@jbrowse/plugin-wiggle/esm/WiggleRPC/getScoreMatrix.js

JBrowse 2 wiggle adapters, tracks, etc.

import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache';
import { groupBy } from '@jbrowse/core/util';
import { checkStopToken2 } from '@jbrowse/core/util/stopToken';
import { firstValueFrom, toArray } from 'rxjs';
export async function getScoreMatrix({ pluginManager, args, }) {
    const { sources, regions, adapterConfig, sessionId, bpPerPx, stopTokenCheck, } = args;
    const adapter = await getAdapter(pluginManager, sessionId, adapterConfig);
    const dataAdapter = adapter.dataAdapter;
    const r0 = regions[0];
    const r0len = r0.end - r0.start;
    const w = Math.floor(r0len / bpPerPx);
    const feats = await firstValueFrom(dataAdapter.getFeatures(r0, args).pipe(toArray()));
    const groups = groupBy(feats, f => f.get('source'));
    const rows = {};
    const r0Start = r0.start;
    const invBpPerPx = 1 / bpPerPx;
    for (const source of sources) {
        const { name } = source;
        const features = groups[name] || [];
        const arr = new Float32Array(w);
        for (const feat of features) {
            const fstart = feat.get('start');
            const fend = feat.get('end');
            const score = feat.get('score');
            const startX = Math.max(0, ((fstart - r0Start) * invBpPerPx) | 0);
            const endX = Math.min(w, ((fend - r0Start) * invBpPerPx) | 0);
            for (let x = startX; x < endX; x++) {
                if (arr[x] === 0) {
                    arr[x] = score;
                }
            }
        }
        rows[name] = Array.from(arr);
        checkStopToken2(stopTokenCheck);
    }
    return rows;
}