test_on_push.yml

on:
  push:
    branches: [ main ]
    paths-ignore:
      - '**/*.md'
  pull_request:
    branches: [ main ]
    paths-ignore:
      - '**/*.md'

name: build and test

jobs:
  build_and_test:
    runs-on: ubuntu-20.04
    steps:
      - uses: actions/checkout@v2
      - name: Install required packages
        run: sudo apt-get update && sudo apt-get install -y
          git
          bash
          cmake
          make
          g++
          python3-dev
          libatomic-ops-dev
          autoconf
          libgsl-dev
          zlib1g-dev
          libdeflate-dev
          libhts-dev
          samtools
          libjemalloc-dev
          bedtools
      - name: Init and update submodules
        run: git submodule update --init --recursive
      - name: Build wfmash
        run: cmake -H. -Bbuild -D CMAKE_BUILD_TYPE=Debug -DWFA_PNG_AND_TSV=ON && cmake --build build -- -j 2
      - name: Test mapping coverage with 8 yeast genomes (PAF output)
        run: ASAN_OPTIONS=detect_leaks=1:symbolize=1 LSAN_OPTIONS=verbosity=0:log_threads=1 build/bin/wfmash data/scerevisiae8.fa.gz -p 95 -n 7 -m -L -Y '#' > scerevisiae8.paf; scripts/test.sh data/scerevisiae8.fa.gz.fai scerevisiae8.paf 0.92
      - name: Test mapping+alignment with a subset of the LPA dataset (PAF output)
        run: ASAN_OPTIONS=detect_leaks=1:symbolize=1 LSAN_OPTIONS=verbosity=0:log_threads=1 build/bin/wfmash data/LPA.subset.fa.gz -n 10 -L > LPA.subset.paf && head LPA.subset.paf
      - name: Test mapping+alignment with a subset of the LPA dataset (SAM output)
        run: ASAN_OPTIONS=detect_leaks=1:symbolize=1 LSAN_OPTIONS=verbosity=0:log_threads=1 build/bin/wfmash data/LPA.subset.fa.gz -N -a -L > LPA.subset.sam && samtools view LPA.subset.sam -bS | samtools sort > LPA.subset.bam && samtools index LPA.subset.bam && samtools view LPA.subset.bam | head | cut -f 1-9
      - name: Test mapping+alignment with short reads (500 bps) to a reference (SAM output)
        run: ASAN_OPTIONS=detect_leaks=1:symbolize=1 LSAN_OPTIONS=verbosity=0:log_threads=1 build/bin/wfmash data/reference.fa.gz data/reads.500bps.fa.gz -s 0.5k -N -a > reads.500bps.sam && samtools view reads.500bps.sam -bS | samtools sort > reads.500bps.bam && samtools index reads.500bps.bam && samtools view reads.500bps.bam | head
      - name: Test mapping+alignment with short reads (255bps) (PAF output)
        run: ASAN_OPTIONS=detect_leaks=1:symbolize=1 LSAN_OPTIONS=verbosity=0:log_threads=1 build/bin/wfmash data/reads.255bps.fa.gz -w 16 -s 100 -L > reads.255bps.paf && head reads.255bps.paf
      - name: Install Rust and Cargo
        uses: actions-rs/toolchain@v1
        with:
          toolchain: stable
          override: true
      - name: Install wgatools
        run: cargo install --git https://github.com/wjwei-handsome/wgatools.git
      - name: Install wgatools
        run: cargo install --git https://github.com/ekg/pafcheck.git
      - name: Run wfmash and generate PAF
        run: build/bin/wfmash -t 8 -T SGDref -Q S288C -Y '#' data/scerevisiae8.fa.gz > test.paf
      - name: check PAF coordinates and extended CIGAR validity
        run: pafcheck --query-fasta data/scerevisiae8.fa.gz --paf test.paf
      - name: Convert PAF to MAF using wgatools
        run: wgatools paf2maf --target data/scerevisiae8.fa.gz --query data/scerevisiae8.fa.gz test.paf > test.maf
      - name: Check if MAF file is not empty
        run: |
          if [ -s test.maf ]; then
            echo "MAF file is not empty. Test passed."
          else
            echo "MAF file is empty. Test failed."
            exit 1
          fi