@jbrowse/core/esm/util/fetchSeq.js

JBrowse 2 core libraries used by plugins

import { getConf } from "../configuration/index.js";
export async function fetchSeq({ start, end, refName, assemblyName, session, }) {
    const { rpcManager, assemblyManager } = session;
    const assembly = await assemblyManager.waitForAssembly(assemblyName);
    if (!assembly) {
        throw new Error('assembly not found');
    }
    const sessionId = 'getSequence';
    const adapterConfig = getConf(assembly, ['sequence', 'adapter']);
    const canonicalRefName = assembly.getCanonicalRefName2(refName);
    const seqAdapterRefName = assembly.getSeqAdapterRefName(canonicalRefName);
    const seq = (await rpcManager.call(sessionId, 'CoreGetSequence', {
        adapterConfig,
        sessionId,
        region: {
            start,
            end,
            refName: seqAdapterRefName,
            assemblyName,
        },
    }));
    return seq ?? '';
}