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

JBrowse 2 core libraries used by plugins

"use strict";
Object.defineProperty(exports, "__esModule", { value: true });
const util_1 = require("../../util");
const io_1 = require("../../util/io");
const BaseAdapter_1 = require("../BaseAdapter");
class CytobandAdapter extends BaseAdapter_1.BaseAdapter {
    async getData(opts) {
        const conf = this.getConf('cytobandLocation');
        if (conf.uri === '' || conf.uri === '/path/to/cytoband.txt.gz') {
            return [];
        }
        const text = await (0, util_1.fetchAndMaybeUnzipText)((0, io_1.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 util_1.SimpleFeature({
                uniqueId: `${i}`,
                refName: refName,
                start: +start,
                end: +end,
                name,
                type,
                gieStain: type || name,
            });
        });
    }
}
exports.default = CytobandAdapter;