Merge pull request #2 from Sentieon/dev #3
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: CI | |
| on: | |
| push: | |
| pull_request: | |
| jobs: | |
| ci: | |
| strategy: | |
| fail-fast: true | |
| matrix: | |
| python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"] | |
| os: [ubuntu-22.04] #, macos-latest, windows-latest] | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Test | |
| run: | | |
| PYTHONPATH=$(pwd) python example/filter_dp.py \ | |
| --input_vcf tests/hc_subset.vcf.gz \ | |
| --output_vcf tests/hc_subset_dp.vcf.gz | |
| if [ ! -f tests/hc_subset_dp.vcf.gz ]; then exit 1; fi | |
| if [ ! -f tests/hc_subset_dp.vcf.gz.tbi ]; then exit 1; fi | |
| - name: Test csi | |
| run: | | |
| rm tests/hc_subset.vcf.gz.tbi | |
| PYTHONPATH=$(pwd) VCF_INDEX_TYPE=2 python example/filter_dp.py \ | |
| --input_vcf tests/hc_subset.vcf.gz \ | |
| --output_vcf tests/hc_subset_dp.vcf.gz | |
| if [ ! -f tests/hc_subset_dp.vcf.gz ]; then exit 1; fi | |
| if [ ! -f tests/hc_subset_dp.vcf.gz.csi ]; then exit 1; fi |