biocheck-cli 0.1.0__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- biocheck_cli-0.1.0/.github/workflows/ci.yml +33 -0
- biocheck_cli-0.1.0/.gitignore +11 -0
- biocheck_cli-0.1.0/.pre-commit-hooks.yaml +6 -0
- biocheck_cli-0.1.0/Cargo.lock +872 -0
- biocheck_cli-0.1.0/Cargo.toml +27 -0
- biocheck_cli-0.1.0/LICENSE +21 -0
- biocheck_cli-0.1.0/PKG-INFO +275 -0
- biocheck_cli-0.1.0/README.md +257 -0
- biocheck_cli-0.1.0/pyproject.toml +27 -0
- biocheck_cli-0.1.0/src/fixer.rs +339 -0
- biocheck_cli-0.1.0/src/lib.rs +62 -0
- biocheck_cli-0.1.0/src/linters/bed.rs +275 -0
- biocheck_cli-0.1.0/src/linters/fasta.rs +211 -0
- biocheck_cli-0.1.0/src/linters/fastq.rs +202 -0
- biocheck_cli-0.1.0/src/linters/gff.rs +271 -0
- biocheck_cli-0.1.0/src/linters/mod.rs +96 -0
- biocheck_cli-0.1.0/src/linters/sam.rs +202 -0
- biocheck_cli-0.1.0/src/linters/vcf.rs +350 -0
- biocheck_cli-0.1.0/src/main.rs +241 -0
- biocheck_cli-0.1.0/src/reporter.rs +121 -0
- biocheck_cli-0.1.0/src/rules_doc.rs +360 -0
- biocheck_cli-0.1.0/src/types.rs +127 -0
- biocheck_cli-0.1.0/src/utils/chr.rs +50 -0
- biocheck_cli-0.1.0/src/utils/compression.rs +35 -0
- biocheck_cli-0.1.0/src/utils/mod.rs +2 -0
- biocheck_cli-0.1.0/tests/fixtures/bad_fields.gff3 +1 -0
- biocheck_cli-0.1.0/tests/fixtures/bad_header.fasta +3 -0
- biocheck_cli-0.1.0/tests/fixtures/duplicate_id.fasta +4 -0
- biocheck_cli-0.1.0/tests/fixtures/inverted.bed +1 -0
- biocheck_cli-0.1.0/tests/fixtures/mismatched_len.fastq +4 -0
- biocheck_cli-0.1.0/tests/fixtures/mixed_chr.vcf +4 -0
- biocheck_cli-0.1.0/tests/fixtures/negative.bed +1 -0
- biocheck_cli-0.1.0/tests/fixtures/spaces.bed +1 -0
- biocheck_cli-0.1.0/tests/fixtures/spaces_instead_of_tabs.vcf +4 -0
- biocheck_cli-0.1.0/tests/fixtures/truncated.fastq +7 -0
- biocheck_cli-0.1.0/tests/fixtures/unsorted.vcf +4 -0
- biocheck_cli-0.1.0/tests/fixtures/valid.bed +3 -0
- biocheck_cli-0.1.0/tests/fixtures/valid.fasta +4 -0
- biocheck_cli-0.1.0/tests/fixtures/valid.fastq +8 -0
- biocheck_cli-0.1.0/tests/fixtures/valid.gff3 +3 -0
- biocheck_cli-0.1.0/tests/fixtures/valid.vcf +6 -0
- biocheck_cli-0.1.0/tests/fixtures/valid.vcf.gz +0 -0
- biocheck_cli-0.1.0/tests/integration_tests.rs +213 -0
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name: CI
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on:
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push:
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branches: [ "main" ]
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pull_request:
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branches: [ "main" ]
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jobs:
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test:
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name: Test (${{ 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, windows-latest]
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steps:
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- uses: actions/checkout@v4
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- uses: dtolnay/rust-toolchain@stable
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- name: Run tests
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run: cargo test --verbose
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lint:
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name: Formatting & Linting
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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- uses: dtolnay/rust-toolchain@stable
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with:
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components: rustfmt, clippy
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- name: Check format
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run: cargo fmt -- --check
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- name: Run clippy
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run: cargo clippy -- -D warnings
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