Penalize far apart pairs not more than as if they were two single ends #1375
Workflow file for this run
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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@v3 | |
| - 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@v3 | |
| - name: Build | |
| run: | | |
| cmake -B build -DCMAKE_BUILD_TYPE=RelWithDebInfo | |
| cd build | |
| make -j3 | |
| make install | |
| - 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 | |
| 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@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.10" | |
| - 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@v3 | |
| - run: cat tests/baseline-commit.txt >> $GITHUB_ENV | |
| - uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ env.baseline_commit }} | |
| path: baseline | |
| - name: Install Linux dependencies | |
| if: runner.os == 'Linux' | |
| run: sudo apt-get install samtools python3-pysam picard-tools | |
| - name: Install macOS dependencies | |
| if: runner.os == 'macOS' | |
| run: brew install samtools pysam picard-tools | |
| - name: Cache test dataset | |
| uses: actions/cache@v3 | |
| with: | |
| key: test-data-${{ hashFiles('tests/download.sh') }} | |
| path: tests/drosophila/ | |
| - name: Download test dataset | |
| run: tests/download.sh | |
| - name: Cache baseline BAM | |
| id: cache-baseline-bam | |
| uses: actions/cache@v3 | |
| with: | |
| key: baseline-bam-${{ hashFiles('tests/baseline-commit.txt') }} | |
| path: baseline.bam | |
| - name: Generate baseline BAM | |
| if: ${{ steps.cache-baseline-bam.outputs.cache-hit != 'true' }} | |
| run: | | |
| ( cd baseline && cmake -B build ) | |
| make -j3 -C baseline/build | |
| baseline/build/strobealign tests/drosophila/ref.fasta tests/drosophila/reads.1.fastq.gz tests/drosophila/reads.2.fastq.gz | samtools view -o baseline.bam | |
| - name: Build HEAD version | |
| run: | | |
| cmake -B build -DCMAKE_BUILD_TYPE=RelWithDebInfo | |
| make -j3 -C build | |
| - name: Generate HEAD BAM | |
| run: build/strobealign tests/drosophila/ref.fasta tests/drosophila/reads.1.fastq.gz tests/drosophila/reads.2.fastq.gz | samtools view -o head.bam | |
| - name: Compare | |
| run: python3 tests/samdiff.py baseline.bam head.bam | |
| - name: Validate with Picard | |
| run: | | |
| PicardCommandLine ValidateSamFile IGNORE=RECORD_MISSING_READ_GROUP IGNORE=MISSING_READ_GROUP I=head.bam |