@jbrowse/plugin-variants 2.16.1 → 2.18.0

package/dist/MultiLinearVariantMatrixDisplay/renderSvg.js

@@ -0,0 +1,21 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.renderSvg = renderSvg;
+const react_1 = __importDefault(require("react"));
+const util_1 = require("@jbrowse/core/util");
+const mobx_1 = require("mobx");
+const LegendBar_1 = __importDefault(require("../shared/LegendBar"));
+const LinesConnectingMatrixToGenomicPosition_1 = __importDefault(require("./components/LinesConnectingMatrixToGenomicPosition"));
+async function renderSvg(model, opts, superRenderSvg) {
+    await (0, mobx_1.when)(() => !!model.regionCannotBeRenderedText);
+    const { offsetPx } = (0, util_1.getContainingView)(model);
+    return (react_1.default.createElement(react_1.default.Fragment, null,
+        react_1.default.createElement("g", { transform: `translate(${Math.max(-offsetPx, 0)})` },
+            react_1.default.createElement(LinesConnectingMatrixToGenomicPosition_1.default, { exportSVG: true, model: model }),
+            react_1.default.createElement("g", { transform: `translate(0,${model.lineZoneHeight})` },
+                react_1.default.createElement("g", null, await superRenderSvg(opts)),
+                react_1.default.createElement(LegendBar_1.default, { model: model, orientation: "left", exportSVG: true })))));
+}

package/dist/MultiLinearVariantMatrixRenderer/LinearVariantMatrixRenderer.d.ts

@@ -0,0 +1,62 @@
+import BoxRendererType from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import type { Source } from '../util';
+import type { RenderArgsDeserialized as BoxRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';
+import type { Feature } from '@jbrowse/core/util';
+export interface SortParams {
+    type: string;
+    pos: number;
+    refName: string;
+    assemblyName: string;
+    tag?: string;
+}
+export interface RenderArgsDeserialized extends BoxRenderArgsDeserialized {
+    sources: {
+        name: string;
+    }[];
+    mafFilter: number;
+    highResolutionScaling: number;
+    height: number;
+}
+export interface RenderArgsDeserializedWithFeaturesAndLayout extends RenderArgsDeserialized {
+    sources: Source[];
+    features: Map<string, Feature>;
+}
+export default class LinearVariantMatrixRenderer extends BoxRendererType {
+    supportsSVG: boolean;
+    makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }: {
+        ctx: CanvasRenderingContext2D;
+        canvasWidth: number;
+        canvasHeight: number;
+        renderArgs: RenderArgsDeserializedWithFeaturesAndLayout;
+    }): {
+        mafs: Feature[];
+    };
+    render(renderProps: RenderArgsDeserialized): Promise<{
+        features: Map<any, any>;
+        simplifiedFeatures: any;
+        height: number;
+        width: number;
+        canvasRecordedData: any;
+        layout: import("@jbrowse/core/util/layouts").BaseLayout<Feature>;
+        reactElement?: import("react").ReactElement;
+        html?: string;
+    } | {
+        features: Map<any, any>;
+        simplifiedFeatures: any;
+        height: number;
+        width: number;
+        reactElement: React.JSX.Element;
+        layout: import("@jbrowse/core/util/layouts").BaseLayout<Feature>;
+        html?: string;
+    } | {
+        features: Map<any, any>;
+        simplifiedFeatures: any;
+        height: number;
+        width: number;
+        imageData: any;
+        layout: import("@jbrowse/core/util/layouts").BaseLayout<Feature>;
+        reactElement?: import("react").ReactElement;
+        html?: string;
+    }>;
+}
+export type { RenderArgs, RenderArgsSerialized, RenderResults, ResultsDeserialized, ResultsSerialized, } from '@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType';

package/dist/MultiLinearVariantMatrixRenderer/LinearVariantMatrixRenderer.js

@@ -0,0 +1,106 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const BoxRendererType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/BoxRendererType"));
+const util_1 = require("@jbrowse/core/util");
+const util_2 = require("../util");
+const fudgeFactor = 0.6;
+const f2 = fudgeFactor / 2;
+class LinearVariantMatrixRenderer extends BoxRendererType_1.default {
+    constructor() {
+        super(...arguments);
+        this.supportsSVG = true;
+    }
+    makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }) {
+        const { mafFilter, sources, features } = renderArgs;
+        const feats = [...features.values()];
+        const h = canvasHeight / sources.length;
+        const mafs = [];
+        for (const feat of feats) {
+            let c = 0;
+            let c2 = 0;
+            const samp = feat.get('genotypes');
+            if (feat.get('end') - feat.get('start') <= 10) {
+                for (const { name } of sources) {
+                    const s = samp[name];
+                    if (s === '0|0' || s === './.') {
+                        c2++;
+                    }
+                    else if (s === '1|0' || s === '0|1') {
+                        c++;
+                    }
+                    else if (s === '1|1') {
+                        c++;
+                        c2++;
+                    }
+                    else {
+                        c++;
+                    }
+                }
+                if (c / sources.length > mafFilter &&
+                    c2 / sources.length < 1 - mafFilter) {
+                    mafs.push(feat);
+                }
+            }
+        }
+        const w = canvasWidth / mafs.length;
+        for (let i = 0; i < mafs.length; i++) {
+            const f = mafs[i];
+            if (f.get('end') - f.get('start') <= 10) {
+                const samp = f.get('genotypes');
+                const x = (i / mafs.length) * canvasWidth;
+                for (let j = 0; j < sources.length; j++) {
+                    const y = (j / sources.length) * canvasHeight;
+                    const { name } = sources[j];
+                    ctx.fillStyle = (0, util_2.getCol)(samp[name]);
+                    ctx.fillRect(x - f2, y - f2, w + f2, h + f2);
+                }
+            }
+        }
+        return { mafs };
+    }
+    async render(renderProps) {
+        const features = await this.getFeatures(renderProps);
+        const { height, sources, regions, bpPerPx } = renderProps;
+        const region = regions[0];
+        const { end, start } = region;
+        const width = (end - start) / bpPerPx;
+        const { mafs, ...res } = await (0, util_1.renderToAbstractCanvas)(width, height, renderProps, ctx => {
+            return this.makeImageData({
+                ctx,
+                canvasWidth: width,
+                canvasHeight: height,
+                renderArgs: {
+                    ...renderProps,
+                    features,
+                    sources,
+                },
+            });
+        });
+        const results = await super.render({
+            ...renderProps,
+            ...res,
+            features,
+            height,
+            width,
+        });
+        return {
+            ...results,
+            ...res,
+            features: new Map(),
+            simplifiedFeatures: mafs.map((s) => new util_1.SimpleFeature({
+                id: s.id(),
+                data: {
+                    start: s.get('start'),
+                    end: s.get('end'),
+                    refName: s.get('refName'),
+                },
+            })),
+            height,
+            width,
+        };
+    }
+}
+exports.default = LinearVariantMatrixRenderer;

package/dist/MultiLinearVariantMatrixRenderer/components/LinearVariantMatrixRendering.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+declare const LinearVariantMatrixRendering: (props: {
+    width: number;
+    height: number;
+}) => React.JSX.Element;
+export default LinearVariantMatrixRendering;

package/dist/MultiLinearVariantMatrixRenderer/components/LinearVariantMatrixRendering.js

@@ -0,0 +1,12 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importDefault(require("react"));
+const ui_1 = require("@jbrowse/core/ui");
+const mobx_react_1 = require("mobx-react");
+const LinearVariantMatrixRendering = (0, mobx_react_1.observer)(function (props) {
+    return react_1.default.createElement(ui_1.PrerenderedCanvas, { ...props });
+});
+exports.default = LinearVariantMatrixRendering;

package/dist/MultiLinearVariantMatrixRenderer/configSchema.d.ts

@@ -0,0 +1,2 @@
+declare const LinearVariantMatrixRenderer: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+export default LinearVariantMatrixRenderer;

package/dist/MultiLinearVariantMatrixRenderer/configSchema.js

@@ -0,0 +1,6 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
+function x() { }
+const LinearVariantMatrixRenderer = (0, configuration_1.ConfigurationSchema)('LinearVariantMatrixRenderer', {}, { explicitlyTyped: true });
+exports.default = LinearVariantMatrixRenderer;

package/dist/MultiLinearVariantMatrixRenderer/index.d.ts

@@ -0,0 +1,2 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function LinearVariantMatrixRendererF(pluginManager: PluginManager): void;

package/dist/MultiLinearVariantMatrixRenderer/index.js

@@ -0,0 +1,20 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = LinearVariantMatrixRendererF;
+const ui_1 = require("@jbrowse/core/ui");
+const LinearVariantMatrixRenderer_1 = __importDefault(require("./LinearVariantMatrixRenderer"));
+const configSchema_1 = __importDefault(require("./configSchema"));
+function LinearVariantMatrixRendererF(pluginManager) {
+    pluginManager.addRendererType(() => {
+        return new LinearVariantMatrixRenderer_1.default({
+            name: 'LinearVariantMatrixRenderer',
+            displayName: 'Linear variant matrix renderer',
+            ReactComponent: ui_1.PrerenderedCanvas,
+            configSchema: configSchema_1.default,
+            pluginManager,
+        });
+    });
+}

package/dist/MultiLinearVariantRenderer/MultiVariantRenderer.d.ts

@@ -0,0 +1,48 @@
+import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import type { Source } from '../util';
+import type { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import type { Feature } from '@jbrowse/core/util';
+import type { ThemeOptions } from '@mui/material';
+export interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {
+    bpPerPx: number;
+    height: number;
+    highResolutionScaling: number;
+    themeOptions: ThemeOptions;
+}
+export interface RenderArgsDeserializedWithFeatures extends RenderArgsDeserialized {
+    features: Map<string, Feature>;
+}
+export interface MultiRenderArgsDeserialized extends RenderArgsDeserializedWithFeatures {
+    sources: Source[];
+    rowHeight: number;
+    scrollTop: number;
+}
+export default class MultiVariantBaseRenderer extends FeatureRendererType {
+    supportsSVG: boolean;
+    render(renderProps: MultiRenderArgsDeserialized): Promise<{
+        features: Map<string, Feature>;
+        height: number;
+        width: number;
+        containsNoTransferables: boolean;
+        canvasRecordedData: any;
+        reactElement?: import("react").ReactElement;
+        html?: string;
+    } | {
+        features: Map<string, Feature>;
+        height: number;
+        width: number;
+        containsNoTransferables: boolean;
+        reactElement: React.JSX.Element;
+        html?: string;
+    } | {
+        features: Map<string, Feature>;
+        height: number;
+        width: number;
+        containsNoTransferables: boolean;
+        imageData: any;
+        reactElement?: import("react").ReactElement;
+        html?: string;
+    }>;
+    draw(ctx: CanvasRenderingContext2D, props: MultiRenderArgsDeserialized): Promise<void>;
+}
+export type { RenderArgsSerialized, RenderResults, ResultsDeserialized, ResultsSerialized, } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';

package/dist/MultiLinearVariantRenderer/MultiVariantRenderer.js

@@ -0,0 +1,60 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const FeatureRendererType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType"));
+const util_1 = require("@jbrowse/core/util");
+const util_2 = require("../util");
+class MultiVariantBaseRenderer extends FeatureRendererType_1.default {
+    constructor() {
+        super(...arguments);
+        this.supportsSVG = true;
+    }
+    async render(renderProps) {
+        const features = await this.getFeatures(renderProps);
+        const { height, regions, bpPerPx } = renderProps;
+        const region = regions[0];
+        const width = (region.end - region.start) / bpPerPx;
+        const rest = await (0, util_1.renderToAbstractCanvas)(width, height, renderProps, async (ctx) => {
+            await this.draw(ctx, {
+                ...renderProps,
+                features,
+            });
+            return undefined;
+        });
+        const results = await super.render({
+            ...renderProps,
+            ...rest,
+            features,
+            height,
+            width,
+        });
+        return {
+            ...results,
+            ...rest,
+            features: new Map(),
+            height,
+            width,
+            containsNoTransferables: true,
+        };
+    }
+    async draw(ctx, props) {
+        const { scrollTop, sources, rowHeight, features, regions, bpPerPx } = props;
+        const region = regions[0];
+        for (const feature of features.values()) {
+            if (feature.get('end') - feature.get('start') <= 10) {
+                const [leftPx, rightPx] = (0, util_1.featureSpanPx)(feature, region, bpPerPx);
+                const w = Math.max(Math.round(rightPx - leftPx), 2);
+                const genotypes = feature.get('genotypes');
+                let t = -scrollTop;
+                for (const { name } of sources) {
+                    ctx.fillStyle = (0, util_2.getCol)(genotypes[name]);
+                    ctx.fillRect(Math.floor(leftPx), t, w, Math.max(t + rowHeight, 1));
+                    t += rowHeight;
+                }
+            }
+        }
+    }
+}
+exports.default = MultiVariantBaseRenderer;

package/dist/MultiLinearVariantRenderer/MultiVariantRendering.d.ts

@@ -0,0 +1,18 @@
+import React from 'react';
+import type { Source } from '../util';
+import type { Feature } from '@jbrowse/core/util';
+import type { Region } from '@jbrowse/core/util/types';
+declare const MultiVariantRendering: (props: {
+    regions: Region[];
+    features: Map<string, Feature>;
+    bpPerPx: number;
+    width: number;
+    height: number;
+    sources: Source[];
+    scrollTop: number;
+    totalHeight: number;
+    onMouseLeave?: (event: React.MouseEvent) => void;
+    onMouseMove?: (event: React.MouseEvent, arg?: Feature) => void;
+    onFeatureClick?: (event: React.MouseEvent, arg?: Feature) => void;
+}) => React.JSX.Element;
+export default MultiVariantRendering;

package/dist/MultiLinearVariantRenderer/MultiVariantRendering.js

@@ -0,0 +1,43 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const react_1 = __importStar(require("react"));
+const ui_1 = require("@jbrowse/core/ui");
+const mobx_react_1 = require("mobx-react");
+const MultiVariantRendering = (0, mobx_react_1.observer)(function (props) {
+    const { totalHeight, scrollTop } = props;
+    const ref = (0, react_1.useRef)(null);
+    return (react_1.default.createElement("div", { ref: ref, style: {
+            overflow: 'visible',
+            position: 'relative',
+            height: totalHeight,
+        } },
+        react_1.default.createElement(ui_1.PrerenderedCanvas, { ...props, style: {
+                position: 'absolute',
+                left: 0,
+                top: scrollTop,
+            } })));
+});
+exports.default = MultiVariantRendering;

package/dist/MultiLinearVariantRenderer/configSchema.d.ts

@@ -0,0 +1,34 @@
+declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
+    color: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    posColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    negColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    clipColor: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
+    bicolorPivot: {
+        type: string;
+        model: import("mobx-state-tree").ISimpleType<string>;
+        description: string;
+        defaultValue: string;
+    };
+    bicolorPivotValue: {
+        type: string;
+        defaultValue: number;
+        description: string;
+    };
+}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>, undefined>>;
+export default configSchema;

package/dist/MultiLinearVariantRenderer/configSchema.js

@@ -0,0 +1,13 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const configuration_1 = require("@jbrowse/core/configuration");
+const configSchema_1 = __importDefault(require("../configSchema"));
+function x() { }
+const configSchema = (0, configuration_1.ConfigurationSchema)('MultiVariantRenderer', {}, {
+    baseConfiguration: configSchema_1.default,
+    explicitlyTyped: true,
+});
+exports.default = configSchema;

package/dist/MultiLinearVariantRenderer/index.d.ts

@@ -0,0 +1,2 @@
+import type PluginManager from '@jbrowse/core/PluginManager';
+export default function MultiVariantRendererF(pluginManager: PluginManager): void;

package/dist/MultiLinearVariantRenderer/index.js

@@ -0,0 +1,19 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = MultiVariantRendererF;
+const MultiVariantRenderer_1 = __importDefault(require("./MultiVariantRenderer"));
+const MultiVariantRendering_1 = __importDefault(require("./MultiVariantRendering"));
+const configSchema_1 = __importDefault(require("./configSchema"));
+function MultiVariantRendererF(pluginManager) {
+    pluginManager.addRendererType(() => {
+        return new MultiVariantRenderer_1.default({
+            name: 'MultiVariantRenderer',
+            ReactComponent: MultiVariantRendering_1.default,
+            configSchema: configSchema_1.default,
+            pluginManager,
+        });
+    });
+}

package/dist/MultiVariantBaseRenderer.d.ts

@@ -0,0 +1,46 @@
+import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import type { Source } from './util';
+import type { RenderArgsDeserialized as FeatureRenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
+import type { Feature } from '@jbrowse/core/util';
+import type { ThemeOptions } from '@mui/material';
+export interface RenderArgsDeserialized extends FeatureRenderArgsDeserialized {
+    bpPerPx: number;
+    height: number;
+    highResolutionScaling: number;
+    themeOptions: ThemeOptions;
+}
+export interface RenderArgsDeserializedWithFeatures extends RenderArgsDeserialized {
+    features: Map<string, Feature>;
+}
+export interface MultiRenderArgsDeserialized extends RenderArgsDeserializedWithFeatures {
+    sources: Source[];
+}
+export default abstract class MultiVariantBaseRenderer extends FeatureRendererType {
+    supportsSVG: boolean;
+    render(renderProps: RenderArgsDeserialized): Promise<{
+        features: Map<string, Feature>;
+        height: number;
+        width: number;
+        containsNoTransferables: boolean;
+        canvasRecordedData: any;
+        reactElement?: import("react").ReactElement;
+        html?: string;
+    } | {
+        features: Map<string, Feature>;
+        height: number;
+        width: number;
+        containsNoTransferables: boolean;
+        reactElement: React.JSX.Element;
+        html?: string;
+    } | {
+        features: Map<string, Feature>;
+        height: number;
+        width: number;
+        containsNoTransferables: boolean;
+        imageData: any;
+        reactElement?: import("react").ReactElement;
+        html?: string;
+    }>;
+    abstract draw<T extends RenderArgsDeserializedWithFeatures>(ctx: CanvasRenderingContext2D, props: T): Promise<Record<string, unknown> | undefined>;
+}
+export type { RenderArgsSerialized, RenderResults, ResultsDeserialized, ResultsSerialized, } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';

package/dist/MultiVariantBaseRenderer.js

@@ -0,0 +1,39 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const FeatureRendererType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType"));
+const util_1 = require("@jbrowse/core/util");
+class MultiVariantBaseRenderer extends FeatureRendererType_1.default {
+    constructor() {
+        super(...arguments);
+        this.supportsSVG = true;
+    }
+    async render(renderProps) {
+        const features = await this.getFeatures(renderProps);
+        const { height, regions, bpPerPx } = renderProps;
+        const region = regions[0];
+        const width = (region.end - region.start) / bpPerPx;
+        const rest = await (0, util_1.renderToAbstractCanvas)(width, height, renderProps, ctx => this.draw(ctx, {
+            ...renderProps,
+            features,
+        }));
+        const results = await super.render({
+            ...renderProps,
+            ...rest,
+            features,
+            height,
+            width,
+        });
+        return {
+            ...results,
+            ...rest,
+            features: new Map(),
+            height,
+            width,
+            containsNoTransferables: true,
+        };
+    }
+}
+exports.default = MultiVariantBaseRenderer;

package/dist/StructuralVariantChordRenderer/Chord.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
-import { Feature } from '@jbrowse/core/util';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Feature } from '@jbrowse/core/util';
 export interface Region {
     end: number;
     start: number;

package/dist/StructuralVariantChordRenderer/Chord.js

@@ -24,10 +24,10 @@ var __importStar = (this && this.__importStar) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
-const mobx_react_1 = require("mobx-react");
-const util_1 = require("@jbrowse/core/util");
-const configuration_1 = require("@jbrowse/core/configuration");
 const vcf_1 = require("@gmod/vcf");
+const configuration_1 = require("@jbrowse/core/configuration");
+const util_1 = require("@jbrowse/core/util");
+const mobx_react_1 = require("mobx-react");
 function bpToRadians(block, pos) {
     const blockStart = block.region.elided ? 0 : block.region.start;
     const blockEnd = block.region.elided ? 0 : block.region.end;
@@ -37,7 +37,6 @@ function bpToRadians(block, pos) {
 const Chord = (0, mobx_react_1.observer)(function Chord({ feature, blocksForRefs, radius, config, bezierRadius, selected, onClick, }) {
     var _a, _b, _c, _d, _e;
     const [hovered, setHovered] = (0, react_1.useState)(false);
-    // find the blocks that our start and end points belong to
     const startBlock = blocksForRefs[feature.get('refName')];
     if (!startBlock) {
         return null;
@@ -56,28 +55,25 @@ const Chord = (0, mobx_react_1.observer)(function Chord({ feature, blocksForRefs
     const bnd = alt && (0, vcf_1.parseBreakend)(alt);
     const startPos = feature.get('start');
     if (bnd) {
-        // VCF BND
         const matePosition = bnd.MatePosition.split(':');
         endPosition = +matePosition[1];
         endBlock = blocksForRefs[matePosition[0]];
     }
     else if (alt === '<TRA>') {
-        // VCF TRA
         const chr2 = (_c = (_b = feature.get('INFO')) === null || _b === void 0 ? void 0 : _b.CHR2) === null || _c === void 0 ? void 0 : _c[0];
         const end = (_e = (_d = feature.get('INFO')) === null || _d === void 0 ? void 0 : _d.END) === null || _e === void 0 ? void 0 : _e[0];
         endPosition = Number.parseInt(end, 10);
         endBlock = blocksForRefs[chr2];
     }
     else if (svType === 'mate') {
-        // generic simplefeatures arcs
         const mate = feature.get('mate');
         const chr2 = mate.refName;
         endPosition = mate.start;
         endBlock = blocksForRefs[chr2];
     }
     else {
-        console.warn('unknown sv type', svType);
-        endPosition = startPos + 1;
+        endBlock = startBlock;
+        endPosition = feature.get('end');
     }
     if (endBlock) {
         const startRadians = bpToRadians(startBlock, startPos);

package/dist/StructuralVariantChordRenderer/ReactComponent.d.ts

@@ -1,7 +1,7 @@
 import React from 'react';
-import { Feature } from '@jbrowse/core/util';
-import { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import { Block, AnyRegion } from './Chord';
+import type { AnyRegion, Block } from './Chord';
+import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
+import type { Feature } from '@jbrowse/core/util';
 declare const StructuralVariantChordsReactComponent: ({ features, config, blockDefinitions, radius, bezierRadius, displayModel, onChordClick, }: {
     features: Map<string, Feature>;
     radius: number;