gbz-base

library0.1.0-alpha.1jsnpmunverified

A prototype for storing a GBZ pangenome graph in an SQLite database, enabling interactive applications that need immediate access to parts of the graph without full in-memory loading. Currently at version 0.1.0-alpha.1, pre-stable. Key differentiators: uses SQLite for direct querying of graph slices, targets WASM for browser usage, and is intended to become an optional feature of GBWT-rs once stabilized. Released via npm as .wasm files, no JavaScript wrapper included.

database

npm install gbz-base

github ↗package ↗homepage ↗

INSTALL

IMPORT

SIG · GBZ-BASE

gbz-base

databasejavascriptv0.1.0-alpha.1

harness data pending

Install & Compatibility

Where this runs

No compatibility data collected yet for this library.

Code

Verified usage

Verified import paths — ran on the pinned version, not inferred.

gbz2db.wasm

✓ const gbz2db = await import('gbz-base/gbz2db.wasm')

Webpack resolves .wasm imports and exports a URL as default. Use dynamic import in browser environments.

query.wasm

✓ const query = await import('gbz-base/query.wasm')

Same as gbz2db.wasm. The .wasm files are WASI modules, not ES modules; need a WASI shim to execute.

full path for Node.js

✓ const fs = require('fs'); const wasm = fs.readFileSync(require.resolve('gbz-base/target/wasm32-wasi/release/query.wasm'))

✗ const query = require('gbz-base/query.wasm')

Node cannot import or require .wasm files directly. Must read the file from its actual filesystem path under node_modules.

Demonstrates loading query.wasm in the browser using dynamic import and browser-wasi-shim for WASI syscalls.

// Browser quickstart with browser-wasi-shim import { WASI, File, OpenFile, ConsoleStdout } from 'browser-wasi-shim'; // Fetch the WASM module const queryUrl = await import('gbz-base/query.wasm'); const response = await fetch(queryUrl.default); const wasmBytes = await response.arrayBuffer(); // Set up a WASI instance with a virtual filesystem const fds = [ new OpenFile(new File([])), // stdin ConsoleStdout(), ConsoleStdout(), ]; const wasi = new WASI([], [], fds); // Instantiate the WebAssembly module const { instance } = await WebAssembly.instantiate(wasmBytes, { wasi_snapshot_preview1: wasi.wasiImport, }); wasi.start(instance); // Query the graph with example graph 'example.gbz' // Note: actual usage requires passing arguments and files

Debug

Known issues

breakingVersion 0.x: API not stable. Breaking changes possible at any time.

fix

Pin to exact version and expect manual migration.

affects: <1.0.0

deprecatedPre-alpha state: No JavaScript helper or loader provided; user must handle .wasm loading manually.

fix

Use your own loader or wait for stable release with bundled JS.

affects: >=0.1.0-alpha.1

gotchaNode.js cannot import or require .wasm files as modules. Using `require('gbz-base/query.wasm')` will fail.

fix

Read the .wasm file from its actual path: require.resolve('gbz-base/target/wasm32-wasi/release/query.wasm')

affects: all

gotchaThe .wasm files target WASI, not bare WebAssembly. They need a WASI shim in non-WASI runtimes (browser, Node without --experimental-wasi-unstable).

fix

Use a WASI implementation like browser-wasi-shim or Node's built-in WASI (experimental).

affects: all

Errors

Common errors & fixes

Cannot find module 'gbz-base/query.wasm'

Wrong import path for the .wasm file.

fix

Use dynamic import with full path if using Webpack: await import('gbz-base/query.wasm')

TypeError: WebAssembly.instantiate(): Imports argument must be present and must be an object

Missing WASI import object when instantiating the .wasm module outside a WASM runtime.

fix

Provide a valid wasi_snapshot_preview1 import object, e.g., from browser-wasi-shim.

Error: The module 'gbz-base/query.wasm' cannot be imported because it's not an ES Module

Trying to use `import` statement on a .wasm file in Node.js without proper loader.

fix

Read the .wasm file with fs.readFileSync and compile it manually.

Upgrade

Version history

0.1.0-alpha.1latest on npm

Audit

Dependencies

No dependency data recorded yet.

Agent activity

14 hits · last 30 days

node

Resources

githubhttps://github.com/jltsiren/gbz-base ↗

packagegbz-base ↗

homepagehttps://github.com/jltsiren/gbz-base ↗