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hangsuUNChangsuUNC
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added github actions
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‎.github/workflows/ci.yml‎

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name: CI
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on:
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push:
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branches: [ main, master, develop ]
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pull_request:
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branches: [ main, master, develop ]
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workflow_dispatch:
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env:
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CARGO_TERM_COLOR: always
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RUST_BACKTRACE: 1
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jobs:
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test:
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name: Test on ${{ matrix.os }}
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [ubuntu-latest, macos-latest]
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rust: [stable, beta]
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include:
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- os: ubuntu-latest
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rust: stable
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cache-key: linux-stable
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- os: macos-latest
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rust: stable
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cache-key: macos-stable
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Install system dependencies (Ubuntu)
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if: matrix.os == 'ubuntu-latest'
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run: |
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sudo apt-get update
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sudo apt-get install -y \
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libcurl4-openssl-dev \
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libssl-dev \
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zlib1g-dev \
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libbz2-dev \
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liblzma-dev \
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samtools \
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bcftools
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- name: Install system dependencies (macOS)
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if: matrix.os == 'macos-latest'
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run: |
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brew install samtools bcftools || true
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- name: Install Rust toolchain
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uses: dtolnay/rust-toolchain@stable
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with:
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toolchain: ${{ matrix.rust }}
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- name: Cache cargo registry
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uses: actions/cache@v4
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with:
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path: |
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~/.cargo/bin/
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~/.cargo/registry/index/
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~/.cargo/registry/cache/
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~/.cargo/git/db/
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target/
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key: ${{ runner.os }}-cargo-${{ matrix.cache-key }}-${{ hashFiles('**/Cargo.lock') }}
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restore-keys: |
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${{ runner.os }}-cargo-${{ matrix.cache-key }}-
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- name: Build project
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run: cargo build --release --verbose
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- name: Test help command
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run: |
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cargo run --release -- --help || true
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cargo run --release -- quick-start --help || true
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cargo run --release -- filter --help || true
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cargo run --release -- build --help || true
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cargo run --release -- correct --help || true
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cargo run --release -- call --help || true
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cargo run --release -- asm --help || true
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cargo run --release -- methyl --help || true
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integration-test:
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name: Integration Test
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runs-on: ubuntu-latest
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needs: test
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Install system dependencies
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run: |
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sudo apt-get update
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sudo apt-get install -y \
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libcurl4-openssl-dev \
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libssl-dev \
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zlib1g-dev \
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libbz2-dev \
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liblzma-dev \
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samtools \
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bcftools
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- name: Install Rust toolchain
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uses: dtolnay/rust-toolchain@stable
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- name: Build project
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run: cargo build --release
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- name: Test Himito quick-start command
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run: |
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if [ -f "test_data/HG005_100x.bam" ] && [ -f "test_data/HG005_100x.bai" ]; then
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cargo run --release -- quick-start \
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-i test_data/HG005_100x.bam \
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-c "chrM" \
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-k 21 \
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--sampleid HG005 \
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-r test_data/rCRS.fasta \
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--output-prefix test_output/himito_test || echo "Himito test skipped - may require additional dependencies"
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else
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echo "Test data not available, skipping evaluate test"
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fi
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- name: Cleanup test outputs
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if: always()
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run: |
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rm -rf test_output test_data || true
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lint:
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name: Lint
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runs-on: ubuntu-latest
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Install Rust toolchain
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uses: dtolnay/rust-toolchain@stable
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- name: Check for common issues
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run: |
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# Check for unsafe code usage
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if grep -r "unsafe" src/ --include="*.rs" | grep -v "// SAFETY" | grep -v "unsafe {"; then
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echo "Warning: Found unsafe code without safety comments"
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fi
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‎.github/workflows/release.yml‎

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name: Release
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on:
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release:
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types: [created]
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workflow_dispatch:
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inputs:
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version:
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description: 'Release version'
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required: true
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jobs:
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build-release:
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name: Build Release Artifacts
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runs-on: ${{ matrix.os }}
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strategy:
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matrix:
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os: [ubuntu-latest, macos-latest, windows-latest]
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include:
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- os: ubuntu-latest
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artifact_name: haplograph-linux-x86_64
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binary_name: haplograph
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- os: macos-latest
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artifact_name: haplograph-macos-x86_64
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binary_name: haplograph
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- os: windows-latest
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artifact_name: haplograph-windows-x86_64
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binary_name: haplograph.exe
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Install system dependencies (Ubuntu)
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if: matrix.os == 'ubuntu-latest'
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run: |
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sudo apt-get update
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sudo apt-get install -y \
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libcurl4-openssl-dev \
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libssl-dev \
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zlib1g-dev \
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libbz2-dev \
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liblzma-dev
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- name: Install system dependencies (macOS)
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if: matrix.os == 'macos-latest'
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run: |
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brew install openssl || true
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- name: Install Rust toolchain
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uses: dtolnay/rust-toolchain@stable
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- name: Build release binary
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run: cargo build --release --verbose
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- name: Create release archive
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shell: bash
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run: |
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mkdir -p release
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cp target/release/${{ matrix.binary_name }} release/
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tar czf ${{ matrix.artifact_name }}.tar.gz -C release ${{ matrix.binary_name }}
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if [ "${{ matrix.os }}" == "windows-latest" ]; then
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zip -r ${{ matrix.artifact_name }}.zip release/
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fi
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- name: Upload artifacts
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uses: actions/upload-artifact@v4
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with:
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name: ${{ matrix.artifact_name }}
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path: |
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${{ matrix.artifact_name }}.tar.gz
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${{ matrix.artifact_name }}.zip
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‎.github/workflows/test-small.yml‎

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name: Small Integration Tests
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on:
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push:
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branches: [ main, master ]
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pull_request:
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branches: [ main, master ]
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workflow_dispatch:
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jobs:
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quick-test:
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name: Quick Integration Test
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runs-on: ubuntu-latest
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timeout-minutes: 30
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steps:
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Install system dependencies
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run: |
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sudo apt-get update
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sudo apt-get install -y \
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libcurl4-openssl-dev \
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libssl-dev \
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zlib1g-dev \
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libbz2-dev \
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liblzma-dev \
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samtools \
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bcftools
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- name: Install Rust toolchain
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uses: dtolnay/rust-toolchain@stable
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- name: Build project
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run: cargo build --release
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- name: Test help command
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run: |
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cargo run --release -- --help || true
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cargo run --release -- quick-start --help || true
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cargo run --release -- filter --help || true
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cargo run --release -- build --help || true
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cargo run --release -- correct --help || true
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cargo run --release -- call --help || true
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cargo run --release -- asm --help || true
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cargo run --release -- methyl --help || true
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- name: Test Himito quick-start command
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run: |
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if [ -f "test_data/HG005_100x.bam" ] && [ -f "test_data/HG005_100x.bai" ]; then
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cargo run --release -- quick-start \
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-i test_data/HG005_100x.bam \
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-c "chrM" \
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-k 21 \
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--sampleid HG005 \
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-r test_data/rCRS.fasta \
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--output-prefix test_output/himito_test || echo "Himito test skipped - may require additional dependencies"
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else
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echo "Test data not available, skipping evaluate test"
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fi
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- name: Cleanup
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if: always()
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run: rm -rf test_output test_data
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