@jbrowse/plugin-variants 3.3.0 → 3.4.0

package/dist/LinearVariantDisplay/model.d.ts

@@ -200,7 +200,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: Feature): void;
+    selectFeature(feature: Feature): Promise<void>;
     navToFeature(feature: Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;

package/dist/MultiLinearVariantDisplay/model.d.ts

@@ -208,7 +208,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): Promise<void>;
     navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;

package/dist/MultiLinearVariantMatrixDisplay/model.d.ts

@@ -208,7 +208,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): Promise<void>;
     navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;

package/dist/MultiLinearVariantMatrixRenderer/MultiLinearVariantMatrixRenderer.d.ts

@@ -1,7 +1,6 @@
 import BoxRendererType from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
 import { SimpleFeature } from '@jbrowse/core/util';
 import type { RenderArgsDeserialized } from './types';
-import type { Feature } from '@jbrowse/core/util';
 export default class LinearVariantMatrixRenderer extends BoxRendererType {
     supportsSVG: boolean;
     render(renderProps: RenderArgsDeserialized): Promise<{
@@ -10,8 +9,8 @@ export default class LinearVariantMatrixRenderer extends BoxRendererType {
         height: number;
         width: number;
         arr: string[][];
-        canvasRecordedData: any;
-        layout: import("@jbrowse/core/util/layouts").BaseLayout<Feature>;
+        canvasRecordedData: Record<string, unknown>;
+        layout: import("@jbrowse/core/util/layouts/BaseLayout").BaseLayout<import("@jbrowse/core/util").Feature>;
         reactElement?: React.ReactElement;
         html?: string;
     } | {
@@ -20,8 +19,9 @@ export default class LinearVariantMatrixRenderer extends BoxRendererType {
         height: number;
         width: number;
         arr: string[][];
-        reactElement: import("react/jsx-runtime").JSX.Element;
-        layout: import("@jbrowse/core/util/layouts").BaseLayout<Feature>;
+        imageData: any;
+        layout: import("@jbrowse/core/util/layouts/BaseLayout").BaseLayout<import("@jbrowse/core/util").Feature>;
+        reactElement?: React.ReactElement;
         html?: string;
     } | {
         features: Map<any, any>;
@@ -29,9 +29,8 @@ export default class LinearVariantMatrixRenderer extends BoxRendererType {
         height: number;
         width: number;
         arr: string[][];
-        imageData: any;
-        layout: import("@jbrowse/core/util/layouts").BaseLayout<Feature>;
-        reactElement?: React.ReactElement;
+        reactElement: React.ReactElement;
+        layout: import("@jbrowse/core/util/layouts/BaseLayout").BaseLayout<import("@jbrowse/core/util").Feature>;
         html?: string;
     }>;
 }

package/dist/MultiLinearVariantMatrixRenderer/MultiLinearVariantMatrixRenderer.js

@@ -50,7 +50,7 @@ class LinearVariantMatrixRenderer extends BoxRendererType_1.default {
         const { end, start } = region;
         const width = (end - start) / bpPerPx;
         const { makeImageData } = await Promise.resolve().then(() => __importStar(require('./makeImageData')));
-        const { mafs, ...res } = await (0, util_1.renderToAbstractCanvas)(width, height, renderProps, ctx => makeImageData({
+        const { mafs, ...rest } = await (0, util_1.renderToAbstractCanvas)(width, height, renderProps, ctx => makeImageData({
             ctx,
             canvasWidth: width,
             canvasHeight: height,
@@ -62,14 +62,14 @@ class LinearVariantMatrixRenderer extends BoxRendererType_1.default {
         }));
         const results = await super.render({
             ...renderProps,
-            ...res,
+            ...rest,
             features,
             height,
             width,
         });
         return {
             ...results,
-            ...res,
+            ...rest,
             features: new Map(),
             simplifiedFeatures: mafs.map(({ feature }) => new util_1.SimpleFeature({
                 id: feature.id(),

package/dist/MultiLinearVariantMatrixRenderer/makeImageData.d.ts

@@ -8,7 +8,7 @@ export declare function makeImageData({ ctx, canvasWidth, canvasHeight, renderAr
     mafs: {
         feature: import("@jbrowse/core/util").Feature;
         mostFrequentAlt: string;
-        alleleCounts: Map<string, number>;
+        alleleCounts: Record<string, number>;
     }[];
     arr: string[][];
 }>;

package/dist/MultiLinearVariantMatrixRenderer/makeImageData.js

@@ -12,17 +12,18 @@ async function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }) {
     const { statusCallback = () => { } } = renderArgs;
     const h = canvasHeight / sources.length;
     (0, stopToken_1.checkStopToken)(stopToken);
-    const mafs = (0, minorAlleleFrequencyUtils_1.getFeaturesThatPassMinorAlleleFrequencyFilter)({
+    const mafs = await (0, util_1.updateStatus)('Calculating stats', statusCallback, () => (0, minorAlleleFrequencyUtils_1.getFeaturesThatPassMinorAlleleFrequencyFilter)({
         stopToken,
         features: features.values(),
         minorAlleleFrequencyFilter,
         lengthCutoffFilter,
-    });
+    }));
     (0, stopToken_1.checkStopToken)(stopToken);
     const arr = [];
     const m = mafs.length;
     const w = canvasWidth / m;
     await (0, util_1.updateStatus)('Drawing variant matrix', statusCallback, () => {
+        const colorCache = {};
         (0, util_1.forEachWithStopTokenCheck)(mafs, stopToken, ({ feature, mostFrequentAlt }, idx) => {
             var _a, _b, _c;
             const arr2 = [];
@@ -52,8 +53,35 @@ async function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }) {
                                 }
                             }
                             else {
-                                const alleles = genotype.split(/[/|]/);
-                                (0, drawAlleleCount_1.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 = (0, drawAlleleCount_1.getColorAlleleCount)(ref, alt, alt2, uncalled, total, true);
+                                    colorCache[genotype] = c;
+                                }
+                                if (c) {
+                                    (0, drawAlleleCount_1.drawColorAlleleCount)(c, ctx, x, y, w, h);
+                                }
                             }
                         }
                     }
@@ -81,8 +109,35 @@ async function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }) {
                             }
                         }
                         else {
-                            const alleles = genotype.split(/[/|]/);
-                            (0, drawAlleleCount_1.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 = (0, drawAlleleCount_1.getColorAlleleCount)(ref, alt, alt2, uncalled, total, true);
+                                colorCache[genotype] = c;
+                            }
+                            if (c) {
+                                (0, drawAlleleCount_1.drawColorAlleleCount)(c, ctx, x, y, w, h);
+                            }
                         }
                     }
                 }

package/dist/MultiLinearVariantRenderer/MultiVariantRenderer.d.ts

@@ -18,7 +18,7 @@ export default class MultiVariantBaseRenderer extends FeatureRendererType {
                 length: number;
             };
         };
-        canvasRecordedData: any;
+        canvasRecordedData: Record<string, unknown>;
         reactElement?: React.ReactElement;
         html?: string;
     } | {
@@ -36,7 +36,8 @@ export default class MultiVariantBaseRenderer extends FeatureRendererType {
                 length: number;
             };
         };
-        reactElement: import("react/jsx-runtime").JSX.Element;
+        imageData: any;
+        reactElement?: React.ReactElement;
         html?: string;
     } | {
         features: Map<string, Feature>;
@@ -53,8 +54,7 @@ export default class MultiVariantBaseRenderer extends FeatureRendererType {
                 length: number;
             };
         };
-        imageData: any;
-        reactElement?: React.ReactElement;
+        reactElement: React.ReactElement;
         html?: string;
     }>;
 }

package/dist/MultiLinearVariantRenderer/MultiVariantRenderer.js

@@ -49,7 +49,7 @@ class MultiVariantBaseRenderer extends FeatureRendererType_1.default {
         const region = regions[0];
         const width = (region.end - region.start) / bpPerPx;
         const { makeImageData } = await Promise.resolve().then(() => __importStar(require('./makeImageData')));
-        const rest = await (0, util_1.renderToAbstractCanvas)(width, height, renderProps, ctx => {
+        const ret = await (0, util_1.renderToAbstractCanvas)(width, height, renderProps, ctx => {
             if (referenceDrawingMode === 'skip') {
                 ctx.fillStyle = '#ccc';
                 ctx.fillRect(0, 0, width, height);
@@ -61,14 +61,14 @@ class MultiVariantBaseRenderer extends FeatureRendererType_1.default {
         });
         const results = await super.render({
             ...renderProps,
-            ...rest,
+            ...ret,
             features,
             height,
             width,
         });
         return {
             ...results,
-            ...rest,
+            ...ret,
             features: new Map(),
             height,
             width,

package/dist/MultiLinearVariantRenderer/makeImageData.js

@@ -14,32 +14,90 @@ const minorAlleleFrequencyUtils_1 = require("../shared/minorAlleleFrequencyUtils
 async function makeImageData(ctx, props) {
     const { scrollTop, minorAlleleFrequencyFilter, sources, rowHeight, features, regions, bpPerPx, renderingMode, stopToken, lengthCutoffFilter, referenceDrawingMode, } = props;
     const region = regions[0];
+    const { statusCallback = () => { } } = props;
     (0, stopToken_1.checkStopToken)(stopToken);
-    const mafs = (0, minorAlleleFrequencyUtils_1.getFeaturesThatPassMinorAlleleFrequencyFilter)({
+    const mafs = await (0, util_1.updateStatus)('Calculating stats', statusCallback, () => (0, minorAlleleFrequencyUtils_1.getFeaturesThatPassMinorAlleleFrequencyFilter)({
         stopToken,
         features: features.values(),
         minorAlleleFrequencyFilter,
         lengthCutoffFilter,
-    });
+    }));
     (0, stopToken_1.checkStopToken)(stopToken);
     const rbush = new rbush_1.default();
-    (0, util_1.forEachWithStopTokenCheck)(mafs, stopToken, ({ mostFrequentAlt, feature }) => {
-        const [leftPx, rightPx] = (0, util_1.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;
-        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 ((0, drawPhased_1.drawPhased)(alleles, ctx, x, y, w, h, HP, undefined, referenceDrawingMode === 'draw')) {
+    await (0, util_1.updateStatus)('Drawing variants', statusCallback, () => {
+        (0, util_1.forEachWithStopTokenCheck)(mafs, stopToken, ({ mostFrequentAlt, feature }) => {
+            const [leftPx, rightPx] = (0, util_1.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 ((0, drawPhased_1.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 - constants_1.f2, y - constants_1.f2, w + constants_1.f2, h + constants_1.f2);
+                        }
+                    }
+                    y += rowHeight;
+                }
+            }
+            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 = (0, drawAlleleCount_1.getColorAlleleCount)(ref, alt, alt2, uncalled, total, referenceDrawingMode === 'draw');
+                            colorCache[genotype] = c;
+                        }
+                        if (c) {
+                            (0, drawAlleleCount_1.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,
@@ -51,37 +109,10 @@ async function makeImageData(ctx, props) {
                             });
                         }
                     }
-                    else {
-                        ctx.fillStyle = 'black';
-                        ctx.fillRect(x - constants_1.f2, y - constants_1.f2, w + constants_1.f2, h + constants_1.f2);
-                    }
-                }
-                y += rowHeight;
-            }
-        }
-        else {
-            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) {
-                    const alleles = genotype.split(/[/|]/);
-                    if ((0, drawAlleleCount_1.drawColorAlleleCount)(alleles, ctx, x, y, w, h, mostFrequentAlt, referenceDrawingMode === 'draw', feature.get('type'), feature.get('strand'), 0.75)) {
-                        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(),

package/dist/MultiLinearVariantRenderer/types.d.ts

@@ -17,4 +17,5 @@ export interface MultiRenderArgsDeserialized extends RenderArgsDeserializedWithF
     scrollTop: number;
     minorAlleleFrequencyFilter: number;
     lengthCutoffFilter: number;
+    statusCallback?: (arg: string) => void;
 }

package/dist/MultiVariantBaseRenderer.d.ts

@@ -22,7 +22,7 @@ export default abstract class MultiVariantBaseRenderer extends FeatureRendererTy
         height: number;
         width: number;
         containsNoTransferables: boolean;
-        canvasRecordedData: any;
+        canvasRecordedData: Record<string, unknown>;
         reactElement?: React.ReactElement;
         html?: string;
     } | {
@@ -30,15 +30,15 @@ export default abstract class MultiVariantBaseRenderer extends FeatureRendererTy
         height: number;
         width: number;
         containsNoTransferables: boolean;
-        reactElement: import("react/jsx-runtime").JSX.Element;
+        imageData: any;
+        reactElement?: React.ReactElement;
         html?: string;
     } | {
         features: Map<string, Feature>;
         height: number;
         width: number;
         containsNoTransferables: boolean;
-        imageData: any;
-        reactElement?: React.ReactElement;
+        reactElement: React.ReactElement;
         html?: string;
     }>;
     abstract draw<T extends RenderArgsDeserializedWithFeatures>(ctx: CanvasRenderingContext2D, props: T): Promise<Record<string, unknown> | undefined>;

package/dist/SplitVcfTabixAdapter/SplitVcfTabixAdapter.d.ts

@@ -15,5 +15,4 @@ export default class SplitVcfTabixAdapter extends BaseFeatureDataAdapter {
     getSources(): Promise<{
         name: string;
     }[]>;
-    freeResources(): void;
 }

package/dist/SplitVcfTabixAdapter/SplitVcfTabixAdapter.js

@@ -88,6 +88,5 @@ class SplitVcfTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 .filter(f => s.has(f.name));
         }
     }
-    freeResources() { }
 }
 exports.default = SplitVcfTabixAdapter;

package/dist/VariantFeatureWidget/VariantFeatureWidget.js

@@ -82,10 +82,9 @@ function LaunchBreakendWidgetArea({ model, }) {
             },
         }, model: model, locStrings: [`${feat.refName}:${feat.end}`] })) : null;
 }
-const VariantFeatureWidget = (0, mobx_react_1.observer)(function (props) {
-    const { model } = props;
-    const { featureData, descriptions } = model;
-    const feat = JSON.parse(JSON.stringify(featureData));
+const FeatDefined = (0, mobx_react_1.observer)(function (props) {
+    const { feat, model } = props;
+    const { descriptions } = model;
     const { samples, ...rest } = feat;
     const { REF } = rest;
     return ((0, jsx_runtime_1.jsxs)(material_1.Paper, { "data-testid": "variant-side-drawer", children: [(0, jsx_runtime_1.jsx)(FeatureDetails_1.default, { feature: rest, descriptions: {
@@ -95,4 +94,10 @@ const VariantFeatureWidget = (0, mobx_react_1.observer)(function (props) {
                     return key === 'ALT' ? ((0, jsx_runtime_1.jsx)(AltFormatter_1.default, { value: `${value}`, ref: REF })) : ((0, jsx_runtime_1.jsx)(Formatter_1.default, { value: value }));
                 }, ...props }), (0, jsx_runtime_1.jsxs)(react_1.Suspense, { fallback: null, children: [(0, jsx_runtime_1.jsx)(CsqPanel, { feature: rest, descriptions: descriptions }), (0, jsx_runtime_1.jsx)(AnnPanel, { feature: rest, descriptions: descriptions }), (0, jsx_runtime_1.jsx)(LaunchBreakendWidgetArea, { model: model })] }), (0, jsx_runtime_1.jsx)(VariantSampleGrid_1.default, { feature: feat, ...props, descriptions: descriptions })] }));
 });
+const VariantFeatureWidget = (0, mobx_react_1.observer)(function (props) {
+    const { model } = props;
+    const { featureData } = model;
+    const feat = structuredClone(featureData);
+    return feat ? ((0, jsx_runtime_1.jsx)(FeatDefined, { feat: feat, ...props })) : ((0, jsx_runtime_1.jsx)("div", { children: "No feature loaded, may not be available after page refresh because it was too large for localStorage" }));
+});
 exports.default = VariantFeatureWidget;

package/dist/VariantFeatureWidget/stateModelFactory.d.ts

@@ -3,9 +3,9 @@ import type { Instance } from 'mobx-state-tree';
 export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
-    featureData: import("mobx-state-tree").IType<any, any, any>;
+    featureData: import("mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
     formattedFields: import("mobx-state-tree").IType<any, any, any>;
-    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
+    unformattedFeatureData: import("mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
     track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -35,15 +35,16 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     } & {
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+    descriptions: import("mobx-state-tree").IType<Record<string, unknown> | undefined, Record<string, unknown> | undefined, Record<string, unknown> | undefined>;
 } & {
     type: import("mobx-state-tree").ISimpleType<"VariantFeatureWidget">;
     descriptions: import("mobx-state-tree").IType<any, any, any>;
 }, {
     error: unknown;
 } & {
-    setFeatureData(featureData: Record<string, unknown>): void;
+    setFeatureData(featureData: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
     clearFeatureData(): void;
-    setFormattedData(feat: Record<string, unknown>): void;
+    setFormattedData(feat: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
     setExtra(type?: string, trackId?: string, maxDepth?: number): void;
     setError(e: unknown): void;
 } & {
@@ -53,9 +54,9 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
 } & Partial<import("mobx-state-tree/dist/internal").ExtractCFromProps<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
-    featureData: import("mobx-state-tree").IType<any, any, any>;
+    featureData: import("mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
     formattedFields: import("mobx-state-tree").IType<any, any, any>;
-    unformattedFeatureData: import("mobx-state-tree").IType<any, any, any>;
+    unformattedFeatureData: import("mobx-state-tree").IType<import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat, import("@jbrowse/core/BaseFeatureWidget/types").MaybeSerializedFeat>;
     view: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
     track: import("mobx-state-tree").IMaybe<import("mobx-state-tree").IReferenceType<import("mobx-state-tree").IAnyType>>;
     trackId: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
@@ -85,6 +86,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     } & {
         afterAttach(): void;
     }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>, [undefined]>;
+    descriptions: import("mobx-state-tree").IType<Record<string, unknown> | undefined, Record<string, unknown> | undefined, Record<string, unknown> | undefined>;
 }>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
     type: "BaseFeatureWidget";
     id: string;
@@ -95,6 +97,7 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     maxDepth: number | undefined;
     sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
     formattedFields: any;
+    descriptions: Record<string, unknown> | undefined;
     finalizedFeatureData: any;
 } & import("mobx-state-tree")._NotCustomized>;
 export type VariantFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;

package/dist/VariantRPC/getGenotypeMatrix.js

@@ -17,11 +17,12 @@ async function getGenotypeMatrix({ pluginManager, args, }) {
         features: await (0, rxjs_1.firstValueFrom)(dataAdapter.getFeaturesInMultipleRegions(regions, args).pipe((0, rxjs_1.toArray)())),
     });
     for (const { alleleCounts } of mafs) {
-        for (const alt of alleleCounts.keys()) {
+        for (const alt of Object.keys(alleleCounts)) {
             genotypeFactor.add(alt);
         }
     }
     const rows = {};
+    const cacheSplit = {};
     (0, util_1.forEachWithStopTokenCheck)(mafs, stopToken, ({ feature }) => {
         const genotypes = feature.get('genotypes');
         for (const { name } of sources) {
@@ -29,7 +30,14 @@ async function getGenotypeMatrix({ pluginManager, args, }) {
                 rows[name] = [];
             }
             const val = genotypes[name];
-            const alleles = val.split(/[/|]/);
+            let alleles;
+            if (cacheSplit[val]) {
+                alleles = cacheSplit[val];
+            }
+            else {
+                alleles = val.split(/[/|]/);
+                cacheSplit[val] = alleles;
+            }
             let genotypeStatus = 0;
             let nonRefCount = 0;
             let uncalledCount = 0;

package/dist/VcfAdapter/VcfAdapter.d.ts

@@ -31,6 +31,5 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
     getSources(): Promise<{
         name: string;
     }[]>;
-    freeResources(): void;
 }
 export {};

package/dist/VcfAdapter/VcfAdapter.js

@@ -140,7 +140,6 @@ class VcfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 .filter(f => s.has(f.name));
         }
     }
-    freeResources() { }
 }
 VcfAdapter.capabilities = ['getFeatures', 'getRefNames'];
 exports.default = VcfAdapter;

package/dist/VcfTabixAdapter/VcfTabixAdapter.d.ts

@@ -22,5 +22,4 @@ export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
     getSources(): Promise<{
         name: string;
     }[]>;
-    freeResources(): void;
 }

package/dist/VcfTabixAdapter/VcfTabixAdapter.js

@@ -113,6 +113,5 @@ class VcfTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
             return metadataLines.filter(f => vcfSampleSet.has(f.name));
         }
     }
-    freeResources() { }
 }
 exports.default = VcfTabixAdapter;

package/dist/shared/MultiVariantBaseModel.d.ts

@@ -205,7 +205,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: Feature): void;
+    selectFeature(feature: Feature): Promise<void>;
     navToFeature(feature: Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;

package/dist/shared/SharedVariantMixin.d.ts

@@ -193,7 +193,7 @@ export default function SharedVariantMixin(configSchema: AnyConfigurationSchemaT
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: Feature): void;
+    selectFeature(feature: Feature): Promise<void>;
     navToFeature(feature: Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;

package/dist/shared/drawAlleleCount.d.ts

@@ -1 +1,2 @@
-export declare function drawColorAlleleCount(alleles: string[], ctx: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, mostFrequentAlt: string, drawReference?: boolean, featureType?: string, featureStrand?: number, alpha?: number): any;
+export declare function getColorAlleleCount(ref: number, alt: number, alt2: number, uncalled: number, total: number, drawReference?: boolean): any;
+export declare function drawColorAlleleCount(c: string, ctx: CanvasRenderingContext2D, x: number, y: number, w: number, h: number, featureType?: string, featureStrand?: number, alpha?: number): void;