@jbrowse/plugin-alignments 2.18.0 → 3.0.1

package/dist/CramAdapter/CramAdapter.js

@@ -29,7 +29,9 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
         const pm = this.pluginManager;
         const cram = new cram_1.IndexedCramFile({
             cramFilehandle: (0, io_1.openLocation)(cramLocation, pm),
-            index: new cram_1.CraiIndex({ filehandle: (0, io_1.openLocation)(craiLocation, pm) }),
+            index: new cram_1.CraiIndex({
+                filehandle: (0, io_1.openLocation)(craiLocation, pm),
+            }),
             seqFetch: (...args) => this.seqFetch(...args),
             checkSequenceMD5: false,
         });
@@ -115,7 +117,10 @@ class CramAdapter extends BaseAdapter_1.BaseFeatureDataAdapter {
                 .map(rgLine => { var _a; return (_a = rgLine.data.find(item => item.tag === 'ID')) === null || _a === void 0 ? void 0 : _a.value; });
             const data = { idToName, nameToId, readGroups };
             this.samHeader = data;
-            return { samHeader: data, ...conf };
+            return {
+                samHeader: data,
+                ...conf,
+            };
         });
     }
     async setup(opts) {

package/dist/CramAdapter/CramTestAdapters.d.ts

@@ -1,7 +1,7 @@
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import SimpleFeature from '@jbrowse/core/util/simpleFeature';
 import { Observable } from 'rxjs';
-import type { GenericFilehandle } from 'generic-filehandle';
+import type { GenericFilehandle } from 'generic-filehandle2';
 export declare function parseSmallFasta(text: string): {
     id: string;
     description: string;

package/dist/CramAdapter/CramTestAdapters.js

@@ -28,7 +28,8 @@ function parseSmallFasta(text) {
 class FetchableSmallFasta {
     constructor(filehandle) {
         this.data = filehandle.readFile().then(buffer => {
-            const text = buffer.toString('utf8');
+            const decoder = new TextDecoder('utf8');
+            const text = decoder.decode(buffer);
             return parseSmallFasta(text);
         });
     }

package/dist/CramAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : 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;
-};
+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 };
 };

package/dist/GuessAlignmentsTypes/index.js

@@ -1,48 +1,33 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = GuessAlignmentsTypesF;
+const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
 function GuessAlignmentsTypesF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {
-            const regexGuess = /\.cram$/i;
-            const adapterName = 'CramAdapter';
-            const fileName = (0, tracks_1.getFileName)(file);
-            const obj = {
-                type: adapterName,
-                cramLocation: file,
-                craiLocation: index || (0, tracks_1.makeIndex)(file, '.crai'),
-            };
-            if (regexGuess.test(fileName) && !adapterHint) {
-                return obj;
-            }
-            if (adapterHint === adapterName) {
-                return obj;
-            }
-            return adapterGuesser(file, index, adapterHint);
-        };
-    });
-    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-        return (file, index, adapterHint) => {
-            const regexGuess = /\.bam$/i;
-            const adapterName = 'BamAdapter';
             const fileName = (0, tracks_1.getFileName)(file);
             const indexName = index && (0, tracks_1.getFileName)(index);
-            const obj = {
-                type: adapterName,
-                bamLocation: file,
-                index: {
-                    location: index || (0, tracks_1.makeIndex)(file, '.bai'),
-                    indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'BAI'),
-                },
-            };
-            if (regexGuess.test(fileName) && !adapterHint) {
-                return obj;
+            if ((0, util_1.testAdapter)(fileName, /\.bam$/i, adapterHint, 'BamAdapter')) {
+                return {
+                    type: 'BamAdapter',
+                    bamLocation: file,
+                    index: {
+                        location: index || (0, tracks_1.makeIndex)(file, '.bai'),
+                        indexType: (0, tracks_1.makeIndexType)(indexName, 'CSI', 'BAI'),
+                    },
+                };
+            }
+            else if ((0, util_1.testAdapter)(fileName, /\.cram$/i, adapterHint, 'CramAdapter')) {
+                return {
+                    type: 'CramAdapter',
+                    cramLocation: file,
+                    craiLocation: index || (0, tracks_1.makeIndex)(file, '.crai'),
+                };
             }
-            if (adapterHint === adapterName) {
-                return obj;
+            else {
+                return adapterGuesser(file, index, adapterHint);
             }
-            return adapterGuesser(file, index, adapterHint);
         };
     });
     pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {

package/dist/HtsgetBamAdapter/index.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : 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;
-};
+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 };
 };

package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts

@@ -1,6 +1,5 @@
-import React from 'react';
 import type { LinearAlignmentsDisplayModel } from '../model';
 declare const AlignmentsDisplay: ({ model, }: {
     model: LinearAlignmentsDisplayModel;
-}) => React.JSX.Element | null;
+}) => import("react/jsx-runtime").JSX.Element | null;
 export default AlignmentsDisplay;

package/dist/LinearAlignmentsDisplay/components/AlignmentsDisplay.js

@@ -1,9 +1,6 @@
 "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 jsx_runtime_1 = require("react/jsx-runtime");
 const configuration_1 = require("@jbrowse/core/configuration");
 const ui_1 = require("@jbrowse/core/ui");
 const mobx_react_1 = require("mobx-react");
@@ -23,17 +20,12 @@ const AlignmentsDisplay = (0, mobx_react_1.observer)(function AlignmentsDisplay(
         return null;
     }
     const top = (_a = SNPCoverageDisplay.height) !== null && _a !== void 0 ? _a : 100;
-    return (react_1.default.createElement("div", { "data-testid": `display-${(0, configuration_1.getConf)(model, 'displayId')}`, style: { position: 'relative' } },
-        react_1.default.createElement("div", { "data-testid": "Blockset-snpcoverage" },
-            react_1.default.createElement(SNPCoverageDisplay.RenderingComponent, { model: SNPCoverageDisplay })),
-        react_1.default.createElement(ui_1.ResizeHandle, { onDrag: delta => {
-                SNPCoverageDisplay.setHeight(SNPCoverageDisplay.height + delta);
-                return delta;
-            }, className: classes.resizeHandle, style: { top: top - 4 } }),
-        react_1.default.createElement("div", { "data-testid": "Blockset-pileup", style: {
-                position: 'absolute',
-                top,
-            } },
-            react_1.default.createElement(PileupDisplay.RenderingComponent, { model: PileupDisplay }))));
+    return ((0, jsx_runtime_1.jsxs)("div", { "data-testid": `display-${(0, configuration_1.getConf)(model, 'displayId')}`, style: { position: 'relative' }, children: [(0, jsx_runtime_1.jsx)("div", { "data-testid": "Blockset-snpcoverage", children: (0, jsx_runtime_1.jsx)(SNPCoverageDisplay.RenderingComponent, { model: SNPCoverageDisplay }) }), (0, jsx_runtime_1.jsx)(ui_1.ResizeHandle, { onDrag: delta => {
+                    SNPCoverageDisplay.setHeight(SNPCoverageDisplay.height + delta);
+                    return delta;
+                }, className: classes.resizeHandle, style: { top: top - 4 } }), (0, jsx_runtime_1.jsx)("div", { "data-testid": "Blockset-pileup", style: {
+                    position: 'absolute',
+                    top,
+                }, children: (0, jsx_runtime_1.jsx)(PileupDisplay.RenderingComponent, { model: PileupDisplay }) })] }));
 });
 exports.default = AlignmentsDisplay;

package/dist/LinearAlignmentsDisplay/model.d.ts

@@ -1,4 +1,3 @@
-import React from 'react';
 import type { FilterBy } from '../shared/types';
 import type PluginManager from '@jbrowse/core/PluginManager';
 import type { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
@@ -104,7 +103,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     afterAttach(): void;
     renderSvg(opts: {
         rasterizeLayers?: boolean;
-    }): Promise<React.JSX.Element>;
+    }): Promise<import("react/jsx-runtime").JSX.Element>;
 } & {
     trackMenuItems(): MenuItem[];
 }, import("mobx-state-tree").ModelCreationType<import("mobx-state-tree/dist/internal").ExtractCFromProps<{

package/dist/LinearAlignmentsDisplay/model.js

@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importDefault(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
 const configuration_1 = require("@jbrowse/core/configuration");
 const models_1 = require("@jbrowse/core/pluggableElementTypes/models");
 const fast_deep_equal_1 = __importDefault(require("fast-deep-equal"));
@@ -165,12 +165,10 @@ function stateModelFactory(pluginManager, configSchema) {
             const pileupHeight = self.height - self.SNPCoverageDisplay.height;
             await (0, mobx_1.when)(() => !self.PileupDisplay.renderProps().notReady &&
                 !self.SNPCoverageDisplay.renderProps().notReady);
-            return (react_1.default.createElement(react_1.default.Fragment, null,
-                react_1.default.createElement("g", null, await self.SNPCoverageDisplay.renderSvg(opts)),
-                react_1.default.createElement("g", { transform: `translate(0 ${self.SNPCoverageDisplay.height})` }, await self.PileupDisplay.renderSvg({
-                    ...opts,
-                    overrideHeight: pileupHeight,
-                }))));
+            return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("g", { children: await self.SNPCoverageDisplay.renderSvg(opts) }), (0, jsx_runtime_1.jsx)("g", { transform: `translate(0 ${self.SNPCoverageDisplay.height})`, children: await self.PileupDisplay.renderSvg({
+                            ...opts,
+                            overrideHeight: pileupHeight,
+                        }) })] }));
         },
     }))
         .views(self => {

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts

@@ -38,7 +38,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
@@ -88,6 +88,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     colorBySetting: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
     filterBySetting: import("mobx-state-tree").IType<FilterBy | undefined, FilterBy | undefined, FilterBy | undefined>;
     jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    hideSmallIndelsSetting: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
 }, {
     rendererTypeName: string;
     error: unknown;
@@ -179,13 +180,13 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
 } & {
     readonly statsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react").JSX.Element | null;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
     featureIdUnderMouse: undefined | string;
     contextMenuFeature: undefined | Feature;
 } & {
-    readonly DisplayMessageComponent: import("react").FC<any> | undefined;
-    readonly blockType: "dynamicBlocks" | "staticBlocks";
+    readonly DisplayMessageComponent: undefined | React.FC<any>;
+    readonly blockType: "staticBlocks" | "dynamicBlocks";
     readonly blockDefinitions: import("@jbrowse/core/util/blockTypes").BlockSet;
 } & {
     readonly renderDelay: number;
@@ -212,7 +213,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     contextMenuItems(): import("@jbrowse/core/ui").MenuItem[];
     renderProps(): any;
 } & {
-    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react").JSX.Element>;
+    renderSvg(opts: import("@jbrowse/plugin-linear-genome-view").ExportSvgDisplayOptions): Promise<import("react/jsx-runtime").JSX.Element>;
     afterAttach(): void;
 } & {
     colorTagMap: import("mobx").ObservableMap<string, string>;
@@ -223,6 +224,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     readonly filterBy: any;
 } & {
     readonly autorunReady: boolean;
+    readonly hideSmallIndels: boolean | undefined;
 } & {
     setTagsReady(flag: boolean): void;
     setMaxHeight(n?: number): void;
@@ -236,6 +238,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     setConfig(conf: AnyConfigurationModel): void;
     setFilterBy(filter: FilterBy): void;
     setJexlFilters(filters: string[]): void;
+    setHideSmallIndels(arg: boolean): void;
 } & {
     readonly rendererConfig: {
         [x: string]: any;
@@ -271,18 +274,28 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
         model: {
             sortedBy?: import("../shared/types").SortedBy;
         };
-    }) => import("react").JSX.Element | null;
+    }) => import("react/jsx-runtime").JSX.Element | null;
     renderPropsPre(): any;
     colorSchemeSubMenuItems(): {
         label: string;
         onClick: () => void;
     }[];
     trackMenuItems(): (import("@jbrowse/core/ui").MenuDivider | import("@jbrowse/core/ui").MenuSubHeader | import("@jbrowse/core/ui").NormalMenuItem | import("@jbrowse/core/ui").CheckboxMenuItem | import("@jbrowse/core/ui").RadioMenuItem | import("@jbrowse/core/ui").SubMenuItem | {
+        label: string;
+        priority: number;
+        type: string;
+        checked: boolean | undefined;
+        onClick: () => void;
+        icon?: undefined;
+    } | {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
             muiName: string;
         };
         onClick: () => void;
+        priority?: undefined;
+        type?: undefined;
+        checked?: undefined;
     })[];
 } & {
     renderProps(): any;
@@ -323,7 +336,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
@@ -373,6 +386,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     colorBySetting: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
     filterBySetting: import("mobx-state-tree").IType<FilterBy | undefined, FilterBy | undefined, FilterBy | undefined>;
     jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;
+    hideSmallIndelsSetting: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
 }>>, {
     id: string;
     type: string;

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js

@@ -15,13 +15,23 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : 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;
-};
+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 };
 };
@@ -61,6 +71,7 @@ function SharedLinearPileupDisplayMixin(configSchema) {
         colorBySetting: mobx_state_tree_1.types.frozen(),
         filterBySetting: mobx_state_tree_1.types.frozen(),
         jexlFilters: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.array(mobx_state_tree_1.types.string), []),
+        hideSmallIndelsSetting: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
     }))
         .volatile(() => ({
         colorTagMap: mobx_1.observable.map({}),
@@ -82,6 +93,9 @@ function SharedLinearPileupDisplayMixin(configSchema) {
             const view = (0, util_1.getContainingView)(self);
             return view.initialized && self.statsReadyAndRegionNotTooLarge;
         },
+        get hideSmallIndels() {
+            return self.hideSmallIndelsSetting;
+        },
     }))
         .actions(self => ({
         setTagsReady(flag) {
@@ -157,18 +171,20 @@ function SharedLinearPileupDisplayMixin(configSchema) {
         setJexlFilters(filters) {
             self.jexlFilters = (0, mobx_state_tree_1.cast)(filters);
         },
+        setHideSmallIndels(arg) {
+            self.hideSmallIndelsSetting = arg;
+        },
     }))
         .views(self => ({
         get rendererConfig() {
-            const { featureHeight, noSpacing, trackMaxHeight, rendererTypeName } = self;
+            const { featureHeight: height, noSpacing, hideSmallIndels, trackMaxHeight: maxHeight, rendererTypeName, } = self;
             const configBlob = (0, configuration_1.getConf)(self, ['renderers', rendererTypeName]) || {};
             return self.rendererType.configSchema.create({
                 ...configBlob,
-                ...(featureHeight !== undefined ? { height: featureHeight } : {}),
+                ...(hideSmallIndels !== undefined ? { hideSmallIndels } : {}),
+                ...(height !== undefined ? { height } : {}),
                 ...(noSpacing !== undefined ? { noSpacing } : {}),
-                ...(trackMaxHeight !== undefined
-                    ? { maxHeight: trackMaxHeight }
-                    : {}),
+                ...(maxHeight !== undefined ? { maxHeight } : {}),
             }, (0, util_1.getEnv)(self));
         },
     }))
@@ -394,6 +410,15 @@ function SharedLinearPileupDisplayMixin(configSchema) {
                             },
                         ],
                     },
+                    {
+                        label: 'Hide small indels (<10bp)',
+                        priority: -1,
+                        type: 'checkbox',
+                        checked: self.hideSmallIndels,
+                        onClick: () => {
+                            self.setHideSmallIndels(!self.hideSmallIndels);
+                        },
+                    },
                     {
                         label: 'Set max height...',
                         priority: -1,
@@ -488,11 +513,11 @@ function SharedLinearPileupDisplayMixin(configSchema) {
     }))
         .preProcessSnapshot(snap => {
         if (snap) {
-            const { colorBy, filterBy, ...rest } = snap;
+            const { colorBy, colorBySetting, filterBySetting, filterBy, ...rest } = snap;
             return {
                 ...rest,
-                filterBySetting: filterBy,
-                colorBySetting: colorBy,
+                filterBySetting: filterBySetting || filterBy,
+                colorBySetting: colorBySetting || colorBy,
             };
         }
         return snap;

package/dist/LinearPileupDisplay/components/ColorByTagDialog.d.ts

@@ -1,4 +1,3 @@
-import React from 'react';
 interface Tag {
     type: string;
     tag: string;
@@ -8,5 +7,5 @@ declare const ColorByTagDialog: ({ model, handleClose, }: {
         setColorScheme: (arg: Tag) => void;
     };
     handleClose: () => void;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default ColorByTagDialog;

package/dist/LinearPileupDisplay/components/ColorByTagDialog.js

@@ -1,49 +1,20 @@
 "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 jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const ui_1 = require("@jbrowse/core/ui");
 const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
 const ColorByTagDialog = (0, mobx_react_1.observer)(function ({ model, handleClose, }) {
     const [tag, setTag] = (0, react_1.useState)('');
     const validTag = /^[A-Za-z][A-Za-z0-9]$/.exec(tag);
-    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Color by tag" },
-        react_1.default.createElement(material_1.DialogContent, { style: { overflowX: 'hidden' } },
-            react_1.default.createElement(material_1.Typography, null, "Enter tag to color by: "),
-            react_1.default.createElement(material_1.Typography, { color: "textSecondary" }, "Examples: XS or TS for RNA-seq inferred read strand, ts (lower-case) for minimap2 read strand, HP for haplotype, RG for read group, etc."),
-            react_1.default.createElement(material_1.TextField, { value: tag, onChange: event => {
-                    setTag(event.target.value);
-                }, placeholder: "Enter tag name", error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '', autoComplete: "off", slotProps: {
-                    htmlInput: { maxLength: 2 },
-                } }),
-            react_1.default.createElement(material_1.DialogActions, null,
-                react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", onClick: () => {
-                        model.setColorScheme({ type: 'tag', tag });
-                        handleClose();
-                    }, disabled: !validTag }, "Submit"),
-                react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: handleClose }, "Cancel")))));
+    return ((0, jsx_runtime_1.jsx)(ui_1.Dialog, { open: true, onClose: handleClose, title: "Color by tag", children: (0, jsx_runtime_1.jsxs)(material_1.DialogContent, { style: { overflowX: 'hidden' }, children: [(0, jsx_runtime_1.jsx)(material_1.Typography, { children: "Enter tag to color by: " }), (0, jsx_runtime_1.jsx)(material_1.Typography, { color: "textSecondary", children: "Examples: XS or TS for RNA-seq inferred read strand, ts (lower-case) for minimap2 read strand, HP for haplotype, RG for read group, etc." }), (0, jsx_runtime_1.jsx)(material_1.TextField, { value: tag, onChange: event => {
+                        setTag(event.target.value);
+                    }, placeholder: "Enter tag name", error: tag.length === 2 && !validTag, helperText: tag.length === 2 && !validTag ? 'Not a valid tag' : '', autoComplete: "off", slotProps: {
+                        htmlInput: { maxLength: 2 },
+                    } }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "primary", onClick: () => {
+                                model.setColorScheme({ type: 'tag', tag });
+                                handleClose();
+                            }, disabled: !validTag, children: "Submit" }), (0, jsx_runtime_1.jsx)(material_1.Button, { variant: "contained", color: "secondary", onClick: handleClose, children: "Cancel" })] })] }) }));
 });
 exports.default = ColorByTagDialog;

package/dist/LinearPileupDisplay/components/GroupByDialog.d.ts

@@ -1,4 +1,3 @@
-import React from 'react';
 import type { AnyConfigurationModel } from '@jbrowse/core/configuration';
 import type { IAnyStateTreeNode } from 'mobx-state-tree';
 declare const GroupByTagDialog: (props: {
@@ -7,5 +6,5 @@ declare const GroupByTagDialog: (props: {
         configuration: AnyConfigurationModel;
     } & IAnyStateTreeNode;
     handleClose: () => void;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default GroupByTagDialog;