@jbrowse/bandage-core

Pangenome graph layout and drawing with no host, the engine behind jbrowse-plugin-graphgenomeviewer and BandageJS.

npm install @jbrowse/bandage-core

• GFA and rGFA text in (loadGraph)

• Layouts: Bandage's FMMM engine as WASM (loadBandage, forceLayout), ordered, anchored, sample rows, walk rows, tube map

• A Canvas2D renderer (buildGeometry, Canvas2DRenderer), hit testing and label placement

• Bubbles, deletion edges, path colors, gbz-base windows cut to GFA

• Walks lifted out of the drawing (walkLift), one facet panel per walk (facetLifts, facetGrid) and each walk's key in words (walkKey)

• Which assembly a backbone lies on (graphBackbone, backboneAssembly, assemblyWalk), and the genes on it: featuresOnBackbone renames an assembly's genes onto the backbone's refNames, and genePins pins only those

• Figures: figureSvg draws a graph and its lifted walks to a standalone SVG, and the bandage-figure CLI makes one from a JSON spec with no browser: npx -p @jbrowse/bandage-core bandage-figure spec.json -o figure.svg. See docs/figures.md

Nothing here imports React, MobX or a JBrowse host. BandageJS's src/main.ts is the worked example.

Developing

pnpm install
pnpm test          # unit tests
pnpm build         # dist/ with declarations
pnpm test:wasm     # the committed layout engine still loads

The Bandage layout engine is OGDF's FMMM compiled to WASM and committed at src/bandage/bandage-layout.js; src/bandage/README.md says how to rebuild it from src/bandage/native and the vendored vendor/ogdf. A weekly workflow proves the committed artifact still reproduces.

CI also packs the core and runs BandageJS and jbrowse-plugin-graphgenomeviewer against it. An API change lands with the consumer's side on a core-next branch in that repo, which CI tests in place of main until the release.

Release with pnpm version patch: it lints, tests, stamps src/version.ts, writes the changelog with git-cliff and pushes the v* tag, and publish.yml publishes to npm with trusted publishing.

License

Both Bandage and OGDF are GPL, which is why this package is GPL-3.0-or-later.