@jbrowse/plugin-variants 3.2.0 → 3.4.0

package/esm/MultiLinearVariantMatrixRenderer/components/MultiLinearVariantMatrixRendering.js

@@ -0,0 +1,39 @@
+import { jsx as _jsx } from "react/jsx-runtime";
+import { useRef } from 'react';
+import { PrerenderedCanvas } from '@jbrowse/core/ui';
+import { observer } from 'mobx-react';
+const MultiLinearVariantMatrixRendering = observer(function (props) {
+    const { arr, width, height, displayModel } = props;
+    const ref = useRef(null);
+    function getFeatureUnderMouse(eventClientX, eventClientY) {
+        var _a, _b, _c;
+        if (!ref.current) {
+            return;
+        }
+        const r = ref.current.getBoundingClientRect();
+        const offsetX = eventClientX - r.left;
+        const offsetY = eventClientY - r.top;
+        const dimY = arr.length;
+        const dimX = ((_a = arr[0]) === null || _a === void 0 ? void 0 : _a.length) || 0;
+        const name = (_b = displayModel.sources[Math.floor((offsetY / height) * dimX)]) === null || _b === void 0 ? void 0 : _b.name;
+        const genotype = (_c = arr[Math.floor((offsetX / width) * dimY)]) === null || _c === void 0 ? void 0 : _c[Math.floor((offsetY / height) * dimX)];
+        return genotype && name
+            ? {
+                name,
+                genotype,
+            }
+            : undefined;
+    }
+    return (_jsx("div", { ref: ref, onMouseMove: e => {
+            displayModel.setHoveredGenotype(getFeatureUnderMouse(e.clientX, e.clientY));
+        }, onMouseLeave: () => {
+            displayModel.setHoveredGenotype(undefined);
+        }, onMouseOut: () => {
+            displayModel.setHoveredGenotype(undefined);
+        }, style: {
+            overflow: 'visible',
+            position: 'relative',
+            height,
+        }, children: _jsx(PrerenderedCanvas, { ...props }) }));
+});
+export default MultiLinearVariantMatrixRendering;

package/esm/MultiLinearVariantMatrixRenderer/index.js

@@ -1,12 +1,12 @@
-import LinearVariantMatrixRenderer from './LinearVariantMatrixRenderer';
-import PrerenderedCanvas from './components/LinearVariantMatrixRendering';
+import MultiLinearVariantMatrixRenderer from './MultiLinearVariantMatrixRenderer';
+import ReactComponent from './components/MultiLinearVariantMatrixRendering';
 import configSchema from './configSchema';
 export default function LinearVariantMatrixRendererF(pluginManager) {
     pluginManager.addRendererType(() => {
-        return new LinearVariantMatrixRenderer({
+        return new MultiLinearVariantMatrixRenderer({
             name: 'LinearVariantMatrixRenderer',
             displayName: 'Linear variant matrix renderer',
-            ReactComponent: PrerenderedCanvas,
+            ReactComponent,
             configSchema,
             pluginManager,
         });

package/esm/MultiLinearVariantMatrixRenderer/makeImageData.d.ts

@@ -1,14 +1,14 @@
-import type { RenderArgsDeserializedWithFeaturesAndLayout } from './types';
+import type { RenderArgsDeserialized } from './types';
 export declare function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }: {
     ctx: CanvasRenderingContext2D;
     canvasWidth: number;
     canvasHeight: number;
-    renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
+    renderArgs: RenderArgsDeserialized;
 }): Promise<{
     mafs: {
         feature: import("@jbrowse/core/util").Feature;
         mostFrequentAlt: string;
-        alleleCounts: Map<string, number>;
+        alleleCounts: Record<string, number>;
     }[];
     arr: string[][];
 }>;

package/esm/MultiLinearVariantMatrixRenderer/makeImageData.js

@@ -1,33 +1,33 @@
-import { updateStatus } from '@jbrowse/core/util';
+import { forEachWithStopTokenCheck, updateStatus } from '@jbrowse/core/util';
 import { checkStopToken } from '@jbrowse/core/util/stopToken';
 import { f2 } from '../shared/constants';
-import { drawColorAlleleCount } from '../shared/drawAlleleCount';
+import { drawColorAlleleCount, getColorAlleleCount, } from '../shared/drawAlleleCount';
 import { drawPhased } from '../shared/drawPhased';
 import { getFeaturesThatPassMinorAlleleFrequencyFilter } from '../shared/minorAlleleFrequencyUtils';
 export async function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }) {
-    const { renderingMode: renderingMode, minorAlleleFrequencyFilter, sources, features, stopToken, } = renderArgs;
+    const { renderingMode, minorAlleleFrequencyFilter, sources, features, stopToken, lengthCutoffFilter, } = renderArgs;
     const { statusCallback = () => { } } = renderArgs;
     const h = canvasHeight / sources.length;
     checkStopToken(stopToken);
-    const mafs = getFeaturesThatPassMinorAlleleFrequencyFilter(features.values(), minorAlleleFrequencyFilter);
+    const mafs = await updateStatus('Calculating stats', statusCallback, () => getFeaturesThatPassMinorAlleleFrequencyFilter({
+        stopToken,
+        features: features.values(),
+        minorAlleleFrequencyFilter,
+        lengthCutoffFilter,
+    }));
     checkStopToken(stopToken);
     const arr = [];
     const m = mafs.length;
     const w = canvasWidth / m;
     await updateStatus('Drawing variant matrix', statusCallback, () => {
-        var _a, _b, _c;
-        let start = performance.now();
-        for (let i = 0; i < m; i++) {
-            if (performance.now() - start > 400) {
-                checkStopToken(stopToken);
-                start = performance.now();
-            }
+        const colorCache = {};
+        forEachWithStopTokenCheck(mafs, stopToken, ({ feature, mostFrequentAlt }, idx) => {
+            var _a, _b, _c;
             const arr2 = [];
-            const { feature, mostFrequentAlt } = mafs[i];
             const hasPhaseSet = (_a = feature.get('FORMAT')) === null || _a === void 0 ? void 0 : _a.includes('PS');
             if (hasPhaseSet) {
                 const samp = feature.get('samples');
-                const x = (i / mafs.length) * canvasWidth;
+                const x = (idx / mafs.length) * canvasWidth;
                 const sln = sources.length;
                 for (let j = 0; j < sln; j++) {
                     const y = (j / sln) * canvasHeight;
@@ -50,8 +50,35 @@ export async function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs
                                 }
                             }
                             else {
-                                const alleles = genotype.split(/[/|]/);
-                                drawColorAlleleCount(alleles, ctx, x, y, w, h, mostFrequentAlt);
+                                let c = colorCache[genotype];
+                                if (c === undefined) {
+                                    let alt = 0;
+                                    let uncalled = 0;
+                                    let alt2 = 0;
+                                    let ref = 0;
+                                    const alleles = genotype.split(/[/|]/);
+                                    const total = alleles.length;
+                                    for (let i = 0; i < total; i++) {
+                                        const allele = alleles[i];
+                                        if (allele === mostFrequentAlt) {
+                                            alt++;
+                                        }
+                                        else if (allele === '0') {
+                                            ref++;
+                                        }
+                                        else if (allele === '.') {
+                                            uncalled++;
+                                        }
+                                        else {
+                                            alt2++;
+                                        }
+                                    }
+                                    c = getColorAlleleCount(ref, alt, alt2, uncalled, total, true);
+                                    colorCache[genotype] = c;
+                                }
+                                if (c) {
+                                    drawColorAlleleCount(c, ctx, x, y, w, h);
+                                }
                             }
                         }
                     }
@@ -59,7 +86,7 @@ export async function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs
             }
             else {
                 const samp = feature.get('genotypes');
-                const x = (i / mafs.length) * canvasWidth;
+                const x = (idx / mafs.length) * canvasWidth;
                 const sln = sources.length;
                 for (let j = 0; j < sln; j++) {
                     const y = (j / sln) * canvasHeight;
@@ -79,14 +106,41 @@ export async function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs
                             }
                         }
                         else {
-                            const alleles = genotype.split(/[/|]/);
-                            drawColorAlleleCount(alleles, ctx, x, y, w, h, mostFrequentAlt);
+                            let c = colorCache[genotype];
+                            if (c === undefined) {
+                                let alt = 0;
+                                let uncalled = 0;
+                                let alt2 = 0;
+                                let ref = 0;
+                                const alleles = genotype.split(/[/|]/);
+                                const total = alleles.length;
+                                for (let i = 0; i < total; i++) {
+                                    const allele = alleles[i];
+                                    if (allele === mostFrequentAlt) {
+                                        alt++;
+                                    }
+                                    else if (allele === '0') {
+                                        ref++;
+                                    }
+                                    else if (allele === '.') {
+                                        uncalled++;
+                                    }
+                                    else {
+                                        alt2++;
+                                    }
+                                }
+                                c = getColorAlleleCount(ref, alt, alt2, uncalled, total, true);
+                                colorCache[genotype] = c;
+                            }
+                            if (c) {
+                                drawColorAlleleCount(c, ctx, x, y, w, h);
+                            }
                         }
                     }
                 }
             }
             arr.push(arr2);
-        }
+        });
     });
     return {
         mafs,

package/esm/MultiLinearVariantMatrixRenderer/types.d.ts

@@ -6,11 +6,9 @@ export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
     minorAlleleFrequencyFilter: number;
     highResolutionScaling: number;
     height: number;
-    renderingMode: string;
-}
-export interface RenderArgsDeserializedWithFeaturesAndLayout extends RenderArgsDeserialized {
-    sources: Source[];
     features: Map<string, Feature>;
     renderingMode: string;
     statusCallback?: (arg: string) => void;
+    lengthCutoffFilter: number;
+    stopToken: string;
 }

package/esm/MultiLinearVariantRenderer/MultiVariantRenderer.d.ts

@@ -8,7 +8,17 @@ export default class MultiVariantBaseRenderer extends FeatureRendererType {
         height: number;
         width: number;
         containsNoTransferables: boolean;
-        canvasRecordedData: any;
+        rbush: any;
+        featureGenotypeMap: {
+            [k: string]: {
+                alt: any;
+                ref: any;
+                name: any;
+                description: any;
+                length: number;
+            };
+        };
+        canvasRecordedData: Record<string, unknown>;
         reactElement?: React.ReactElement;
         html?: string;
     } | {
@@ -16,16 +26,35 @@ export default class MultiVariantBaseRenderer extends FeatureRendererType {
         height: number;
         width: number;
         containsNoTransferables: boolean;
-        reactElement: import("react/jsx-runtime").JSX.Element;
+        rbush: any;
+        featureGenotypeMap: {
+            [k: string]: {
+                alt: any;
+                ref: any;
+                name: any;
+                description: any;
+                length: number;
+            };
+        };
+        imageData: any;
+        reactElement?: React.ReactElement;
         html?: string;
     } | {
         features: Map<string, Feature>;
         height: number;
         width: number;
         containsNoTransferables: boolean;
-        imageData: any;
-        reactElement?: React.ReactElement;
+        rbush: any;
+        featureGenotypeMap: {
+            [k: string]: {
+                alt: any;
+                ref: any;
+                name: any;
+                description: any;
+                length: number;
+            };
+        };
+        reactElement: React.ReactElement;
         html?: string;
     }>;
 }
-export type { RenderArgsSerialized, RenderResults, ResultsDeserialized, ResultsSerialized, } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';

package/esm/MultiLinearVariantRenderer/MultiVariantRenderer.js

@@ -7,24 +7,30 @@ export default class MultiVariantBaseRenderer extends FeatureRendererType {
     }
     async render(renderProps) {
         const features = await this.getFeatures(renderProps);
-        const { height, regions, bpPerPx } = renderProps;
+        const { height, referenceDrawingMode, regions, bpPerPx } = renderProps;
         const region = regions[0];
         const width = (region.end - region.start) / bpPerPx;
         const { makeImageData } = await import('./makeImageData');
-        const rest = await renderToAbstractCanvas(width, height, renderProps, ctx => makeImageData(ctx, {
-            ...renderProps,
-            features,
-        }));
+        const ret = await renderToAbstractCanvas(width, height, renderProps, ctx => {
+            if (referenceDrawingMode === 'skip') {
+                ctx.fillStyle = '#ccc';
+                ctx.fillRect(0, 0, width, height);
+            }
+            return makeImageData(ctx, {
+                ...renderProps,
+                features,
+            });
+        });
         const results = await super.render({
             ...renderProps,
-            ...rest,
+            ...ret,
             features,
             height,
             width,
         });
         return {
             ...results,
-            ...rest,
+            ...ret,
             features: new Map(),
             height,
             width,

package/esm/MultiLinearVariantRenderer/components/{MultiVariantRendering.d.ts → MultiLinearVariantRendering.d.ts}

@@ -1,7 +1,14 @@
-import RBush from 'rbush';
 import type { Source } from '../../shared/types';
 import type { Feature } from '@jbrowse/core/util';
 import type { Region } from '@jbrowse/core/util/types';
+type SerializedRBush = any;
+interface MinimizedVariantRecord {
+    alt: string[];
+    ref: string;
+    name: string;
+    description: string;
+    length: number;
+}
 declare const MultiVariantRendering: (props: {
     regions: Region[];
     features: Map<string, Feature>;
@@ -10,10 +17,9 @@ declare const MultiVariantRendering: (props: {
     height: number;
     sources: Source[];
     scrollTop: number;
+    featureGenotypeMap: Record<string, MinimizedVariantRecord>;
     totalHeight: number;
-    rbush: RBush<{
-        genotype: string;
-    }>;
+    rbush: SerializedRBush;
     displayModel: any;
     onMouseLeave?: (event: React.MouseEvent) => void;
     onMouseMove?: (event: React.MouseEvent, arg?: Feature) => void;

package/esm/MultiLinearVariantRenderer/components/{MultiVariantRendering.js → MultiLinearVariantRendering.js}

@@ -1,29 +1,47 @@
 import { jsx as _jsx } from "react/jsx-runtime";
 import { useMemo, useRef } from 'react';
 import { PrerenderedCanvas } from '@jbrowse/core/ui';
+import { getBpDisplayStr } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
 import RBush from 'rbush';
+import { minElt } from './util';
+import { makeSimpleAltString } from '../../VcfFeature/util';
 const MultiVariantRendering = observer(function (props) {
-    const { totalHeight, scrollTop } = props;
+    const { featureGenotypeMap, totalHeight, scrollTop } = props;
     const { rbush, displayModel } = props;
     const ref = useRef(null);
     const rbush2 = useMemo(() => new RBush().fromJSON(rbush), [rbush]);
     function getFeatureUnderMouse(eventClientX, eventClientY) {
-        var _a;
         let offsetX = 0;
         let offsetY = 0;
         if (ref.current) {
             const r = ref.current.getBoundingClientRect();
             offsetX = eventClientX - r.left;
-            offsetY = eventClientY - r.top;
+            offsetY = eventClientY - r.top - ((displayModel === null || displayModel === void 0 ? void 0 : displayModel.scrollTop) || 0);
         }
-        const ret = rbush2.search({
+        const x = rbush2.search({
             minX: offsetX,
-            maxX: offsetX + 3,
+            maxX: offsetX + 1,
             minY: offsetY,
-            maxY: offsetY + 3,
+            maxY: offsetY + 1,
         });
-        return (_a = ret[0]) === null || _a === void 0 ? void 0 : _a.genotype;
+        if (x.length) {
+            const { minX, minY, maxX, maxY, genotype, featureId, ...rest } = minElt(x, elt => elt.maxX - elt.minX);
+            const ret = featureGenotypeMap[featureId];
+            if (ret) {
+                const { ref, alt, name, description, length } = ret;
+                const alleles = makeSimpleAltString(genotype, ref, alt);
+                return {
+                    ...rest,
+                    genotype,
+                    alleles,
+                    featureName: name,
+                    description: alt.length >= 3 ? 'multiple ALT alleles' : description,
+                    length: getBpDisplayStr(length),
+                };
+            }
+        }
+        return undefined;
     }
     return (_jsx("div", { ref: ref, onMouseMove: e => {
             var _a;

package/esm/MultiLinearVariantRenderer/components/util.d.ts

@@ -0,0 +1 @@
+export declare function minElt<T>(arr: Iterable<T>, cb: (arg: T) => number): T | undefined;

package/esm/MultiLinearVariantRenderer/components/util.js

@@ -0,0 +1,12 @@
+export function minElt(arr, cb) {
+    let min = Infinity;
+    let minElement;
+    for (const entry of arr) {
+        const val = cb(entry);
+        if (val < min) {
+            min = val;
+            minElement = entry;
+        }
+    }
+    return minElement;
+}

package/esm/MultiLinearVariantRenderer/index.js

@@ -1,5 +1,5 @@
 import MultiVariantRenderer from './MultiVariantRenderer';
-import ReactComponent from './components/MultiVariantRendering';
+import ReactComponent from './components/MultiLinearVariantRendering';
 import configSchema from './configSchema';
 export default function MultiVariantRendererF(pluginManager) {
     pluginManager.addRendererType(() => {

package/esm/MultiLinearVariantRenderer/makeImageData.d.ts

@@ -1,4 +1,13 @@
 import type { MultiRenderArgsDeserialized } from './types';
 export declare function makeImageData(ctx: CanvasRenderingContext2D, props: MultiRenderArgsDeserialized): Promise<{
     rbush: any;
+    featureGenotypeMap: {
+        [k: string]: {
+            alt: any;
+            ref: any;
+            name: any;
+            description: any;
+            length: number;
+        };
+    };
 }>;

package/esm/MultiLinearVariantRenderer/makeImageData.js

@@ -1,61 +1,124 @@
-import { featureSpanPx } from '@jbrowse/core/util';
+import { featureSpanPx, forEachWithStopTokenCheck, updateStatus, } from '@jbrowse/core/util';
 import { checkStopToken } from '@jbrowse/core/util/stopToken';
 import RBush from 'rbush';
 import { f2 } from '../shared/constants';
-import { drawColorAlleleCount } from '../shared/drawAlleleCount';
+import { drawColorAlleleCount, getColorAlleleCount, } from '../shared/drawAlleleCount';
 import { drawPhased } from '../shared/drawPhased';
 import { getFeaturesThatPassMinorAlleleFrequencyFilter } from '../shared/minorAlleleFrequencyUtils';
 export async function makeImageData(ctx, props) {
-    const { scrollTop, minorAlleleFrequencyFilter, sources, rowHeight, features, regions, bpPerPx, renderingMode, stopToken, } = props;
+    const { scrollTop, minorAlleleFrequencyFilter, sources, rowHeight, features, regions, bpPerPx, renderingMode, stopToken, lengthCutoffFilter, referenceDrawingMode, } = props;
     const region = regions[0];
+    const { statusCallback = () => { } } = props;
     checkStopToken(stopToken);
-    const mafs = getFeaturesThatPassMinorAlleleFrequencyFilter(features.values(), minorAlleleFrequencyFilter);
+    const mafs = await updateStatus('Calculating stats', statusCallback, () => getFeaturesThatPassMinorAlleleFrequencyFilter({
+        stopToken,
+        features: features.values(),
+        minorAlleleFrequencyFilter,
+        lengthCutoffFilter,
+    }));
     checkStopToken(stopToken);
     const rbush = new RBush();
-    let start = performance.now();
-    for (const { mostFrequentAlt, feature } of mafs) {
-        if (performance.now() - start > 400) {
-            checkStopToken(stopToken);
-            start = performance.now();
-        }
-        const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
-        const w = Math.max(Math.round(rightPx - leftPx), 2);
-        const samp = feature.get('genotypes');
-        let y = -scrollTop;
-        const s = sources.length;
-        for (let j = 0; j < s; j++) {
-            const { name, HP } = sources[j];
-            const genotype = samp[name];
-            const x = Math.floor(leftPx);
-            const h = Math.max(rowHeight, 1);
-            if (genotype) {
-                rbush.insert({
-                    minX: x - f2,
-                    maxX: x + w + f2,
-                    minY: y - f2,
-                    maxY: y + h + f2,
-                    genotype,
-                });
-                const isPhased = genotype.includes('|');
-                if (renderingMode === 'phased') {
-                    if (isPhased) {
-                        const alleles = genotype.split('|');
-                        drawPhased(alleles, ctx, x, y, w, h, HP);
-                    }
-                    else {
-                        ctx.fillStyle = 'black';
-                        ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
+    await updateStatus('Drawing variants', statusCallback, () => {
+        forEachWithStopTokenCheck(mafs, stopToken, ({ mostFrequentAlt, feature }) => {
+            const [leftPx, rightPx] = featureSpanPx(feature, region, bpPerPx);
+            const flen = feature.get('end') - feature.get('start');
+            const w = Math.max(Math.round(rightPx - leftPx), 2);
+            const samp = feature.get('genotypes');
+            let y = -scrollTop;
+            const s = sources.length;
+            if (renderingMode === 'phased') {
+                for (let j = 0; j < s; j++) {
+                    const { name, HP } = sources[j];
+                    const genotype = samp[name];
+                    const x = Math.floor(leftPx);
+                    const h = Math.max(rowHeight, 1);
+                    if (genotype) {
+                        const isPhased = genotype.includes('|');
+                        if (isPhased) {
+                            const alleles = genotype.split('|');
+                            if (drawPhased(alleles, ctx, x, y, w, h, HP, undefined, referenceDrawingMode === 'draw')) {
+                                rbush.insert({
+                                    minX: x,
+                                    maxX: x + w,
+                                    minY: y,
+                                    maxY: y + h,
+                                    genotype,
+                                    name,
+                                    featureId: feature.id(),
+                                });
+                            }
+                        }
+                        else {
+                            ctx.fillStyle = 'black';
+                            ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
+                        }
                     }
+                    y += rowHeight;
                 }
-                else {
-                    const alleles = genotype.split(/[/|]/);
-                    drawColorAlleleCount(alleles, ctx, x, y, w, h, mostFrequentAlt);
+            }
+            else {
+                const colorCache = {};
+                for (let j = 0; j < s; j++) {
+                    const { name } = sources[j];
+                    const genotype = samp[name];
+                    const x = Math.floor(leftPx);
+                    const h = Math.max(rowHeight, 1);
+                    if (genotype) {
+                        let c = colorCache[genotype];
+                        if (c === undefined) {
+                            let alt = 0;
+                            let uncalled = 0;
+                            let alt2 = 0;
+                            let ref = 0;
+                            const alleles = genotype.split(/[/|]/);
+                            const total = alleles.length;
+                            for (let i = 0; i < total; i++) {
+                                const allele = alleles[i];
+                                if (allele === mostFrequentAlt) {
+                                    alt++;
+                                }
+                                else if (allele === '0') {
+                                    ref++;
+                                }
+                                else if (allele === '.') {
+                                    uncalled++;
+                                }
+                                else {
+                                    alt2++;
+                                }
+                            }
+                            c = getColorAlleleCount(ref, alt, alt2, uncalled, total, referenceDrawingMode === 'draw');
+                            colorCache[genotype] = c;
+                        }
+                        if (c) {
+                            drawColorAlleleCount(c, ctx, x, y, w, h, feature.get('type'), feature.get('strand'), flen > 5 ? 0.75 : 1);
+                            rbush.insert({
+                                minX: x,
+                                maxX: x + w,
+                                minY: y,
+                                maxY: y + h,
+                                genotype,
+                                name,
+                                featureId: feature.id(),
+                            });
+                        }
+                    }
+                    y += rowHeight;
                 }
             }
-            y += rowHeight;
-        }
-    }
+        });
+    });
     return {
         rbush: rbush.toJSON(),
+        featureGenotypeMap: Object.fromEntries(mafs.map(({ feature }) => [
+            feature.id(),
+            {
+                alt: feature.get('ALT'),
+                ref: feature.get('REF'),
+                name: feature.get('name'),
+                description: feature.get('description'),
+                length: feature.get('end') - feature.get('start'),
+            },
+        ])),
     };
 }

package/esm/MultiLinearVariantRenderer/types.d.ts

@@ -16,4 +16,6 @@ export interface MultiRenderArgsDeserialized extends RenderArgsDeserializedWithF
     rowHeight: number;
     scrollTop: number;
     minorAlleleFrequencyFilter: number;
+    lengthCutoffFilter: number;
+    statusCallback?: (arg: string) => void;
 }