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reference](docs/getting-started/cli-usage.md),\n[JavaScript API](docs/getting-started/api-usage.md), or\n[browser/package capability guide](docs/guide/browser-and-package.md). The latter\nincludes website bundle setup and in-memory VCF, pedigree, feature and scoring\nexamples, with the Node-only filesystem features identified explicitly.\n\n## Quick Start\n\n### Installation\n\nRequires Node.js 22.14 or later. Install the CLI with\n`npm install --global variant-linker`, or the library with `npm install variant-linker`.\nThe APIs documented in this checkout target 4.0.0; until that release is published,\nbuild this checkout to use the new in-memory parsers and browser helpers.\nFor development from source:\n\n```bash\ngit clone https://github.com/berntpopp/variant-linker.git\ncd variant-linker\nnpm ci\nnpm link  # Optional: for global CLI access\n```\n\n#### Windows Installation Issues\n\nIf the `variant-linker` command isn't recognized on Windows PowerShell:\n\n**Option 1: Use npx (recommended)**\n\n```powershell\nnpx variant-linker --help\n```\n\n**Option 2: Reinstall globally**\n\n```powershell\nnpm uninstall -g variant-linker\nnpm install -g variant-linker\n```\n\n### Basic Usage\n\n```bash\n# Analyze a single variant\nvariant-linker --variant \"rs6025\" --output JSON\n\n# Analyze a copy number variant (CNV)\nvariant-linker --variant \"7:117559600-117559609:DEL\" --output JSON\n\n# Process VCF file with inheritance analysis\nvariant-linker --vcf-input sample.vcf --ped family.ped --calculate-inheritance --output VCF\n\n# Liftover hg19 coordinates to hg38 for annotation\nvariant-linker --assembly hg19tohg38 --variant \"chr17-7578406-C-A\" --output JSON\n\n# Batch processing with custom scoring\nvariant-linker --variants-file variants.txt --scoring_config_path scoring/nephro_variant_score/ --output CSV\n\n# Use HTTP proxy for API requests\nvariant-linker --variant \"rs6025\" --proxy http://proxy.company.com:8080 --output JSON\n\n# Use authenticated proxy\nvariant-linker --variant \"rs6025\" --proxy http://user:pass@proxy.company.com:8080 --output JSON\n```\n\n## Key Features\n\n- 🔄 **Variant Translation** - Convert between rsID, HGVS, VCF, and CNV formats\n- 📊 **VEP Annotations** - Comprehensive variant effect predictions including CNV-specific annotations\n- 🧬 **Genome Assembly Liftover** - Transparent hg19→hg38 coordinate conversion\n- 👨‍👩‍👧‍👦 **Family Analysis** - Inheritance pattern detection from PED files\n- 🗂️ **VCF Support** - Full VCF input/output with header preservation\n- ⚡ **Batch Processing** - Efficient handling of large variant datasets\n- 🌊 **Streaming Support** - Memory-efficient stdin processing for pipeline integration\n- 🎯 **Custom Scoring** - Configurable variant prioritization models\n- 📋 **Multiple Formats** - JSON, validated SCHEMA JSON-LD, CSV, TSV, and VCF output options\n- 🎨 **Custom Annotations** - Overlay variants with BED regions, gene lists, and JSON metadata\n\n## Library Usage\n\nUse Variant-Linker as a library in your Node.js projects:\n\n```javascript\nconst { analyzeVariant } = require('variant-linker');\n\nasync function main() {\n  const result = await analyzeVariant({\n    variants: ['rs6025', 'rs1799963'],\n    vepOptions: { CADD: '1', hgvs: '1' },\n    requestOptions: { timeoutMs: 60000, postConcurrency: 1 },\n    output: 'JSON',\n  });\n  console.log(result);\n}\nmain().catch(console.error);\n```\n\nESM applications can use `import VariantLinker from 'variant-linker'`. Websites\ncan serve `dist/variant-linker.bundle.js`, which exposes `globalThis.VariantLinker`.\nPublic in-memory parsers include `parseVcfText`, `parsePedigreeText`,\n`parseBedText`, `parseGeneListText`, `parseJsonGenesData`, and `buildFeatures`.\nSee the [integration guide](docs/guide/browser-and-package.md) for full examples.\n\nAnnotation sends the supplied variant identifiers/coordinates to Ensembl or an\nexplicitly configured compatible service. Handle rejected promises and per-input\nerror records; usable output can accompany failed inputs. Operational defaults\nlive in the [documented JSON configuration files](docs/guide/browser-and-package.md#configuration-and-environment-boundaries).\n\n## Contributing\n\nContributions are welcome! Please feel free to submit a Pull Request. For major changes, please open an issue first to discuss what you would like to change.\n\n### Development Setup\n\n```bash\ngit clone https://github.com/berntpopp/variant-linker.git\ncd variant-linker\nnpm ci\nnpm --prefix docs ci\nnpm run verify\n```\n\nSee our [Contributing Guide](https://berntpopp.github.io/variant-linker/contributing) for detailed information.\n\nUse Node.js >=22.14. `npm run verify` runs the local and CI gates, including strict\nlint/types/formatting, files below 650 lines, offline tests and >=81% coverage.\n[AGENTS.md](AGENTS.md) defines the shared agent development contract.\n\nFor large VCFs, use `--stream --chunk-size 100`; inheritance requires full-file mode.\nJSON/SCHEMA streams emit one compact JSON document per chunk. `--spreadsheet-safe`\nprotects CSV/TSV text cells for spreadsheet import. Scoring formulas and conditions use a **restricted expression language** with\nexplicitly allowed operators and functions; arbitrary JavaScript is rejected.\nSee [reliable processing](docs/guide/reliable-processing.md) for output, cache,\nliftover, benchmark and failure semantics.\n\n## License\n\nThis project is licensed under the [MIT License](LICENSE).\n\n## Acknowledgements\n\nThis tool utilizes the Ensembl Variant Recoder and Variant Effect Predictor APIs, provided by the Ensembl project.\n","readmeFilename":"README.md"}