@jbrowse/plugin-variants 3.0.3 → 3.0.5

package/dist/MultiLinearVariantMatrixDisplay/components/LinesConnectingMatrixToGenomicPosition.js

@@ -1,8 +1,19 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 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 mobx_react_1 = require("mobx-react");
+const mui_1 = require("tss-react/mui");
+const useStyles = (0, mui_1.makeStyles)()({
+    resizeHandle: {
+        height: 4,
+        background: '#ccc',
+        boxSizing: 'border-box',
+        borderTop: '1px solid #fafafa',
+    },
+});
 const Wrapper = (0, mobx_react_1.observer)(function ({ children, model, exportSVG, }) {
     const { height } = model;
     const { width, offsetPx } = (0, util_1.getContainingView)(model);
@@ -11,12 +22,31 @@ const Wrapper = (0, mobx_react_1.observer)(function ({ children, model, exportSV
             position: 'absolute',
             top: 0,
             left,
-            pointerEvents: 'none',
             height,
             width,
         }, children: children }));
 });
 const LinesConnectingMatrixToGenomicPosition = (0, mobx_react_1.observer)(function ({ model, exportSVG, }) {
+    var _a;
+    const { classes } = useStyles();
+    const { assemblyManager } = (0, util_1.getSession)(model);
+    const view = (0, util_1.getContainingView)(model);
+    const [mouseOverLine, setMouseOverLine] = (0, react_1.useState)();
+    const { lineZoneHeight, featuresVolatile } = model;
+    const { assemblyNames, dynamicBlocks } = view;
+    const assembly = assemblyManager.get(assemblyNames[0]);
+    const b0 = ((_a = dynamicBlocks.contentBlocks[0]) === null || _a === void 0 ? void 0 : _a.widthPx) || 0;
+    const w = b0 / ((featuresVolatile === null || featuresVolatile === void 0 ? void 0 : featuresVolatile.length) || 1);
+    return assembly && featuresVolatile ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsxs)(Wrapper, { exportSVG: exportSVG, model: model, children: [(0, jsx_runtime_1.jsx)(AllLines, { model: model, setMouseOverLine: setMouseOverLine }), mouseOverLine ? ((0, jsx_runtime_1.jsx)("line", { stroke: "#f00c", strokeWidth: 2, style: {
+                            pointerEvents: 'none',
+                        }, x1: mouseOverLine.idx * w + w / 2, x2: mouseOverLine.c, y1: lineZoneHeight, y2: 0, onMouseLeave: () => {
+                            setMouseOverLine(undefined);
+                        } })) : null] }), !exportSVG ? ((0, jsx_runtime_1.jsx)(ui_1.ResizeHandle, { style: {
+                    position: 'absolute',
+                    top: lineZoneHeight - 4,
+                }, onDrag: n => model.setLineZoneHeight(lineZoneHeight + n), className: classes.resizeHandle })) : null] })) : null;
+});
+const AllLines = (0, mobx_react_1.observer)(function ({ model, setMouseOverLine, }) {
     var _a;
     const { assemblyManager } = (0, util_1.getSession)(model);
     const view = (0, util_1.getContainingView)(model);
@@ -26,14 +56,18 @@ const LinesConnectingMatrixToGenomicPosition = (0, mobx_react_1.observer)(functi
     const b0 = ((_a = dynamicBlocks.contentBlocks[0]) === null || _a === void 0 ? void 0 : _a.widthPx) || 0;
     const w = b0 / ((featuresVolatile === null || featuresVolatile === void 0 ? void 0 : featuresVolatile.length) || 1);
     const l = Math.max(offsetPx, 0);
-    return assembly && featuresVolatile ? ((0, jsx_runtime_1.jsx)(Wrapper, { exportSVG: exportSVG, model: model, children: featuresVolatile.map((f, i) => {
+    return assembly && featuresVolatile ? ((0, jsx_runtime_1.jsx)(jsx_runtime_1.Fragment, { children: featuresVolatile.map((f, i) => {
             var _a;
             const ref = f.get('refName');
             const c = (((_a = view.bpToPx({
                 refName: assembly.getCanonicalRefName(ref) || ref,
                 coord: f.get('start'),
             })) === null || _a === void 0 ? void 0 : _a.offsetPx) || 0) - l;
-            return ((0, jsx_runtime_1.jsx)("line", { stroke: "#0004", x1: i * w + w / 2, x2: c, y1: lineZoneHeight, y2: 0 }, f.id()));
+            return ((0, jsx_runtime_1.jsx)("line", { stroke: "#0004", strokeWidth: 1, x1: i * w + w / 2, x2: c, y1: lineZoneHeight, y2: 0, onMouseEnter: () => {
+                    setMouseOverLine({ f, idx: i, c });
+                }, onMouseLeave: () => {
+                    setMouseOverLine(undefined);
+                } }, f.id()));
         }) })) : null;
 });
 exports.default = LinesConnectingMatrixToGenomicPosition;

package/dist/MultiLinearVariantMatrixDisplay/model.d.ts

@@ -92,6 +92,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearVariantMatrixDisplay">;
     rowHeightSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    lineZoneHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -338,8 +339,6 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     readonly totalHeight: number;
 } & {
     renderProps(): any;
-} & {
-    lineZoneHeight: number;
 } & {
     readonly nrow: number;
     readonly blockType: string;
@@ -349,6 +348,9 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     renderProps(): any;
     readonly canDisplayLabels: boolean;
 } & {
+    setLineZoneHeight(n: number): number;
+} & {
+    setLineZoneHeight(n: number): number;
     afterAttach(): void;
     renderSvg(opts: ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/dist/MultiLinearVariantMatrixDisplay/model.js

@@ -45,8 +45,6 @@ function stateModelFactory(configSchema) {
         .compose('LinearVariantMatrixDisplay', (0, MultiVariantBaseModel_1.default)(configSchema), mobx_state_tree_1.types.model({
         type: mobx_state_tree_1.types.literal('LinearVariantMatrixDisplay'),
         rowHeightSetting: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.number, 1),
-    }))
-        .volatile(() => ({
         lineZoneHeight: 20,
     }))
         .views(self => ({
@@ -83,10 +81,20 @@ function stateModelFactory(configSchema) {
         get canDisplayLabels() {
             return self.rowHeight > 8 && self.showSidebarLabelsSetting;
         },
+    }))
+        .actions(self => ({
+        setLineZoneHeight(n) {
+            self.lineZoneHeight = (0, util_1.clamp)(n, 10, 1000);
+            return self.lineZoneHeight;
+        },
     }))
         .actions(self => {
         const { renderSvg: superRenderSvg } = self;
         return {
+            setLineZoneHeight(n) {
+                self.lineZoneHeight = (0, util_1.clamp)(n, 10, 1000);
+                return self.lineZoneHeight;
+            },
             afterAttach() {
                 ;
                 (async () => {

package/dist/MultiLinearVariantMatrixRenderer/makeImageData.js

@@ -15,11 +15,11 @@ async function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }) {
     const m = mafs.length;
     const w = canvasWidth / m;
     await (0, util_1.updateStatus)('Drawing variant matrix', statusCallback, () => {
-        var _a, _b;
+        var _a, _b, _c;
         for (let i = 0; i < m; i++) {
             const arr2 = [];
             const { feature, mostFrequentAlt } = mafs[i];
-            const hasPhaseSet = feature.get('format').includes('PS');
+            const hasPhaseSet = (_a = feature.get('FORMAT')) === null || _a === void 0 ? void 0 : _a.includes('PS');
             if (hasPhaseSet) {
                 const samp = feature.get('samples');
                 const x = (i / mafs.length) * canvasWidth;
@@ -29,13 +29,13 @@ async function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs, }) {
                     const { name, HP } = sources[j];
                     const s = samp[name];
                     if (s) {
-                        const genotype = (_a = s.GT) === null || _a === void 0 ? void 0 : _a[0];
+                        const genotype = (_b = s.GT) === null || _b === void 0 ? void 0 : _b[0];
                         if (genotype) {
                             arr2.push(genotype);
                             const isPhased = genotype.includes('|');
                             if (renderingMode === 'phased') {
                                 if (isPhased) {
-                                    const PS = (_b = s.PS) === null || _b === void 0 ? void 0 : _b[0];
+                                    const PS = (_c = s.PS) === null || _c === void 0 ? void 0 : _c[0];
                                     const alleles = genotype.split('|');
                                     (0, drawPhased_1.drawPhased)(alleles, ctx, x, y, w, h, HP, PS);
                                 }

package/dist/SplitVcfTabixAdapter/SplitVcfTabixAdapter.d.ts

@@ -0,0 +1,19 @@
+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;
+    }[]>;
+    freeResources(): void;
+}

package/dist/SplitVcfTabixAdapter/SplitVcfTabixAdapter.js

@@ -0,0 +1,93 @@
+"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));
+        }
+    }
+    freeResources() { }
+}
+exports.default = SplitVcfTabixAdapter;

package/dist/SplitVcfTabixAdapter/configSchema.d.ts

@@ -0,0 +1,23 @@
+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

@@ -0,0 +1,27 @@
+"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 is the sample names',
+            locationType: 'UriLocation',
+        },
+    },
+}, { explicitlyTyped: true });
+exports.default = SplitVcfTabixAdapter;

package/dist/SplitVcfTabixAdapter/index.d.ts

@@ -0,0 +1,3 @@
+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

@@ -0,0 +1,52 @@
+"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/VariantFeatureWidget/{LaunchBreakendPanel.d.ts → LaunchBreakendPanel/LaunchBreakendPanel.d.ts}

@@ -1,4 +1,4 @@
-import type { VariantFeatureWidgetModel } from './stateModelFactory';
+import type { VariantFeatureWidgetModel } from '../stateModelFactory';
 import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
 export default function LaunchBreakendPanel(props: {
     locStrings: string[];

package/dist/VariantFeatureWidget/{LaunchBreakendWidgetArea.d.ts → LaunchBreakendPanel/LaunchBreakendWidgetArea.d.ts}

@@ -1,4 +1,4 @@
-import type { VariantFeatureWidgetModel } from './stateModelFactory';
+import type { VariantFeatureWidgetModel } from '../stateModelFactory';
 export default function LaunchBreakendWidgetArea({ model, }: {
     model: VariantFeatureWidgetModel;
 }): import("react/jsx-runtime").JSX.Element;

package/dist/VariantFeatureWidget/LaunchBreakendPanel/index.d.ts

@@ -0,0 +1 @@
+export { default } from './LaunchBreakendPanel';

package/dist/VariantFeatureWidget/LaunchBreakendPanel/index.js

@@ -0,0 +1,8 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = void 0;
+var LaunchBreakendPanel_1 = require("./LaunchBreakendPanel");
+Object.defineProperty(exports, "default", { enumerable: true, get: function () { return __importDefault(LaunchBreakendPanel_1).default; } });

package/dist/VariantFeatureWidget/VariantFeatureWidget.js

@@ -42,9 +42,9 @@ const vcf_1 = require("@gmod/vcf");
 const FeatureDetails_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails"));
 const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
-const VariantSampleGrid_1 = __importDefault(require("./VariantSampleGrid"));
+const VariantSampleGrid_1 = __importDefault(require("./VariantSampleGrid/VariantSampleGrid"));
 const variantFieldDescriptions_1 = require("./variantFieldDescriptions");
-const LaunchBreakendPanel = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./LaunchBreakendPanel'))));
+const LaunchBreakendPanel = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./LaunchBreakendPanel/LaunchBreakendPanel'))));
 const VariantConsequenceDataGrid = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./VariantConsequenceDataGrid'))));
 function AnnPanel({ descriptions, feature, }) {
     var _a, _b, _c, _d, _e;

package/dist/VariantFeatureWidget/VariantSampleGrid/index.d.ts

@@ -0,0 +1 @@
+export { default } from './VariantSampleGrid';

package/dist/VariantFeatureWidget/VariantSampleGrid/index.js

@@ -0,0 +1,8 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.default = void 0;
+var VariantSampleGrid_1 = require("./VariantSampleGrid");
+Object.defineProperty(exports, "default", { enumerable: true, get: function () { return __importDefault(VariantSampleGrid_1).default; } });

package/dist/VcfFeature/index.js

@@ -2,7 +2,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const util_1 = require("./util");
 function dataFromVariant(variant, parser) {
-    const { FORMAT, REF = '', ALT, POS, CHROM, ID } = variant;
+    const { REF = '', ALT, POS, CHROM, ID } = variant;
     const start = POS - 1;
     const [type, description] = (0, util_1.getSOTermAndDescription)(REF, ALT, parser);
     return {
@@ -13,7 +13,6 @@ function dataFromVariant(variant, parser) {
         type,
         name: ID === null || ID === void 0 ? void 0 : ID.join(','),
         aliases: ID && ID.length > 1 ? ID.slice(1) : undefined,
-        format: FORMAT,
     };
 }
 function getEnd(variant) {

package/dist/VcfTabixAdapter/VcfTabixAdapter.d.ts

@@ -17,6 +17,7 @@ export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
     }>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getHeader(opts?: BaseOptions): Promise<string>;
+    getMetadata(opts?: BaseOptions): Promise<any>;
     getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     getSources(): Promise<{
         name: string;

package/dist/VcfTabixAdapter/VcfTabixAdapter.js

@@ -55,6 +55,10 @@ class VcfTabixAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const { vcf } = await this.configure(opts);
         return vcf.getHeader();
     }
+    async getMetadata(opts) {
+        const { parser } = await this.configure(opts);
+        return parser.getMetadata();
+    }
     getFeatures(query, opts = {}) {
         return (0, rxjs_1.ObservableCreate)(async (observer) => {
             const { refName, start, end } = query;

package/dist/index.js

@@ -11,6 +11,7 @@ const MultiLinearVariantDisplay_1 = __importDefault(require("./MultiLinearVarian
 const MultiLinearVariantMatrixDisplay_1 = __importDefault(require("./MultiLinearVariantMatrixDisplay"));
 const MultiLinearVariantMatrixRenderer_1 = __importDefault(require("./MultiLinearVariantMatrixRenderer"));
 const MultiLinearVariantRenderer_1 = __importDefault(require("./MultiLinearVariantRenderer"));
+const SplitVcfTabixAdapter_1 = __importDefault(require("./SplitVcfTabixAdapter"));
 const StructuralVariantChordRenderer_1 = __importDefault(require("./StructuralVariantChordRenderer"));
 const VariantFeatureWidget_1 = __importDefault(require("./VariantFeatureWidget"));
 const MultiVariantGetGenotypeMatrix_1 = require("./VariantRPC/MultiVariantGetGenotypeMatrix");
@@ -28,6 +29,7 @@ class VariantsPlugin extends Plugin_1.default {
     install(pluginManager) {
         (0, VcfAdapter_1.default)(pluginManager);
         (0, VcfTabixAdapter_1.default)(pluginManager);
+        (0, SplitVcfTabixAdapter_1.default)(pluginManager);
         (0, VariantFeatureWidget_1.default)(pluginManager);
         (0, VariantTrack_1.default)(pluginManager);
         (0, extensionPoints_1.default)(pluginManager);

package/dist/shared/MultiVariantBaseModel.js

@@ -229,10 +229,9 @@ function MultiVariantBaseModelF(configSchema) {
                                 },
                             },
                             {
-                                label: 'Phased' +
-                                    (!self.hasPhased
-                                        ? ' (disabled, no phased variants found)'
-                                        : ''),
+                                label: `Phased${!self.hasPhased
+                                    ? ' (disabled, no phased variants found)'
+                                    : ''}`,
                                 disabled: !self.hasPhased,
                                 checked: self.renderingMode === 'phased',
                                 type: 'radio',

package/dist/shared/drawAlleleCount.js

@@ -27,14 +27,19 @@ function getColorAlleleCount(alleles, mostFrequentAlt) {
         return `#ccc`;
     }
     else {
-        let a1 = (0, colord_1.colord)(`hsl(200,50%,${80 - (alt / total) * 50}%)`);
+        let a1;
+        if (alt) {
+            a1 = (0, colord_1.colord)(`hsl(200,50%,${80 - (alt / total) * 50}%)`);
+        }
         if (alt2) {
-            a1 = a1.mix(`hsla(0,100%,20%,${alt2 / total})`);
+            const l = `hsla(0,100%,20%,${alt2 / total})`;
+            a1 = a1 ? a1.mix(l) : (0, colord_1.colord)(l);
         }
         if (uncalled) {
-            a1 = a1.mix(`hsla(50,50%,50%,${uncalled / total / 2})`);
+            const l = `hsl(50,50%,50%,${uncalled / total})`;
+            a1 = a1 ? a1.mix(l) : (0, colord_1.colord)(l);
         }
-        return a1.toHex();
+        return (a1 === null || a1 === void 0 ? void 0 : a1.toHex()) || 'black';
     }
 }
 function drawColorAlleleCount(alleles, ctx, x, y, w, h, mostFrequentAlt) {

package/esm/MultiLinearVariantMatrixDisplay/components/LinesConnectingMatrixToGenomicPosition.js

@@ -1,6 +1,17 @@
-import { jsx as _jsx } from "react/jsx-runtime";
+import { jsx as _jsx, jsxs as _jsxs, Fragment as _Fragment } from "react/jsx-runtime";
+import { useState } from 'react';
+import { ResizeHandle } from '@jbrowse/core/ui';
 import { getContainingView, getSession } from '@jbrowse/core/util';
 import { observer } from 'mobx-react';
+import { makeStyles } from 'tss-react/mui';
+const useStyles = makeStyles()({
+    resizeHandle: {
+        height: 4,
+        background: '#ccc',
+        boxSizing: 'border-box',
+        borderTop: '1px solid #fafafa',
+    },
+});
 const Wrapper = observer(function ({ children, model, exportSVG, }) {
     const { height } = model;
     const { width, offsetPx } = getContainingView(model);
@@ -9,12 +20,31 @@ const Wrapper = observer(function ({ children, model, exportSVG, }) {
             position: 'absolute',
             top: 0,
             left,
-            pointerEvents: 'none',
             height,
             width,
         }, children: children }));
 });
 const LinesConnectingMatrixToGenomicPosition = observer(function ({ model, exportSVG, }) {
+    var _a;
+    const { classes } = useStyles();
+    const { assemblyManager } = getSession(model);
+    const view = getContainingView(model);
+    const [mouseOverLine, setMouseOverLine] = useState();
+    const { lineZoneHeight, featuresVolatile } = model;
+    const { assemblyNames, dynamicBlocks } = view;
+    const assembly = assemblyManager.get(assemblyNames[0]);
+    const b0 = ((_a = dynamicBlocks.contentBlocks[0]) === null || _a === void 0 ? void 0 : _a.widthPx) || 0;
+    const w = b0 / ((featuresVolatile === null || featuresVolatile === void 0 ? void 0 : featuresVolatile.length) || 1);
+    return assembly && featuresVolatile ? (_jsxs(_Fragment, { children: [_jsxs(Wrapper, { exportSVG: exportSVG, model: model, children: [_jsx(AllLines, { model: model, setMouseOverLine: setMouseOverLine }), mouseOverLine ? (_jsx("line", { stroke: "#f00c", strokeWidth: 2, style: {
+                            pointerEvents: 'none',
+                        }, x1: mouseOverLine.idx * w + w / 2, x2: mouseOverLine.c, y1: lineZoneHeight, y2: 0, onMouseLeave: () => {
+                            setMouseOverLine(undefined);
+                        } })) : null] }), !exportSVG ? (_jsx(ResizeHandle, { style: {
+                    position: 'absolute',
+                    top: lineZoneHeight - 4,
+                }, onDrag: n => model.setLineZoneHeight(lineZoneHeight + n), className: classes.resizeHandle })) : null] })) : null;
+});
+const AllLines = observer(function ({ model, setMouseOverLine, }) {
     var _a;
     const { assemblyManager } = getSession(model);
     const view = getContainingView(model);
@@ -24,14 +54,18 @@ const LinesConnectingMatrixToGenomicPosition = observer(function ({ model, expor
     const b0 = ((_a = dynamicBlocks.contentBlocks[0]) === null || _a === void 0 ? void 0 : _a.widthPx) || 0;
     const w = b0 / ((featuresVolatile === null || featuresVolatile === void 0 ? void 0 : featuresVolatile.length) || 1);
     const l = Math.max(offsetPx, 0);
-    return assembly && featuresVolatile ? (_jsx(Wrapper, { exportSVG: exportSVG, model: model, children: featuresVolatile.map((f, i) => {
+    return assembly && featuresVolatile ? (_jsx(_Fragment, { children: featuresVolatile.map((f, i) => {
             var _a;
             const ref = f.get('refName');
             const c = (((_a = view.bpToPx({
                 refName: assembly.getCanonicalRefName(ref) || ref,
                 coord: f.get('start'),
             })) === null || _a === void 0 ? void 0 : _a.offsetPx) || 0) - l;
-            return (_jsx("line", { stroke: "#0004", x1: i * w + w / 2, x2: c, y1: lineZoneHeight, y2: 0 }, f.id()));
+            return (_jsx("line", { stroke: "#0004", strokeWidth: 1, x1: i * w + w / 2, x2: c, y1: lineZoneHeight, y2: 0, onMouseEnter: () => {
+                    setMouseOverLine({ f, idx: i, c });
+                }, onMouseLeave: () => {
+                    setMouseOverLine(undefined);
+                } }, f.id()));
         }) })) : null;
 });
 export default LinesConnectingMatrixToGenomicPosition;

package/esm/MultiLinearVariantMatrixDisplay/model.d.ts

@@ -92,6 +92,7 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearVariantMatrixDisplay">;
     rowHeightSetting: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<number>, [undefined]>;
+    lineZoneHeight: import("mobx-state-tree").IType<number | undefined, number, number>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -338,8 +339,6 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     readonly totalHeight: number;
 } & {
     renderProps(): any;
-} & {
-    lineZoneHeight: number;
 } & {
     readonly nrow: number;
     readonly blockType: string;
@@ -349,6 +348,9 @@ export default function stateModelFactory(configSchema: AnyConfigurationSchemaTy
     renderProps(): any;
     readonly canDisplayLabels: boolean;
 } & {
+    setLineZoneHeight(n: number): number;
+} & {
+    setLineZoneHeight(n: number): number;
     afterAttach(): void;
     renderSvg(opts: ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
 }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>;

package/esm/MultiLinearVariantMatrixDisplay/model.js

@@ -1,4 +1,4 @@
-import { getSession } from '@jbrowse/core/util';
+import { clamp, getSession } from '@jbrowse/core/util';
 import { isAlive, types } from 'mobx-state-tree';
 import MultiVariantBaseModelF from '../shared/MultiVariantBaseModel';
 export default function stateModelFactory(configSchema) {
@@ -6,8 +6,6 @@ export default function stateModelFactory(configSchema) {
         .compose('LinearVariantMatrixDisplay', MultiVariantBaseModelF(configSchema), types.model({
         type: types.literal('LinearVariantMatrixDisplay'),
         rowHeightSetting: types.optional(types.number, 1),
-    }))
-        .volatile(() => ({
         lineZoneHeight: 20,
     }))
         .views(self => ({
@@ -44,10 +42,20 @@ export default function stateModelFactory(configSchema) {
         get canDisplayLabels() {
             return self.rowHeight > 8 && self.showSidebarLabelsSetting;
         },
+    }))
+        .actions(self => ({
+        setLineZoneHeight(n) {
+            self.lineZoneHeight = clamp(n, 10, 1000);
+            return self.lineZoneHeight;
+        },
     }))
         .actions(self => {
         const { renderSvg: superRenderSvg } = self;
         return {
+            setLineZoneHeight(n) {
+                self.lineZoneHeight = clamp(n, 10, 1000);
+                return self.lineZoneHeight;
+            },
             afterAttach() {
                 ;
                 (async () => {

package/esm/MultiLinearVariantMatrixRenderer/makeImageData.js

@@ -12,11 +12,11 @@ export async function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs
     const m = mafs.length;
     const w = canvasWidth / m;
     await updateStatus('Drawing variant matrix', statusCallback, () => {
-        var _a, _b;
+        var _a, _b, _c;
         for (let i = 0; i < m; i++) {
             const arr2 = [];
             const { feature, mostFrequentAlt } = mafs[i];
-            const hasPhaseSet = feature.get('format').includes('PS');
+            const hasPhaseSet = (_a = feature.get('FORMAT')) === null || _a === void 0 ? void 0 : _a.includes('PS');
             if (hasPhaseSet) {
                 const samp = feature.get('samples');
                 const x = (i / mafs.length) * canvasWidth;
@@ -26,13 +26,13 @@ export async function makeImageData({ ctx, canvasWidth, canvasHeight, renderArgs
                     const { name, HP } = sources[j];
                     const s = samp[name];
                     if (s) {
-                        const genotype = (_a = s.GT) === null || _a === void 0 ? void 0 : _a[0];
+                        const genotype = (_b = s.GT) === null || _b === void 0 ? void 0 : _b[0];
                         if (genotype) {
                             arr2.push(genotype);
                             const isPhased = genotype.includes('|');
                             if (renderingMode === 'phased') {
                                 if (isPhased) {
-                                    const PS = (_b = s.PS) === null || _b === void 0 ? void 0 : _b[0];
+                                    const PS = (_c = s.PS) === null || _c === void 0 ? void 0 : _c[0];
                                     const alleles = genotype.split('|');
                                     drawPhased(alleles, ctx, x, y, w, h, HP, PS);
                                 }

package/esm/SplitVcfTabixAdapter/SplitVcfTabixAdapter.d.ts

@@ -0,0 +1,19 @@
+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;
+    }[]>;
+    freeResources(): void;
+}

package/esm/SplitVcfTabixAdapter/SplitVcfTabixAdapter.js

@@ -0,0 +1,87 @@
+import { TabixIndexedFile } from '@gmod/tabix';
+import VcfParser from '@gmod/vcf';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { fetchAndMaybeUnzipText, updateStatus } from '@jbrowse/core/util';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import VcfFeature from '../VcfFeature';
+export default class SplitVcfTabixAdapter extends 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 = openLocation(vcfGzLocation, this.pluginManager);
+        const isCSI = indexType === 'CSI';
+        const vcf = new TabixIndexedFile({
+            filehandle,
+            csiFilehandle: isCSI
+                ? openLocation(indexLocation, this.pluginManager)
+                : undefined,
+            tbiFilehandle: !isCSI
+                ? openLocation(indexLocation, this.pluginManager)
+                : undefined,
+            chunkCacheSize: 50 * 2 ** 20,
+        });
+        return {
+            vcf,
+            parser: new VcfParser({
+                header: await vcf.getHeader(),
+            }),
+        };
+    }
+    async configure(refName, opts) {
+        const { statusCallback = () => { } } = opts || {};
+        return updateStatus('Downloading index', statusCallback, () => this.configurePre(refName));
+    }
+    async getRefNames() {
+        return Object.keys(this.getConf('vcfGzLocationMap'));
+    }
+    getFeatures(query, opts = {}) {
+        return ObservableCreate(async (observer) => {
+            const { refName, start, end } = query;
+            const { statusCallback = () => { } } = opts;
+            const { vcf, parser } = await this.configure(query.refName, opts);
+            await updateStatus('Downloading variants', statusCallback, () => vcf.getLines(refName, start, end, {
+                lineCallback: (line, fileOffset) => {
+                    observer.next(new VcfFeature({
+                        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 fetchAndMaybeUnzipText(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));
+        }
+    }
+    freeResources() { }
+}

package/esm/SplitVcfTabixAdapter/configSchema.d.ts

@@ -0,0 +1,23 @@
+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/esm/SplitVcfTabixAdapter/configSchema.js

@@ -0,0 +1,25 @@
+import { ConfigurationSchema } from '@jbrowse/core/configuration';
+function x() { }
+const SplitVcfTabixAdapter = 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 is the sample names',
+            locationType: 'UriLocation',
+        },
+    },
+}, { explicitlyTyped: true });
+export default SplitVcfTabixAdapter;

package/esm/SplitVcfTabixAdapter/index.d.ts

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

package/esm/SplitVcfTabixAdapter/index.js

@@ -0,0 +1,11 @@
+import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType';
+import configSchema from './configSchema';
+export { default as configSchema } from './configSchema';
+export default function VcfTabixAdapterF(pluginManager) {
+    pluginManager.addAdapterType(() => new AdapterType({
+        name: 'SplitVcfTabixAdapter',
+        displayName: 'VCF tabix adapter (split across multiple files)',
+        configSchema,
+        getAdapterClass: () => import('./SplitVcfTabixAdapter').then(r => r.default),
+    }));
+}

package/esm/VariantFeatureWidget/{LaunchBreakendPanel.d.ts → LaunchBreakendPanel/LaunchBreakendPanel.d.ts}

@@ -1,4 +1,4 @@
-import type { VariantFeatureWidgetModel } from './stateModelFactory';
+import type { VariantFeatureWidgetModel } from '../stateModelFactory';
 import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
 export default function LaunchBreakendPanel(props: {
     locStrings: string[];

package/esm/VariantFeatureWidget/{LaunchBreakendWidgetArea.d.ts → LaunchBreakendPanel/LaunchBreakendWidgetArea.d.ts}

@@ -1,4 +1,4 @@
-import type { VariantFeatureWidgetModel } from './stateModelFactory';
+import type { VariantFeatureWidgetModel } from '../stateModelFactory';
 export default function LaunchBreakendWidgetArea({ model, }: {
     model: VariantFeatureWidgetModel;
 }): import("react/jsx-runtime").JSX.Element;

package/esm/VariantFeatureWidget/LaunchBreakendPanel/index.d.ts

@@ -0,0 +1 @@
+export { default } from './LaunchBreakendPanel';

package/esm/VariantFeatureWidget/LaunchBreakendPanel/index.js

@@ -0,0 +1 @@
+export { default } from './LaunchBreakendPanel';

package/esm/VariantFeatureWidget/VariantFeatureWidget.js

@@ -4,9 +4,9 @@ import { parseBreakend } from '@gmod/vcf';
 import FeatureDetails from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails';
 import { Paper } from '@mui/material';
 import { observer } from 'mobx-react';
-import VariantSampleGrid from './VariantSampleGrid';
+import VariantSampleGrid from './VariantSampleGrid/VariantSampleGrid';
 import { variantFieldDescriptions } from './variantFieldDescriptions';
-const LaunchBreakendPanel = lazy(() => import('./LaunchBreakendPanel'));
+const LaunchBreakendPanel = lazy(() => import('./LaunchBreakendPanel/LaunchBreakendPanel'));
 const VariantConsequenceDataGrid = lazy(() => import('./VariantConsequenceDataGrid'));
 function AnnPanel({ descriptions, feature, }) {
     var _a, _b, _c, _d, _e;

package/esm/VariantFeatureWidget/VariantSampleGrid/index.d.ts

@@ -0,0 +1 @@
+export { default } from './VariantSampleGrid';

package/esm/VariantFeatureWidget/VariantSampleGrid/index.js

@@ -0,0 +1 @@
+export { default } from './VariantSampleGrid';

package/esm/VcfFeature/index.js

@@ -1,6 +1,6 @@
 import { getSOTermAndDescription } from './util';
 function dataFromVariant(variant, parser) {
-    const { FORMAT, REF = '', ALT, POS, CHROM, ID } = variant;
+    const { REF = '', ALT, POS, CHROM, ID } = variant;
     const start = POS - 1;
     const [type, description] = getSOTermAndDescription(REF, ALT, parser);
     return {
@@ -11,7 +11,6 @@ function dataFromVariant(variant, parser) {
         type,
         name: ID === null || ID === void 0 ? void 0 : ID.join(','),
         aliases: ID && ID.length > 1 ? ID.slice(1) : undefined,
-        format: FORMAT,
     };
 }
 function getEnd(variant) {

package/esm/VcfTabixAdapter/VcfTabixAdapter.d.ts

@@ -17,6 +17,7 @@ export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
     }>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
     getHeader(opts?: BaseOptions): Promise<string>;
+    getMetadata(opts?: BaseOptions): Promise<any>;
     getFeatures(query: NoAssemblyRegion, opts?: BaseOptions): import("rxjs").Observable<Feature>;
     getSources(): Promise<{
         name: string;

package/esm/VcfTabixAdapter/VcfTabixAdapter.js

@@ -50,6 +50,10 @@ export default class VcfTabixAdapter extends BaseFeatureDataAdapter {
         const { vcf } = await this.configure(opts);
         return vcf.getHeader();
     }
+    async getMetadata(opts) {
+        const { parser } = await this.configure(opts);
+        return parser.getMetadata();
+    }
     getFeatures(query, opts = {}) {
         return ObservableCreate(async (observer) => {
             const { refName, start, end } = query;

package/esm/index.js

@@ -5,6 +5,7 @@ import MultiLinearVariantDisplayF from './MultiLinearVariantDisplay';
 import LinearVariantMatrixDisplayF from './MultiLinearVariantMatrixDisplay';
 import LinearVariantMatrixRendererF from './MultiLinearVariantMatrixRenderer';
 import MultiVariantRendererF from './MultiLinearVariantRenderer';
+import SplitVcfTabixAdapterF from './SplitVcfTabixAdapter';
 import StructuralVariantChordRendererF from './StructuralVariantChordRenderer';
 import VariantFeatureWidgetF from './VariantFeatureWidget';
 import { MultiVariantGetGenotypeMatrix } from './VariantRPC/MultiVariantGetGenotypeMatrix';
@@ -22,6 +23,7 @@ export default class VariantsPlugin extends Plugin {
     install(pluginManager) {
         VcfAdapterF(pluginManager);
         VcfTabixAdapterF(pluginManager);
+        SplitVcfTabixAdapterF(pluginManager);
         VariantFeatureWidgetF(pluginManager);
         VariantTrackF(pluginManager);
         ExtensionPointsF(pluginManager);

package/esm/shared/MultiVariantBaseModel.js

@@ -190,10 +190,9 @@ export default function MultiVariantBaseModelF(configSchema) {
                                 },
                             },
                             {
-                                label: 'Phased' +
-                                    (!self.hasPhased
-                                        ? ' (disabled, no phased variants found)'
-                                        : ''),
+                                label: `Phased${!self.hasPhased
+                                    ? ' (disabled, no phased variants found)'
+                                    : ''}`,
                                 disabled: !self.hasPhased,
                                 checked: self.renderingMode === 'phased',
                                 type: 'radio',

package/esm/shared/drawAlleleCount.js

@@ -24,14 +24,19 @@ function getColorAlleleCount(alleles, mostFrequentAlt) {
         return `#ccc`;
     }
     else {
-        let a1 = colord(`hsl(200,50%,${80 - (alt / total) * 50}%)`);
+        let a1;
+        if (alt) {
+            a1 = colord(`hsl(200,50%,${80 - (alt / total) * 50}%)`);
+        }
         if (alt2) {
-            a1 = a1.mix(`hsla(0,100%,20%,${alt2 / total})`);
+            const l = `hsla(0,100%,20%,${alt2 / total})`;
+            a1 = a1 ? a1.mix(l) : colord(l);
         }
         if (uncalled) {
-            a1 = a1.mix(`hsla(50,50%,50%,${uncalled / total / 2})`);
+            const l = `hsl(50,50%,50%,${uncalled / total})`;
+            a1 = a1 ? a1.mix(l) : colord(l);
         }
-        return a1.toHex();
+        return (a1 === null || a1 === void 0 ? void 0 : a1.toHex()) || 'black';
     }
 }
 export function drawColorAlleleCount(alleles, ctx, x, y, w, h, mostFrequentAlt) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-variants",
-  "version": "3.0.3",
+  "version": "3.0.5",
   "description": "JBrowse 2 variant adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -40,10 +40,10 @@
     "@gmod/bgzf-filehandle": "^2.0.1",
     "@gmod/tabix": "^2.0.0",
     "@gmod/vcf": "^6.0.8",
-    "@jbrowse/core": "^3.0.3",
-    "@jbrowse/plugin-circular-view": "^3.0.3",
-    "@jbrowse/plugin-linear-genome-view": "^3.0.3",
-    "@jbrowse/sv-core": "^3.0.3",
+    "@jbrowse/core": "^3.0.5",
+    "@jbrowse/plugin-circular-view": "^3.0.5",
+    "@jbrowse/plugin-linear-genome-view": "^3.0.5",
+    "@jbrowse/sv-core": "^3.0.5",
     "@mui/icons-material": "^6.0.0",
     "@mui/material": "^6.0.0",
     "@mui/x-data-grid": "^7.0.0",
@@ -62,5 +62,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "f516540428282351d26e46743e69a724651bfb2c"
+  "gitHead": "a03749efe19e51609922272b845a331897346789"
 }