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

JBrowse 2 core libraries used by plugins

import { firstValueFrom } from 'rxjs';
import { reduce } from 'rxjs/operators';
export function calcStdFromSums(sum, sumSquares, n, population = false) {
    if (n === 0) {
        return 0;
    }
    let variance;
    if (population) {
        variance = sumSquares / n - (sum * sum) / (n * n);
    }
    else {
        variance = sumSquares - (sum * sum) / n;
        if (n > 1) {
            variance /= n - 1;
        }
    }
    return variance < 0 ? 0 : Math.sqrt(variance);
}
export function rectifyStats(s) {
    return {
        ...s,
        scoreMean: (s.scoreSum || 0) / (s.featureCount || s.basesCovered || 1),
        scoreStdDev: calcStdFromSums(s.scoreSum, s.scoreSumSquares, s.featureCount || s.basesCovered),
        featureDensity: (s.featureCount || 1) / s.basesCovered,
    };
}
export async function scoresToStats(region, feats) {
    const { start, end } = region;
    const seed = {
        scoreMin: Number.MAX_VALUE,
        scoreMax: Number.MIN_VALUE,
        scoreMeanMin: Number.MAX_VALUE,
        scoreMeanMax: Number.MIN_VALUE,
        scoreSum: 0,
        scoreSumSquares: 0,
        featureCount: 0,
    };
    let found = false;
    const { scoreMin, scoreMax, scoreMeanMin, scoreMeanMax, scoreSum, scoreSumSquares, featureCount, } = await firstValueFrom(feats.pipe(reduce((acc, f) => {
        const s = f.get('score');
        const summary = f.get('summary');
        const { scoreMax, scoreMin } = acc;
        acc.scoreMax = Math.max(scoreMax, summary ? f.get('maxScore') : s);
        acc.scoreMin = Math.min(scoreMin, summary ? f.get('minScore') : s);
        acc.scoreMeanMin = Math.min(acc.scoreMeanMin, s);
        acc.scoreMeanMax = Math.max(acc.scoreMeanMax, s);
        acc.scoreSum += s;
        acc.scoreSumSquares += s * s;
        acc.featureCount += 1;
        found = true;
        return acc;
    }, seed)));
    return found
        ? rectifyStats({
            scoreMax,
            scoreMin,
            scoreMeanMin,
            scoreMeanMax,
            scoreSum,
            scoreSumSquares,
            featureCount,
            basesCovered: end - start + 1,
        })
        : blankStats();
}
export function blankStats() {
    return {
        scoreMin: 0,
        scoreMax: 0,
        scoreMean: 0,
        scoreStdDev: 0,
        scoreSum: 0,
        scoreSumSquares: 0,
        featureCount: 0,
        featureDensity: 0,
        basesCovered: 0,
    };
}