@jbrowse/plugin-alignments 2.18.0 → 3.0.1

package/dist/LinearPileupDisplay/model.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 };
 };
@@ -123,11 +133,12 @@ function stateModelFactory(configSchema) {
             return [...self.visibleModifications.keys()];
         },
         get rendererConfig() {
-            const { featureHeight, noSpacing, trackMaxHeight, mismatchAlpha, rendererTypeName, } = self;
+            const { featureHeight, noSpacing, trackMaxHeight, mismatchAlpha, rendererTypeName, hideSmallIndels, } = self;
             const configBlob = (0, configuration_1.getConf)(self, ['renderers', rendererTypeName]) || {};
             return self.rendererType.configSchema.create({
                 ...configBlob,
                 ...(featureHeight !== undefined ? { height: featureHeight } : {}),
+                ...(hideSmallIndels !== undefined ? { hideSmallIndels } : {}),
                 ...(noSpacing !== undefined ? { noSpacing } : {}),
                 ...(mismatchAlpha !== undefined ? { mismatchAlpha } : {}),
                 ...(trackMaxHeight !== undefined

package/dist/LinearReadArcsDisplay/components/ReactComponent.d.ts

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

package/dist/LinearReadArcsDisplay/components/ReactComponent.js

@@ -1,32 +1,10 @@
 "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;
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 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 util_1 = require("@jbrowse/core/util");
 const mobx_react_1 = require("mobx-react");
 const BaseDisplayComponent_1 = __importDefault(require("../../shared/components/BaseDisplayComponent"));
@@ -37,10 +15,9 @@ const Arcs = (0, mobx_react_1.observer)(function ({ model, }) {
     const cb = (0, react_1.useCallback)((ref) => {
         model.setRef(ref);
     }, [model, width, height]);
-    return (react_1.default.createElement("canvas", { "data-testid": "arc-canvas", ref: cb, style: { width, height, position: 'absolute' }, width: width * 2, height: height * 2 }));
+    return ((0, jsx_runtime_1.jsx)("canvas", { "data-testid": "arc-canvas", ref: cb, style: { width, height, position: 'absolute' }, width: width * 2, height: height * 2 }));
 });
 const LinearReadArcsReactComponent = (0, mobx_react_1.observer)(function ({ model, }) {
-    return (react_1.default.createElement(BaseDisplayComponent_1.default, { model: model },
-        react_1.default.createElement(Arcs, { model: model })));
+    return ((0, jsx_runtime_1.jsx)(BaseDisplayComponent_1.default, { model: model, children: (0, jsx_runtime_1.jsx)(Arcs, { model: model }) }));
 });
 exports.default = LinearReadArcsReactComponent;

package/dist/LinearReadArcsDisplay/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/LinearReadArcsDisplay/model.d.ts

@@ -112,7 +112,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     readonly statsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): React.JSX.Element | null;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
     loading: boolean;
     chainData: ChainData | undefined;

package/dist/LinearReadArcsDisplay/model.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/LinearReadCloudDisplay/components/ReactComponent.d.ts

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

package/dist/LinearReadCloudDisplay/components/ReactComponent.js

@@ -1,32 +1,10 @@
 "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;
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 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 util_1 = require("@jbrowse/core/util");
 const mobx_react_1 = require("mobx-react");
 const BaseDisplayComponent_1 = __importDefault(require("../../shared/components/BaseDisplayComponent"));
@@ -37,10 +15,9 @@ const Cloud = (0, mobx_react_1.observer)(function ({ model, }) {
     const cb = (0, react_1.useCallback)((ref) => {
         model.setRef(ref);
     }, [model, width, height]);
-    return (react_1.default.createElement("canvas", { "data-testid": "cloud-canvas", ref: cb, style: { width, height, position: 'absolute' }, width: width * 2, height: height * 2 }));
+    return ((0, jsx_runtime_1.jsx)("canvas", { "data-testid": "cloud-canvas", ref: cb, style: { width, height, position: 'absolute' }, width: width * 2, height: height * 2 }));
 });
 const LinearReadCloudReactComponent = (0, mobx_react_1.observer)(function ({ model, }) {
-    return (react_1.default.createElement(BaseDisplayComponent_1.default, { model: model },
-        react_1.default.createElement(Cloud, { model: model })));
+    return ((0, jsx_runtime_1.jsx)(BaseDisplayComponent_1.default, { model: model, children: (0, jsx_runtime_1.jsx)(Cloud, { model: model }) }));
 });
 exports.default = LinearReadCloudReactComponent;

package/dist/LinearReadCloudDisplay/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/LinearReadCloudDisplay/model.d.ts

@@ -109,7 +109,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     readonly statsReadyAndRegionNotTooLarge: boolean;
     regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
-    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): React.JSX.Element | null;
+    regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): import("react/jsx-runtime").JSX.Element | null;
 } & {
     loading: boolean;
     chainData: ChainData | undefined;

package/dist/LinearReadCloudDisplay/model.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/LinearSNPCoverageDisplay/components/Tooltip.d.ts

@@ -1,4 +1,3 @@
-import React from 'react';
 import type { Feature } from '@jbrowse/core/util';
 type Coord = [number, number];
 declare const SNPCoverageTooltip: (props: {
@@ -9,5 +8,5 @@ declare const SNPCoverageTooltip: (props: {
     offsetMouseCoord: Coord;
     clientMouseCoord: Coord;
     clientRect?: DOMRect;
-}) => React.JSX.Element | null;
+}) => import("react/jsx-runtime").JSX.Element | null;
 export default SNPCoverageTooltip;

package/dist/LinearSNPCoverageDisplay/components/Tooltip.js

@@ -1,9 +1,7 @@
 "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 react_1 = require("react");
 const util_1 = require("@jbrowse/core/util");
 const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
 const mobx_react_1 = require("mobx-react");
@@ -15,7 +13,7 @@ const useStyles = (0, mui_1.makeStyles)()(() => ({
 }));
 const toP = (s = 0) => +(+s).toFixed(1);
 const pct = (n, total = 1) => `${toP((n / (total || 1)) * 100)}%`;
-const TooltipContents = react_1.default.forwardRef(function TooltipContents2(props, reactRef) {
+const TooltipContents = (0, react_1.forwardRef)(function TooltipContents2(props, reactRef) {
     const { feature, model } = props;
     const { classes } = useStyles();
     const start = feature.get('start') + 1;
@@ -28,58 +26,21 @@ const TooltipContents = react_1.default.forwardRef(function TooltipContents2(pro
     ]
         .filter(f => !!f)
         .join(':');
-    return (react_1.default.createElement("div", { ref: reactRef },
-        react_1.default.createElement("table", null,
-            react_1.default.createElement("caption", null, loc),
-            react_1.default.createElement("thead", null,
-                react_1.default.createElement("tr", null,
-                    react_1.default.createElement("th", null),
-                    react_1.default.createElement("th", null, "Base"),
-                    react_1.default.createElement("th", null, "Count"),
-                    react_1.default.createElement("th", null, "% of Total"),
-                    react_1.default.createElement("th", null, "Strands"))),
-            react_1.default.createElement("tbody", null,
-                react_1.default.createElement("tr", null,
-                    react_1.default.createElement("td", null),
-                    react_1.default.createElement("td", null, "Total"),
-                    react_1.default.createElement("td", null, readsCounted),
-                    react_1.default.createElement("td", null, " "),
-                    react_1.default.createElement("td", null, " ")),
-                react_1.default.createElement("tr", null,
-                    react_1.default.createElement("td", null),
-                    react_1.default.createElement("td", null,
-                        "REF ",
-                        refbase ? `(${refbase.toUpperCase()})` : ''),
-                    react_1.default.createElement("td", null, ref.entryDepth),
-                    react_1.default.createElement("td", null, pct(ref.entryDepth, readsCounted)),
-                    react_1.default.createElement("td", null,
-                        ref['-1'] ? `${ref['-1']}(-)` : '',
-                        ref['1'] ? `${ref['1']}(+)` : '')),
-                Object.entries(info).map(([key, entry]) => Object.entries(entry).map(([base, score]) => (react_1.default.createElement("tr", { key: `${key}_${base}` },
-                    react_1.default.createElement("td", null,
-                        react_1.default.createElement(ColorSquare, { model: model, base: base })),
-                    react_1.default.createElement("td", null,
-                        base.toUpperCase(),
-                        " "),
-                    react_1.default.createElement("td", { className: classes.td }, [
-                        score.entryDepth,
-                        score.avgProbability !== undefined
-                            ? `(avg. ${pct(score.avgProbability)} prob.)`
-                            : '',
-                    ]
-                        .filter(f => !!f)
-                        .join(' ')),
-                    react_1.default.createElement("td", null, base === 'depth' || base === 'skip'
-                        ? '---'
-                        : pct(score.entryDepth, readsCounted)),
-                    react_1.default.createElement("td", null,
-                        score['-1'] ? `${score['-1']}(-)` : '',
-                        score['1'] ? `${score['1']}(+)` : '')))))))));
+    return ((0, jsx_runtime_1.jsx)("div", { ref: reactRef, children: (0, jsx_runtime_1.jsxs)("table", { children: [(0, jsx_runtime_1.jsx)("caption", { children: loc }), (0, jsx_runtime_1.jsx)("thead", { children: (0, jsx_runtime_1.jsxs)("tr", { children: [(0, jsx_runtime_1.jsx)("th", {}), (0, jsx_runtime_1.jsx)("th", { children: "Base" }), (0, jsx_runtime_1.jsx)("th", { children: "Count" }), (0, jsx_runtime_1.jsx)("th", { children: "% of Total" }), (0, jsx_runtime_1.jsx)("th", { children: "Strands" })] }) }), (0, jsx_runtime_1.jsxs)("tbody", { children: [(0, jsx_runtime_1.jsxs)("tr", { children: [(0, jsx_runtime_1.jsx)("td", {}), (0, jsx_runtime_1.jsx)("td", { children: "Total" }), (0, jsx_runtime_1.jsx)("td", { children: readsCounted }), (0, jsx_runtime_1.jsx)("td", { children: " " }), (0, jsx_runtime_1.jsx)("td", { children: " " })] }), (0, jsx_runtime_1.jsxs)("tr", { children: [(0, jsx_runtime_1.jsx)("td", {}), (0, jsx_runtime_1.jsxs)("td", { children: ["REF ", refbase ? `(${refbase.toUpperCase()})` : ''] }), (0, jsx_runtime_1.jsx)("td", { children: ref.entryDepth }), (0, jsx_runtime_1.jsx)("td", { children: pct(ref.entryDepth, readsCounted) }), (0, jsx_runtime_1.jsxs)("td", { children: [ref['-1'] ? `${ref['-1']}(-)` : '', ref['1'] ? `${ref['1']}(+)` : ''] })] }), Object.entries(info).map(([key, entry]) => Object.entries(entry).map(([base, score]) => ((0, jsx_runtime_1.jsxs)("tr", { children: [(0, jsx_runtime_1.jsx)("td", { children: (0, jsx_runtime_1.jsx)(ColorSquare, { model: model, base: base }) }), (0, jsx_runtime_1.jsxs)("td", { children: [base.toUpperCase(), " "] }), (0, jsx_runtime_1.jsx)("td", { className: classes.td, children: [
+                                        score.entryDepth,
+                                        score.avgProbability !== undefined
+                                            ? `(avg. ${pct(score.avgProbability)} prob.)`
+                                            : '',
+                                    ]
+                                        .filter(f => !!f)
+                                        .join(' ') }), (0, jsx_runtime_1.jsx)("td", { children: base === 'depth' || base === 'skip'
+                                        ? '---'
+                                        : pct(score.entryDepth, readsCounted) }), (0, jsx_runtime_1.jsxs)("td", { children: [score['-1'] ? `${score['-1']}(-)` : '', score['1'] ? `${score['1']}(+)` : ''] })] }, `${key}_${base}`))))] })] }) }));
 });
 function ColorSquare({ base, model, }) {
     var _a;
     const { visibleModifications } = model;
-    return base.startsWith('mod_') ? (react_1.default.createElement("div", { style: {
+    return base.startsWith('mod_') ? ((0, jsx_runtime_1.jsx)("div", { style: {
             width: 10,
             height: 10,
             background: (_a = visibleModifications.get(base.replace('mod_', ''))) === null || _a === void 0 ? void 0 : _a.color,
@@ -88,6 +49,6 @@ function ColorSquare({ base, model, }) {
 const SNPCoverageTooltip = (0, mobx_react_1.observer)(function (props) {
     const { model } = props;
     const { featureUnderMouse: feat } = model;
-    return feat && feat.get('type') === 'skip' ? null : (react_1.default.createElement(plugin_wiggle_1.Tooltip, { TooltipContents: TooltipContents, ...props }));
+    return feat && feat.get('type') === 'skip' ? null : ((0, jsx_runtime_1.jsx)(plugin_wiggle_1.Tooltip, { TooltipContents: TooltipContents, ...props }));
 });
 exports.default = SNPCoverageTooltip;

package/dist/LinearSNPCoverageDisplay/model.d.ts

@@ -36,7 +36,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
                 status?: string;
                 reactElement?: React.ReactElement;
             };
-        }) => import("react").JSX.Element | undefined;
+        }) => import("react/jsx-runtime").JSX.Element | undefined;
         renderProps: any;
     } & {
         doReload(): void;
@@ -99,9 +99,9 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     type: import("mobx-state-tree").ISimpleType<"LinearWiggleDisplay">;
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearSNPCoverageDisplay">;
-    drawInterbaseCounts: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    drawIndicators: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
-    drawArcs: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    showInterbaseCounts: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    showInterbaseIndicators: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
+    showArcs: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<boolean>>;
     filterBySetting: import("mobx-state-tree").IType<FilterBy | undefined, FilterBy | undefined, FilterBy | undefined>;
     colorBySetting: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
     jexlFilters: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IArrayType<import("mobx-state-tree").ISimpleType<string>>, [undefined]>;

package/dist/LinearSNPCoverageDisplay/model.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 };
 };
@@ -31,6 +41,7 @@ const configuration_1 = require("@jbrowse/core/configuration");
 const serializableFilterChain_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain"));
 const util_1 = require("@jbrowse/core/util");
 const plugin_wiggle_1 = require("@jbrowse/plugin-wiggle");
+const Visibility_1 = __importDefault(require("@mui/icons-material/Visibility"));
 const mobx_1 = require("mobx");
 const mobx_state_tree_1 = require("mobx-state-tree");
 const getUniqueModifications_1 = require("../shared/getUniqueModifications");
@@ -41,9 +52,9 @@ function stateModelFactory(pluginManager, configSchema) {
     return mobx_state_tree_1.types
         .compose('LinearSNPCoverageDisplay', (0, plugin_wiggle_1.linearWiggleDisplayModelFactory)(pluginManager, configSchema), mobx_state_tree_1.types.model({
         type: mobx_state_tree_1.types.literal('LinearSNPCoverageDisplay'),
-        drawInterbaseCounts: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-        drawIndicators: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
-        drawArcs: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
+        showInterbaseCounts: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
+        showInterbaseIndicators: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
+        showArcs: mobx_state_tree_1.types.maybe(mobx_state_tree_1.types.boolean),
         filterBySetting: mobx_state_tree_1.types.frozen(),
         colorBySetting: 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), []),
@@ -97,25 +108,25 @@ function stateModelFactory(pluginManager, configSchema) {
         return {
             get rendererConfig() {
                 const configBlob = (0, configuration_1.getConf)(self, ['renderers', self.rendererTypeName]) || {};
-                const { drawArcs, drawInterbaseCounts, drawIndicators } = self;
+                const { showArcs, showInterbaseCounts, showInterbaseIndicators } = self;
                 return self.rendererType.configSchema.create({
                     ...configBlob,
-                    drawInterbaseCounts: drawInterbaseCounts !== null && drawInterbaseCounts !== void 0 ? drawInterbaseCounts : configBlob.drawInterbaseCounts,
-                    drawIndicators: drawIndicators !== null && drawIndicators !== void 0 ? drawIndicators : configBlob.drawIndicators,
-                    drawArcs: drawArcs !== null && drawArcs !== void 0 ? drawArcs : configBlob.drawArcs,
+                    showInterbaseCounts: showInterbaseCounts !== null && showInterbaseCounts !== void 0 ? showInterbaseCounts : configBlob.showInterbaseCounts,
+                    showInterbaseIndicators: showInterbaseIndicators !== null && showInterbaseIndicators !== void 0 ? showInterbaseIndicators : configBlob.showInterbaseIndicators,
+                    showArcs: showArcs !== null && showArcs !== void 0 ? showArcs : configBlob.showArcs,
                 }, (0, mobx_state_tree_1.getEnv)(self));
             },
-            get drawArcsSetting() {
+            get showArcsSetting() {
                 var _a;
-                return ((_a = self.drawArcs) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'drawArcs'));
+                return ((_a = self.showArcs) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'showArcs'));
             },
-            get drawInterbaseCountsSetting() {
+            get showInterbaseCountsSetting() {
                 var _a;
-                return ((_a = self.drawInterbaseCounts) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'drawInterbaseCounts'));
+                return ((_a = self.showInterbaseCounts) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'showInterbaseCounts'));
             },
-            get drawIndicatorsSetting() {
+            get showInterbaseIndicatorsSetting() {
                 var _a;
-                return ((_a = self.drawIndicators) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'drawIndicators'));
+                return ((_a = self.showInterbaseIndicators) !== null && _a !== void 0 ? _a : (0, configuration_1.readConfObject)(this.rendererConfig, 'showInterbaseIndicators'));
             },
             get autorunReady() {
                 const view = (0, util_1.getContainingView)(self);
@@ -138,14 +149,14 @@ function stateModelFactory(pluginManager, configSchema) {
         setModificationsReady(flag) {
             self.modificationsReady = flag;
         },
-        toggleDrawIndicators() {
-            self.drawIndicators = !self.drawIndicatorsSetting;
+        setShowInterbaseIndicators(arg) {
+            self.showInterbaseIndicators = arg;
         },
-        toggleDrawInterbaseCounts() {
-            self.drawInterbaseCounts = !self.drawInterbaseCountsSetting;
+        setShowInterbaseCounts(arg) {
+            self.showInterbaseCounts = arg;
         },
-        toggleDrawArcs() {
-            self.drawArcs = !self.drawArcsSetting;
+        setShowArcs(arg) {
+            self.showArcs = arg;
         },
     }))
         .actions(self => ({
@@ -217,27 +228,30 @@ function stateModelFactory(pluginManager, configSchema) {
                 return [
                     ...superTrackMenuItems(),
                     {
-                        label: 'Draw insertion/clipping indicators',
+                        label: 'Show insertion/clipping indicators',
+                        icon: Visibility_1.default,
                         type: 'checkbox',
-                        checked: self.drawIndicatorsSetting,
+                        checked: self.showInterbaseIndicatorsSetting,
                         onClick: () => {
-                            self.toggleDrawIndicators();
+                            self.setShowInterbaseIndicators(!self.showInterbaseIndicatorsSetting);
                         },
                     },
                     {
-                        label: 'Draw insertion/clipping counts',
+                        label: 'Show insertion/clipping counts',
+                        icon: Visibility_1.default,
                         type: 'checkbox',
-                        checked: self.drawInterbaseCountsSetting,
+                        checked: self.showInterbaseCountsSetting,
                         onClick: () => {
-                            self.toggleDrawInterbaseCounts();
+                            self.setShowInterbaseCounts(self.showInterbaseCountsSetting);
                         },
                     },
                     {
-                        label: 'Draw arcs',
+                        label: 'Show arcs',
+                        icon: Visibility_1.default,
                         type: 'checkbox',
-                        checked: self.drawArcsSetting,
+                        checked: self.showArcsSetting,
                         onClick: () => {
-                            self.toggleDrawArcs();
+                            self.setShowArcs(self.showArcsSetting);
                         },
                     },
                 ];

package/dist/MismatchParser/cigarToMismatches.d.ts

@@ -1,3 +1,2 @@
 import type { Mismatch } from '../shared/types';
-import type { Buffer } from 'buffer';
-export declare function cigarToMismatches(ops: string[], seq?: string, ref?: string, qual?: Buffer): Mismatch[];
+export declare function cigarToMismatches(ops: string[], seq?: string, ref?: string, qual?: Uint8Array): Mismatch[];

package/dist/MismatchParser/index.d.ts

@@ -1,8 +1,7 @@
 import type { Mismatch } from '../shared/types';
 import type { Feature } from '@jbrowse/core/util';
-import type { Buffer } from 'buffer';
 export declare function parseCigar(cigar?: string): string[];
-export declare function getMismatches(cigar?: string, md?: string, seq?: string, ref?: string, qual?: Buffer): Mismatch[];
+export declare function getMismatches(cigar?: string, md?: string, seq?: string, ref?: string, qual?: Uint8Array): Mismatch[];
 export declare function getOrientedCigar(flip: boolean, cigar: string[]): string[];
 export declare function getOrientedMismatches(flip: boolean, cigar: string): Mismatch[];
 export declare function getLengthOnRef(cigar: string): number;

package/dist/MismatchParser/mdToMismatches.d.ts

@@ -1,3 +1,2 @@
 import type { Mismatch } from '../shared/types';
-import type { Buffer } from 'buffer';
-export declare function mdToMismatches(mdstring: string, ops: string[], cigarMismatches: Mismatch[], seq: string, qual?: Buffer | number[] | null): Mismatch[];
+export declare function mdToMismatches(mdstring: string, ops: string[], cigarMismatches: Mismatch[], seq: string, qual?: Uint8Array): Mismatch[];