added pool and loci filtering after setting loci below some depth thr… #316
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| name: 🚀 | |
| on: | |
| push: | |
| branches: | |
| - main | |
| jobs: | |
| compile: | |
| name: Compile | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Setup | Checkout | |
| uses: actions/checkout@v3 | |
| - name: Setup | Rust | |
| uses: ATiltedTree/setup-rust@v1 | |
| with: | |
| rust-version: stable | |
| - name: Build | Compile | |
| run: cargo check | |
| test: | |
| name: Test | |
| strategy: | |
| matrix: | |
| os: | |
| - ubuntu-latest | |
| - windows-latest | |
| # - macOS-latest | |
| rust: | |
| - stable | |
| # - beta | |
| # - nightly | |
| runs-on: ${{ matrix.os }} | |
| needs: [compile] | |
| steps: | |
| - name: Setup | Checkout | |
| uses: actions/checkout@v3 | |
| - name: Setup | Rust | |
| uses: ATiltedTree/setup-rust@v1 | |
| with: | |
| rust-version: ${{ matrix.rust }} | |
| - name: Tests | Rust | |
| run: cargo test | |
| - name: Build | Compile | Test on test data | |
| run: | | |
| cargo run -- pileup2sync -f ./tests/test.pileup -p ./tests/test.csv | |
| cargo run -- pileup2sync -f ./tests/test.pileup -p ./tests/test.csv --n-threads 2 --min-quality 0.0001 | |
| cargo run -- pileup2sync -f ./tests/test.pileup -p ./tests/test.csv --n-threads 2 --min-quality 0.0001 --min-coverage 10 | |
| cargo run -- pileup2sync -f ./tests/test.pileup -p ./tests/test.csv --n-threads 2 --min-quality 0.0001 --min-coverage 10 --min-allele-frequency 0.01 | |
| cargo run -- fisher_exact_test -f ./tests/test.sync -p ./tests/test.csv --n-threads 2 | |
| cargo run -- fisher_exact_test -f ./tests/test.sync -p ./tests/test.csv --n-threads 2 --min-coverage 10 --min-allele-frequency 0.01 | |
| cargo run -- chisq_test -f ./tests/test.sync -p ./tests/test.csv --n-threads 2 | |
| cargo run -- chisq_test -f ./tests/test.sync -p ./tests/test.csv --n-threads 2 --min-coverage 10 --min-allele-frequency 0.01 | |
| cargo run -- pearson_corr -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3 --n-threads 2 | |
| cargo run -- pearson_corr -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3 --n-threads 2 --min-coverage 10 --min-allele-frequency 0.01 | |
| cargo run -- ols_iter -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3 --n-threads 2 | |
| cargo run -- ols_iter -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3 --n-threads 2 --min-coverage 10 --min-allele-frequency 0.01 | |
| cargo run -- mle_iter -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3 --n-threads 2 | |
| cargo run -- mle_iter -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3 --n-threads 2 --min-coverage 10 --min-allele-frequency 0.01 | |
| cargo run -- gwalpha -f ./tests/test.sync -p ./tests/test.py --n-threads 2 --gwalpha-method LS | |
| cargo run -- gwalpha -f ./tests/test.sync -p ./tests/test.py --n-threads 2 --gwalpha-method ML | |
| cargo run -- sync2csv -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3 --n-threads 2 | |
| cargo run -- sync2csv -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3 --n-threads 2 --keep-p-minus-1 | |
| cargo run -- fst -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3 --window-size-bp 100 --window-slide-size-bp 50 --min-loci-per-window 10 --n-threads 2 | |
| cargo run -- heterozygosity -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3 --window-size-bp 100 --window-slide-size-bp 50 --min-loci-per-window 10 --n-threads 2 | |
| cargo run -- tajima_d -f ./tests/test.sync -p ./tests/test.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3 --window-size-bp 100 --window-slide-size-bp 50 --min-loci-per-window 10 --n-threads 2 | |
| # cargo run -- genomic_prediction_cross_validation -f ./tests/test_MORE_POOLS.sync -p ./tests/test_MORE_POOLS.csv --phen-delim , --phen-name-col 0 --phen-value-col 2,3 --n-threads 2 |