Add support for the csi index #2
Workflow file for this run
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| 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 |