@jbrowse/plugin-config/esm/RefNameAliasAdapter/RefNameAliasAdapter.js

JBrowse 2 config utilities

import { BaseAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
import { openLocation } from '@jbrowse/core/util/io';
export default class RefNameAliasAdapter extends BaseAdapter {
    async getRefNameAliases() {
        const loc = this.getConf('location');
        if (loc.uri === '' || loc.uri === '/path/to/my/aliases.txt') {
            return [];
        }
        const results = await openLocation(loc, this.pluginManager).readFile('utf8');
        const refColumn = this.getConf('refNameColumn');
        const refColumnHeaderName = this.getConf('refNameColumnHeaderName');
        const lines = results
            .trim()
            .split(/\n|\r\n|\r/)
            .filter(f => !!f);
        const header = lines.filter(f => f.startsWith('#'));
        const headerCol = refColumnHeaderName && header.length
            ? header
                .at(-1)
                .slice(1)
                .split('\t')
                .map(t => t.trim())
                .indexOf(refColumnHeaderName)
            : refColumn;
        return lines
            .filter(f => !f.startsWith('#'))
            .map(row => {
            const aliases = row.split('\t');
            const refName = aliases[headerCol];
            return {
                refName: refName,
                aliases: aliases.filter(f => !!f.trim()),
            };
        });
    }
}