More stuff

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,5 @@
+Thank you for making an issue and making our software better.
+If you are submitting a bug report, it will help us if you include the following information:
+
+- Your version of Julia and all packages installed in your current Julia environment
+- A small example that demonstrates the bug. If possible, please make the code copy-pastable into a fresh REPL.

.github/PULL_REQUEST_TEMPLATE.md

@@ -0,0 +1,7 @@
+Thank you for your contribution! 
+If you have any questions about your PR, or need help completing it, you can ping the maintainers of this repository, who will be happy to help if they can find time.
+
+You can optionally use the following checklist when you work on your PR:
+- [ ] I have updated any relevant documentation and docstrings.
+- [ ] I have added unit tests, and the CodeCov bot shows tests cover my new code.
+- [ ] I have mentioned my changes in the CHANGELOG.md file.

.github/codecov.yml

@@ -0,0 +1,28 @@
+coverage:
+  status:
+    project:
+      default:
+        # basic
+        target: auto
+        threshold: 10%
+        base: auto 
+        flags: 
+          - unittest
+        paths: 
+          - "src"
+       # advanced settings
+        if_ci_failed: ignore
+        informational: true
+    patch:
+      default:
+        # basic
+        target: auto
+        threshold: 10%
+        base: auto 
+        flags: 
+          - unittest
+        paths: 
+          - "src"
+       # advanced settings
+        if_ci_failed: ignore
+        informational: true

.github/workflows/Documentation.yml

@@ -0,0 +1,29 @@
+name: Documentation
+
+on:
+  push:
+    branches:
+      - master # update to match your development branch (master, main, dev, trunk, ...)
+    tags: '*'
+  pull_request:
+
+jobs:
+  build:
+    permissions:
+      contents: write
+      pull-requests: read
+      statuses: write
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: 'nightly'
+      - uses: julia-actions/cache@v1
+      - name: Install dependencies
+        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and deploy
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # If authenticating with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # If authenticating with SSH deploy key
+        run: julia --project=docs/ docs/make.jl

.github/workflows/UnitTesting.yml

@@ -0,0 +1,45 @@
+name: CI
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version:
+          - 'nightly'
+        os: [ ubuntu-latest, windows-latest ]
+        arch: [ x64 ]
+        include:
+          - julia-version: nightly
+            julia-arch: x86
+            os: ubuntu-latest
+            experimental: true
+         # - julia-version: 1
+         #   os: macOS-latest
+         #   experimental: false
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v2
+      - name: Setup Julia
+        uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.julia-version }}
+      - 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

@@ -3,9 +3,27 @@ uuid = "e5b51f81-6ffd-4e20-bbec-f118e37ea906"
 version = "0.1.0"
 authors = ["Jakob Nybo Nissen <[email protected]>"]
 
+[weakdeps]
+BioAlignments = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e"
+
 [deps]
-BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
-MemViews = "a791c907-b98b-4e44-8f4d-e4c2362c6b2f"
+MemoryViews = "a791c907-b98b-4e44-8f4d-e4c2362c6b2f"
+
+[extensions]
+BioAlignmentsExt = "BioAlignments"
 
 [compat]
-BenchmarkTools = "1.5.0"
+BioAlignments = "3.1.0"
+FormatSpecimens = "1.3.0"
+MemoryViews = "0.2.1"
+julia = "1.11"
+Test = "1.11"
+
+[extras]
+BioAlignments = "00701ae9-d1dc-5365-b64a-a3a3ebf5695e"
+FormatSpecimens = "3372ea36-2a1a-11e9-3eb7-996970b6ffbd"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+MemoryViews = "a791c907-b98b-4e44-8f4d-e4c2362c6b2f"
+
+[targets]
+test = ["Test", "MemoryViews", "FormatSpecimens", "BioAlignments"]

ext/BioAlignmentsExt.jl

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+module BioAlignmentsExt
+
+using BioAlignments: BioAlignments as BA
+import CIGARStrings: CIGAR, Anchor, advance, CIGAROp
+
+function BA.AlignmentAnchor(anchor::Anchor, op::CIGAROp)
+    BA.AlignmentAnchor(anchor.query, anchor.ref, anchor.aln, reinterpret(BA.Operation, op))
+end
+
+function BA.Alignment(cigar::CIGAR, refpos::Int)
+    if refpos < 1
+        error("Alignment cannot start before ref position 1")
+    end
+    anchor = Anchor(0, refpos - 1, 0)
+    anchors = Vector{BA.AlignmentAnchor}(undef, length(cigar) + 1)
+    anchors[1] = (BA.AlignmentAnchor(0, anchor.ref, 0, BA.OP_START))
+    for (i, element) in enumerate(cigar)
+        anchor = advance(anchor, element)
+        anchors[i+1] = BA.AlignmentAnchor(anchor, element.op)
+    end
+    # Note: CIGAR constructor checks everything that Alignment needs.
+    BA.Alignment(anchors, false)
+end
+
+end # module BioAlignmentsExt