Better --noSplit
#29
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: Build and test mapping coverage | |
| on: | |
| push: | |
| branches: [ master ] | |
| paths-ignore: | |
| - '**/*.md' | |
| pull_request: | |
| branches: [ master ] | |
| paths-ignore: | |
| - '**/*.md' | |
| env: | |
| # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.) | |
| BUILD_TYPE: DEBUG | |
| jobs: | |
| linux: | |
| # The CMake configure and build commands are platform agnostic and should work equally well on Windows or Mac. | |
| # You can convert this to a matrix build if you need cross-platform coverage. | |
| # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-20.04] | |
| compiler: | |
| - { compiler: GNU, CC: gcc-11, CXX: g++-11 } | |
| steps: | |
| - name: Cancel Workflow Action | |
| uses: styfle/[email protected] | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| with: | |
| submodules: 'true' | |
| - name: Setup apt | |
| run: | | |
| sudo apt install build-essential manpages-dev software-properties-common | |
| sudo add-apt-repository ppa:ubuntu-toolchain-r/test | |
| sudo apt update && sudo apt install | |
| - name: Install Requirements | |
| run: sudo apt install -y | |
| ${{ matrix.compiler.CC }} | |
| ${{ matrix.compiler.CXX }} | |
| libhts-dev | |
| libjemalloc-dev | |
| libgsl-dev | |
| zlib1g-dev | |
| libhts-dev | |
| samtools | |
| bedtools | |
| - name: Build | |
| env: | |
| CC: ${{ matrix.compiler.CC }} | |
| CXX: ${{ matrix.compiler.CXX }} | |
| # Build your program with the given configuration | |
| run: cmake -H. -Bbuild -DCMAKE_BUILD_TYPE=${BUILD_TYPE} && cmake --build build -- | |
| - name: Basic version test | |
| env: | |
| CC: ${{ matrix.compiler.CC }} | |
| CXX: ${{ matrix.compiler.CXX }} | |
| run: build/bin/mashmap -v | |
| - name: Align yeast genomes | |
| run: ASAN_OPTIONS=detect_leaks=1:symbolize=1 LSAN_OPTIONS=verbosity=0:log_threads=1 build/bin/mashmap | |
| -r data/scerevisiae8.fa.gz | |
| -q data/scerevisiae8.fa.gz | |
| --pi 95 -n 1 -Y '#' | |
| --threads $(nproc --all) | |
| -o scerevisiae8.paf; | |
| - name: Test yeast coverage | |
| run: scripts/test.sh data/scerevisiae8.fa.gz.fai scerevisiae8.paf 0.92 | |