@jbrowse/plugin-alignments 2.17.0 → 3.0.0

package/dist/LinearReadCloudDisplay/drawPairChains.js

@@ -13,9 +13,6 @@ function drawPairChains({ ctx, self, chainData, view, asm, }) {
     const type = ((_a = self.colorBy) === null || _a === void 0 ? void 0 : _a.type) || 'insertSizeAndOrientation';
     const { chains, stats } = chainData;
     for (const chain of chains) {
-        // if we're looking at a paired read (flag 1) then assume it is just
-        // two reads (some small cases may defy this assumption such as
-        // secondary alignments but this may be uncommon)
         if (chain.length > 1) {
             const v0 = chain[0];
             const v1 = chain[1];

package/dist/LinearReadCloudDisplay/index.d.ts

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

package/dist/LinearReadCloudDisplay/index.js

@@ -15,23 +15,32 @@ 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 };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = register;
+const react_1 = require("react");
 const DisplayType_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/DisplayType"));
-// locals
 const configSchema_1 = __importDefault(require("./configSchema"));
 const model_1 = __importDefault(require("./model"));
-const react_1 = require("react");
 function register(pluginManager) {
     pluginManager.addDisplayType(() => {
         const configSchema = (0, configSchema_1.default)(pluginManager);

package/dist/LinearReadCloudDisplay/model.d.ts

@@ -1,16 +1,8 @@
-import React from 'react';
-import { Instance } from 'mobx-state-tree';
-import { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
-import { ColorBy, FilterBy } from '../shared/types';
-import { ChainData } from '../shared/fetchChains';
-/**
- * #stateModel LinearReadCloudDisplay
- * it is not a block based track, hence not BaseLinearDisplay
- * extends
- * - [BaseDisplay](../basedisplay)
- * - [TrackHeightMixin](../trackheightmixin)
- * - [FeatureDensityMixin](../featuredensitymixin)
- */
+import type React from 'react';
+import type { ChainData } from '../shared/fetchChains';
+import type { ColorBy, FilterBy } from '../shared/types';
+import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
+import type { Instance } from 'mobx-state-tree';
 declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<string>;
@@ -23,8 +15,8 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     type: import("mobx-state-tree").ISimpleType<"LinearReadCloudDisplay">;
     configuration: AnyConfigurationSchemaType;
-    filterBy: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").IType<FilterBy, FilterBy, FilterBy>, [undefined]>;
-    colorBy: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
+    filterBySetting: import("mobx-state-tree").IType<FilterBy | undefined, FilterBy | undefined, FilterBy | undefined>;
+    colorBySetting: import("mobx-state-tree").IType<ColorBy | undefined, ColorBy | undefined, ColorBy | undefined>;
     drawSingletons: import("mobx-state-tree").IType<boolean | undefined, boolean, boolean>;
 }, {
     rendererTypeName: string;
@@ -62,20 +54,14 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
             error: unknown;
             message: string | undefined;
         } & import("mobx-state-tree").IStateTreeNode<import("mobx-state-tree").IModelType<{
-            id: import(
-            /**
-             * #action
-             */
-            "mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
+            id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
             type: import("mobx-state-tree").ISimpleType<string>;
             rpcDriverName: import("mobx-state-tree").IMaybe<import("mobx-state-tree").ISimpleType<string>>;
         }, {
             rendererTypeName: string;
             error: unknown;
             message: string | undefined;
-        }, import("mobx-state-tree" /**
-         * #action
-         */)._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
+        }, import("mobx-state-tree")._NotCustomized, import("mobx-state-tree")._NotCustomized>>;
     }> | null;
     readonly adapterConfig: any;
     readonly parentTrack: any;
@@ -121,8 +107,9 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly regionTooLarge: boolean;
     readonly regionTooLargeReason: string;
 } & {
+    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;
@@ -130,50 +117,24 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     lastDrawnBpPerPx: number;
     ref: HTMLCanvasElement | null;
 } & {
-    /**
-     * #action
-     */
+    readonly colorBy: any;
+    readonly filterBy: any;
+} & {
     setDrawSingletons(f: boolean): void;
-    /**
-     * #action
-     */
     setLastDrawnOffsetPx(n: number): void;
-    /**
-     * #action
-     */
     setLastDrawnBpPerPx(n: number): void;
-    /**
-     * #action
-     */
     setLoading(f: boolean): void;
-    /**
-     * #action
-     */
     reload(): void;
-    /**
-     * #action
-     * internal, a reference to a HTMLCanvas because we use a autorun to draw
-     * the canvas
-     */
     setRef(ref: HTMLCanvasElement | null): void;
     setColorScheme(colorBy: {
         type: string;
     }): void;
-    /**
-     * #action
-     */
     setChainData(args: ChainData): void;
-    /**
-     * #action
-     */
     setFilterBy(filter: FilterBy): void;
 } & {
     readonly drawn: boolean;
 } & {
     renderProps(): any;
-    /**
-     * #method
-     */
     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;
         type: string;
@@ -203,9 +164,6 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
         checked?: undefined;
         onClick?: undefined;
     })[];
-    /**
-     * #method
-     */
     renderSvg(opts: {
         rasterizeLayers?: boolean;
     }): Promise<React.ReactNode>;

package/dist/LinearReadCloudDisplay/model.js

@@ -15,59 +15,43 @@ 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 };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = require("react");
-const mobx_state_tree_1 = require("mobx-state-tree");
-const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
 const configuration_1 = require("@jbrowse/core/configuration");
+const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
 const util_1 = require("@jbrowse/core/util");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
-// icons
-const Palette_1 = __importDefault(require("@mui/icons-material/Palette"));
 const ClearAll_1 = __importDefault(require("@mui/icons-material/ClearAll"));
-const util_2 = require("../shared/util");
-// async
+const Palette_1 = __importDefault(require("@mui/icons-material/Palette"));
+const mobx_state_tree_1 = require("mobx-state-tree");
 const FilterByTagDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('../shared/components/FilterByTagDialog'))));
-/**
- * #stateModel LinearReadCloudDisplay
- * it is not a block based track, hence not BaseLinearDisplay
- * extends
- * - [BaseDisplay](../basedisplay)
- * - [TrackHeightMixin](../trackheightmixin)
- * - [FeatureDensityMixin](../featuredensitymixin)
- */
 function stateModelFactory(configSchema) {
     return mobx_state_tree_1.types
         .compose('LinearReadCloudDisplay', pluggableElementTypes_1.BaseDisplay, (0, plugin_linear_genome_view_1.TrackHeightMixin)(), (0, plugin_linear_genome_view_1.FeatureDensityMixin)(), mobx_state_tree_1.types.model({
-        /**
-         * #property
-         */
         type: mobx_state_tree_1.types.literal('LinearReadCloudDisplay'),
-        /**
-         * #property
-         */
         configuration: (0, configuration_1.ConfigurationReference)(configSchema),
-        /**
-         * #property
-         */
-        filterBy: mobx_state_tree_1.types.optional(mobx_state_tree_1.types.frozen(), util_2.defaultFilterFlags),
-        /**
-         * #property
-         */
-        colorBy: mobx_state_tree_1.types.frozen(),
-        /**
-         * #property
-         */
+        filterBySetting: mobx_state_tree_1.types.frozen(),
+        colorBySetting: mobx_state_tree_1.types.frozen(),
         drawSingletons: true,
     }))
         .volatile(() => ({
@@ -76,62 +60,46 @@ function stateModelFactory(configSchema) {
         lastDrawnOffsetPx: undefined,
         lastDrawnBpPerPx: 0,
         ref: null,
+    }))
+        .views(self => ({
+        get colorBy() {
+            var _a;
+            return (_a = self.colorBySetting) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'colorBy');
+        },
+        get filterBy() {
+            var _a;
+            return (_a = self.filterBySetting) !== null && _a !== void 0 ? _a : (0, configuration_1.getConf)(self, 'filterBy');
+        },
     }))
         .actions(self => ({
-        /**
-         * #action
-         */
         setDrawSingletons(f) {
             self.drawSingletons = f;
         },
-        /**
-         * #action
-         */
         setLastDrawnOffsetPx(n) {
             self.lastDrawnOffsetPx = n;
         },
-        /**
-         * #action
-         */
         setLastDrawnBpPerPx(n) {
             self.lastDrawnBpPerPx = n;
         },
-        /**
-         * #action
-         */
         setLoading(f) {
             self.loading = f;
         },
-        /**
-         * #action
-         */
         reload() {
             self.error = undefined;
         },
-        /**
-         * #action
-         * internal, a reference to a HTMLCanvas because we use a autorun to draw
-         * the canvas
-         */
         setRef(ref) {
             self.ref = ref;
         },
         setColorScheme(colorBy) {
-            self.colorBy = {
+            self.colorBySetting = {
                 ...colorBy,
             };
         },
-        /**
-         * #action
-         */
         setChainData(args) {
             self.chainData = args;
         },
-        /**
-         * #action
-         */
         setFilterBy(filter) {
-            self.filterBy = {
+            self.filterBySetting = {
                 ...filter,
             };
         },
@@ -144,17 +112,12 @@ function stateModelFactory(configSchema) {
         .views(self => {
         const { trackMenuItems: superTrackMenuItems, renderProps: superRenderProps, } = self;
         return {
-            // we don't use a server side renderer, so this fills in minimal
-            // info so as not to crash
             renderProps() {
                 return {
                     ...superRenderProps(),
                     notReady: !self.chainData,
                 };
             },
-            /**
-             * #method
-             */
             trackMenuItems() {
                 return [
                     ...superTrackMenuItems(),
@@ -208,9 +171,6 @@ function stateModelFactory(configSchema) {
                     },
                 ];
             },
-            /**
-             * #method
-             */
             async renderSvg(opts) {
                 const { renderSvg } = await Promise.resolve().then(() => __importStar(require('../shared/renderSvgUtil')));
                 const { drawFeats } = await Promise.resolve().then(() => __importStar(require('./drawFeats')));
@@ -220,7 +180,6 @@ function stateModelFactory(configSchema) {
     })
         .actions(self => ({
         afterAttach() {
-            // eslint-disable-next-line @typescript-eslint/no-floating-promises
             ;
             (async () => {
                 try {

package/dist/LinearReadCloudDisplay/util.js

@@ -2,7 +2,6 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.fillRectCtx = fillRectCtx;
 exports.strokeRectCtx = strokeRectCtx;
-// avoid drawing negative width features for SVG exports
 function fillRectCtx(x, y, width, height, ctx, fillColor) {
     if (width < 0) {
         x += width;

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

@@ -1,5 +1,4 @@
-import React from 'react';
-import { Feature } from '@jbrowse/core/util';
+import type { Feature } from '@jbrowse/core/util';
 type Coord = [number, number];
 declare const SNPCoverageTooltip: (props: {
     model: {
@@ -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

@@ -1,12 +1,10 @@
 "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 mobx_react_1 = require("mobx-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");
 const mui_1 = require("tss-react/mui");
 const useStyles = (0, mui_1.makeStyles)()(() => ({
     td: {
@@ -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/configSchema.d.ts

@@ -1,60 +1,55 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function SNPCoverageConfigFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
     autoscale: {
         type: string;
         defaultValue: string;
         model: import("mobx-state-tree").ISimpleType<string>;
         description: string;
     };
-    /**
-     * #slot
-     */
     minScore: {
         type: string;
         defaultValue: number;
         description: string;
     };
-    /**
-     * #slot
-     */
     maxScore: {
         type: string;
         description: string;
         defaultValue: number;
     };
-    /**
-     * #slot
-     */
     scaleType: {
         type: string;
         model: import("mobx-state-tree").ISimpleType<string>;
         description: string;
         defaultValue: string;
     };
-    /**
-     * #slot
-     */ inverted: {
+    inverted: {
         type: string;
         description: string;
         defaultValue: boolean;
     };
-    /**
-     * #slot
-     */
     multiTicks: {
         type: string;
         description: string;
         defaultValue: boolean;
     };
-    /**
-     * #slot
-     */
     renderers: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
         SNPCoverageRenderer: import("@jbrowse/core/configuration").AnyConfigurationSchemaType;
     }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
+    colorBy: {
+        type: string;
+        description: string;
+        defaultValue: {
+            type: string;
+        };
+    };
+    filterBy: {
+        type: string;
+        description: string;
+        defaultValue: {
+            flagInclude: number;
+            flagExclude: number;
+        };
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     maxFeatureScreenDensity: {
         type: string;