Allow references with up to 2**31 contigs #1860
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| name: CI | |
| on: [push, pull_request] | |
| defaults: | |
| run: | |
| shell: bash # For -o pipefail | |
| jobs: | |
| lint: | |
| # Run for PRs only if they come from a forked repo (avoids duplicate runs) | |
| if: >- | |
| github.event_name != 'pull_request' || | |
| github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Check for tab characters | |
| run: "! grep -P -R '\\t' src/ tests/*.{cpp,py}" | |
| build: | |
| if: >- | |
| github.event_name != 'pull_request' || | |
| github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest, macos-latest] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install Linux dependencies | |
| if: runner.os == 'Linux' | |
| run: sudo apt-get install libisal-dev | |
| - name: Install macOS dependencies | |
| if: runner.os == 'macOS' | |
| run: brew install isa-l | |
| - name: Build | |
| run: | | |
| cmake -B build -DCMAKE_BUILD_TYPE=RelWithDebInfo | |
| cmake --build build -j 3 | |
| cmake --install build | |
| - name: Install Linux dependencies | |
| if: runner.os == 'Linux' | |
| run: sudo apt-get install samtools | |
| - name: Install macOS dependencies | |
| if: runner.os == 'macOS' | |
| run: brew install samtools | |
| - name: Run | |
| run: tests/run.sh | |
| # Test building with a downloaded ISA-L | |
| externalisal: | |
| if: >- | |
| github.event_name != 'pull_request' || | |
| github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Install Linux dependencies | |
| if: runner.os == 'Linux' | |
| run: sudo apt-get install nasm | |
| - name: Install macOS dependencies | |
| if: runner.os == 'macOS' | |
| run: brew install nasm | |
| - uses: actions/checkout@v4 | |
| - name: Build | |
| run: | | |
| cmake -B build -DISAL=download | |
| cmake --build build -j3 | |
| pythonbindings: | |
| if: >- | |
| github.event_name != 'pull_request' || | |
| github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| - name: Install Linux dependencies | |
| if: runner.os == 'Linux' | |
| run: sudo apt-get install libisal-dev | |
| - name: Install macOS dependencies | |
| if: runner.os == 'macOS' | |
| run: brew install isa-l | |
| - name: Install Python dependencies | |
| run: pip install pytest | |
| - name: Install Python bindings | |
| run: pip install . | |
| - name: Run tests | |
| run: pytest tests | |
| compare: | |
| if: >- | |
| github.event_name != 'pull_request' || | |
| github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Baseline comparison needs older commits | |
| - name: Install Linux dependencies | |
| if: runner.os == 'Linux' | |
| run: sudo apt-get install samtools python3-pysam picard-tools libisal-dev | |
| - name: Install macOS dependencies | |
| if: runner.os == 'macOS' | |
| run: brew install samtools pysam picard-tools isa-l | |
| - name: Cache test dataset | |
| uses: actions/cache@v4 | |
| with: | |
| key: test-data-${{ hashFiles('tests/download.sh') }} | |
| path: tests/drosophila/ | |
| - name: Cache baseline BAM | |
| id: cache-baseline-bam | |
| uses: actions/cache@v4 | |
| with: | |
| key: baseline-bam-${{ hashFiles('tests/baseline-commit.txt') }} | |
| path: baseline/bam/ | |
| - name: Compare to baseline | |
| run: tests/compare-baseline.sh | |
| - name: Validate with Picard | |
| run: | | |
| PicardCommandLine ValidateSamFile IGNORE=RECORD_MISSING_READ_GROUP IGNORE=MISSING_READ_GROUP I=head.bam |