This README is the one indexed from the repository at its latest ref, not from the tag for this version.

d4-plot

A native desktop viewer for D4 genomic signal files. D4 Plot compares multiple tracks, displays genomic annotations, exports visible bins or complete BigWig tracks, and creates coverage D4 files from BAM or CRAM.

Windows	macOS	Linux

Documentation

English guide · 日本語ガイド

Install

Download a package from GitHub Releases, or follow the source build guide.

Browser viewer / headless server

Open the bundled local IGV.js viewer with or without D4 tracks, without starting the native desktop UI:

# Either entry point accepts the same options.
d4-plot serve --genome hg38 --open sample.d4
d4-plot-server --genome hg38 --open
d4-plot-server --reference reference.fa --reference-index reference.fa.fai sample.d4
d4-plot-server --contigs-only sample.d4

The server binds only to 127.0.0.1 and prints a token-scoped viewer URL. Use --open to launch it automatically, or paste the printed URL into a browser. --port 0 (the default) selects an available loopback port; stop the server with Ctrl-C. On Windows, run d4-plot-server from a terminal when you need to copy the printed URL. In the macOS DMG, the standalone binary is inside the application bundle at d4-plot.app/Contents/MacOS/d4-plot-server so it can share the bundle's packaged native libraries.

Reference choices are mutually exclusive: --genome ID, --reference PATH, or --contigs-only. A local FASTA requires an existing FAI (use --reference-index to name a non-default one). A .json reference is treated as an IGV genome JSON and its referenced files must be accessible local files. Preset genomes use IGV's public reference definitions, so their sequence data is not available offline unless a local reference is supplied. With a preset, the browser fetches public reference data directly from IGV/UCSC hosts; the local server does not proxy those requests. Those HTTPS byte-range requests can reveal the reference and approximate viewed genomic intervals to that reference host; use a local FASTA/FAI for fully local reference access.

Development

shards install --frozen
crystal spec spec
ameba
crystal tool format --check src spec examples

See the development guide for native dependencies, platform-specific builds, and UI runtime constraints.

License

MIT. See LICENSE and THIRD_PARTY_NOTICES.md.