block-aligner 0.5.1

SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive block-based algorithm.
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107

name: CI

on:
  push:
    branches: [main]
  pull_request:
    branches: [main]

jobs:
  ci-x86:
    runs-on: ${{matrix.os}}

    strategy:
      matrix:
        os: [ubuntu-latest]

    steps:
    - uses: actions/checkout@v2

    - name: Install Rust Nightly
      uses: actions-rs/toolchain@v1

    - name: Test AVX2
      run: |
        cargo --version
        cargo test --all-targets --features simd_avx2
        cargo test --doc --features simd_avx2

    - name: Test SSE2
      run: |
        cargo --version
        cargo test --all-targets --features simd_sse2
        cargo test --doc --features simd_sse2

    - name: Install Rust Stable
      uses: actions-rs/toolchain@v1
      with:
        toolchain: stable
        override: true

    - name: Test AVX2
      run: |
        cargo --version
        cargo build --features simd_avx2

    - name: Test SSE2
      run: |
        cargo --version
        cargo build --features simd_sse2

  ci-wasm32:
    runs-on: ${{matrix.os}}

    strategy:
      matrix:
        os: [ubuntu-latest]

    steps:
    - uses: actions/checkout@v2

    - name: Install Rust Nightly
      uses: actions-rs/toolchain@v1
      with:
        target: wasm32-wasi

    - name: Test WASM
      run: |
        WASMTIME_DIR=wasmtime-v2.0.2-x86_64-linux
        curl -OL https://github.com/bytecodealliance/wasmtime/releases/download/v2.0.2/${WASMTIME_DIR}.tar.xz
        tar -xvf ${WASMTIME_DIR}.tar.xz
        mv ${WASMTIME_DIR}/wasmtime ./
        cargo --version
        CARGO_TARGET_WASM32_WASI_RUNNER="./wasmtime --wasm-features simd --" cargo test --target=wasm32-wasi --features simd_wasm --all-targets -- --nocapture

    - name: Install Rust Stable
      uses: actions-rs/toolchain@v1
      with:
        toolchain: stable
        override: true
        target: wasm32-wasi

    - name: Test WASM
      run: |
        cargo --version
        cargo build --target=wasm32-wasi --features simd_wasm

  ci-aarch64:
    runs-on: ${{matrix.os}}

    strategy:
      matrix:
        os: [ubuntu-latest]

    steps:
    - uses: actions/checkout@v2

    - name: Install Rust Nightly
      uses: actions-rs/toolchain@v1
      with:
        target: aarch64-unknown-linux-gnu

    - name: Test Neon
      run: |
        sudo apt-get update
        sudo apt-get install -y --no-install-recommends gcc-aarch64-linux-gnu libc6-dev-arm64-cross qemu-user
        cargo --version
        CARGO_TARGET_AARCH64_UNKNOWN_LINUX_GNU_LINKER=aarch64-linux-gnu-gcc CARGO_TARGET_AARCH64_UNKNOWN_LINUX_GNU_RUNNER="qemu-aarch64 -L /usr/aarch64-linux-gnu" cargo test --target=aarch64-unknown-linux-gnu --all-targets --features simd_neon