@jbrowse/plugin-wiggle 2.16.0 → 2.17.0

package/dist/MultiLinearWiggleDisplay/{models/model.js → model.js}

@@ -29,21 +29,19 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.stateModelFactory = stateModelFactory;
 const react_1 = require("react");
 const mobx_state_tree_1 = require("mobx-state-tree");
-const mobx_1 = require("mobx");
 const react_d3_axis_mod_1 = require("react-d3-axis-mod");
 const fast_deep_equal_1 = __importDefault(require("fast-deep-equal"));
 // jbrowse imports
 const configuration_1 = require("@jbrowse/core/configuration");
 const util_1 = require("@jbrowse/core/util");
-const tracks_1 = require("@jbrowse/core/util/tracks");
 const colors_1 = require("@jbrowse/core/ui/colors");
 // locals
-const util_2 = require("../../util");
-const modelShared_1 = __importDefault(require("../../shared/modelShared"));
+const util_2 = require("../util");
+const SharedWiggleMixin_1 = __importDefault(require("../shared/SharedWiggleMixin"));
 const randomColor = () => '#000000'.replaceAll('0', () => (~~(Math.random() * 16)).toString(16));
 // lazies
-const Tooltip = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../components/Tooltip'))));
-const SetColorDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../components/SetColorDialog'))));
+const Tooltip = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/Tooltip'))));
+const SetColorDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./components/SetColorDialog'))));
 // using a map because it preserves order
 const rendererTypes = new Map([
     ['xyplot', 'MultiXYPlotRenderer'],
@@ -59,7 +57,7 @@ const rendererTypes = new Map([
  */
 function stateModelFactory(pluginManager, configSchema) {
     return mobx_state_tree_1.types
-        .compose('MultiLinearWiggleDisplay', (0, modelShared_1.default)(configSchema), mobx_state_tree_1.types.model({
+        .compose('MultiLinearWiggleDisplay', (0, SharedWiggleMixin_1.default)(configSchema), mobx_state_tree_1.types.model({
         /**
          * #property
          */
@@ -159,6 +157,9 @@ function stateModelFactory(pluginManager, configSchema) {
         get needsCustomLegend() {
             return self.rendererTypeName === 'MultiDensityRenderer';
         },
+        /**
+         * #getter
+         */
         get canHaveFill() {
             return (self.rendererTypeName === 'MultiXYPlotRenderer' ||
                 self.rendererTypeName === 'MultiRowXYPlotRenderer');
@@ -197,6 +198,16 @@ function stateModelFactory(pluginManager, configSchema) {
                     (!this.isMultiRow ? colors_1.set1[i] || randomColor() : 'blue'),
             }));
         },
+        /**
+         * #getter
+         */
+        get quantitativeStatsReady() {
+            const view = (0, util_1.getContainingView)(self);
+            return (view.initialized &&
+                self.featureDensityStatsReady &&
+                !self.regionTooLarge &&
+                !self.error);
+        },
     }))
         .views(self => ({
         /**
@@ -218,42 +229,6 @@ function stateModelFactory(pluginManager, configSchema) {
         get useMinimalTicks() {
             return ((0, configuration_1.getConf)(self, 'minimalTicks') || this.rowHeightTooSmallForScalebar);
         },
-    }))
-        .views(self => ({
-        /**
-         * #getter
-         */
-        get ticks() {
-            const { scaleType, domain, isMultiRow, rowHeight, useMinimalTicks } = self;
-            if (!domain) {
-                return undefined;
-            }
-            const offset = isMultiRow ? 0 : util_2.YSCALEBAR_LABEL_OFFSET;
-            const ticks = (0, react_d3_axis_mod_1.axisPropsFromTickScale)((0, util_2.getScale)({
-                scaleType,
-                domain,
-                range: [rowHeight - offset, offset],
-                inverted: (0, configuration_1.getConf)(self, 'inverted'),
-            }), 4);
-            return useMinimalTicks ? { ...ticks, values: domain } : ticks;
-        },
-        /**
-         * #getter
-         */
-        get colors() {
-            return [
-                'red',
-                'blue',
-                'green',
-                'orange',
-                'purple',
-                'cyan',
-                'pink',
-                'darkblue',
-                'darkred',
-                'pink',
-            ];
-        },
     }))
         .views(self => {
         const { renderProps: superRenderProps } = self;
@@ -261,58 +236,114 @@ function stateModelFactory(pluginManager, configSchema) {
             /**
              * #method
              */
-            renderProps() {
+            adapterProps() {
                 const superProps = superRenderProps();
-                const { displayCrossHatches, filters, height, resolution, rpcDriverName, scaleOpts, stats, sources, ticks, rendererConfig: config, } = self;
                 return {
                     ...superProps,
-                    notReady: superProps.notReady || !sources || !stats,
                     displayModel: self,
-                    config,
-                    displayCrossHatches,
-                    filters,
-                    height,
-                    resolution,
-                    rpcDriverName,
-                    scaleOpts,
-                    sources,
-                    ticks,
-                    onMouseMove: (_, f) => {
-                        self.setFeatureUnderMouse(f);
-                    },
-                    onMouseLeave: () => {
-                        self.setFeatureUnderMouse(undefined);
-                    },
+                    config: self.rendererConfig,
+                    filters: self.filters,
+                    resolution: self.resolution,
+                    rpcDriverName: self.rpcDriverName,
+                    sources: self.sources,
                 };
             },
             /**
              * #getter
              */
-            get hasResolution() {
-                return self.adapterCapabilities.includes('hasResolution');
+            get ticks() {
+                const { scaleType, domain, isMultiRow, rowHeight, useMinimalTicks } = self;
+                if (!domain) {
+                    return undefined;
+                }
+                const offset = isMultiRow ? 0 : util_2.YSCALEBAR_LABEL_OFFSET;
+                const ticks = (0, react_d3_axis_mod_1.axisPropsFromTickScale)((0, util_2.getScale)({
+                    scaleType,
+                    domain,
+                    range: [rowHeight - offset, offset],
+                    inverted: (0, configuration_1.getConf)(self, 'inverted'),
+                }), 4);
+                return useMinimalTicks ? { ...ticks, values: domain } : ticks;
             },
             /**
              * #getter
              */
-            get hasGlobalStats() {
-                return self.adapterCapabilities.includes('hasGlobalStats');
+            get colors() {
+                return [
+                    'red',
+                    'blue',
+                    'green',
+                    'orange',
+                    'purple',
+                    'cyan',
+                    'pink',
+                    'darkblue',
+                    'darkred',
+                    'pink',
+                ];
             },
             /**
              * #getter
+             * unused currently
              */
-            get fillSetting() {
-                if (self.filled) {
-                    return 0;
-                }
-                else if (self.minSize === 1) {
-                    return 1;
-                }
-                else {
-                    return 2;
-                }
+            get quantitativeStatsRelevantToCurrentZoom() {
+                var _a;
+                const view = (0, util_1.getContainingView)(self);
+                return ((_a = self.stats) === null || _a === void 0 ? void 0 : _a.currStatsBpPerPx) === view.bpPerPx;
             },
         };
     })
+        .views(self => ({
+        /**
+         * #method
+         */
+        renderProps() {
+            const superProps = self.adapterProps();
+            return {
+                ...superProps,
+                notReady: superProps.notReady || !self.sources || !self.stats,
+                displayModel: self,
+                rpcDriverName: self.rpcDriverName,
+                displayCrossHatches: self.displayCrossHatches,
+                height: self.height,
+                ticks: self.ticks,
+                stats: self.stats,
+                scaleOpts: self.scaleOpts,
+                onMouseMove: (_, f) => {
+                    self.setFeatureUnderMouse(f);
+                },
+                onMouseLeave: () => {
+                    self.setFeatureUnderMouse(undefined);
+                },
+            };
+        },
+        /**
+         * #getter
+         */
+        get hasResolution() {
+            return self.adapterCapabilities.includes('hasResolution');
+        },
+        /**
+         * #getter
+         */
+        get hasGlobalStats() {
+            return self.adapterCapabilities.includes('hasGlobalStats');
+        },
+        /**
+         * #getter
+         */
+        get fillSetting() {
+            if (self.filled) {
+                return 0;
+            }
+            else if (self.minSize === 1) {
+                return 1;
+            }
+            else {
+                return 2;
+            }
+        },
+    }))
         .views(self => {
         const { trackMenuItems: superTrackMenuItems } = self;
         const hasRenderings = (0, configuration_1.getConf)(self, 'defaultRendering');
@@ -395,20 +426,20 @@ function stateModelFactory(pluginManager, configSchema) {
                 // eslint-disable-next-line @typescript-eslint/no-floating-promises
                 ;
                 (async () => {
-                    const { quantitativeStatsAutorun } = await Promise.resolve().then(() => __importStar(require('../../util')));
-                    quantitativeStatsAutorun(self);
-                    (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
-                        const { rpcManager } = (0, util_1.getSession)(self);
-                        const { adapterConfig } = self;
-                        const sessionId = (0, tracks_1.getRpcSessionId)(self);
-                        const sources = (await rpcManager.call(sessionId, 'MultiWiggleGetSources', {
-                            sessionId,
-                            adapterConfig,
-                        }));
+                    try {
+                        const [{ getMultiWiggleSourcesAutorun }, { getQuantitativeStatsAutorun },] = await Promise.all([
+                            Promise.resolve().then(() => __importStar(require('../getMultiWiggleSourcesAutorun'))),
+                            Promise.resolve().then(() => __importStar(require('../getQuantitativeStatsAutorun'))),
+                        ]);
+                        getQuantitativeStatsAutorun(self);
+                        getMultiWiggleSourcesAutorun(self);
+                    }
+                    catch (e) {
                         if ((0, mobx_state_tree_1.isAlive)(self)) {
-                            self.setSources(sources);
+                            console.error(e);
+                            (0, util_1.getSession)(self).notifyError(`${e}`, e);
                         }
-                    }));
+                    }
                 })();
             },
             /**

package/dist/MultiLinearWiggleDisplay/{models/renderSvg.js → renderSvg.js}

@@ -7,7 +7,7 @@ exports.renderSvg = renderSvg;
 const react_1 = __importDefault(require("react"));
 const util_1 = require("@jbrowse/core/util");
 const mobx_1 = require("mobx");
-const YScaleBars_1 = __importDefault(require("../components/YScaleBars"));
+const YScaleBars_1 = __importDefault(require("./components/YScaleBars"));
 async function renderSvg(self, opts, superRenderSvg) {
     await (0, mobx_1.when)(() => !!self.stats && !!self.regionCannotBeRenderedText);
     const { offsetPx } = (0, util_1.getContainingView)(self);

package/dist/MultiRowXYPlotRenderer/configSchema.js

@@ -40,7 +40,7 @@ const configSchema = (0, configuration_1.ConfigurationSchema)('MultiRowXYPlotRen
      */
     minSize: {
         type: 'number',
-        defaultValue: 0,
+        defaultValue: 0.7,
     },
 }, {
     /**

package/dist/MultiWiggleAdapter/MultiWiggleAdapter.d.ts

@@ -21,7 +21,7 @@ export default class MultiWiggleAdapter extends BaseFeatureDataAdapter {
     getMultiRegionFeatureDensityStats(_regions: Region[]): Promise<{
         featureDensity: number;
     }>;
-    getSources(): Promise<{
+    getSources(_regions: Region[]): Promise<{
         name: string;
         __name: unknown;
     }[]>;

package/dist/MultiWiggleAdapter/MultiWiggleAdapter.js

@@ -67,11 +67,13 @@ class MultiWiggleAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
     }
     // always render bigwig instead of calculating a feature density for it
     async getMultiRegionFeatureDensityStats(_regions) {
-        return { featureDensity: 0 };
+        return {
+            featureDensity: 0,
+        };
     }
     // in another adapter type, this could be dynamic depending on region or
     // something, but it is static for this particular multi-wiggle adapter type
-    async getSources() {
+    async getSources(_regions) {
         const adapters = await this.getAdapters();
         return adapters.map(({ dataAdapter, source, name, ...rest }) => ({
             name: source,

package/dist/MultiWiggleAddTrackWorkflow/AddTrackWorkflow.js

@@ -30,9 +30,6 @@ const mui_1 = require("tss-react/mui");
 const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
 const useStyles = (0, mui_1.makeStyles)()(theme => ({
-    textbox: {
-        width: '100%',
-    },
     paper: {
         margin: theme.spacing(),
         padding: theme.spacing(),
@@ -43,6 +40,16 @@ const useStyles = (0, mui_1.makeStyles)()(theme => ({
         display: 'block',
     },
 }));
+// on electron, use path to LocalFileLocation, on web, use the BlobLocation
+function makeFileLocation(file) {
+    const { webUtils } = window.require('electron');
+    return util_1.isElectron
+        ? {
+            localPath: webUtils.getPathForFile(file),
+            locationType: 'LocalPathLocation',
+        }
+        : (0, tracks_1.storeBlobLocation)({ blob: file });
+}
 function MultiWiggleWidget({ model }) {
     const { classes } = useStyles();
     const [val, setVal] = (0, react_1.useState)('');
@@ -51,64 +58,65 @@ function MultiWiggleWidget({ model }) {
         react_1.default.createElement("ul", null,
             react_1.default.createElement("li", null, "Enter list of URLs for bigwig files in the textbox"),
             react_1.default.createElement("li", null, "Or, use the button below the text box to select files from your computer")),
-        react_1.default.createElement(material_1.TextField, { multiline: true, rows: 10, value: val, onChange: event => {
+        react_1.default.createElement(material_1.TextField, { multiline: true, fullWidth: true, rows: 10, value: val, placeholder: "Paste list of URLs here, or use file selector below", variant: "outlined", onChange: event => {
                 setVal(event.target.value);
-            }, placeholder: 'Paste list of URLs here, or use file selector below', variant: "outlined", className: classes.textbox }),
+            } }),
         react_1.default.createElement(material_1.Button, { variant: "outlined", component: "label" },
             "Choose Files from your computer",
             react_1.default.createElement("input", { type: "file", hidden: true, multiple: true, onChange: ({ target }) => {
                     const res = [...(target.files || [])].map(file => ({
                         type: 'BigWigAdapter',
-                        bigWigLocation: util_1.isElectron
-                            ? {
-                                localPath: file.path,
-                                locationType: 'LocalPathLocation',
-                            }
-                            : (0, tracks_1.storeBlobLocation)({ blob: file }),
+                        bigWigLocation: makeFileLocation(file),
                         source: file.name,
                     }));
                     setVal(JSON.stringify(res, null, 2));
                 } })),
-        react_1.default.createElement(material_1.TextField, { value: trackName, onChange: event => {
+        react_1.default.createElement(material_1.TextField, { value: trackName, helperText: "Track name", onChange: event => {
                 setTrackName(event.target.value);
-            }, helperText: "Track name" }),
+            } }),
         react_1.default.createElement(material_1.Button, { variant: "contained", className: classes.submit, onClick: () => {
                 var _a;
                 const session = (0, util_1.getSession)(model);
-                const trackId = [
-                    `${trackName.toLowerCase().replaceAll(' ', '_')}-${Date.now()}`,
-                    session.adminMode ? '' : '-sessionTrack',
-                ].join('');
-                // allow list of bigwigs in JSON format or line-by-line
-                let bigWigs;
                 try {
-                    bigWigs = JSON.parse(val);
+                    const trackId = [
+                        `${trackName.toLowerCase().replaceAll(' ', '_')}-${Date.now()}`,
+                        session.adminMode ? '' : '-sessionTrack',
+                    ].join('');
+                    // allow list of bigwigs in JSON format or line-by-line
+                    let bigWigs;
+                    try {
+                        bigWigs = JSON.parse(val);
+                    }
+                    catch (e) {
+                        bigWigs = val
+                            .split(/\n|\r\n|\r/)
+                            .map(f => f.trim())
+                            .filter(f => !!f);
+                    }
+                    const obj = typeof bigWigs[0] === 'string'
+                        ? { bigWigs }
+                        : { subadapters: bigWigs };
+                    if ((0, util_1.isSessionWithAddTracks)(session)) {
+                        session.addTrackConf({
+                            trackId,
+                            type: 'MultiQuantitativeTrack',
+                            name: trackName,
+                            assemblyNames: [model.assembly],
+                            adapter: {
+                                type: 'MultiWiggleAdapter',
+                                ...obj,
+                            },
+                        });
+                        (_a = model.view) === null || _a === void 0 ? void 0 : _a.showTrack(trackId);
+                    }
+                    model.clearData();
+                    if ((0, util_1.isSessionModelWithWidgets)(session)) {
+                        session.hideWidget(model);
+                    }
                 }
                 catch (e) {
-                    bigWigs = val
-                        .split(/\n|\r\n|\r/)
-                        .map(f => f.trim())
-                        .filter(f => !!f);
-                }
-                const obj = typeof bigWigs[0] === 'string'
-                    ? { bigWigs }
-                    : { subadapters: bigWigs };
-                if ((0, util_1.isSessionWithAddTracks)(session)) {
-                    session.addTrackConf({
-                        trackId,
-                        type: 'MultiQuantitativeTrack',
-                        name: trackName,
-                        assemblyNames: [model.assembly],
-                        adapter: {
-                            type: 'MultiWiggleAdapter',
-                            ...obj,
-                        },
-                    });
-                    (_a = model.view) === null || _a === void 0 ? void 0 : _a.showTrack(trackId);
-                }
-                model.clearData();
-                if ((0, util_1.isSessionModelWithWidgets)(session)) {
-                    session.hideWidget(model);
+                    console.error(e);
+                    session.notifyError(`${e}`, e);
                 }
             } }, "Submit"),
         react_1.default.createElement("p", null, "Additional notes: "),

package/dist/MultiXYPlotRenderer/configSchema.js

@@ -40,7 +40,7 @@ const configSchema = (0, configuration_1.ConfigurationSchema)('MultiXYPlotRender
      */
     minSize: {
         type: 'number',
-        defaultValue: 0,
+        defaultValue: 0.7,
     },
 }, {
     /**

package/dist/WiggleBaseRenderer.d.ts

@@ -54,4 +54,4 @@ export default abstract class WiggleBaseRenderer extends FeatureRendererType {
      */
     abstract draw<T extends RenderArgsDeserializedWithFeatures>(ctx: CanvasRenderingContext2D, props: T): Promise<Record<string, unknown> | undefined>;
 }
-export { type RenderArgsSerialized, type RenderResults, type ResultsDeserialized, type ResultsSerialized, } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+export type { RenderArgsSerialized, RenderResults, ResultsDeserialized, ResultsSerialized, } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';

package/dist/XYPlotRenderer/configSchema.js

@@ -40,7 +40,7 @@ const configSchema = (0, configuration_1.ConfigurationSchema)('XYPlotRenderer',
      */
     minSize: {
         type: 'number',
-        defaultValue: 0,
+        defaultValue: 0.7,
     },
 }, {
     /**

package/dist/getMultiWiggleSourcesAutorun.d.ts

@@ -0,0 +1,17 @@
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export interface Source {
+    name: string;
+    color?: string;
+    group?: string;
+}
+export declare function getMultiWiggleSourcesAutorun(self: {
+    quantitativeStatsReady: boolean;
+    configuration: AnyConfigurationModel;
+    adapterConfig: AnyConfigurationModel;
+    autoscaleType: string;
+    adapterProps: () => Record<string, unknown>;
+    setStatsLoading: (aborter: AbortController) => void;
+    setError: (error: unknown) => void;
+    setMessage: (str: string) => void;
+    setSources: (sources: Source[]) => void;
+}): void;

package/dist/getMultiWiggleSourcesAutorun.js

@@ -0,0 +1,35 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getMultiWiggleSourcesAutorun = getMultiWiggleSourcesAutorun;
+const mobx_1 = require("mobx");
+const mobx_state_tree_1 = require("mobx-state-tree");
+// jbrowse
+const util_1 = require("@jbrowse/core/util");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+function getMultiWiggleSourcesAutorun(self) {
+    (0, mobx_state_tree_1.addDisposer)(self, (0, mobx_1.autorun)(async () => {
+        try {
+            const { rpcManager } = (0, util_1.getSession)(self);
+            const { adapterConfig } = self;
+            const sessionId = (0, tracks_1.getRpcSessionId)(self);
+            const view = (0, util_1.getContainingView)(self);
+            if (!view.initialized) {
+                return;
+            }
+            const sources = (await rpcManager.call(sessionId, 'MultiWiggleGetSources', {
+                regions: view.staticBlocks.contentBlocks,
+                sessionId,
+                adapterConfig,
+            }));
+            if ((0, mobx_state_tree_1.isAlive)(self)) {
+                self.setSources(sources);
+            }
+        }
+        catch (e) {
+            if (!(0, util_1.isAbortException)(e) && (0, mobx_state_tree_1.isAlive)(self)) {
+                console.error(e);
+                (0, util_1.getSession)(self).notifyError(`${e}`, e);
+            }
+        }
+    }));
+}

package/dist/getQuantitativeStats.d.ts

@@ -0,0 +1,13 @@
+import { QuantitativeStats } from '@jbrowse/core/util/stats';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export declare function getQuantitativeStats(self: {
+    adapterConfig: AnyConfigurationModel;
+    configuration: AnyConfigurationModel;
+    autoscaleType: string;
+    setMessage: (str: string) => void;
+}, opts: {
+    headers?: Record<string, string>;
+    signal?: AbortSignal;
+    filters: string[];
+    currStatsBpPerPx: number;
+}): Promise<QuantitativeStats>;

package/dist/getQuantitativeStats.js

@@ -0,0 +1,78 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getQuantitativeStats = getQuantitativeStats;
+const mobx_state_tree_1 = require("mobx-state-tree");
+// jbrowse
+const util_1 = require("@jbrowse/core/util");
+const tracks_1 = require("@jbrowse/core/util/tracks");
+const configuration_1 = require("@jbrowse/core/configuration");
+async function getQuantitativeStats(self, opts) {
+    const { rpcManager } = (0, util_1.getSession)(self);
+    const numStdDev = (0, configuration_1.getConf)(self, 'numStdDev') || 3;
+    const { adapterConfig, autoscaleType } = self;
+    const sessionId = (0, tracks_1.getRpcSessionId)(self);
+    const { currStatsBpPerPx } = opts;
+    const params = {
+        sessionId,
+        adapterConfig,
+        statusCallback: (message) => {
+            if ((0, mobx_state_tree_1.isAlive)(self)) {
+                self.setMessage(message);
+            }
+        },
+        ...opts,
+    };
+    if (autoscaleType === 'global' || autoscaleType === 'globalsd') {
+        const results = (await rpcManager.call(sessionId, 'WiggleGetGlobalQuantitativeStats', params));
+        const { scoreMin, scoreMean, scoreStdDev } = results;
+        // globalsd uses heuristic to avoid unnecessary scoreMin<0
+        //
+        // if the scoreMin is never less than 0 helps with most coverage bigwigs
+        // just being >0
+        return autoscaleType === 'globalsd'
+            ? {
+                ...results,
+                scoreMin: scoreMin >= 0 ? 0 : scoreMean - numStdDev * scoreStdDev,
+                scoreMax: scoreMean + numStdDev * scoreStdDev,
+                currStatsBpPerPx,
+            }
+            : {
+                ...results,
+                currStatsBpPerPx,
+            };
+    }
+    if (autoscaleType === 'local' || autoscaleType === 'localsd') {
+        const { dynamicBlocks, bpPerPx } = (0, util_1.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),
+                };
+            }),
+            bpPerPx,
+        }));
+        const { scoreMin, scoreMean, scoreStdDev } = results;
+        // localsd uses heuristic to avoid unnecessary scoreMin<0 if the
+        // scoreMin is never less than 0 helps with most coverage bigwigs
+        // just being >0
+        return autoscaleType === 'localsd'
+            ? {
+                ...results,
+                scoreMin: scoreMin >= 0 ? 0 : scoreMean - numStdDev * scoreStdDev,
+                scoreMax: scoreMean + numStdDev * scoreStdDev,
+                currStatsBpPerPx,
+            }
+            : {
+                ...results,
+                currStatsBpPerPx,
+            };
+    }
+    if (autoscaleType === 'zscale') {
+        return rpcManager.call(sessionId, 'WiggleGetGlobalQuantitativeStats', params);
+    }
+    throw new Error(`invalid autoscaleType '${autoscaleType}'`);
+}

package/dist/getQuantitativeStatsAutorun.d.ts

@@ -0,0 +1,13 @@
+import { QuantitativeStats } from '@jbrowse/core/util/stats';
+import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+export declare function getQuantitativeStatsAutorun(self: {
+    quantitativeStatsReady: boolean;
+    configuration: AnyConfigurationModel;
+    adapterConfig: AnyConfigurationModel;
+    autoscaleType: string;
+    adapterProps: () => Record<string, unknown>;
+    setStatsLoading: (aborter: AbortController) => void;
+    setError: (error: unknown) => void;
+    setMessage: (str: string) => void;
+    updateQuantitativeStats: (stats: QuantitativeStats, region: string) => void;
+}): void;