Make BAM input compatible with --interleaved, -1/2 and -U
#75
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| name: Random Tests | |
| on: | |
| push: | |
| branches: | |
| - 'bug_fixes' | |
| - 'master' | |
| paths: | |
| - '**.h' | |
| - '**.cpp' | |
| - 'bowtie2' | |
| - 'bowtie2-build' | |
| - 'bowtie2-inspect' | |
| - 'Makefile' | |
| - 'scripts/sim/**' | |
| - 'scripts/test/**' | |
| pull_request: | |
| branches: | |
| - 'master' | |
| paths: | |
| - '**.h' | |
| - '**.cpp' | |
| - 'bowtie2' | |
| - 'bowtie2-build' | |
| - 'bowtie2-inspect' | |
| - 'Makefile' | |
| - 'scripts/sim/**' | |
| - 'scripts/test/**' | |
| jobs: | |
| setup: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out repository code | |
| uses: actions/checkout@v2 | |
| - name: Install zlib development files | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install zlib1g-dev | |
| linux: | |
| runs-on: ubuntu-latest | |
| needs: setup | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Run random tests | |
| run: | | |
| make clean; make -j4 allall | |
| export NUM_CORES=1 | |
| make random-test | |
| linux-avx2: | |
| runs-on: ubuntu-latest | |
| needs: linux | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Run random tests using avx2 | |
| run: | | |
| export SSE_AVX2=1 | |
| make clean; make -j4 allall | |
| export NUM_CORES=1 | |
| make random-test | |
| macos: | |
| runs-on: macos-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Pull submodules | |
| run: | | |
| git submodule init | |
| git submodule update | |
| - name: Run random tests | |
| run: | | |
| make clean; make -j4 allall | |
| export NUM_CORES=1 | |
| make random-test |