@jbrowse/plugin-alignments 3.4.0 → 3.5.1

package/dist/LinearAlignmentsDisplay/model.d.ts

@@ -91,6 +91,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     readonly DisplayBlurb: any;
     readonly sortedBy: any;
     readonly coverageConf: any;
+    notReady(): any;
 } & {
     setSNPCoverageDisplay(configuration: AnyConfigurationModel): void;
     setFeatureDensityStatsLimit(stats?: FeatureDensityStats): void;

package/dist/LinearAlignmentsDisplay/model.js

@@ -98,6 +98,10 @@ function stateModelFactory(pluginManager, configSchema) {
                 displayId: `${self.configuration.displayId}_snpcoverage_xyz`,
             };
         },
+        notReady() {
+            return (self.PileupDisplay.renderProps().notReady ||
+                self.SNPCoverageDisplay.renderProps().notReady);
+        },
     }))
         .actions(self => ({
         setSNPCoverageDisplay(configuration) {
@@ -163,8 +167,7 @@ function stateModelFactory(pluginManager, configSchema) {
         },
         async renderSvg(opts) {
             const pileupHeight = self.height - self.SNPCoverageDisplay.height;
-            await (0, mobx_1.when)(() => !self.PileupDisplay.renderProps().notReady &&
-                !self.SNPCoverageDisplay.renderProps().notReady);
+            await (0, mobx_1.when)(() => !self.notReady());
             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,

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts

@@ -1,5 +1,4 @@
 import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
-import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
 import type { ColorBy, FilterBy } from '../shared/types';
 import type { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import type { Feature } from '@jbrowse/core/util';
@@ -192,6 +191,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     readonly renderDelay: number;
     readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
     readonly selectedFeatureId: string | undefined;
+    copyInfoToClipboard(feature: Feature): void;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
     readonly featureUnderMouse: Feature | undefined;
@@ -201,7 +201,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: Feature): Promise<void>;
+    selectFeature(feature: Feature): void;
     navToFeature(feature: Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
@@ -234,12 +234,12 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     updateColorTagMap(uniqueTag: string[]): void;
     setFeatureUnderMouse(feat?: Feature): void;
     selectFeature(feature: Feature): void;
-    copyFeatureToClipboard(feature: Feature): void;
     setConfig(conf: AnyConfigurationModel): void;
     setFilterBy(filter: FilterBy): void;
     setJexlFilters(filters: string[]): void;
     setHideSmallIndels(arg: boolean): void;
 } & {
+    copyFeatureToClipboard(feature: Feature): void;
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -259,17 +259,13 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     readonly filters: SerializableFilterChain;
 } & {
     readonly rendererTypeName: string;
-    contextMenuItems(): ({
+    contextMenuItems(): {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
             muiName: string;
         };
         onClick: () => void;
-    } | {
-        label: string;
-        icon: typeof ContentCopyIcon;
-        onClick: () => void;
-    })[];
+    }[];
     readonly DisplayBlurb: ({ model, }: {
         model: {
             sortedBy?: import("../shared/types").SortedBy;

package/dist/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js

@@ -40,11 +40,11 @@ exports.SharedLinearPileupDisplayMixin = SharedLinearPileupDisplayMixin;
 const react_1 = require("react");
 const configuration_1 = require("@jbrowse/core/configuration");
 const serializableFilterChain_1 = __importDefault(require("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain"));
-const Icons_1 = require("@jbrowse/core/ui/Icons");
 const util_1 = require("@jbrowse/core/util");
 const tracks_1 = require("@jbrowse/core/util/tracks");
 const plugin_linear_genome_view_1 = require("@jbrowse/plugin-linear-genome-view");
 const ClearAll_1 = __importDefault(require("@mui/icons-material/ClearAll"));
+const ContentCopy_1 = __importDefault(require("@mui/icons-material/ContentCopy"));
 const MenuOpen_1 = __importDefault(require("@mui/icons-material/MenuOpen"));
 const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
 const mobx_1 = require("mobx");
@@ -154,12 +154,6 @@ function SharedLinearPileupDisplayMixin(configSchema) {
             }
             session.setSelection(feature);
         },
-        copyFeatureToClipboard(feature) {
-            const { uniqueId, ...rest } = feature.toJSON();
-            const session = (0, util_1.getSession)(self);
-            (0, copy_to_clipboard_1.default)(JSON.stringify(rest, null, 4));
-            session.notify('Copied to clipboard', 'success');
-        },
         setConfig(conf) {
             self.configuration = conf;
         },
@@ -176,6 +170,12 @@ function SharedLinearPileupDisplayMixin(configSchema) {
         },
     }))
         .views(self => ({
+        copyFeatureToClipboard(feature) {
+            const { uniqueId, ...rest } = feature.toJSON();
+            const session = (0, util_1.getSession)(self);
+            (0, copy_to_clipboard_1.default)(JSON.stringify(rest, null, 4));
+            session.notify('Copied to clipboard', 'success');
+        },
         get rendererConfig() {
             const { featureHeight: height, noSpacing, hideSmallIndels, trackMaxHeight: maxHeight, rendererTypeName, } = self;
             const configBlob = (0, configuration_1.getConf)(self, ['renderers', rendererTypeName]) || {};
@@ -225,14 +225,12 @@ function SharedLinearPileupDisplayMixin(configSchema) {
                             icon: MenuOpen_1.default,
                             onClick: () => {
                                 self.clearFeatureSelection();
-                                self.selectFeature(feat).catch((e) => {
-                                    (0, util_1.getSession)(self).notifyError(`${e}`, e);
-                                });
+                                self.selectFeature(feat);
                             },
                         },
                         {
                             label: 'Copy info to clipboard',
-                            icon: Icons_1.ContentCopy,
+                            icon: ContentCopy_1.default,
                             onClick: () => {
                                 self.copyFeatureToClipboard(feat);
                             },
@@ -273,7 +271,7 @@ function SharedLinearPileupDisplayMixin(configSchema) {
                                     rendererType: 'PileupRenderer',
                                 }));
                                 if ((0, mobx_state_tree_1.isAlive)(self) && feature) {
-                                    await self.selectFeature(new util_1.SimpleFeature(feature));
+                                    self.selectFeature(new util_1.SimpleFeature(feature));
                                 }
                             }
                         }

package/dist/LinearPileupDisplay/model.d.ts

@@ -196,6 +196,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly renderDelay: number;
     readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
     readonly selectedFeatureId: string | undefined;
+    copyInfoToClipboard(feature: import("@jbrowse/core/util").Feature): void;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
@@ -205,7 +206,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: import("@jbrowse/core/util").Feature): Promise<void>;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
@@ -238,12 +239,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     updateColorTagMap(uniqueTag: string[]): void;
     setFeatureUnderMouse(feat?: import("@jbrowse/core/util").Feature): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
-    copyFeatureToClipboard(feature: import("@jbrowse/core/util").Feature): void;
     setConfig(conf: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
     setFilterBy(filter: import("../shared/types").FilterBy): void;
     setJexlFilters(filters: string[]): void;
     setHideSmallIndels(arg: boolean): void;
 } & {
+    copyFeatureToClipboard(feature: import("@jbrowse/core/util").Feature): void;
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -263,17 +264,13 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly filters: import("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain").default;
 } & {
     readonly rendererTypeName: string;
-    contextMenuItems(): ({
+    contextMenuItems(): {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
             muiName: string;
         };
         onClick: () => void;
-    } | {
-        label: string;
-        icon: typeof import("@jbrowse/core/ui/Icons").ContentCopy;
-        onClick: () => void;
-    })[];
+    }[];
     readonly DisplayBlurb: ({ model, }: {
         model: {
             sortedBy?: SortedBy;

package/dist/LinearSNPCoverageDisplay/components/Tooltip.js

@@ -1,54 +1,15 @@
 "use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 const jsx_runtime_1 = require("react/jsx-runtime");
-const react_1 = require("react");
-const 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: {
-        whiteSpace: 'nowrap',
-    },
-}));
-const toP = (s = 0) => +(+s).toFixed(1);
-const pct = (n, total = 1) => `${toP((n / (total || 1)) * 100)}%`;
-const TooltipContents = (0, react_1.forwardRef)(function TooltipContents2(props, reactRef) {
-    const { feature, model } = props;
-    const { classes } = useStyles();
-    const start = feature.get('start') + 1;
-    const end = feature.get('end');
-    const name = feature.get('refName');
-    const { refbase, readsCounted, depth, ref, ...info } = feature.get('snpinfo');
-    const loc = [
-        name,
-        start === end ? (0, util_1.toLocale)(start) : `${(0, util_1.toLocale)(start)}..${(0, util_1.toLocale)(end)}`,
-    ]
-        .filter(f => !!f)
-        .join(':');
-    return ((0, jsx_runtime_1.jsx)("div", { ref: reactRef, children: (0, jsx_runtime_1.jsxs)("table", { children: [(0, jsx_runtime_1.jsx)("caption", { children: loc }), (0, jsx_runtime_1.jsx)("thead", { children: (0, jsx_runtime_1.jsxs)("tr", { children: [(0, jsx_runtime_1.jsx)("th", {}), (0, jsx_runtime_1.jsx)("th", { children: "Base" }), (0, jsx_runtime_1.jsx)("th", { children: "Count" }), (0, jsx_runtime_1.jsx)("th", { children: "% of Total" }), (0, jsx_runtime_1.jsx)("th", { children: "Strands" })] }) }), (0, jsx_runtime_1.jsxs)("tbody", { children: [(0, jsx_runtime_1.jsxs)("tr", { children: [(0, jsx_runtime_1.jsx)("td", {}), (0, jsx_runtime_1.jsx)("td", { children: "Total" }), (0, jsx_runtime_1.jsx)("td", { children: readsCounted }), (0, jsx_runtime_1.jsx)("td", { children: " " }), (0, jsx_runtime_1.jsx)("td", { children: " " })] }), (0, jsx_runtime_1.jsxs)("tr", { children: [(0, jsx_runtime_1.jsx)("td", {}), (0, jsx_runtime_1.jsxs)("td", { children: ["REF ", refbase ? `(${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_') ? ((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,
-        } })) : null;
-}
+const TooltipContents_1 = __importDefault(require("./TooltipContents"));
 const SNPCoverageTooltip = (0, mobx_react_1.observer)(function (props) {
     const { model } = props;
     const { featureUnderMouse: feat } = model;
-    return feat && feat.get('type') === 'skip' ? null : ((0, jsx_runtime_1.jsx)(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_1.default, ...props }));
 });
 exports.default = SNPCoverageTooltip;

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

@@ -0,0 +1,11 @@
+import type { Feature } from '@jbrowse/core/util';
+interface Props {
+    feature: Feature;
+    model: {
+        visibleModifications: Map<string, {
+            color: string;
+        }>;
+    };
+}
+declare const TooltipContents: import("react").ForwardRefExoticComponent<Props & import("react").RefAttributes<HTMLDivElement>>;
+export default TooltipContents;

package/dist/LinearSNPCoverageDisplay/components/TooltipContents.js

@@ -0,0 +1,48 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
+const util_1 = require("@jbrowse/core/util");
+const mui_1 = require("tss-react/mui");
+const useStyles = (0, mui_1.makeStyles)()(() => ({
+    td: {
+        whiteSpace: 'nowrap',
+    },
+}));
+const toP = (s = 0) => +(+s).toFixed(1);
+const pct = (n, total = 1) => `${toP((n / (total || 1)) * 100)}%`;
+function ColorSquare({ base, model, }) {
+    var _a;
+    const { visibleModifications } = model;
+    return base.startsWith('mod_') ? ((0, jsx_runtime_1.jsx)("div", { style: {
+            width: 10,
+            height: 10,
+            background: (_a = visibleModifications.get(base.replace('mod_', ''))) === null || _a === void 0 ? void 0 : _a.color,
+        } })) : null;
+}
+const TooltipContents = (0, react_1.forwardRef)(function TooltipContents2(props, reactRef) {
+    const { feature, model } = props;
+    const { classes } = useStyles();
+    const start = feature.get('start') + 1;
+    const end = feature.get('end');
+    const name = feature.get('refName');
+    const { refbase, readsCounted, depth, ref, ...info } = feature.get('snpinfo');
+    return ((0, jsx_runtime_1.jsx)("div", { ref: reactRef, children: (0, jsx_runtime_1.jsxs)("table", { children: [(0, jsx_runtime_1.jsx)("caption", { children: [
+                        name,
+                        start === end
+                            ? (0, util_1.toLocale)(start)
+                            : `${(0, util_1.toLocale)(start)}..${(0, util_1.toLocale)(end)}`,
+                    ]
+                        .filter(f => !!f)
+                        .join(':') }), (0, jsx_runtime_1.jsx)("thead", { children: (0, jsx_runtime_1.jsxs)("tr", { children: [(0, jsx_runtime_1.jsx)("th", {}), (0, jsx_runtime_1.jsx)("th", { children: "Base" }), (0, jsx_runtime_1.jsx)("th", { children: "Count" }), (0, jsx_runtime_1.jsx)("th", { children: "% of Total" }), (0, jsx_runtime_1.jsx)("th", { children: "Strands" })] }) }), (0, jsx_runtime_1.jsxs)("tbody", { children: [(0, jsx_runtime_1.jsxs)("tr", { children: [(0, jsx_runtime_1.jsx)("td", {}), (0, jsx_runtime_1.jsx)("td", { children: "Total" }), (0, jsx_runtime_1.jsx)("td", { children: readsCounted }), (0, jsx_runtime_1.jsx)("td", { children: " " }), (0, jsx_runtime_1.jsx)("td", { children: " " })] }), (0, jsx_runtime_1.jsxs)("tr", { children: [(0, jsx_runtime_1.jsx)("td", {}), (0, jsx_runtime_1.jsxs)("td", { children: ["REF ", refbase ? `(${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}`))))] })] }) }));
+});
+exports.default = TooltipContents;

package/dist/LinearSNPCoverageDisplay/model.js

@@ -189,18 +189,15 @@ function stateModelFactory(pluginManager, configSchema) {
         .views(self => {
         const { renderProps: superRenderProps, trackMenuItems: superTrackMenuItems, } = self;
         return {
-            get renderReady() {
+            renderReady() {
                 const superProps = superRenderProps();
                 return !superProps.notReady && self.modificationsReady;
             },
-            get ready() {
-                return this.renderReady;
-            },
             renderProps() {
                 const { colorBy, visibleModifications } = self;
                 return {
                     ...superRenderProps(),
-                    notReady: !this.ready,
+                    notReady: !this.renderReady(),
                     colorBy,
                     visibleModifications: Object.fromEntries(visibleModifications.toJSON()),
                 };

package/dist/MismatchParser/index.d.ts

@@ -1,6 +1,6 @@
 import type { Mismatch } from '../shared/types';
 import type { Feature } from '@jbrowse/core/util';
-export declare function parseCigar(cigar?: string): string[];
+export declare function parseCigar(s?: string): string[];
 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[];

package/dist/MismatchParser/index.js

@@ -13,11 +13,26 @@ exports.getTag = getTag;
 exports.featurizeSA = featurizeSA;
 const cigarToMismatches_1 = require("./cigarToMismatches");
 const mdToMismatches_1 = require("./mdToMismatches");
-const cigarRegex = new RegExp(/([MIDNSHPX=])/);
 const startClip = new RegExp(/(\d+)[SH]$/);
 const endClip = new RegExp(/^(\d+)([SH])/);
-function parseCigar(cigar = '') {
-    return cigar.split(cigarRegex).slice(0, -1);
+function parseCigar(s = '') {
+    let currLen = '';
+    let len;
+    let op;
+    const ret = [];
+    for (let i = 0, l = s.length; i < l; i++) {
+        const c = s[i];
+        if (c >= '0' && c <= '9') {
+            currLen = currLen + c;
+        }
+        else {
+            len = currLen;
+            op = c;
+            currLen = '';
+            ret.push(len, op);
+        }
+    }
+    return ret;
 }
 function getMismatches(cigar, md, seq, ref, qual) {
     let mismatches = [];

package/dist/shared/fetchChains.js

@@ -2,8 +2,9 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.fetchChains = fetchChains;
 const util_1 = require("@jbrowse/core/util");
+const tracks_1 = require("@jbrowse/core/util/tracks");
 async function fetchChains(self) {
-    const { rpcSessionId: sessionId } = (0, util_1.getContainingTrack)(self);
+    const sessionId = (0, tracks_1.getRpcSessionId)(self);
     const { rpcManager } = (0, util_1.getSession)(self);
     const view = (0, util_1.getContainingView)(self);
     if (!view.initialized || self.error || !self.statsReadyAndRegionNotTooLarge) {

package/esm/LinearAlignmentsDisplay/model.d.ts

@@ -91,6 +91,7 @@ declare function stateModelFactory(pluginManager: PluginManager, configSchema: A
     readonly DisplayBlurb: any;
     readonly sortedBy: any;
     readonly coverageConf: any;
+    notReady(): any;
 } & {
     setSNPCoverageDisplay(configuration: AnyConfigurationModel): void;
     setFeatureDensityStatsLimit(stats?: FeatureDensityStats): void;

package/esm/LinearAlignmentsDisplay/model.js

@@ -93,6 +93,10 @@ function stateModelFactory(pluginManager, configSchema) {
                 displayId: `${self.configuration.displayId}_snpcoverage_xyz`,
             };
         },
+        notReady() {
+            return (self.PileupDisplay.renderProps().notReady ||
+                self.SNPCoverageDisplay.renderProps().notReady);
+        },
     }))
         .actions(self => ({
         setSNPCoverageDisplay(configuration) {
@@ -158,8 +162,7 @@ function stateModelFactory(pluginManager, configSchema) {
         },
         async renderSvg(opts) {
             const pileupHeight = self.height - self.SNPCoverageDisplay.height;
-            await when(() => !self.PileupDisplay.renderProps().notReady &&
-                !self.SNPCoverageDisplay.renderProps().notReady);
+            await when(() => !self.notReady());
             return (_jsxs(_Fragment, { children: [_jsx("g", { children: await self.SNPCoverageDisplay.renderSvg(opts) }), _jsx("g", { transform: `translate(0 ${self.SNPCoverageDisplay.height})`, children: await self.PileupDisplay.renderSvg({
                             ...opts,
                             overrideHeight: pileupHeight,

package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.d.ts

@@ -1,5 +1,4 @@
 import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
-import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
 import type { ColorBy, FilterBy } from '../shared/types';
 import type { AnyConfigurationModel, AnyConfigurationSchemaType } from '@jbrowse/core/configuration';
 import type { Feature } from '@jbrowse/core/util';
@@ -192,6 +191,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     readonly renderDelay: number;
     readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
     readonly selectedFeatureId: string | undefined;
+    copyInfoToClipboard(feature: Feature): void;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, Feature>;
     readonly featureUnderMouse: Feature | undefined;
@@ -201,7 +201,7 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: Feature): Promise<void>;
+    selectFeature(feature: Feature): void;
     navToFeature(feature: Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
@@ -234,12 +234,12 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     updateColorTagMap(uniqueTag: string[]): void;
     setFeatureUnderMouse(feat?: Feature): void;
     selectFeature(feature: Feature): void;
-    copyFeatureToClipboard(feature: Feature): void;
     setConfig(conf: AnyConfigurationModel): void;
     setFilterBy(filter: FilterBy): void;
     setJexlFilters(filters: string[]): void;
     setHideSmallIndels(arg: boolean): void;
 } & {
+    copyFeatureToClipboard(feature: Feature): void;
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -259,17 +259,13 @@ export declare function SharedLinearPileupDisplayMixin(configSchema: AnyConfigur
     readonly filters: SerializableFilterChain;
 } & {
     readonly rendererTypeName: string;
-    contextMenuItems(): ({
+    contextMenuItems(): {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
             muiName: string;
         };
         onClick: () => void;
-    } | {
-        label: string;
-        icon: typeof ContentCopyIcon;
-        onClick: () => void;
-    })[];
+    }[];
     readonly DisplayBlurb: ({ model, }: {
         model: {
             sortedBy?: import("../shared/types").SortedBy;

package/esm/LinearPileupDisplay/SharedLinearPileupDisplayMixin.js

@@ -1,11 +1,11 @@
 import { lazy } from 'react';
 import { ConfigurationReference, getConf, readConfObject, } from '@jbrowse/core/configuration';
 import SerializableFilterChain from '@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain';
-import { ContentCopy as ContentCopyIcon } from '@jbrowse/core/ui/Icons';
 import { SimpleFeature, getContainingTrack, getContainingView, getEnv, getSession, isSessionModelWithWidgets, } from '@jbrowse/core/util';
 import { getRpcSessionId } from '@jbrowse/core/util/tracks';
 import { BaseLinearDisplay } from '@jbrowse/plugin-linear-genome-view';
 import FilterListIcon from '@mui/icons-material/ClearAll';
+import ContentCopyIcon from '@mui/icons-material/ContentCopy';
 import MenuOpenIcon from '@mui/icons-material/MenuOpen';
 import copy from 'copy-to-clipboard';
 import { autorun, observable } from 'mobx';
@@ -115,12 +115,6 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
             }
             session.setSelection(feature);
         },
-        copyFeatureToClipboard(feature) {
-            const { uniqueId, ...rest } = feature.toJSON();
-            const session = getSession(self);
-            copy(JSON.stringify(rest, null, 4));
-            session.notify('Copied to clipboard', 'success');
-        },
         setConfig(conf) {
             self.configuration = conf;
         },
@@ -137,6 +131,12 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
         },
     }))
         .views(self => ({
+        copyFeatureToClipboard(feature) {
+            const { uniqueId, ...rest } = feature.toJSON();
+            const session = getSession(self);
+            copy(JSON.stringify(rest, null, 4));
+            session.notify('Copied to clipboard', 'success');
+        },
         get rendererConfig() {
             const { featureHeight: height, noSpacing, hideSmallIndels, trackMaxHeight: maxHeight, rendererTypeName, } = self;
             const configBlob = getConf(self, ['renderers', rendererTypeName]) || {};
@@ -186,9 +186,7 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
                             icon: MenuOpenIcon,
                             onClick: () => {
                                 self.clearFeatureSelection();
-                                self.selectFeature(feat).catch((e) => {
-                                    getSession(self).notifyError(`${e}`, e);
-                                });
+                                self.selectFeature(feat);
                             },
                         },
                         {
@@ -234,7 +232,7 @@ export function SharedLinearPileupDisplayMixin(configSchema) {
                                     rendererType: 'PileupRenderer',
                                 }));
                                 if (isAlive(self) && feature) {
-                                    await self.selectFeature(new SimpleFeature(feature));
+                                    self.selectFeature(new SimpleFeature(feature));
                                 }
                             }
                         }

package/esm/LinearPileupDisplay/model.d.ts

@@ -196,6 +196,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly renderDelay: number;
     readonly TooltipComponent: import("@jbrowse/core/util").AnyReactComponentType;
     readonly selectedFeatureId: string | undefined;
+    copyInfoToClipboard(feature: import("@jbrowse/core/util").Feature): void;
 } & {
     readonly features: import("@jbrowse/core/util/compositeMap").default<string, import("@jbrowse/core/util").Feature>;
     readonly featureUnderMouse: import("@jbrowse/core/util").Feature | undefined;
@@ -205,7 +206,7 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
 } & {
     addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
     deleteBlock(key: string): void;
-    selectFeature(feature: import("@jbrowse/core/util").Feature): Promise<void>;
+    selectFeature(feature: import("@jbrowse/core/util").Feature): void;
     navToFeature(feature: import("@jbrowse/core/util").Feature): void;
     clearFeatureSelection(): void;
     setFeatureIdUnderMouse(feature?: string): void;
@@ -238,12 +239,12 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     updateColorTagMap(uniqueTag: string[]): void;
     setFeatureUnderMouse(feat?: import("@jbrowse/core/util").Feature): void;
     selectFeature(feature: import("@jbrowse/core/util").Feature): void;
-    copyFeatureToClipboard(feature: import("@jbrowse/core/util").Feature): void;
     setConfig(conf: import("@jbrowse/core/configuration").AnyConfigurationModel): void;
     setFilterBy(filter: import("../shared/types").FilterBy): void;
     setJexlFilters(filters: string[]): void;
     setHideSmallIndels(arg: boolean): void;
 } & {
+    copyFeatureToClipboard(feature: import("@jbrowse/core/util").Feature): void;
     readonly rendererConfig: {
         [x: string]: any;
     } & import("mobx-state-tree/dist/internal").NonEmptyObject & {
@@ -263,17 +264,13 @@ declare function stateModelFactory(configSchema: AnyConfigurationSchemaType): im
     readonly filters: import("@jbrowse/core/pluggableElementTypes/renderers/util/serializableFilterChain").default;
 } & {
     readonly rendererTypeName: string;
-    contextMenuItems(): ({
+    contextMenuItems(): {
         label: string;
         icon: import("@mui/material/OverridableComponent").OverridableComponent<import("@mui/material").SvgIconTypeMap<{}, "svg">> & {
             muiName: string;
         };
         onClick: () => void;
-    } | {
-        label: string;
-        icon: typeof import("@jbrowse/core/ui/Icons").ContentCopy;
-        onClick: () => void;
-    })[];
+    }[];
     readonly DisplayBlurb: ({ model, }: {
         model: {
             sortedBy?: SortedBy;

package/esm/LinearSNPCoverageDisplay/components/Tooltip.js

@@ -1,49 +1,7 @@
-import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
-import { forwardRef } from 'react';
-import { toLocale } from '@jbrowse/core/util';
+import { jsx as _jsx } from "react/jsx-runtime";
 import { Tooltip } from '@jbrowse/plugin-wiggle';
 import { observer } from 'mobx-react';
-import { makeStyles } from 'tss-react/mui';
-const useStyles = makeStyles()(() => ({
-    td: {
-        whiteSpace: 'nowrap',
-    },
-}));
-const toP = (s = 0) => +(+s).toFixed(1);
-const pct = (n, total = 1) => `${toP((n / (total || 1)) * 100)}%`;
-const TooltipContents = forwardRef(function TooltipContents2(props, reactRef) {
-    const { feature, model } = props;
-    const { classes } = useStyles();
-    const start = feature.get('start') + 1;
-    const end = feature.get('end');
-    const name = feature.get('refName');
-    const { refbase, readsCounted, depth, ref, ...info } = feature.get('snpinfo');
-    const loc = [
-        name,
-        start === end ? toLocale(start) : `${toLocale(start)}..${toLocale(end)}`,
-    ]
-        .filter(f => !!f)
-        .join(':');
-    return (_jsx("div", { ref: reactRef, children: _jsxs("table", { children: [_jsx("caption", { children: loc }), _jsx("thead", { children: _jsxs("tr", { children: [_jsx("th", {}), _jsx("th", { children: "Base" }), _jsx("th", { children: "Count" }), _jsx("th", { children: "% of Total" }), _jsx("th", { children: "Strands" })] }) }), _jsxs("tbody", { children: [_jsxs("tr", { children: [_jsx("td", {}), _jsx("td", { children: "Total" }), _jsx("td", { children: readsCounted }), _jsx("td", { children: " " }), _jsx("td", { children: " " })] }), _jsxs("tr", { children: [_jsx("td", {}), _jsxs("td", { children: ["REF ", refbase ? `(${refbase.toUpperCase()})` : ''] }), _jsx("td", { children: ref.entryDepth }), _jsx("td", { children: pct(ref.entryDepth, readsCounted) }), _jsxs("td", { children: [ref['-1'] ? `${ref['-1']}(-)` : '', ref['1'] ? `${ref['1']}(+)` : ''] })] }), Object.entries(info).map(([key, entry]) => Object.entries(entry).map(([base, score]) => (_jsxs("tr", { children: [_jsx("td", { children: _jsx(ColorSquare, { model: model, base: base }) }), _jsxs("td", { children: [base.toUpperCase(), " "] }), _jsx("td", { className: classes.td, children: [
-                                        score.entryDepth,
-                                        score.avgProbability !== undefined
-                                            ? `(avg. ${pct(score.avgProbability)} prob.)`
-                                            : '',
-                                    ]
-                                        .filter(f => !!f)
-                                        .join(' ') }), _jsx("td", { children: base === 'depth' || base === 'skip'
-                                        ? '---'
-                                        : pct(score.entryDepth, readsCounted) }), _jsxs("td", { children: [score['-1'] ? `${score['-1']}(-)` : '', score['1'] ? `${score['1']}(+)` : ''] })] }, `${key}_${base}`))))] })] }) }));
-});
-function ColorSquare({ base, model, }) {
-    var _a;
-    const { visibleModifications } = model;
-    return base.startsWith('mod_') ? (_jsx("div", { style: {
-            width: 10,
-            height: 10,
-            background: (_a = visibleModifications.get(base.replace('mod_', ''))) === null || _a === void 0 ? void 0 : _a.color,
-        } })) : null;
-}
+import TooltipContents from './TooltipContents';
 const SNPCoverageTooltip = observer(function (props) {
     const { model } = props;
     const { featureUnderMouse: feat } = model;

package/esm/LinearSNPCoverageDisplay/components/TooltipContents.d.ts

@@ -0,0 +1,11 @@
+import type { Feature } from '@jbrowse/core/util';
+interface Props {
+    feature: Feature;
+    model: {
+        visibleModifications: Map<string, {
+            color: string;
+        }>;
+    };
+}
+declare const TooltipContents: import("react").ForwardRefExoticComponent<Props & import("react").RefAttributes<HTMLDivElement>>;
+export default TooltipContents;

package/esm/LinearSNPCoverageDisplay/components/TooltipContents.js

@@ -0,0 +1,46 @@
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { forwardRef } from 'react';
+import { toLocale } from '@jbrowse/core/util';
+import { makeStyles } from 'tss-react/mui';
+const useStyles = makeStyles()(() => ({
+    td: {
+        whiteSpace: 'nowrap',
+    },
+}));
+const toP = (s = 0) => +(+s).toFixed(1);
+const pct = (n, total = 1) => `${toP((n / (total || 1)) * 100)}%`;
+function ColorSquare({ base, model, }) {
+    var _a;
+    const { visibleModifications } = model;
+    return base.startsWith('mod_') ? (_jsx("div", { style: {
+            width: 10,
+            height: 10,
+            background: (_a = visibleModifications.get(base.replace('mod_', ''))) === null || _a === void 0 ? void 0 : _a.color,
+        } })) : null;
+}
+const TooltipContents = forwardRef(function TooltipContents2(props, reactRef) {
+    const { feature, model } = props;
+    const { classes } = useStyles();
+    const start = feature.get('start') + 1;
+    const end = feature.get('end');
+    const name = feature.get('refName');
+    const { refbase, readsCounted, depth, ref, ...info } = feature.get('snpinfo');
+    return (_jsx("div", { ref: reactRef, children: _jsxs("table", { children: [_jsx("caption", { children: [
+                        name,
+                        start === end
+                            ? toLocale(start)
+                            : `${toLocale(start)}..${toLocale(end)}`,
+                    ]
+                        .filter(f => !!f)
+                        .join(':') }), _jsx("thead", { children: _jsxs("tr", { children: [_jsx("th", {}), _jsx("th", { children: "Base" }), _jsx("th", { children: "Count" }), _jsx("th", { children: "% of Total" }), _jsx("th", { children: "Strands" })] }) }), _jsxs("tbody", { children: [_jsxs("tr", { children: [_jsx("td", {}), _jsx("td", { children: "Total" }), _jsx("td", { children: readsCounted }), _jsx("td", { children: " " }), _jsx("td", { children: " " })] }), _jsxs("tr", { children: [_jsx("td", {}), _jsxs("td", { children: ["REF ", refbase ? `(${refbase.toUpperCase()})` : ''] }), _jsx("td", { children: ref.entryDepth }), _jsx("td", { children: pct(ref.entryDepth, readsCounted) }), _jsxs("td", { children: [ref['-1'] ? `${ref['-1']}(-)` : '', ref['1'] ? `${ref['1']}(+)` : ''] })] }), Object.entries(info).map(([key, entry]) => Object.entries(entry).map(([base, score]) => (_jsxs("tr", { children: [_jsx("td", { children: _jsx(ColorSquare, { model: model, base: base }) }), _jsxs("td", { children: [base.toUpperCase(), " "] }), _jsx("td", { className: classes.td, children: [
+                                        score.entryDepth,
+                                        score.avgProbability !== undefined
+                                            ? `(avg. ${pct(score.avgProbability)} prob.)`
+                                            : '',
+                                    ]
+                                        .filter(f => !!f)
+                                        .join(' ') }), _jsx("td", { children: base === 'depth' || base === 'skip'
+                                        ? '---'
+                                        : pct(score.entryDepth, readsCounted) }), _jsxs("td", { children: [score['-1'] ? `${score['-1']}(-)` : '', score['1'] ? `${score['1']}(+)` : ''] })] }, `${key}_${base}`))))] })] }) }));
+});
+export default TooltipContents;

package/esm/LinearSNPCoverageDisplay/model.js

@@ -151,18 +151,15 @@ function stateModelFactory(pluginManager, configSchema) {
         .views(self => {
         const { renderProps: superRenderProps, trackMenuItems: superTrackMenuItems, } = self;
         return {
-            get renderReady() {
+            renderReady() {
                 const superProps = superRenderProps();
                 return !superProps.notReady && self.modificationsReady;
             },
-            get ready() {
-                return this.renderReady;
-            },
             renderProps() {
                 const { colorBy, visibleModifications } = self;
                 return {
                     ...superRenderProps(),
-                    notReady: !this.ready,
+                    notReady: !this.renderReady(),
                     colorBy,
                     visibleModifications: Object.fromEntries(visibleModifications.toJSON()),
                 };

package/esm/MismatchParser/index.d.ts

@@ -1,6 +1,6 @@
 import type { Mismatch } from '../shared/types';
 import type { Feature } from '@jbrowse/core/util';
-export declare function parseCigar(cigar?: string): string[];
+export declare function parseCigar(s?: string): string[];
 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[];

package/esm/MismatchParser/index.js

@@ -1,10 +1,25 @@
 import { cigarToMismatches } from './cigarToMismatches';
 import { mdToMismatches } from './mdToMismatches';
-const cigarRegex = new RegExp(/([MIDNSHPX=])/);
 const startClip = new RegExp(/(\d+)[SH]$/);
 const endClip = new RegExp(/^(\d+)([SH])/);
-export function parseCigar(cigar = '') {
-    return cigar.split(cigarRegex).slice(0, -1);
+export function parseCigar(s = '') {
+    let currLen = '';
+    let len;
+    let op;
+    const ret = [];
+    for (let i = 0, l = s.length; i < l; i++) {
+        const c = s[i];
+        if (c >= '0' && c <= '9') {
+            currLen = currLen + c;
+        }
+        else {
+            len = currLen;
+            op = c;
+            currLen = '';
+            ret.push(len, op);
+        }
+    }
+    return ret;
 }
 export function getMismatches(cigar, md, seq, ref, qual) {
     let mismatches = [];

package/esm/shared/fetchChains.js

@@ -1,6 +1,7 @@
-import { getContainingTrack, getContainingView, getSession, } from '@jbrowse/core/util';
+import { getContainingView, getSession } from '@jbrowse/core/util';
+import { getRpcSessionId } from '@jbrowse/core/util/tracks';
 export async function fetchChains(self) {
-    const { rpcSessionId: sessionId } = getContainingTrack(self);
+    const sessionId = getRpcSessionId(self);
     const { rpcManager } = getSession(self);
     const view = getContainingView(self);
     if (!view.initialized || self.error || !self.statsReadyAndRegionNotTooLarge) {

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-alignments",
-  "version": "3.4.0",
+  "version": "3.5.1",
   "description": "JBrowse 2 alignments adapters, tracks, etc.",
   "keywords": [
     "jbrowse",
@@ -38,10 +38,10 @@
   "dependencies": {
     "@gmod/bam": "^6.0.1",
     "@gmod/cram": "^5.0.4",
-    "@jbrowse/core": "^3.4.0",
-    "@jbrowse/plugin-linear-genome-view": "^3.4.0",
-    "@jbrowse/plugin-wiggle": "^3.4.0",
-    "@jbrowse/sv-core": "^3.4.0",
+    "@jbrowse/core": "^3.5.1",
+    "@jbrowse/plugin-linear-genome-view": "^3.5.1",
+    "@jbrowse/plugin-wiggle": "^3.5.1",
+    "@jbrowse/sv-core": "^3.5.1",
     "@mui/icons-material": "^7.0.0",
     "@mui/material": "^7.0.0",
     "canvas2svg": "^1.0.16",
@@ -63,5 +63,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "a9f1ac35fc2dd810bae92cdaf1fc19995bee4413"
+  "gitHead": "cb8859da9d838ad2594964777c5c54f385d98f5e"
 }