@jbrowse/plugin-variants 3.6.4 → 3.7.0

package/dist/LinearVariantDisplay/model.d.ts

@@ -181,6 +181,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
+    mouseoverExtraInformation: string | undefined;
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | Feature;
 } & {
@@ -195,9 +196,22 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
     readonly featureUnderMouse: Feature | undefined;
+    readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, [number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]>;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
-    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
-    searchFeatureByID(id: string): [number, number, number, number] | undefined;
+    getFeatureByID(blockKey: string, id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
+    searchFeatureByID(id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
@@ -206,6 +220,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
     setContextMenuFeature(feature?: Feature): void;
+    setMouseoverExtraInformation(extra?: string): void;
 } & {
     reload(): Promise<void>;
 } & {

package/dist/MultiLinearVariantDisplay/model.d.ts

@@ -189,6 +189,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
+    mouseoverExtraInformation: string | undefined;
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
 } & {
@@ -203,9 +204,22 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
+    readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, [number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]>;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
-    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
-    searchFeatureByID(id: string): [number, number, number, number] | undefined;
+    getFeatureByID(blockKey: string, id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
+    searchFeatureByID(id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
@@ -214,6 +228,7 @@ export declare function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature): void;
+    setMouseoverExtraInformation(extra?: string): void;
 } & {
     reload(): Promise<void>;
 } & {

package/dist/MultiLinearVariantMatrixDisplay/model.d.ts

@@ -189,6 +189,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
+    mouseoverExtraInformation: string | undefined;
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | import("@jbrowse/core/util").Feature;
 } & {
@@ -203,9 +204,22 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
+    readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, [number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]>;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
-    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
-    searchFeatureByID(id: string): [number, number, number, number] | undefined;
+    getFeatureByID(blockKey: string, id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
+    searchFeatureByID(id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
@@ -214,6 +228,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
     setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature): void;
+    setMouseoverExtraInformation(extra?: string): void;
 } & {
     reload(): Promise<void>;
 } & {

package/dist/MultiLinearVariantMatrixRenderer/makeImageData.js

@@ -53,7 +53,8 @@ async function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }) {
                                 }
                             }
                             else {
-                                let c = colorCache[genotype];
+                                const cacheKey = `${genotype}:${mostFrequentAlt}`;
+                                let c = colorCache[cacheKey];
                                 if (c === undefined) {
                                     let alt = 0;
                                     let uncalled = 0;
@@ -77,7 +78,7 @@ async function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }) {
                                         }
                                     }
                                     c = (0, drawAlleleCount_1.getColorAlleleCount)(ref, alt, alt2, uncalled, total, true);
-                                    colorCache[genotype] = c;
+                                    colorCache[cacheKey] = c;
                                 }
                                 if (c) {
                                     (0, drawAlleleCount_1.drawColorAlleleCount)(c, ctx, x, y, w, h);
@@ -109,7 +110,8 @@ async function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }) {
                             }
                         }
                         else {
-                            let c = colorCache[genotype];
+                            const cacheKey = `${genotype}:${mostFrequentAlt}`;
+                            let c = colorCache[cacheKey];
                             if (c === undefined) {
                                 let alt = 0;
                                 let uncalled = 0;
@@ -133,7 +135,7 @@ async function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }) {
                                     }
                                 }
                                 c = (0, drawAlleleCount_1.getColorAlleleCount)(ref, alt, alt2, uncalled, total, true);
-                                colorCache[genotype] = c;
+                                colorCache[cacheKey] = c;
                             }
                             if (c) {
                                 (0, drawAlleleCount_1.drawColorAlleleCount)(c, ctx, x, y, w, h);

package/dist/MultiLinearVariantRenderer/MultiVariantRenderer.d.ts

@@ -8,7 +8,8 @@ export default class MultiVariantBaseRenderer extends FeatureRendererType {
         height: number;
         width: number;
         containsNoTransferables: boolean;
-        rbush: any;
+        flatbush: ArrayBufferLike;
+        items: any[];
         featureGenotypeMap: {
             [k: string]: {
                 alt: any;
@@ -26,7 +27,8 @@ export default class MultiVariantBaseRenderer extends FeatureRendererType {
         height: number;
         width: number;
         containsNoTransferables: boolean;
-        rbush: any;
+        flatbush: ArrayBufferLike;
+        items: any[];
         featureGenotypeMap: {
             [k: string]: {
                 alt: any;
@@ -44,7 +46,8 @@ export default class MultiVariantBaseRenderer extends FeatureRendererType {
         height: number;
         width: number;
         containsNoTransferables: boolean;
-        rbush: any;
+        flatbush: ArrayBufferLike;
+        items: any[];
         featureGenotypeMap: {
             [k: string]: {
                 alt: any;

package/dist/MultiLinearVariantRenderer/components/MultiLinearVariantRendering.d.ts

@@ -1,7 +1,11 @@
 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 Item {
+    genotype: string;
+    featureId: string;
+    bpLen: number;
+}
 interface MinimizedVariantRecord {
     alt: string[];
     ref: string;
@@ -19,7 +23,8 @@ declare const MultiVariantRendering: (props: {
     scrollTop: number;
     featureGenotypeMap: Record<string, MinimizedVariantRecord>;
     totalHeight: number;
-    rbush: SerializedRBush;
+    flatbush: any;
+    items: Item[];
     displayModel: any;
     onMouseLeave?: (event: React.MouseEvent) => void;
     onMouseMove?: (event: React.MouseEvent, arg?: Feature) => void;

package/dist/MultiLinearVariantRenderer/components/MultiLinearVariantRendering.js

@@ -7,33 +7,30 @@ const jsx_runtime_1 = require("react/jsx-runtime");
 const react_1 = require("react");
 const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
+const flatbush_1 = __importDefault(require("@jbrowse/core/util/flatbush"));
 const mobx_react_1 = require("mobx-react");
-const rbush_1 = __importDefault(require("rbush"));
 const util_2 = require("./util");
 const util_3 = require("../../VcfFeature/util");
 const MultiVariantRendering = (0, mobx_react_1.observer)(function (props) {
-    const { featureGenotypeMap, totalHeight, scrollTop } = props;
-    const { rbush, displayModel } = props;
+    const { flatbush, items, displayModel, featureGenotypeMap, totalHeight, scrollTop, } = props;
     const ref = (0, react_1.useRef)(null);
-    const rbush2 = (0, react_1.useMemo)(() => new rbush_1.default().fromJSON(rbush), [rbush]);
+    const flatbush2 = (0, react_1.useMemo)(() => flatbush_1.default.from(flatbush), [flatbush]);
     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 - ((displayModel === null || displayModel === void 0 ? void 0 : displayModel.scrollTop) || 0);
+        if (!ref.current) {
+            return;
         }
-        const x = rbush2.search({
-            minX: offsetX,
-            maxX: offsetX + 1,
-            minY: offsetY,
-            maxY: offsetY + 1,
-        });
+        const rect = ref.current.getBoundingClientRect();
+        offsetX = eventClientX - rect.left;
+        offsetY = eventClientY - rect.top - ((displayModel === null || displayModel === void 0 ? void 0 : displayModel.scrollTop) || 0);
+        const x = flatbush2.search(offsetX, offsetY, offsetX + 1, offsetY + 1);
         if (x.length) {
-            const { minX, minY, maxX, maxY, genotype, featureId, ...rest } = (0, util_2.minElt)(x, elt => elt.maxX - elt.minX);
-            const ret = featureGenotypeMap[featureId];
-            if (ret) {
+            const res = (0, util_2.minElt)(x, idx => { var _a, _b; return (_b = (_a = items[idx]) === null || _a === void 0 ? void 0 : _a.bpLen) !== null && _b !== void 0 ? _b : 0; });
+            const { bpLen, genotype, featureId, ...rest } = (_a = items[res]) !== null && _a !== void 0 ? _a : {};
+            const ret = featureId !== undefined ? featureGenotypeMap[featureId] : undefined;
+            if (ret && genotype) {
                 const { ref, alt, name, description, length } = ret;
                 const alleles = (0, util_3.makeSimpleAltString)(genotype, ref, alt);
                 return {

package/dist/MultiLinearVariantRenderer/makeImageData.d.ts

@@ -1,6 +1,7 @@
 import type { MultiRenderArgsDeserialized } from './types';
 export declare function makeImageData(ctx: CanvasRenderingContext2D, props: MultiRenderArgsDeserialized): Promise<{
-    rbush: any;
+    flatbush: ArrayBufferLike;
+    items: any[];
     featureGenotypeMap: {
         [k: string]: {
             alt: any;

package/dist/MultiLinearVariantRenderer/makeImageData.js

@@ -5,8 +5,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.makeImageData = makeImageData;
 const util_1 = require("@jbrowse/core/util");
+const flatbush_1 = __importDefault(require("@jbrowse/core/util/flatbush"));
 const stopToken_1 = require("@jbrowse/core/util/stopToken");
-const rbush_1 = __importDefault(require("rbush"));
 const constants_1 = require("../shared/constants");
 const drawAlleleCount_1 = require("../shared/drawAlleleCount");
 const drawPhased_1 = require("../shared/drawPhased");
@@ -23,11 +23,14 @@ async function makeImageData(ctx, props) {
         lengthCutoffFilter,
     }));
     (0, stopToken_1.checkStopToken)(stopToken);
-    const rbush = new rbush_1.default();
+    const coords = [];
+    const items = [];
+    const colorCache = {};
     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 featureId = feature.id();
+            const bpLen = feature.get('end') - feature.get('start');
             const w = Math.max(Math.round(rightPx - leftPx), 2);
             const samp = feature.get('genotypes');
             let y = -scrollTop;
@@ -43,15 +46,13 @@ async function makeImageData(ctx, props) {
                         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,
+                                items.push({
                                     name,
-                                    featureId: feature.id(),
+                                    genotype,
+                                    featureId,
+                                    bpLen,
                                 });
+                                coords.push(x, y, x + w, y + h);
                             }
                         }
                         else {
@@ -63,14 +64,14 @@ async function makeImageData(ctx, props) {
                 }
             }
             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];
+                        const cacheKey = `${genotype}:${mostFrequentAlt}`;
+                        let c = colorCache[cacheKey];
                         if (c === undefined) {
                             let alt = 0;
                             let uncalled = 0;
@@ -94,19 +95,17 @@ async function makeImageData(ctx, props) {
                                 }
                             }
                             c = (0, drawAlleleCount_1.getColorAlleleCount)(ref, alt, alt2, uncalled, total, referenceDrawingMode === 'draw');
-                            colorCache[genotype] = c;
+                            colorCache[cacheKey] = 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,
-                                minY: y,
-                                maxY: y + h,
-                                genotype,
+                            (0, drawAlleleCount_1.drawColorAlleleCount)(c, ctx, x, y, w, h, feature.get('type'), feature.get('strand'), bpLen > 5 ? 0.75 : 1);
+                            items.push({
                                 name,
-                                featureId: feature.id(),
+                                genotype,
+                                featureId,
+                                bpLen,
                             });
+                            coords.push(x, y, x + w, y + h);
                         }
                     }
                     y += rowHeight;
@@ -114,8 +113,19 @@ async function makeImageData(ctx, props) {
             }
         });
     });
+    const flatbush = new flatbush_1.default(Math.max(items.length, 1));
+    if (items.length) {
+        for (let i = 0; i < coords.length; i += 4) {
+            flatbush.add(coords[i], coords[i + 1], coords[i + 2], coords[i + 3]);
+        }
+    }
+    else {
+        flatbush.add(0, 0);
+    }
+    flatbush.finish();
     return {
-        rbush: rbush.toJSON(),
+        flatbush: flatbush.data,
+        items,
         featureGenotypeMap: Object.fromEntries(mafs.map(({ feature }) => [
             feature.id(),
             {

package/dist/StructuralVariantChordRenderer/ReactComponent.js

@@ -23,7 +23,7 @@ const StructuralVariantChordsReactComponent = (0, mobx_react_1.observer)(functio
     }, [blockDefinitions]);
     return ((0, jsx_runtime_1.jsx)("g", { "data-testid": "structuralVariantChordRenderer", children: [...features.values()].map(feature => {
             const id = feature.id();
-            const selected = String(selectedFeatureId) === String(id);
+            const selected = selectedFeatureId === id;
             return ((0, jsx_runtime_1.jsx)(Chord_1.default, { feature: feature, config: config, radius: radius, bezierRadius: bezierRadius, blocksForRefs: blocksForRefsMemo, selected: selected, onClick: onChordClick }, id));
         }) }));
 });

package/dist/VariantFeatureWidget/AltFormatter.d.ts

@@ -1,4 +1,4 @@
-export default function AltFormatter({ value, ref, }: {
+export default function AltFormatter({ value, refString, }: {
     value: string;
-    ref: string;
+    refString: string;
 }): string | import("react/jsx-runtime").JSX.Element;

package/dist/VariantFeatureWidget/AltFormatter.js

@@ -4,10 +4,10 @@ exports.default = AltFormatter;
 const jsx_runtime_1 = require("react/jsx-runtime");
 const react_1 = require("react");
 const util_1 = require("../VcfFeature/util");
-function AltFormatter({ value, ref, }) {
+function AltFormatter({ value, refString, }) {
     const [show, setShow] = (0, react_1.useState)(false);
-    const alt = (0, util_1.getMinimalDesc)(ref, value);
+    const alt = (0, react_1.useMemo)(() => (0, util_1.getMinimalDesc)(refString, value), [refString, value]);
     return alt !== value ? ((0, jsx_runtime_1.jsxs)("div", { children: [(0, jsx_runtime_1.jsx)("button", { onClick: () => {
                     setShow(!show);
-                }, children: show ? 'Show simplified ALT' : 'Show raw ALT' }), ' ', show ? value : (0, util_1.getMinimalDesc)(ref, value)] })) : (value);
+                }, children: show ? 'Show simplified ALT' : 'Show raw ALT' }), ' ', show ? value : alt] })) : (value);
 }

package/dist/VariantFeatureWidget/VariantFeatureWidget.js

@@ -91,7 +91,7 @@ const FeatDefined = (0, mobx_react_1.observer)(function (props) {
                     ...variantFieldDescriptions_1.variantFieldDescriptions,
                     ...descriptions,
                 }, formatter: (value, key) => {
-                    return key === 'ALT' ? ((0, jsx_runtime_1.jsx)(AltFormatter_1.default, { value: `${value}`, ref: REF })) : ((0, jsx_runtime_1.jsx)(Formatter_1.default, { value: value }));
+                    return key === 'ALT' ? ((0, jsx_runtime_1.jsx)(AltFormatter_1.default, { value: `${value}`, refString: 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) {

package/dist/VariantFeatureWidget/stateModelFactory.d.ts

@@ -18,14 +18,14 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         upperCaseCDS: boolean;
         charactersPerRow: number;
         feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
-        mode: string;
+        mode: "" | "genomic" | "gene" | "gene_collapsed_intron" | "gene_updownstream" | "cdna" | "cds" | "genomic_sequence_updownstream" | "protein";
     } & {
         setFeature(f: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
         setUpDownBp(f: number): void;
         setIntronBp(f: number): void;
         setUpperCaseCDS(f: boolean): void;
         setShowCoordinates(f: "none" | "relative" | "genomic"): void;
-        setMode(mode: string): void;
+        setMode(mode: "" | "genomic" | "gene" | "gene_collapsed_intron" | "gene_updownstream" | "cdna" | "cds" | "genomic_sequence_updownstream" | "protein"): void;
     } & {
         readonly showCoordinates: boolean;
         readonly showGenomicCoordsOption: boolean;
@@ -69,14 +69,14 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
         upperCaseCDS: boolean;
         charactersPerRow: number;
         feature: import("@jbrowse/core/util").SimpleFeatureSerialized | undefined;
-        mode: string;
+        mode: "" | "genomic" | "gene" | "gene_collapsed_intron" | "gene_updownstream" | "cdna" | "cds" | "genomic_sequence_updownstream" | "protein";
     } & {
         setFeature(f: import("@jbrowse/core/util").SimpleFeatureSerialized): void;
         setUpDownBp(f: number): void;
         setIntronBp(f: number): void;
         setUpperCaseCDS(f: boolean): void;
         setShowCoordinates(f: "none" | "relative" | "genomic"): void;
-        setMode(mode: string): void;
+        setMode(mode: "" | "genomic" | "gene" | "gene_collapsed_intron" | "gene_updownstream" | "cdna" | "cds" | "genomic_sequence_updownstream" | "protein"): void;
     } & {
         readonly showCoordinates: boolean;
         readonly showGenomicCoordsOption: boolean;

package/dist/VcfAdapter/VcfAdapter.d.ts

@@ -1,15 +1,15 @@
-import IntervalTree from '@flatten-js/interval-tree';
+import { IntervalTree } from '@flatten-js/interval-tree';
 import VcfParser from '@gmod/vcf';
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
 import type { Feature, Region } from '@jbrowse/core/util';
 type StatusCallback = (arg: string) => void;
 export default class VcfAdapter extends BaseFeatureDataAdapter {
-    calculatedIntervalTreeMap: Record<string, IntervalTree>;
+    calculatedIntervalTreeMap: Record<string, IntervalTree<Feature>>;
     vcfFeatures?: Promise<{
         header: string;
         parser: VcfParser;
-        intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree>;
+        intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree<Feature>>;
     }>;
     static capabilities: string[];
     getHeader(): Promise<string>;
@@ -18,13 +18,13 @@ export default class VcfAdapter extends BaseFeatureDataAdapter {
         header: string;
         parser: VcfParser;
         intervalTreeMap: {
-            [k: string]: (sc?: (arg: string) => void) => IntervalTree<any>;
+            [k: string]: (sc?: (arg: string) => void) => IntervalTree<Feature>;
         };
     }>;
     setup(): Promise<{
         header: string;
         parser: VcfParser;
-        intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree>;
+        intervalTreeMap: Record<string, (sc?: StatusCallback) => IntervalTree<Feature>>;
     }>;
     getRefNames(_?: BaseOptions): Promise<string[]>;
     getFeatures(region: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;

package/dist/VcfAdapter/VcfAdapter.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const interval_tree_1 = __importDefault(require("@flatten-js/interval-tree"));
+const interval_tree_1 = require("@flatten-js/interval-tree");
 const vcf_1 = __importDefault(require("@gmod/vcf"));
 const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
 const util_1 = require("@jbrowse/core/util");
@@ -36,7 +36,7 @@ class VcfAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 if (!this.calculatedIntervalTreeMap[refName]) {
                     sc === null || sc === void 0 ? void 0 : sc('Parsing VCF data');
                     let idx = 0;
-                    const intervalTree = new interval_tree_1.default();
+                    const intervalTree = new interval_tree_1.IntervalTree();
                     for (const line of lines) {
                         const f = new VcfFeature_1.default({
                             variant: parser.parseLine(line),

package/dist/VcfFeature/index.d.ts

@@ -1,6 +1,6 @@
+import { type Feature } from '@jbrowse/core/util';
 import type VCFParser from '@gmod/vcf';
 import type { Variant } from '@gmod/vcf';
-import type { Feature } from '@jbrowse/core/util';
 export default class VCFFeature implements Feature {
     private variant;
     private parser;

package/dist/VcfFeature/index.js

@@ -1,10 +1,11 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-const util_1 = require("./util");
+const util_1 = require("@jbrowse/core/util");
+const util_2 = require("./util");
 function dataFromVariant(variant, parser) {
     const { REF = '', ALT, POS, CHROM, ID } = variant;
     const start = POS - 1;
-    const [type, description] = (0, util_1.getSOTermAndDescription)(REF, ALT, parser);
+    const [type, description] = (0, util_2.getSOTermAndDescription)(REF, ALT, parser);
     return {
         refName: CHROM,
         start,
@@ -15,15 +16,30 @@ function dataFromVariant(variant, parser) {
     };
 }
 function getEnd(variant) {
-    const { POS, REF = '', ALT } = variant;
-    const isTRA = ALT === null || ALT === void 0 ? void 0 : ALT.includes('<TRA>');
+    var _a;
+    const { POS, REF = '', ALT = [] } = variant;
+    const isTRA = ALT.includes('<TRA>');
     const start = POS - 1;
-    const isSymbolic = ALT === null || ALT === void 0 ? void 0 : ALT.some(f => f.includes('<'));
+    const isSymbolic = ALT.some(f => f.includes('<'));
     if (isSymbolic) {
         const info = variant.INFO;
         if (info.END && !isTRA) {
             return +info.END[0];
         }
+        const lens = [];
+        if (info.SVLEN && !isTRA) {
+            const svlens = info.SVLEN;
+            for (let i = 0; i < svlens.length; i++) {
+                const svlen = svlens[i];
+                if ((_a = ALT[i]) === null || _a === void 0 ? void 0 : _a.startsWith('<INS')) {
+                    lens.push(1);
+                }
+                else {
+                    lens.push(Math.abs(+svlen));
+                }
+            }
+            return start + (0, util_1.max)(lens);
+        }
     }
     return start + REF.length;
 }

package/dist/shared/MultiVariantBaseModel.d.ts

@@ -186,6 +186,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
     regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
+    mouseoverExtraInformation: string | undefined;
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | Feature;
 } & {
@@ -200,9 +201,22 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
     readonly featureUnderMouse: Feature | undefined;
+    readonly layoutFeatures: import("@jbrowse/core/util/compositeMap").default<string, [number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]>;
     getFeatureOverlapping(blockKey: string, x: number, y: number): string | undefined;
-    getFeatureByID(blockKey: string, id: string): [number, number, number, number] | undefined;
-    searchFeatureByID(id: string): [number, number, number, number] | undefined;
+    getFeatureByID(blockKey: string, id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
+    searchFeatureByID(id: string): ([number, number, number, number] | [number, number, number, number, {
+        label?: string;
+        description?: string;
+        refName: string;
+    }]) | undefined;
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
@@ -211,6 +225,7 @@ export default function MultiVariantBaseModelF(configSchema: AnyConfigurationSch
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
     setContextMenuFeature(feature?: Feature): void;
+    setMouseoverExtraInformation(extra?: string): void;
 } & {
     reload(): Promise<void>;
 } & {