Fixed slight slow down in build mode introduced in the previous ver…
#14
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| name: GitHub Actions CI | |
| on: | |
| push: | |
| branches: [ master, develop] | |
| paths-ignore: | |
| - '**.md' | |
| workflow_dispatch: | |
| jobs: | |
| ######################################################################################## | |
| make: | |
| name: Make | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| machine: [ubuntu-latest, macOS-12] | |
| runs-on: ['${{ matrix.machine }}'] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: make | |
| run: | | |
| g++ --version | |
| make -j CXX=g++-12 | |
| - name: tar artifacts | |
| run: tar -cvf kmer-db.tar ./kmer-db ./test/virus | |
| - uses: actions/upload-artifact@v4 | |
| with: | |
| name: executable-artifact-${{ matrix.machine }} | |
| path: ./kmer-db.tar | |
| ######################################################################################## | |
| virus: | |
| needs: make | |
| name: Virus data | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| machine: [ubuntu-latest, macOS-12] | |
| runs-on: ['${{ matrix.machine }}'] | |
| env: | |
| INPUT_DIR: ./test/virus | |
| steps: | |
| - uses: actions/download-artifact@v4 | |
| with: | |
| name: executable-artifact-${{ matrix.machine }} | |
| path: ./ | |
| - name: untar artifacts | |
| run: | | |
| tar -xf kmer-db.tar | |
| - name: build | |
| run: | | |
| ./kmer-db build ${INPUT_DIR}/seqs.part1.list k18.parts.db | |
| - name: new2all | |
| run: | | |
| ./kmer-db new2all k18.parts.db ${INPUT_DIR}/seqs.part2.list k18.n2a.csv | |
| cmp k18.n2a.csv ${INPUT_DIR}/k18.n2a.csv | |
| - name: new2all (sparse) | |
| run: | | |
| ./kmer-db new2all -sparse k18.parts.db ${INPUT_DIR}/seqs.part2.list k18.n2a.sparse.csv | |
| cmp k18.n2a.sparse.csv ${INPUT_DIR}/k18.n2a.sparse.csv | |
| - name: extend | |
| run: | | |
| ./kmer-db build -extend -k 25 ${INPUT_DIR}/seqs.part2.list k18.parts.db | |
| - name: all2all | |
| run: | | |
| ./kmer-db all2all k18.parts.db k18.csv | |
| cmp k18.csv ${INPUT_DIR}/k18.csv | |
| - name: all2all (sparse) | |
| run: | | |
| ./kmer-db all2all -sparse k18.parts.db k18.sparse.csv | |
| cmp k18.sparse.csv ${INPUT_DIR}/k18.sparse.csv | |
| - name: distance | |
| run: | | |
| ./kmer-db distance jaccard k18.csv k18.csv.jaccard | |
| ./kmer-db distance min k18.csv k18.csv.min | |
| ./kmer-db distance max k18.csv k18.csv.max | |
| ./kmer-db distance cosine k18.csv k18.csv.cosine | |
| ./kmer-db distance mash k18.csv k18.csv.mash | |
| cmp k18.csv.jaccard ${INPUT_DIR}/k18.csv.jaccard | |
| cmp k18.csv.min ${INPUT_DIR}/k18.csv.min | |
| cmp k18.csv.max ${INPUT_DIR}/k18.csv.max | |
| cmp k18.csv.cosine ${INPUT_DIR}/k18.csv.cosine | |
| cmp k18.csv.mash ${INPUT_DIR}/k18.csv.mash | |
| - name: build (default k) + all2all | |
| run: | | |
| ./kmer-db build ${INPUT_DIR}/seqs.list k18.db | |
| ./kmer-db all2all k18.db k18.csv | |
| cmp k18.csv ${INPUT_DIR}/k18.csv | |
| - name: build (default k, multifasta) + all2all | |
| run: | | |
| ./kmer-db build -multisample-fasta ${INPUT_DIR}/multi.list k18.multi.db | |
| ./kmer-db all2all k18.multi.db k18.multi.csv | |
| cmp k18.multi.csv ${INPUT_DIR}/k18.csv | |
| - name: build (default k, 2 x multifasta) + all2all | |
| run: | | |
| ./kmer-db build -multisample-fasta ${INPUT_DIR}/multi.split.list k18.multi.split.db | |
| ./kmer-db all2all k18.multi.split.db k18.multi.split.csv | |
| cmp k18.multi.split.csv ${INPUT_DIR}/k18.csv | |
| - name: build (default k) + extend + all2all | |
| run: | | |
| ./kmer-db build ${INPUT_DIR}/seqs.part1.list k18.parts.db | |
| ./kmer-db build -extend -k 25 ${INPUT_DIR}/seqs.part2.list k18.parts.db | |
| ./kmer-db all2all k18.parts.db k18.parts.csv | |
| cmp k18.parts.csv ${INPUT_DIR}/k18.csv | |
| - name: build (default k, fraction 0.1) + all2all | |
| run: | | |
| ./kmer-db build -f 0.1 ${INPUT_DIR}/seqs.list k18.frac.db | |
| ./kmer-db all2all k18.frac.db k18.frac.csv | |
| cmp k18.frac.csv ${INPUT_DIR}/k18.frac.csv | |
| - name: minhash (default k, fraction 0.1) + build + all2all | |
| run: | | |
| ./kmer-db minhash -f 0.1 ${INPUT_DIR}/seqs.list | |
| ./kmer-db build -from-minhash ${INPUT_DIR}/seqs.list k18.minhash.db | |
| ./kmer-db all2all k18.minhash.db k18.minhash.csv | |
| cmp k18.minhash.csv ${INPUT_DIR}/k18.frac.csv | |
| - name: build (k=24) + all2all | |
| run: | | |
| ./kmer-db build -k 24 ${INPUT_DIR}/seqs.list k24.db | |
| ./kmer-db all2all k24.db k24.csv | |
| cmp k24.csv ${INPUT_DIR}/k24.csv | |
| - name: build (k=25, f=0.1) + one2all | |
| run: | | |
| ./kmer-db build -k 25 -f 0.1 ${INPUT_DIR}/seqs.part1.list k25.db | |
| ./kmer-db one2all k25.db ${INPUT_DIR}/data/MT159713 MT159713.csv | |
| cmp MT159713.csv ${INPUT_DIR}/MT159713.csv | |
| - name: new2all (against itself) | |
| run: | | |
| ./kmer-db new2all k18.db ${INPUT_DIR}/seqs.list k18.n2a.itself.csv | |
| cmp k18.n2a.itself.csv ${INPUT_DIR}/k18.n2a.itself.csv | |