binseq 0.9.0

A high efficiency binary format for sequencing data
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

name: CI

on: [push, pull_request]

env:
  CARGO_TERM_COLOR: always

jobs:
  build:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - name: Build
        run: cargo build --verbose
      - name: Run tests
        run: cargo test --verbose
      - name: Run tests (release)
        run: cargo test --verbose --release

  fmt_lint:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - name: Formatting
        run: cargo fmt --check
      - name: Linting
        run: cargo clippy --verbose

  example_grep:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        ext: [bq, vbq, cbq]
    steps:
      - uses: actions/checkout@v3
      - name: run example ${{ matrix.ext }}
        run: cargo run --release --example grep -- ./data/subset.${{ matrix.ext }} "ACGTACGT"

  example_range:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        ext: [bq, vbq, cbq]
    steps:
      - uses: actions/checkout@v3
      - name: run example ${{ matrix.ext }}
        run: cargo run --release --example parallel_range -- ./data/subset.${{ matrix.ext }} 4 30 200

  example_write:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        ext: [bq, vbq, cbq]
    steps:
      - uses: actions/checkout@v3
      - name: run example (single) ${{ matrix.ext }}
        run: cargo run --release --example write -- ./data/subset_R1.fastq.gz -o ./output.${{ matrix.ext }}
      - name: run example (paired) ${{ matrix.ext }}
        run: cargo run --release --example write -- ./data/subset_R1.fastq.gz ./data/subset_R2.fastq.gz -o ./output.${{ matrix.ext }}

  example_read:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        ext: [bq, vbq, cbq]
    steps:
      - uses: actions/checkout@v3
      - name: run example ${{ matrix.ext }}
        run: cargo run --release --example read -- ./data/subset.${{ matrix.ext }}