@jbrowse/core/esm/data_adapters/CytobandAdapter/CytobandAdapter.js

JBrowse 2 core libraries used by plugins

import { SimpleFeature, fetchAndMaybeUnzipText } from "../../util/index.js";
import { openLocation } from "../../util/io/index.js";
import { BaseAdapter } from "../BaseAdapter/index.js";
export default class CytobandAdapter extends BaseAdapter {
    async getData(opts) {
        const conf = this.getConf('cytobandLocation');
        if (conf.uri === '' || conf.uri === '/path/to/cytoband.txt.gz') {
            return [];
        }
        const text = await fetchAndMaybeUnzipText(openLocation(conf, this.pluginManager), opts);
        return text
            .split(/\n|\r\n|\r/)
            .filter(f => !!f.trim())
            .filter(f => !f.startsWith('#'))
            .map((line, i) => {
            const [refName, start, end, name, type] = line.split('\t');
            return new SimpleFeature({
                uniqueId: `${i}`,
                refName: refName,
                start: +start,
                end: +end,
                name,
                type,
                gieStain: type || name,
            });
        });
    }
}