@jbrowse/plugin-variants 3.7.0 → 4.0.0

package/dist/MultiLinearVariantRenderer/index.js

@@ -1,19 +0,0 @@
-"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 MultiLinearVariantRendering_1 = __importDefault(require("./components/MultiLinearVariantRendering"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-function MultiVariantRendererF(pluginManager) {
-    pluginManager.addRendererType(() => {
-        return new MultiVariantRenderer_1.default({
-            name: 'MultiVariantRenderer',
-            ReactComponent: MultiLinearVariantRendering_1.default,
-            configSchema: configSchema_1.default,
-            pluginManager,
-        });
-    });
-}

package/dist/MultiLinearVariantRenderer/makeImageData.d.ts

@@ -1,14 +0,0 @@
-import type { MultiRenderArgsDeserialized } from './types';
-export declare function makeImageData(ctx: CanvasRenderingContext2D, props: MultiRenderArgsDeserialized): Promise<{
-    flatbush: ArrayBufferLike;
-    items: any[];
-    featureGenotypeMap: {
-        [k: string]: {
-            alt: any;
-            ref: any;
-            name: any;
-            description: any;
-            length: number;
-        };
-    };
-}>;

package/dist/MultiLinearVariantRenderer/makeImageData.js

@@ -1,140 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": 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 constants_1 = require("../shared/constants");
-const drawAlleleCount_1 = require("../shared/drawAlleleCount");
-const drawPhased_1 = require("../shared/drawPhased");
-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 = await (0, util_1.updateStatus)('Calculating stats', statusCallback, () => (0, minorAlleleFrequencyUtils_1.getFeaturesThatPassMinorAlleleFrequencyFilter)({
-        stopToken,
-        features: features.values(),
-        minorAlleleFrequencyFilter,
-        lengthCutoffFilter,
-    }));
-    (0, stopToken_1.checkStopToken)(stopToken);
-    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 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;
-            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')) {
-                                items.push({
-                                    name,
-                                    genotype,
-                                    featureId,
-                                    bpLen,
-                                });
-                                coords.push(x, y, x + w, y + h);
-                            }
-                        }
-                        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 cacheKey = `${genotype}:${mostFrequentAlt}`;
-                        let c = colorCache[cacheKey];
-                        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[cacheKey] = c;
-                        }
-                        if (c) {
-                            (0, drawAlleleCount_1.drawColorAlleleCount)(c, ctx, x, y, w, h, feature.get('type'), feature.get('strand'), bpLen > 5 ? 0.75 : 1);
-                            items.push({
-                                name,
-                                genotype,
-                                featureId,
-                                bpLen,
-                            });
-                            coords.push(x, y, x + w, y + h);
-                        }
-                    }
-                    y += rowHeight;
-                }
-            }
-        });
-    });
-    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 {
-        flatbush: flatbush.data,
-        items,
-        featureGenotypeMap: Object.fromEntries(mafs.map(({ feature }) => [
-            feature.id(),
-            {
-                alt: feature.get('ALT'),
-                ref: feature.get('REF'),
-                name: feature.get('name'),
-                description: feature.get('description'),
-                length: feature.get('end') - feature.get('start'),
-            },
-        ])),
-    };
-}

package/dist/MultiLinearVariantRenderer/types.d.ts

@@ -1,21 +0,0 @@
-import type { Source } from '../shared/types';
-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;
-    minorAlleleFrequencyFilter: number;
-    lengthCutoffFilter: number;
-    statusCallback?: (arg: string) => void;
-}

package/dist/MultiLinearVariantRenderer/types.js

@@ -1,2 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });

package/dist/MultiVariantBaseRenderer.d.ts

@@ -1,46 +0,0 @@
-import FeatureRendererType from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
-import type { Source } from './shared/types';
-import type { RenderArgsDeserialized } from '@jbrowse/core/pluggableElementTypes/renderers/FeatureRendererType';
-import type { Feature } from '@jbrowse/core/util';
-import type { ThemeOptions } from '@mui/material';
-export interface RenderArgs extends RenderArgsDeserialized {
-    bpPerPx: number;
-    height: number;
-    highResolutionScaling: number;
-    themeOptions: ThemeOptions;
-}
-export interface RenderArgsDeserializedWithFeatures extends RenderArgs {
-    features: Map<string, Feature>;
-}
-export interface MultiRenderArgsDeserialized extends RenderArgsDeserializedWithFeatures {
-    sources: Source[];
-}
-export default abstract class MultiVariantBaseRenderer extends FeatureRendererType {
-    supportsSVG: boolean;
-    render(renderProps: RenderArgs): Promise<{
-        features: Map<string, Feature>;
-        height: number;
-        width: number;
-        containsNoTransferables: boolean;
-        canvasRecordedData: Record<string, unknown>;
-        reactElement?: React.ReactElement;
-        html?: string;
-    } | {
-        features: Map<string, Feature>;
-        height: number;
-        width: number;
-        containsNoTransferables: boolean;
-        imageData: any;
-        reactElement?: React.ReactElement;
-        html?: string;
-    } | {
-        features: Map<string, Feature>;
-        height: number;
-        width: number;
-        containsNoTransferables: boolean;
-        reactElement: 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

@@ -1,39 +0,0 @@
-"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/SplitVcfTabixAdapter/SplitVcfTabixAdapter.d.ts

@@ -1,18 +0,0 @@
-import { TabixIndexedFile } from '@gmod/tabix';
-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 } from '@jbrowse/core/util';
-import type { NoAssemblyRegion } from '@jbrowse/core/util/types';
-export default class SplitVcfTabixAdapter extends BaseFeatureDataAdapter {
-    private configurePre;
-    configure(refName: string, opts?: BaseOptions): Promise<{
-        vcf: TabixIndexedFile;
-        parser: VcfParser;
-    }>;
-    getRefNames(): Promise<string[]>;
-    getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    getSources(): Promise<{
-        name: string;
-    }[]>;
-}

package/dist/SplitVcfTabixAdapter/SplitVcfTabixAdapter.js

@@ -1,92 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const tabix_1 = require("@gmod/tabix");
-const vcf_1 = __importDefault(require("@gmod/vcf"));
-const BaseAdapter_1 = require("@jbrowse/core/data_adapters/BaseAdapter");
-const util_1 = require("@jbrowse/core/util");
-const io_1 = require("@jbrowse/core/util/io");
-const rxjs_1 = require("@jbrowse/core/util/rxjs");
-const VcfFeature_1 = __importDefault(require("../VcfFeature"));
-class SplitVcfTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
-    async configurePre(refName) {
-        const indexType = this.getConf('indexType');
-        const vcfGzLocation = this.getConf('vcfGzLocationMap')[refName];
-        const indexLocation = this.getConf('indexLocationMap')[refName] || {
-            uri: `${vcfGzLocation.uri}.${indexType.toLowerCase()}`,
-        };
-        const filehandle = (0, io_1.openLocation)(vcfGzLocation, this.pluginManager);
-        const isCSI = indexType === 'CSI';
-        const vcf = new tabix_1.TabixIndexedFile({
-            filehandle,
-            csiFilehandle: isCSI
-                ? (0, io_1.openLocation)(indexLocation, this.pluginManager)
-                : undefined,
-            tbiFilehandle: !isCSI
-                ? (0, io_1.openLocation)(indexLocation, this.pluginManager)
-                : undefined,
-            chunkCacheSize: 50 * 2 ** 20,
-        });
-        return {
-            vcf,
-            parser: new vcf_1.default({
-                header: await vcf.getHeader(),
-            }),
-        };
-    }
-    async configure(refName, opts) {
-        const { statusCallback = () => { } } = opts || {};
-        return (0, util_1.updateStatus)('Downloading index', statusCallback, () => this.configurePre(refName));
-    }
-    async getRefNames() {
-        return Object.keys(this.getConf('vcfGzLocationMap'));
-    }
-    getFeatures(query, opts = {}) {
-        return (0, rxjs_1.ObservableCreate)(async (observer) => {
-            const { refName, start, end } = query;
-            const { statusCallback = () => { } } = opts;
-            const { vcf, parser } = await this.configure(query.refName, opts);
-            await (0, util_1.updateStatus)('Downloading variants', statusCallback, () => vcf.getLines(refName, start, end, {
-                lineCallback: (line, fileOffset) => {
-                    observer.next(new VcfFeature_1.default({
-                        variant: parser.parseLine(line),
-                        parser,
-                        id: `${this.id}-vcf-${fileOffset}`,
-                    }));
-                },
-                ...opts,
-            }));
-            observer.complete();
-        }, opts.stopToken);
-    }
-    async getSources() {
-        const conf = this.getConf('samplesTsvLocation');
-        const r = Object.keys(this.getConf('vcfGzLocationMap'))[0];
-        if (conf.uri === '' || conf.uri === '/path/to/samples.tsv') {
-            const { parser } = await this.configure(r);
-            return parser.samples.map(name => ({
-                name,
-            }));
-        }
-        else {
-            const txt = await (0, util_1.fetchAndMaybeUnzipText)((0, io_1.openLocation)(conf, this.pluginManager));
-            const lines = txt.split(/\n|\r\n|\r/);
-            const header = lines[0].split('\t');
-            const { parser } = await this.configure(r);
-            const s = new Set(parser.samples);
-            return lines
-                .slice(1)
-                .map(line => {
-                const cols = line.split('\t');
-                return {
-                    name: cols[0],
-                    ...Object.fromEntries(cols.slice(1).map((c, idx) => [header[idx + 1], c])),
-                };
-            })
-                .filter(f => s.has(f.name));
-        }
-    }
-}
-exports.default = SplitVcfTabixAdapter;

package/dist/SplitVcfTabixAdapter/configSchema.d.ts

@@ -1,23 +0,0 @@
-declare const SplitVcfTabixAdapter: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    vcfGzLocationMap: {
-        type: string;
-        defaultValue: {};
-    };
-    indexLocationMap: {
-        type: string;
-        defaultValue: {};
-    };
-    indexType: {
-        type: string;
-        defaultValue: string;
-    };
-    samplesTsvLocation: {
-        type: string;
-        defaultValue: {
-            uri: string;
-            description: string;
-            locationType: string;
-        };
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default SplitVcfTabixAdapter;

package/dist/SplitVcfTabixAdapter/configSchema.js

@@ -1,29 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const configuration_1 = require("@jbrowse/core/configuration");
-function x() { }
-const SplitVcfTabixAdapter = (0, configuration_1.ConfigurationSchema)('SplitVcfTabixAdapter', {
-    vcfGzLocationMap: {
-        type: 'frozen',
-        defaultValue: {},
-    },
-    indexLocationMap: {
-        type: 'frozen',
-        defaultValue: {},
-    },
-    indexType: {
-        type: 'string',
-        defaultValue: 'TBI',
-    },
-    samplesTsvLocation: {
-        type: 'fileLocation',
-        defaultValue: {
-            uri: '/path/to/samples.tsv',
-            description: 'tsv with header like "name\tpopulation\tetc" where the first column is required, and corresponds to the sample names in the VCF files',
-            locationType: 'UriLocation',
-        },
-    },
-}, {
-    explicitlyTyped: true,
-});
-exports.default = SplitVcfTabixAdapter;

package/dist/SplitVcfTabixAdapter/index.d.ts

@@ -1,3 +0,0 @@
-import type PluginManager from '@jbrowse/core/PluginManager';
-export { default as configSchema } from './configSchema';
-export default function VcfTabixAdapterF(pluginManager: PluginManager): void;

package/dist/SplitVcfTabixAdapter/index.js

@@ -1,52 +0,0 @@
-"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 () {
-    var ownKeys = function(o) {
-        ownKeys = Object.getOwnPropertyNames || function (o) {
-            var ar = [];
-            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
-            return ar;
-        };
-        return ownKeys(o);
-    };
-    return function (mod) {
-        if (mod && mod.__esModule) return mod;
-        var result = {};
-        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
-        __setModuleDefault(result, mod);
-        return result;
-    };
-})();
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.configSchema = void 0;
-exports.default = VcfTabixAdapterF;
-const AdapterType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/AdapterType"));
-const configSchema_1 = __importDefault(require("./configSchema"));
-var configSchema_2 = require("./configSchema");
-Object.defineProperty(exports, "configSchema", { enumerable: true, get: function () { return __importDefault(configSchema_2).default; } });
-function VcfTabixAdapterF(pluginManager) {
-    pluginManager.addAdapterType(() => new AdapterType_1.default({
-        name: 'SplitVcfTabixAdapter',
-        displayName: 'VCF tabix adapter (split across multiple files)',
-        configSchema: configSchema_1.default,
-        getAdapterClass: () => Promise.resolve().then(() => __importStar(require('./SplitVcfTabixAdapter'))).then(r => r.default),
-    }));
-}

package/dist/StructuralVariantChordRenderer/Chord.d.ts

@@ -1,13 +0,0 @@
-import type { AnyRegion, Block } from './types';
-import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
-import type { Feature } from '@jbrowse/core/util';
-declare const Chord: ({ feature, blocksForRefs, radius, config, bezierRadius, selected, onClick, }: {
-    feature: Feature;
-    blocksForRefs: Record<string, Block>;
-    radius: number;
-    config: AnyConfigurationModel;
-    bezierRadius: number;
-    selected: boolean;
-    onClick: (feat: Feature, reg: AnyRegion, end: AnyRegion, evt: unknown) => void;
-}) => import("react/jsx-runtime").JSX.Element | null;
-export default Chord;

package/dist/StructuralVariantChordRenderer/Chord.js

@@ -1,82 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-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;
-    const bpOffset = block.flipped ? blockEnd - pos : pos - blockStart;
-    return bpOffset / block.bpPerRadian + block.startRadians;
-}
-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);
-    const startBlock = blocksForRefs[feature.get('refName')];
-    if (!startBlock) {
-        return null;
-    }
-    let svType;
-    if (feature.get('INFO')) {
-        ;
-        [svType] = feature.get('INFO').SVTYPE || [];
-    }
-    else if (feature.get('mate')) {
-        svType = 'mate';
-    }
-    let endPosition;
-    let endBlock;
-    const alt = (_a = feature.get('ALT')) === null || _a === void 0 ? void 0 : _a[0];
-    const bnd = alt && (0, vcf_1.parseBreakend)(alt);
-    const startPos = feature.get('start');
-    if (bnd) {
-        const matePosition = bnd.MatePosition.split(':');
-        endPosition = +matePosition[1];
-        endBlock = blocksForRefs[matePosition[0]];
-    }
-    else if (alt === '<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') {
-        const mate = feature.get('mate');
-        const chr2 = mate.refName;
-        endPosition = mate.start;
-        endBlock = blocksForRefs[chr2];
-    }
-    else {
-        endBlock = startBlock;
-        endPosition = feature.get('end');
-    }
-    if (endBlock) {
-        const startRadians = bpToRadians(startBlock, startPos);
-        const endRadians = bpToRadians(endBlock, endPosition);
-        const startXY = (0, util_1.polarToCartesian)(radius, startRadians);
-        const endXY = (0, util_1.polarToCartesian)(radius, endRadians);
-        const controlXY = (0, util_1.polarToCartesian)(bezierRadius, (endRadians + startRadians) / 2);
-        const strokeColor = selected
-            ? (0, configuration_1.readConfObject)(config, 'strokeColorSelected', { feature })
-            : (0, configuration_1.readConfObject)(config, 'strokeColor', { feature });
-        const hoverStrokeColor = (0, configuration_1.readConfObject)(config, 'strokeColorHover', {
-            feature,
-        });
-        return ((0, jsx_runtime_1.jsx)("path", { "data-testid": `chord-${feature.id()}`, cursor: "crosshair", fill: "none", d: ['M', ...startXY, 'Q', ...controlXY, ...endXY].join(' '), ...(0, util_1.getStrokeProps)(hovered ? hoverStrokeColor : strokeColor), strokeWidth: hovered ? 3 : 1, onClick: evt => {
-                onClick(feature, startBlock.region, endBlock.region, evt);
-            }, onMouseOver: () => {
-                if (!selected) {
-                    setHovered(true);
-                }
-            }, onMouseOut: () => {
-                if (!selected) {
-                    setHovered(false);
-                }
-            } }));
-    }
-    return null;
-});
-exports.default = Chord;

package/dist/StructuralVariantChordRenderer/ReactComponent.d.ts

@@ -1,16 +0,0 @@
-import type { AnyRegion, Block } from './types';
-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;
-    config: AnyConfigurationModel;
-    displayModel?: {
-        id: string;
-        selectedFeatureId: string;
-    };
-    blockDefinitions: Block[];
-    bezierRadius: number;
-    onChordClick: (feature: Feature, reg: AnyRegion, endBlock: AnyRegion, evt: unknown) => void;
-}) => import("react/jsx-runtime").JSX.Element;
-export default StructuralVariantChordsReactComponent;

package/dist/StructuralVariantChordRenderer/ReactComponent.js

@@ -1,30 +0,0 @@
-"use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const mobx_react_1 = require("mobx-react");
-const Chord_1 = __importDefault(require("./Chord"));
-const StructuralVariantChordsReactComponent = (0, mobx_react_1.observer)(function ({ features, config, blockDefinitions, radius, bezierRadius, displayModel, onChordClick, }) {
-    const { selectedFeatureId } = displayModel || {};
-    const blocksForRefsMemo = (0, react_1.useMemo)(() => {
-        const blocksForRefs = {};
-        for (const block of blockDefinitions) {
-            const regions = block.region.elided
-                ? block.region.regions
-                : [block.region];
-            for (const region of regions) {
-                blocksForRefs[region.refName] = block;
-            }
-        }
-        return blocksForRefs;
-    }, [blockDefinitions]);
-    return ((0, jsx_runtime_1.jsx)("g", { "data-testid": "structuralVariantChordRenderer", children: [...features.values()].map(feature => {
-            const id = feature.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));
-        }) }));
-});
-exports.default = StructuralVariantChordsReactComponent;