SamUtils PairOrientation is confusingly ambiguous about paired reads needing to map to the same contig #330
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| # This is a github actions workflow which runs htsjdk tests and spotbugs. | |
| name: Build and Test | |
| on: | |
| push: | |
| branches: [master] | |
| pull_request: | |
| workflow_dispatch: | |
| jobs: | |
| test: | |
| env: | |
| HTSJDK_SAMTOOLS_BIN: /usr/bin/samtools | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| java: [ 17 ] | |
| experimental: [false] | |
| fail-fast: false | |
| continue-on-error: ${{ matrix.experimental }} | |
| name: Java ${{ matrix.Java }} build and test | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up java ${{ matrix.Java }} | |
| uses: actions/setup-java@v3 | |
| with: | |
| java-version: ${{ matrix.Java }} | |
| distribution: 'adopt' | |
| cache: gradle | |
| - name: Grant execute permission for gradlew | |
| run: chmod +x gradlew | |
| - name: Compile with Gradle | |
| run: ./gradlew compileJava | |
| - name: Install Samtools | |
| run: scripts/install-samtools.sh | |
| - name: Start the htsget server | |
| run: scripts/htsget-scripts/start-htsget-test-server.sh | |
| - name: Run tests | |
| run: ./gradlew test jacocoTestReport | |
| - name: Upload test results | |
| if: always() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: test-results-${{ matrix.Java }} | |
| path: build/reports/tests | |
| testExternalApis: | |
| continue-on-error: true | |
| runs-on: ubuntu-latest | |
| name: Tests that require external APIs | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up java 17 | |
| uses: actions/setup-java@v3 | |
| with: | |
| java-version: '17' | |
| distribution: 'adopt' | |
| cache: gradle | |
| - name: Grant execute permission for gradlew | |
| run: chmod +x gradlew | |
| - name: Compile with Gradle | |
| run: ./gradlew compileJava | |
| - name: Run tests | |
| run: ./gradlew testFTP jacocoTestReport | |
| # - name: Upload to codecov | |
| # run: bash <(curl -s https://raw.githubusercontent.com/broadinstitute/codecov-bash-uploader/main/codecov-verified.bash) | |
| - name: Upload test results | |
| if: always() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: test-results-external-apis | |
| path: build/reports/tests | |
| testFTP: | |
| continue-on-error: true | |
| runs-on: ubuntu-latest | |
| name: FTP tests | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up java 17 | |
| uses: actions/setup-java@v3 | |
| with: | |
| java-version: '17' | |
| distribution: 'adopt' | |
| cache: gradle | |
| - name: Grant execute permission for gradlew | |
| run: chmod +x gradlew | |
| - name: Compile with Gradle | |
| run: ./gradlew compileJava | |
| - name: Run tests | |
| run: ./gradlew testFTP jacocoTestReport | |
| # - name: Upload to codecov | |
| # run: bash <(curl -s https://raw.githubusercontent.com/broadinstitute/codecov-bash-uploader/main/codecov-verified.bash) | |
| - name: Upload test results | |
| if: always() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: test-results-ftp | |
| path: build/reports/tests | |
| spotBugs: | |
| runs-on: ubuntu-latest | |
| name: SpotBugs | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up java 17 | |
| uses: actions/setup-java@v3 | |
| with: | |
| java-version: '17' | |
| distribution: 'adopt' | |
| cache: gradle | |
| - name: Grant execute permission for gradlew | |
| run: chmod +x gradlew | |
| - name: Compile with Gradle | |
| run: ./gradlew spotBugsMain spotBugsTest | |
| - name: Upload spotBugs Report | |
| if: failure() | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: spotBugs-Report | |
| path: build/reports/spotbugs | |