{"name":"@deckyard/abif","description":"Read Applied Biosystems ABIF files: Sanger traces (.ab1), fragment-analysis runs (.fsa) and 3500 HID runs (.hid); every element type, raw and analysed traces, dyes, base calls, qualities, peak locations and run metadata","versions":{"0.1.0":{"version":"0.1.0","kind":"git","url":"https://github.com/deckyard/deck-abif.git","ref":"0.1.0","commit":"4fffec17489fe3f48b4d991fffa3c96332a452b8","checksum":"","yanked":false,"license":"LGPL-3.0-only","requires":{},"engines":{"jennifer":"\u003e=0.26.0"},"capabilities":[],"keywords":["abif","ab1","fsa","sanger","capillary-electrophoresis"],"description":"Read Applied Biosystems ABIF files: Sanger traces (.ab1), fragment-analysis runs (.fsa) and 3500 HID runs (.hid); every element type, raw and analysed traces, dyes, base calls, qualities, peak locations and run metadata","publishedAt":"1794612453","repoId":1457189854,"repoOwnerId":346943577,"repoOwner":"deckyard"}},"readme":"# @deckyard/abif\n\n[![test](https://github.com/deckyard/deck-abif/actions/workflows/test.yml/badge.svg)](https://github.com/deckyard/deck-abif/actions/workflows/test.yml)\n[![Documentation](https://img.shields.io/badge/docs-github%20pages-blue)](https://deckyard.github.io/deck-abif/)\n[![release](https://img.shields.io/github/v/release/deckyard/deck-abif)](https://github.com/deckyard/deck-abif/releases/latest)\n\nRead Applied Biosystems ABIF files in a [Jennifer](https://jennifer-lang.dev/)\nprogram: Sanger traces (`.ab1`), fragment-analysis runs (`.fsa`) and 3500\nHID runs (`.hid`). Every element type, raw and analysed traces per dye, dyes,\nbase calls with qualities and peak locations, and the sample and run\nmetadata. The directory is checked against the file before anything is read.\n\n**[Documentation](https://deckyard.github.io/deck-abif/)**\n\n## Install\n\n```sh\njvc add @deckyard/abif\n```\n\nThis vendors the deck to `vendor/\u003cscope\u003e/abif/`. Without `jvc`, unpack the\n`src/` subtree of a release archive (`\u003cscope\u003e-abif-\u003cversion\u003e.tar.gz`) there.\n\n## Usage\n\n```jennifer\nimport \"@deckyard/abif/\" as abif;\n\ndef f as abif.File init abif.open(\"sample.ab1\");\ndef i as abif.Info init abif.info($f);\ndef c as abif.Calls init abif.calls($f);\nio.printf(\"%s (%s): %d bases\\n\", $i.sample, $i.well, len($c.bases));\n```\n\n## Requirements\n\nJennifer 0.26.0 or newer. No capabilities.\n\nThe traces, peak tables and most dye names of a 3500 HID file are encrypted;\nthe deck reads that file's metadata, not its signal.\n\n## Development\n\n```sh\ntools/check-all.sh                   # the full gate, as CI runs it\njennifer test src/abif_test.j        # the test overlay\ntools/check-docs.sh                  # docs against the code\ntools/pack.sh dist                   # build the release archive\n```\n\n## Licence\n\nLGPL-3.0-only, see [LICENSE](LICENSE). Copyright (C) 2026 mplx \u0026lt;mplx@jennifer-lang.dev\u0026gt;.\n\n`tools/check-headers.sh` checks every source file's SPDX header against\n`deck.toml`. The sample files in `testdata/` have their own licences; see\n[testdata/README.md](testdata/README.md).\n"}