Merge pull request #52 from BioJulia/release/0.3.0

Release v0.3.0

.github/workflows/CompatHelper.yml

@@ -1,17 +1,45 @@
 name: CompatHelper
-
 on:
   schedule:
-    - cron: '0 0 * * *'
-
+    - cron: 0 0 * * *
+  workflow_dispatch:
+permissions:
+  contents: write
+  pull-requests: write
 jobs:
   CompatHelper:
     runs-on: ubuntu-latest
     steps:
-      - name: Add CompatHelper
-        run: julia --color=yes -e 'using Pkg; Pkg.add("CompatHelper")'
-      - name: Run CompatHelper
+           - name: Check if Julia is already available in the PATH
+        id: julia_in_path
+        run: which julia
+        continue-on-error: true
+      - name: Install Julia, but only if it is not already available in the PATH
+        uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+          arch: ${{ runner.arch }}
+        if: steps.julia_in_path.outcome != 'success'
+      - name: "Add the General registry via Git"
+        run: |
+          import Pkg
+          ENV["JULIA_PKG_SERVER"] = ""
+          Pkg.Registry.add("General")
+        shell: julia --color=yes {0}
+      - name: "Install CompatHelper"
+        run: |
+          import Pkg
+          name = "CompatHelper"
+          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
+          version = "3"
+          Pkg.add(; name, uuid, version)
+        shell: julia --color=yes {0}
+      - name: "Run CompatHelper"
+        run: |
+          import CompatHelper
+          CompatHelper.main()
+        shell: julia --color=yes {0}
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}
-        run: julia --color=yes -e 'using CompatHelper; CompatHelper.main(master_branch = "master")'
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}

.github/workflows/Documentation.yml

@@ -1,5 +1,4 @@
-name: Build Documentation
-
+name: Documentation
 on:
   push:
     branches:
@@ -10,17 +9,15 @@ on:
   pull_request:
 
 jobs:
-  build:
+  Documenter:
+    permissions:
+      contents: write
+    name: Documentation    
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
-        with:
-          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
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-docdeploy@v1
         env:
-          # GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
-        run: julia --color=yes --project=docs/ docs/make.jl
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/TagBot.yml

@@ -1,12 +1,22 @@
 name: TagBot
+
 on:
-  schedule:
-    - cron: '0 0 * * *'
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+    inputs:
+      lookback:
+        default: 3
+permissions:
+  contents: write
+
 jobs:
   TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
     runs-on: ubuntu-latest
     steps:
       - uses: JuliaRegistries/TagBot@v1
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          ssh: ${{ secrets.TAGBOT_KEY }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}

.github/workflows/UnitTests.yml

@@ -6,16 +6,20 @@ on:
 
 jobs:
   test:
+    name: Julia ${{ matrix.julia-version }} - ${{ matrix.os }} - ${{ matrix.julia-arch }} - ${{ github.event_name }}
     runs-on: ${{ matrix.os }}
     continue-on-error: ${{ matrix.experimental }}
     strategy:
       fail-fast: false
       matrix:
         julia-version:
-          - '1.0' # LTS
+          - '1.6' # LTS
           - '1'
         julia-arch: [x64, x86]
         os: [ubuntu-latest, windows-latest, macOS-latest]
+        exclude:
+          - os: macOS-latest
+            julia-arch: x86
         experimental: [false]
         include:
           - julia-version: nightly
@@ -31,7 +35,7 @@ jobs:
         with:
           version: ${{ matrix.julia-version }}
       - name: Run Tests
-        uses: julia-actions/julia-runtest@latest
+        uses: julia-actions/julia-runtest@v1
       - name: Create CodeCov
         uses: julia-actions/julia-processcoverage@v1
       - name: Upload CodeCov

CHANGELOG.md

@@ -0,0 +1,27 @@
+# Changelog
+
+All notable changes to HapLink.jl will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+## [0.3.0]
+
+## Added
+
+- Crosschecks for SAM and BAM ([#29](https://github.com/BioJulia/XAM.jl/pull/29))
+- Improved documentation for flags ([#43](https://github.com/BioJulia/XAM.jl/pull/43))
+
+### Changed
+
+- `BAM.quality` performance improved ([#21](https://github.com/BioJulia/XAM.jl/issues/21))
+- Updated BioAlignments to v2.2 and BioSequences to v3 ([#48](https://github.com/BioJulia/XAM.jl/pull/48))
+
+### Fixed
+
+- `BAM.Record` layout now matches the BAM specs ([#26](https://github.com/BioJulia/XAM.jl/pull/26))
+
+[Unreleased]: https://github.com/BioJulia/XAM.jl/compare/v0.3.0...HEAD
+[0.3.0]: https://github.com/BioJulia/XAM.jl/compare/v0.2.8...v0.3.0

Project.toml

@@ -1,7 +1,7 @@
 name = "XAM"
 uuid = "d759349c-bcba-11e9-07c2-5b90f8f05f7c"
 authors = ["Kenta Sato <bicycle1885@gmail.com>", "Ben J. Ward <ward9250@gmail.com>", "Ciarán O'Mara <Ciaran.OMara@utas.edu.au>"]
-version = "0.2.8"
+version = "0.3.0"
 
 [deps]
 Automa = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
@@ -17,18 +17,19 @@ TranscodingStreams = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 [compat]
 Automa = "0.7, 0.8"
 BGZFStreams = "0.3.1"
-BioAlignments = "2"
+BioAlignments = "2.2"
 BioGenerics = "0.1"
-BioSequences = "2.0.4"
+BioSequences = "3"
 FormatSpecimens = "1.1"
 GenomicFeatures = "2"
 Indexes = "0.1"
 TranscodingStreams = "0.6, 0.7, 0.8, 0.9"
-julia = "1"
+julia = "1.6"
 
 [extras]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 FormatSpecimens = "3372ea36-2a1a-11e9-3eb7-996970b6ffbd"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["FormatSpecimens", "Test"]
+test = ["Documenter", "FormatSpecimens", "Test"]

README.md

@@ -5,7 +5,6 @@
 [![MIT license](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/BioJulia/XAM.jl/blob/master/LICENSE)
 [![Stable documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://biojulia.github.io/XAM.jl/stable)
 [![Latest documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://biojulia.github.io/XAM.jl/dev/)
-[![Join the chat at https://gitter.im/BioJulia/XAM.jl](https://badges.gitter.im/BioJulia/XAM.jl.svg)](https://gitter.im/BioJulia/XAM.jl)
 
 > 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/ "original
 blog post").
@@ -66,4 +65,4 @@ Your logo will show up here with a link to your website.
 
 
 ## Questions?
-If you have a question about contributing or using BioJulia software, come on over and chat to us on [Gitter](https://gitter.im/BioJulia/General), or you can try the [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).
+If you have a question about contributing or using BioJulia software, come on over and chat to us on [the Julia Slack workspace](https://julialang.org/slack/), or you can try the [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).

docs/Project.toml

@@ -3,4 +3,4 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 
 [compat]
-Documenter = "0.24"
+Documenter = "0.27"

docs/make.jl

@@ -2,6 +2,8 @@ using Pkg
 using Documenter, XAM
 
 makedocs(
+    checkdocs = :all,
+    linkcheck = true,
     format = Documenter.HTML(
         edit_link = "develop"
     ),

docs/src/index.md

@@ -5,7 +5,6 @@
 [![MIT license](https://img.shields.io/badge/license-MIT-green.svg)](https://github.com/BioJulia/XAM.jl/blob/master/LICENSE)
 [![Stable documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://biojulia.github.io/XAM.jl/stable)
 [![Latest documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://biojulia.github.io/XAM.jl/dev/)
-[![Join the chat at https://gitter.im/BioJulia/XAM.jl](https://badges.gitter.im/BioJulia/XAM.jl.svg)](https://gitter.im/BioJulia/XAM.jl)
 
 > 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/).
 
@@ -65,4 +64,4 @@ Your logo will show up here with a link to your website.
 
 
 ## Questions?
-If you have a question about contributing or using BioJulia software, come on over and chat to us on [Gitter](https://gitter.im/BioJulia/General), or you can try the [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).
+If you have a question about contributing or using BioJulia software, come on over and chat to us on [the Julia Slack workspace](https://julialang.org/slack/), or you can try the [Bio category of the Julia discourse site](https://discourse.julialang.org/c/domain/bio).

src/XAM.jl

@@ -4,6 +4,27 @@ export
     SAM,
     BAM
 
+"""
+    flag(record::Union{SAM.Record, BAM.Record})::UInt16
+
+Get the bitwise flags of `record`. The returned value is a `UInt16` of each flag
+being OR'd together. The possible flags are:
+
+    0x0001 template having multiple segments in sequencing
+    0x0002 each segment properly aligned according to the aligner
+    0x0004 segment unmapped
+    0x0008 next segment in the template unmapped
+    0x0010 SEQ being reverse complemented
+    0x0020 SEQ of the next segment in the template being reverse complemented
+    0x0040 the first segment in the template
+    0x0080 the last segment in the template
+    0x0100 secondary alignment
+    0x0200 not passing filters, such as platform/vendor quality controls
+    0x0400 PCR or optical duplicate
+    0x0800 supplementary alignment
+"""
+function flag end
+
 include("sam/sam.jl")
 include("bam/bam.jl")
 

src/bam/bam.jl

@@ -6,6 +6,7 @@ module BAM
 using BioGenerics
 using GenomicFeatures
 using XAM.SAM
+import ..XAM: flag
 
 import BGZFStreams
 import BioAlignments

src/bam/overlap.jl

@@ -50,12 +50,15 @@ function Base.iterate(iter::OverlapIterator)
     if refindex === nothing
         throw(ArgumentError("sequence name $(iter.refname) is not found in the header"))
     end
-    @assert iter.reader.index !== nothing
+
+    @assert iter.reader.index !== nothing "Reader index cannot be nothing."
+
     chunks = Indexes.overlapchunks(iter.reader.index.index, refindex, iter.interval)
-    if !isempty(chunks)
-        seek(iter.reader, first(chunks).start)
+    if isempty(chunks)
+        return nothing
     end
     state = OverlapIteratorState(refindex, chunks, 1, Record())
+    seek(iter.reader, state.chunks[state.chunkid].start)
     return iterate(iter, state)
 end
 
@@ -65,7 +68,7 @@ function Base.iterate(iter::OverlapIterator, state)
         while BGZFStreams.virtualoffset(iter.reader.stream) < chunk.stop
             read!(iter.reader, state.record)
             c = compare_intervals(state.record, (state.refindex, iter.interval))
-            if c == 0
+            if c == 0  # overlapping
                 return copy(state.record), state
             end
             if c > 0
@@ -78,6 +81,7 @@ function Base.iterate(iter::OverlapIterator, state)
             seek(iter.reader, state.chunks[state.chunkid].start)
         end
     end
+    # no more overlapping records
     return nothing
 end
 
@@ -89,7 +93,7 @@ function compare_intervals(record::Record, interval::Tuple{Int,UnitRange{Int}})
         return -1
     end
 
-    if rid > interval[1] || (rid == interval[1] && position(record) > last(interval[2]))
+    if rid > interval[1] || (rid == interval[1] && leftposition(record) > last(interval[2]))
         # strictly right
         return +1
     end