{"name":"@deckyard/ngs","description":"Streaming NGS file formats, read QC, interval arithmetic and pipeline orchestration","versions":{"0.2.0":{"version":"0.2.0","kind":"git","url":"https://github.com/deckyard/deck-ngs.git","ref":"0.2.0","commit":"fbdf2662661237386b8baa1280df08f25ff912c2","checksum":"","yanked":false,"license":"LGPL-3.0-only","requires":{},"engines":{"jennifer":"\u003e=0.25.0"},"capabilities":["exec"],"keywords":["bioinformatics","ngs","sequencing","fastq","genomics"],"description":"Streaming NGS file formats, read QC, interval arithmetic and pipeline orchestration","publishedAt":"1793743674","repoId":1350405333,"repoOwnerId":346943577,"repoOwner":"deckyard"}},"readme":"# deck-ngs - `@deckyard/ngs`\n\n[![test](https://github.com/deckyard/deck-ngs/actions/workflows/test.yml/badge.svg)](https://github.com/deckyard/deck-ngs/actions/workflows/test.yml)\n[![Documentation](https://img.shields.io/badge/docs-github%20pages-blue)](https://deckyard.github.io/deck-ngs/)\n[![release](https://img.shields.io/github/v/release/deckyard/deck-ngs)](https://github.com/deckyard/deck-ngs/releases/latest)\n\nStreaming FASTQ, SAM, VCF, BED and GFF3/GTF I/O, read QC, trimming, interval\narithmetic and pipeline orchestration for next-generation sequencing data, in\n[Jennifer](https://jennifer-lang.dev/). Memory use does not grow with file size.\nAlignment, assembly, variant calling and BAM/CRAM stay with the native tools,\nwhich the `pipeline` module drives.\n\n## Install\n\n```yaml\n# deck.yaml\ndecks:\n  \"@deckyard/ngs\": \"^0.1.0\"\n```\n\n`jvc` vendors the deck's `src/` into `vendor/deckyard/ngs/`. Release archives\nare named `deckyard-ngs-\u003cversion\u003e.tar.gz`;\n[installing one by hand](https://deckyard.github.io/deck-ngs/getting-started.html)\nis covered in the manual.\n\nNeeds Jennifer 0.25.0 or newer. Streaming gzip and `pipeline` need the `exec`\ncapability (the default `jennifer` binary, not `jennifer-tiny`) and `gzip` and\n`mkfifo` on `PATH`; everything else runs on both binaries.\n\n## Example\n\n```jennifer\nuse io;\nimport \"@deckyard/ngs/qc.j\" as qc;\n\ndef report as qc.Report init qc.analyze(\"sample.fastq.gz\", qc.options());\nio.printf(\"%s\", qc.summary($report));\n```\n\n## Documentation\n\nThe manual is at \u003chttps://deckyard.github.io/deck-ngs/\u003e, built from `docs/`. The\n[cheatsheet](https://deckyard.github.io/deck-ngs/cheatsheet.html) lists every\nexport.\n\n## Licence\n\nLGPL-3.0-only, see [LICENSE](LICENSE). Copyright (C) 2026 mplx \u0026lt;mplx@jennifer-lang.dev\u0026gt;.\n"}