@jbrowse/plugin-wiggle/esm/getQuantitativeStats.js

JBrowse 2 wiggle adapters, tracks, etc.

import { getConf } from '@jbrowse/core/configuration';
import { getContainingTrack, getContainingView, getSession, } from '@jbrowse/core/util';
import { getRpcSessionId } from '@jbrowse/core/util/tracks';
import { isAlive } from '@jbrowse/mobx-state-tree';
export async function getQuantitativeStats(self, opts) {
    const { rpcManager } = getSession(self);
    const numStdDev = getConf(self, 'numStdDev') || 3;
    const { adapterConfig, autoscaleType, effectiveRpcDriverName } = self;
    const sessionId = getRpcSessionId(self);
    const trackInstanceId = getContainingTrack(self).id;
    const { currStatsBpPerPx } = opts;
    const params = {
        sessionId,
        trackInstanceId,
        adapterConfig,
        rpcDriverName: effectiveRpcDriverName,
        statusCallback: (message) => {
            if (isAlive(self)) {
                self.setStatusMessage(message);
            }
        },
        ...opts,
    };
    if (autoscaleType === 'global' || autoscaleType === 'globalsd') {
        const results = (await rpcManager.call(sessionId, 'WiggleGetGlobalQuantitativeStats', params));
        const { scoreMin, scoreMean, scoreStdDev } = results;
        return autoscaleType === 'globalsd'
            ? {
                ...results,
                scoreMin: scoreMin >= 0 ? 0 : scoreMean - numStdDev * scoreStdDev,
                scoreMax: scoreMean + numStdDev * scoreStdDev,
                currStatsBpPerPx,
            }
            : {
                ...results,
                currStatsBpPerPx,
            };
    }
    else if (autoscaleType === 'local' || autoscaleType === 'localsd') {
        const { dynamicBlocks, staticBlocks, bpPerPx } = getContainingView(self);
        const results = (await rpcManager.call(sessionId, 'WiggleGetMultiRegionQuantitativeStats', {
            ...params,
            regions: dynamicBlocks.contentBlocks.map(region => {
                const { start, end } = region;
                return {
                    ...JSON.parse(JSON.stringify(region)),
                    start: Math.floor(start),
                    end: Math.ceil(end),
                };
            }),
            staticBlocks: staticBlocks.contentBlocks.map(region => {
                const { start, end } = region;
                return {
                    ...JSON.parse(JSON.stringify(region)),
                    start: Math.floor(start),
                    end: Math.ceil(end),
                };
            }),
            bpPerPx,
        }));
        const { scoreMin, scoreMean, scoreStdDev } = results;
        return autoscaleType === 'localsd'
            ? {
                ...results,
                scoreMin: scoreMin >= 0 ? 0 : scoreMean - numStdDev * scoreStdDev,
                scoreMax: scoreMean + numStdDev * scoreStdDev,
                currStatsBpPerPx,
            }
            : {
                ...results,
                currStatsBpPerPx,
            };
    }
    else if (autoscaleType === 'zscale') {
        return rpcManager.call(sessionId, 'WiggleGetGlobalQuantitativeStats', params);
    }
    throw new Error(`invalid autoscaleType '${autoscaleType}'`);
}