+    tags: '*'
+  pull_request:
 
 jobs:
   build:
-    runs-on: ${{ matrix.os }}
-    strategy:
-      matrix:
-        julia-version: [1.3.0]
-        julia-arch: [x86]
-        os: [ubuntu-latest]
+    runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v1.0.0
-      - uses: julia-actions/setup-julia@latest
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
         with:
-          version: ${{ matrix.julia-version }}
-      - name: Install dependencies
-        run: |
-          julia ci_prep.jl;
-          julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
-      - name: Build and deploy
+          version: '1'
+      - name: Install Dependencies
+        run: julia --color=yes --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and Deploy
         env:
-          # https://github.com/JuliaDocs/Documenter.jl/issues/1177
           # GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
-        run: julia --project=docs/ --color=yes docs/make.jl
+        run: julia --color=yes --project=docs/ docs/make.jl

.github/workflows/TagBot.yml

@@ -1,7 +1,7 @@
 name: TagBot
 on:
   schedule:
-    - cron: '0 * * * *'
+    - cron: '0 0 * * *'
 jobs:
   TagBot:
     runs-on: ubuntu-latest
@@ -10,4 +10,3 @@ jobs:
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           ssh: ${{ secrets.TAGBOT_KEY }}
-          registry: BioJulia/BioJuliaRegistry

.github/workflows/UnitTests.yml

@@ -1,22 +1,44 @@
-name: Unit tests
+name: Unit Tests
 
-on: [push, pull_request]
+on:
+  - push
+  - pull_request
 
 jobs:
   test:
     runs-on: ${{ matrix.os }}
+    continue-on-error: ${{ matrix.experimental }}
     strategy:
+      fail-fast: false
       matrix:
-        julia-version: ['1.1', '1.2', '1.3']
-        julia-arch: [x64]
+        julia-version:
+          - '1.0' # LTS
+          - '1'
+        julia-arch: [x64, x86]
         os: [ubuntu-latest, windows-latest, macOS-latest]
+        experimental: [false]
+        include:
+          - julia-version: nightly
+            julia-arch: x64
+            os: ubuntu-latest
+            experimental: true
 
     steps:
-      - uses: actions/[email protected]
-      - uses: julia-actions/setup-julia@v1
+      - name: Checkout Repository
+        uses: actions/checkout@v2
+      - name: Setup Julia
+        uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.julia-version }}
-          arch: ${{ matrix.julia-arch }}
-      - name: Install dependencies
-        run: julia ci_prep.jl
-      - uses: julia-actions/julia-runtest@master
+      - name: Run Tests
+        uses: julia-actions/julia-runtest@latest
+      - name: Create CodeCov
+        uses: julia-actions/julia-processcoverage@v1
+      - name: Upload CodeCov
+        uses: codecov/codecov-action@v1
+        with:
+          file: ./lcov.info
+          flags: unittests
+          name: codecov-umbrella
+          fail_ci_if_error: false
+          token: ${{ secrets.CODECOV_TOKEN }}

Project.toml

@@ -1,7 +1,7 @@
 name = "XAM"
 uuid = "d759349c-bcba-11e9-07c2-5b90f8f05f7c"
 authors = ["Kenta Sato <[email protected]>", "Ben J. Ward <[email protected]>", "Ciarán O'Mara <[email protected]>"]
-version = "0.2.4"
+version = "0.2.5"
 
 [deps]
 Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
@@ -19,11 +19,11 @@ Automa = "0.7, 0.8"
 BGZFStreams = "0.3"
 BioAlignments = "2"
 BioGenerics = "0.1"
-BioSequences = "2"
+BioSequences = "2.0.4"
 GenomicFeatures = "2"
 Indexes = "0.1"
 TranscodingStreams = "0.6, 0.7, 0.8, 0.9"
-julia = "1.1"
+julia = "1"
 
 [extras]
 FormatSpecimens = "3372ea36-2a1a-11e9-3eb7-996970b6ffbd"

README.md

@@ -11,18 +11,11 @@
 blog post").
 
 ## Description
-XAM provides I/O and utilities for manipulating SAM and BAM formatted alignment map files.
+The XAM package provides I/O and utilities for manipulating SAM and BAM formatted alignment map files.
 
 ## Installation
-The latest version of XAM is made available to install through BioJulia's package registry.
-By default, Julia's package manager only includes the "General" package registry.
-
-To add the BioJulia registry from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/), press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), then enter the following command:
-```julia
-registry add https://github.com/BioJulia/BioJuliaRegistry.git
-```
-
-Once the registry is added to your configuration, you can install XAM while in [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/) with the following:
+You can install the XAM package from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/).
+Press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), then enter the following command:
 ```julia
 add XAM
 ```

docs/src/index.md

@@ -10,20 +10,11 @@
 > This project follows the [semver](http://semver.org) pro forma and uses the [git-flow branching model](https://nvie.com/posts/a-successful-git-branching-model/).
 
 ## Description
-
-XAM provides I/O and utilities for manipulating SAM and BAM formatted alignment map files.
-
+The XAM package provides I/O and utilities for manipulating SAM and BAM formatted alignment map files.
 
 ## Installation
-The latest version of XAM is made available to install through BioJulia's package registry.
-By default, Julia's package manager only includes the "General" package registry.
-
-To add the BioJulia registry from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/), press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), then enter the following command:
-```julia
-registry add https://github.com/BioJulia/BioJuliaRegistry.git
-```
-
-Once the registry is added to your configuration, you can install XAM while in [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/) with the following:
+You can install the XAM package from the [Julia REPL](https://docs.julialang.org/en/v1/manual/getting-started/).
+Press `]` to enter [pkg mode](https://docs.julialang.org/en/v1/stdlib/Pkg/), then enter the following command:
 ```julia
 add XAM
 ```

docs/src/man/hts-files.md

@@ -287,7 +287,7 @@ SAM.Writer(IOStream(<file my-data.sam>))
 
 ```
 
-To make a BAM Writer is slightly different, as you need to use a specific stream type from the (https://github.com/BioJulia/BGZFStreams.jl)[https://github.com/BioJulia/BGZFStreams.jl] package:
+To make a BAM Writer is slightly different, as you need to use a specific stream type from the [https://github.com/BioJulia/BGZFStreams.jl](https://github.com/BioJulia/BGZFStreams.jl) package:
 
 ```julia
 julia> using BGZFStreams

src/sam/metainfo.jl

@@ -48,7 +48,7 @@ Create a SAM metainfo from `str`.
 
 """
 function MetaInfo(str::AbstractString)
-    return MetaInfo(Vector{UInt8}(str))
+    return MetaInfo(collect(UInt8, str))
 end
 
 """
@@ -198,7 +198,7 @@ function keyvalues(metainfo::MetaInfo)::Vector{Pair{String,String}}
     if iscomment(metainfo)
         throw(ArgumentError("not a dictionary"))
     end
-    return Pair{String,String}[key => val for (key, val) in zip(keys(metainfo), values(metainfo))]
+    return Pair{String, String}.(keys(metainfo), values(metainfo))
 end
 
 function Base.keys(metainfo::MetaInfo)

src/sam/readrecord.jl

@@ -1,12 +1,16 @@
 # Automa.jl generated readrecord! and readmetainfo! functions
 # ========================================
 
+import Automa
+import Automa.RegExp: @re_str
+import Automa.Stream: @mark, @markpos, @relpos, @abspos
+
 # file   = header . body
 # header = metainfo*
 # body   = record*
 const sam_machine_metainfo, sam_machine_record, sam_machine_header, sam_machine_body, sam_machine = (function ()
 
-    isinteractive() && info("compiling SAM")
+    isinteractive() && @info "compiling SAM"
 
     cat = Automa.RegExp.cat
     rep = Automa.RegExp.rep
@@ -161,21 +165,15 @@ function appendfrom!(dst, dpos, src, spos, n)
     if length(dst) < dpos + n - 1
         resize!(dst, dpos + n - 1)
     end
-    copyto!(dst, dpos, src, spos, n)
+    unsafe_copyto!(dst, dpos, src, spos, n)
     return dst
 end
 
 const action_metainfo = quote
+    appendfrom!(metainfo.data, 1, data, @markpos, p-@markpos)
+    metainfo.filled = 1:(p-@markpos)
 
-    let markpos = @markpos()
-
-        appendfrom!(metainfo.data, 1, data, markpos, length(markpos:p-1))
-
-        metainfo.filled = @relpos(markpos):@relpos(p-1)
-
-        found_metainfo = true
-    end
-
+    found_metainfo = true
 end
 
 const sam_actions_metainfo = Dict(
@@ -227,15 +225,11 @@ const sam_actions_record = Dict(
     :record_qual  => :(record.qual  = pos:@relpos(p-1)),
     :record_field => :(push!(record.fields, pos:@relpos(p-1))),
     :record       => quote
-        let markpos = @markpos()
-
-            appendfrom!(record.data, 1, data, markpos, length(markpos:p-1))
-
-            record.filled = @relpos(markpos):@relpos(p-1)
+        appendfrom!(record.data, 1, data, @markpos, p-@markpos)
+        record.filled = 1:(p-@markpos)
 
-            found_record = true
-            @escape
-        end
+        found_record = true
+        @escape
     end
 )
 

src/sam/record.jl

@@ -71,7 +71,7 @@ function Record(str::AbstractString)
 end
 
 function Base.convert(::Type{Record}, str::AbstractString)
-    return Record(Vector{UInt8}(str))
+    return Record(collect(UInt8, str))
 end
 
 function Base.:(==)(a::Record, b::Record)
@@ -399,7 +399,7 @@ function sequence(record::Record)::BioSequences.LongDNASeq
     end
     seqlen = length(record.seq)
     ret = BioSequences.LongDNASeq(seqlen)
-    BioSequences.encode_copy!(ret, 1, record.data, first(record.seq), seqlen)
+    copyto!(ret, 1, record.data, first(record.seq), seqlen)
     return ret
 end
 

src/sam/sam.jl

@@ -5,9 +5,6 @@ module SAM
 
 using BioGenerics
 
-import Automa
-import Automa.RegExp: @re_str
-import Automa.Stream: @mark, @markpos, @relpos, @abspos
 import BioAlignments
 import BioGenerics: BioGenerics, isfilled, header
 import BioGenerics.Exceptions: missingerror