fgumi 0.3.1

High-performance tools for UMI-tagged sequencing data: extraction, grouping, and consensus calling
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
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154

name: Check and Test

on:
  push:
    branches:
      - main
  pull_request:

env:
  CARGO_TERM_COLOR: always
  CARGO_INCREMENTAL: 0
  SCCACHE_GHA_ENABLED: "true"
  RUSTC_WRAPPER: "sccache"

jobs:
  test:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout code
        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
      - name: Install Rust toolchain
        uses: dtolnay/rust-toolchain@29eef336d9b2848a0b548edc03f92a220660cdb8 # stable
      - name: Set up compilation cache (sccache)
        uses: mozilla-actions/sccache-action@9e7fa8a12102821edf02ca5dbea1acd0f89a2696 # v0.0.10
      - name: Install nextest
        uses: taiki-e/install-action@0631aa6515c7d545823c67cfae7ef4fc7f490154 # v2.81.8
        with:
          tool: nextest
      - name: Unit tests
        run: cargo ci-test
  
  lint:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout code
        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
      - name: Install Rust toolchain
        uses: dtolnay/rust-toolchain@29eef336d9b2848a0b548edc03f92a220660cdb8 # stable
        with:
          components: clippy
      - name: Set up compilation cache (sccache)
        uses: mozilla-actions/sccache-action@9e7fa8a12102821edf02ca5dbea1acd0f89a2696 # v0.0.10
      - name: Clippy check
        run: cargo ci-lint

  coverage:
    runs-on: ubuntu-latest
    if: github.actor != 'dependabot[bot]'
    environment: github-actions
    steps:
      - name: Checkout code
        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
      - name: Install Rust toolchain
        uses: dtolnay/rust-toolchain@29eef336d9b2848a0b548edc03f92a220660cdb8 # stable
      - name: Set up compilation cache (sccache)
        uses: mozilla-actions/sccache-action@9e7fa8a12102821edf02ca5dbea1acd0f89a2696 # v0.0.10
      - name: Install cargo-llvm-cov
        uses: taiki-e/install-action@0631aa6515c7d545823c67cfae7ef4fc7f490154 # v2.81.8
        with:
          tool: cargo-llvm-cov
      - name: Install nextest
        uses: taiki-e/install-action@0631aa6515c7d545823c67cfae7ef4fc7f490154 # v2.81.8
        with:
          tool: nextest
      - name: Generate coverage
        run: cargo llvm-cov nextest --features compare,simulate,profile-adjacency --no-tests=pass --lcov --output-path lcov.info
      - name: Upload to Codecov
        uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v6.0.2
        with:
          files: lcov.info
          fail_ci_if_error: true
          token: ${{ secrets.CODECOV_TOKEN }}

  format:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout code
        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
      - name: Install Rust toolchain
        uses: dtolnay/rust-toolchain@29eef336d9b2848a0b548edc03f92a220660cdb8 # stable
        with:
          components: rustfmt
      - name: Set up compilation cache (sccache)
        uses: mozilla-actions/sccache-action@9e7fa8a12102821edf02ca5dbea1acd0f89a2696 # v0.0.10
      - name: Rustfmt check
        run: cargo ci-fmt

  security:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout code
        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
      - name: Install cargo-audit
        uses: taiki-e/install-action@0631aa6515c7d545823c67cfae7ef4fc7f490154 # v2.81.8
        with:
          tool: cargo-audit
      - name: Audit dependencies for known vulnerabilities
        run: cargo audit

  publish-dry-run:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout code
        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
      - name: Install Rust toolchain
        uses: dtolnay/rust-toolchain@29eef336d9b2848a0b548edc03f92a220660cdb8 # stable
      - name: Set up compilation cache (sccache)
        uses: mozilla-actions/sccache-action@9e7fa8a12102821edf02ca5dbea1acd0f89a2696 # v0.0.10
      - name: Package every workspace crate (dry-run)
        # Validates manifest health for every publishable crate: declared
        # dependency versions on path deps, include = [...] paths, features
        # referring to real deps/features, no-publish flags, etc. Uses
        # --no-verify because cargo's workspace dry-run with --verify hits
        # an internal "no hash listed" error (cargo 1.93) when a later
        # crate transitively depends on an earlier crate's freshly packaged
        # tarball. Real-CI publish doesn't hit this -- each predecessor
        # resolves from crates.io with a real hash before the next verify.
        run: cargo publish --workspace --dry-run --allow-dirty --no-verify
      - name: Simulate publish-verify for crates with default-off optional deps
        # `cargo publish --verify` compiles the packaged tarball with DEFAULT
        # features only. For crates whose default feature set does NOT enable
        # every optional dependency, that build path is not exercised by the
        # regular workspace build (other crates often enable the optional
        # feature transitively), so "optional dep used unconditionally" bugs
        # can ship unnoticed and break publish mid-release.
        #
        # Add a crate to this list whenever it gains a default-off optional
        # dep. Current members:
        #   - fgumi-raw-bam: default = [], `noodles`/`anyhow` behind feature
        run: cargo check -p fgumi-raw-bam --no-default-features --all-targets

  no-default-features-check:
    runs-on: ubuntu-latest
    steps:
      - name: Checkout code
        uses: actions/checkout@df4cb1c069e1874edd31b4311f1884172cec0e10 # v6.0.3
      - name: Install Rust toolchain
        uses: dtolnay/rust-toolchain@29eef336d9b2848a0b548edc03f92a220660cdb8 # stable
      - name: Set up compilation cache (sccache)
        uses: mozilla-actions/sccache-action@9e7fa8a12102821edf02ca5dbea1acd0f89a2696 # v0.0.10
      - name: cargo check --workspace --no-default-features --all-targets
        # The regular test/lint jobs run with default features enabled, which
        # pulls in every optional dependency transitively. That hides two
        # classes of bug from CI:
        #   1. Optional deps used unconditionally (library behind a feature
        #      gate referenced from non-gated code).
        #   2. Modules behind a non-default feature referenced from
        #      always-compiled code.
        # Both manifest as compile failures only under
        # `default-features = false`, which is exactly what downstream
        # consumers can opt into. This job compiles every workspace crate
        # (lib + tests + benches) with no default features to surface
        # regressions at PR time.
        run: cargo check --workspace --no-default-features --all-targets