@jbrowse/plugin-alignments 2.16.1 → 2.18.0

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
 declare const AlignmentsFeatureDetails: (props: {
     model: AlignmentFeatureWidgetModel;
 }) => React.JSX.Element;

package/dist/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -27,31 +27,24 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 };
 Object.defineProperty(exports, "__esModule", { value: true });
 const react_1 = __importStar(require("react"));
+const FeatureDetails_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails"));
 const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
-const clone_1 = __importDefault(require("clone"));
-const FeatureDetails_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails"));
-// locals
-const util_1 = require("./util");
-const tagInfo_1 = require("./tagInfo");
-// local components
 const Flags_1 = __importDefault(require("./Flags"));
-const PairLink_1 = __importDefault(require("./PairLink"));
 const Formatter_1 = __importDefault(require("./Formatter"));
-// lazies
+const PairLink_1 = __importDefault(require("./PairLink"));
+const tagInfo_1 = require("./tagInfo");
+const util_1 = require("./util");
 const SupplementaryAlignments = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./SupplementaryAlignments'))));
 const LinkedPairedAlignments = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./LinkedPairedAlignments'))));
-const omit = ['clipPos', 'flags'];
 const AlignmentsFeatureDetails = (0, mobx_react_1.observer)(function (props) {
     const { model } = props;
     const { featureData } = model;
-    const feat = (0, clone_1.default)(featureData);
+    const feat = structuredClone(featureData);
     const SA = (0, util_1.getTag)('SA', feat);
     const { flags } = feat;
     return (react_1.default.createElement(material_1.Paper, { "data-testid": "alignment-side-drawer" },
-        react_1.default.createElement(FeatureDetails_1.default, { ...props, omit: omit, 
-            // @ts-expect-error
-            descriptions: { ...tagInfo_1.tags, tags: tagInfo_1.tags }, feature: feat, formatter: (value, key) => key === 'next_segment_position' ? (react_1.default.createElement(PairLink_1.default, { model: model, locString: value })) : (react_1.default.createElement(Formatter_1.default, { value: value })) }),
+        react_1.default.createElement(FeatureDetails_1.default, { ...props, descriptions: { tags: tagInfo_1.tags }, feature: feat, formatter: (value, key) => key === 'next_segment_position' ? (react_1.default.createElement(PairLink_1.default, { model: model, locString: value })) : (react_1.default.createElement(Formatter_1.default, { value: value })) }),
         SA !== undefined ? (react_1.default.createElement(SupplementaryAlignments, { model: model, tag: SA, feature: feat })) : null,
         flags & 1 ? (react_1.default.createElement(LinkedPairedAlignments, { model: model, feature: feat })) : null,
         flags !== undefined ? react_1.default.createElement(Flags_1.default, { feature: feat, ...props }) : null));

package/dist/AlignmentsFeatureDetail/BreakendMultiLevelOptionDialog.js

@@ -1,6 +1,5 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = void 0;
-// re-exported for react lazy
 var sv_core_1 = require("@jbrowse/sv-core");
 Object.defineProperty(exports, "default", { enumerable: true, get: function () { return sv_core_1.BreakendMultiLevelOptionDialog; } });

package/dist/AlignmentsFeatureDetail/BreakendSingleLevelOptionDialog.js

@@ -1,6 +1,5 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = void 0;
-// re-exported for react lazy
 var sv_core_1 = require("@jbrowse/sv-core");
 Object.defineProperty(exports, "default", { enumerable: true, get: function () { return sv_core_1.BreakendSingleLevelOptionDialog; } });

package/dist/AlignmentsFeatureDetail/Flags.js

@@ -5,10 +5,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = AlignmentFlags;
 const react_1 = __importDefault(require("react"));
-const material_1 = require("@mui/material");
-const mui_1 = require("tss-react/mui");
 const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
 const SimpleField_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/SimpleField"));
+const material_1 = require("@mui/material");
+const mui_1 = require("tss-react/mui");
 const useStyles = (0, mui_1.makeStyles)()({
     compact: {
         paddingRight: 0,

package/dist/AlignmentsFeatureDetail/Formatter.js

@@ -29,9 +29,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = Formatter;
 const react_1 = __importStar(require("react"));
 const copy_to_clipboard_1 = __importDefault(require("copy-to-clipboard"));
-// this 'show more...' used specifically as a formatter on alignments feature
-// details because long SEQ or CRAM files, even a single div full of a ton of
-// data from a long read, can slow down the rest of the app
 function Formatter({ value }) {
     const [show, setShow] = (0, react_1.useState)(false);
     const [copied, setCopied] = (0, react_1.useState)(false);

package/dist/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.d.ts

@@ -1,9 +1,7 @@
 import React from 'react';
-import { SimpleFeatureSerialized } from '@jbrowse/core/util';
-import { ViewType } from '@jbrowse/core/pluggableElementTypes';
-import { AlignmentFeatureWidgetModel } from './stateModelFactory';
-export default function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, viewType, }: {
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
+export default function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, }: {
     model: AlignmentFeatureWidgetModel;
     feature: SimpleFeatureSerialized;
-    viewType: ViewType;
 }): React.JSX.Element;

package/dist/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.js

@@ -25,12 +25,11 @@ var __importStar = (this && this.__importStar) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = LaunchPairedEndBreakpointSplitViewPanel;
 const react_1 = __importStar(require("react"));
-const material_1 = require("@mui/material");
 const util_1 = require("@jbrowse/core/util");
-// lazies
+const material_1 = require("@mui/material");
 const BreakendMultiLevelOptionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BreakendMultiLevelOptionDialog'))));
 const BreakendSingleLevelOptionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BreakendSingleLevelOptionDialog'))));
-function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, viewType, }) {
+function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, }) {
     const session = (0, util_1.getSession)(model);
     const f1 = {
         uniqueId: feature.uniqueId,
@@ -64,10 +63,8 @@ function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, viewType, })
                             BreakendMultiLevelOptionDialog,
                             {
                                 handleClose,
-                                model,
+                                session,
                                 feature: new util_1.SimpleFeature({ ...f1, mate: f2 }),
-                                // @ts-expect-error
-                                viewType,
                                 view: model.view,
                                 assemblyName: model.view.displayedRegions[0].assemblyName,
                             },
@@ -80,10 +77,8 @@ function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, viewType, })
                             BreakendSingleLevelOptionDialog,
                             {
                                 handleClose,
-                                model,
+                                session,
                                 feature: new util_1.SimpleFeature({ ...f1, mate: f2 }),
-                                // @ts-expect-error
-                                viewType,
                                 view: model.view,
                                 assemblyName: model.view.displayedRegions[0].assemblyName,
                             },

package/dist/AlignmentsFeatureDetail/LaunchSupplementaryAlignmentBreakpointSplitViewPanel.d.ts

@@ -1,9 +1,7 @@
 import React from 'react';
-import { SimpleFeatureSerialized } from '@jbrowse/core/util';
-import { ViewType } from '@jbrowse/core/pluggableElementTypes';
-import { AlignmentFeatureWidgetModel } from './stateModelFactory';
-export default function LaunchBreakpointSplitViewPanel({ model, feature, viewType, }: {
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
+export default function LaunchBreakpointSplitViewPanel({ model, feature, }: {
     model: AlignmentFeatureWidgetModel;
     feature: SimpleFeatureSerialized;
-    viewType: ViewType;
 }): React.JSX.Element | null;

package/dist/AlignmentsFeatureDetail/LaunchSupplementaryAlignmentBreakpointSplitViewPanel.js

@@ -25,20 +25,17 @@ var __importStar = (this && this.__importStar) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = LaunchBreakpointSplitViewPanel;
 const react_1 = __importStar(require("react"));
-const material_1 = require("@mui/material");
-const util_1 = require("@jbrowse/core/util");
 const ui_1 = require("@jbrowse/core/ui");
+const util_1 = require("@jbrowse/core/util");
+const material_1 = require("@mui/material");
 const getSAFeatures_1 = require("./getSAFeatures");
-// lazies
 const BreakendMultiLevelOptionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BreakendMultiLevelOptionDialog'))));
 const BreakendSingleLevelOptionDialog = (0, react_1.lazy)(() => Promise.resolve().then(() => __importStar(require('./BreakendSingleLevelOptionDialog'))));
-function LaunchBreakpointSplitViewPanel({ model, feature, viewType, }) {
-    const session = (0, util_1.getSession)(model);
+function LaunchBreakpointSplitViewPanel({ model, feature, }) {
     const { view } = model;
     const [res, setRes] = (0, react_1.useState)();
     const [error, setError] = (0, react_1.useState)();
     (0, react_1.useEffect)(() => {
-        // eslint-disable-next-line @typescript-eslint/no-floating-promises
         ;
         (async () => {
             try {
@@ -75,36 +72,40 @@ function LaunchBreakpointSplitViewPanel({ model, feature, viewType, }) {
                 ":",
                 (0, util_1.toLocale)(f2.strand === 1 ? f2.start : f2.end),
                 ' ',
-                react_1.default.createElement(material_1.Link, { href: "#", onClick: event => {
-                        event.preventDefault();
-                        session.queueDialog(handleClose => [
-                            BreakendMultiLevelOptionDialog,
-                            {
-                                handleClose,
-                                model,
-                                feature: new util_1.SimpleFeature({ ...f1, mate: f2 }),
-                                // @ts-expect-error
-                                viewType,
-                                view: model.view,
-                                assemblyName: model.view.displayedRegions[0].assemblyName,
-                            },
-                        ]);
-                    } }, "(top/bottom)"),
+                react_1.default.createElement(TopBottomSplitViewLink, { model: model, f1: f1, f2: f2 }),
                 ' ',
-                react_1.default.createElement(material_1.Link, { href: "#", onClick: event => {
-                        event.preventDefault();
-                        session.queueDialog(handleClose => [
-                            BreakendSingleLevelOptionDialog,
-                            {
-                                handleClose,
-                                model,
-                                feature: new util_1.SimpleFeature({ ...f1, mate: f2 }),
-                                // @ts-expect-error
-                                viewType,
-                                view: model.view,
-                                assemblyName: model.view.displayedRegions[0].assemblyName,
-                            },
-                        ]);
-                    } }, "(single row)")));
+                react_1.default.createElement(SideBySideViewLink, { model: model, f1: f1, f2: f2 })));
         })))) : null;
 }
+function TopBottomSplitViewLink({ model, f1, f2, }) {
+    return (react_1.default.createElement(material_1.Link, { href: "#", onClick: event => {
+            event.preventDefault();
+            const session = (0, util_1.getSession)(model);
+            session.queueDialog(handleClose => [
+                BreakendMultiLevelOptionDialog,
+                {
+                    handleClose,
+                    session,
+                    feature: new util_1.SimpleFeature({ ...f1, mate: f2 }),
+                    view: model.view,
+                    assemblyName: model.view.displayedRegions[0].assemblyName,
+                },
+            ]);
+        } }, "(top/bottom)"));
+}
+function SideBySideViewLink({ model, f1, f2, }) {
+    return (react_1.default.createElement(material_1.Link, { href: "#", onClick: event => {
+            event.preventDefault();
+            const session = (0, util_1.getSession)(model);
+            session.queueDialog(handleClose => [
+                BreakendSingleLevelOptionDialog,
+                {
+                    handleClose,
+                    session,
+                    feature: new util_1.SimpleFeature({ ...f1, mate: f2 }),
+                    view: model.view,
+                    assemblyName: model.view.displayedRegions[0].assemblyName,
+                },
+            ]);
+        } }, "(single row)"));
+}

package/dist/AlignmentsFeatureDetail/LinkedPairedAlignments.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
-import { SimpleFeatureSerialized } from '@jbrowse/core/util';
-import { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
 export default function SuppAlignments(props: {
     model: AlignmentFeatureWidgetModel;
     feature: SimpleFeatureSerialized;

package/dist/AlignmentsFeatureDetail/LinkedPairedAlignments.js

@@ -12,12 +12,11 @@ function SuppAlignments(props) {
     const { model, feature } = props;
     const session = (0, util_1.getSession)(model);
     const { pluginManager } = (0, util_1.getEnv)(session);
-    let viewType;
+    let hasBreakendSplitView = false;
     try {
-        viewType = pluginManager.getViewType('BreakpointSplitView');
+        hasBreakendSplitView = !!pluginManager.getViewType('BreakpointSplitView');
     }
     catch (e) {
-        // ignore
     }
-    return (react_1.default.createElement(BaseCard_1.default, { ...props, title: "Supplementary alignments" }, viewType ? (react_1.default.createElement(LaunchPairedEndBreakpointSplitViewPanel_1.default, { viewType: viewType, model: model, feature: feature })) : null));
+    return (react_1.default.createElement(BaseCard_1.default, { ...props, title: "Paired alignments" }, hasBreakendSplitView ? (react_1.default.createElement(LaunchPairedEndBreakpointSplitViewPanel_1.default, { model: model, feature: feature })) : null));
 }

package/dist/AlignmentsFeatureDetail/PairLink.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
 export default function PairLink({ locString, model, }: {
     locString: string;
     model: AlignmentFeatureWidgetModel;

package/dist/AlignmentsFeatureDetail/PairLink.js

@@ -10,7 +10,6 @@ const util_1 = require("./util");
 function PairLink({ locString, model, }) {
     return (react_1.default.createElement(material_1.Link, { onClick: event => {
             event.preventDefault();
-            // eslint-disable-next-line @typescript-eslint/no-floating-promises
             (0, util_1.navToLoc)(locString, model);
         }, href: "#" }, locString));
 }

package/dist/AlignmentsFeatureDetail/SupplementaryAlignments.d.ts

@@ -1,6 +1,6 @@
 import React from 'react';
-import { SimpleFeatureSerialized } from '@jbrowse/core/util';
-import { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
 export default function SupplementaryAlignments(props: {
     tag: string;
     model: AlignmentFeatureWidgetModel;

package/dist/AlignmentsFeatureDetail/SupplementaryAlignments.js

@@ -5,22 +5,21 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = SupplementaryAlignments;
 const react_1 = __importDefault(require("react"));
-const util_1 = require("@jbrowse/core/util");
 const BaseCard_1 = __importDefault(require("@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard"));
-const SupplementaryAlignmentsLocStrings_1 = __importDefault(require("./SupplementaryAlignmentsLocStrings"));
+const util_1 = require("@jbrowse/core/util");
 const LaunchSupplementaryAlignmentBreakpointSplitViewPanel_1 = __importDefault(require("./LaunchSupplementaryAlignmentBreakpointSplitViewPanel"));
+const SupplementaryAlignmentsLocStrings_1 = __importDefault(require("./SupplementaryAlignmentsLocStrings"));
 function SupplementaryAlignments(props) {
     const { model, tag, feature } = props;
     const session = (0, util_1.getSession)(model);
     const { pluginManager } = (0, util_1.getEnv)(session);
-    let viewType;
+    let hasBreakendSplitView = false;
     try {
-        viewType = pluginManager.getViewType('BreakpointSplitView');
+        hasBreakendSplitView = !!pluginManager.getViewType('BreakpointSplitView');
     }
     catch (e) {
-        // ignore
     }
     return (react_1.default.createElement(BaseCard_1.default, { ...props, title: "Supplementary alignments" },
         react_1.default.createElement(SupplementaryAlignmentsLocStrings_1.default, { model: model, tag: tag }),
-        viewType ? (react_1.default.createElement(LaunchSupplementaryAlignmentBreakpointSplitViewPanel_1.default, { viewType: viewType, model: model, feature: feature })) : null));
+        hasBreakendSplitView ? (react_1.default.createElement(LaunchSupplementaryAlignmentBreakpointSplitViewPanel_1.default, { model: model, feature: feature })) : null));
 }

package/dist/AlignmentsFeatureDetail/SupplementaryAlignmentsLocStrings.d.ts

@@ -1,5 +1,5 @@
 import React from 'react';
-import { AlignmentFeatureWidgetModel } from './stateModelFactory';
+import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
 export default function SupplementaryAlignmentsLocStrings({ tag, model, }: {
     tag: string;
     model: AlignmentFeatureWidgetModel;

package/dist/AlignmentsFeatureDetail/SupplementaryAlignmentsLocStrings.js

@@ -6,7 +6,6 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = SupplementaryAlignmentsLocStrings;
 const react_1 = __importDefault(require("react"));
 const material_1 = require("@mui/material");
-// locals
 const MismatchParser_1 = require("../MismatchParser");
 const util_1 = require("./util");
 function SupplementaryAlignmentsLocStrings({ tag, model, }) {
@@ -27,12 +26,9 @@ function SupplementaryAlignmentsLocStrings({ tag, model, }) {
             const displayStart = start.toLocaleString('en-US');
             const displayEnd = end.toLocaleString('en-US');
             const displayString = `${saRef}:${displayStart}-${displayEnd} (${saStrand}) [${saLength}bp]`;
-            return (
-            /* biome-ignore lint/suspicious/noArrayIndexKey: */
-            react_1.default.createElement("li", { key: `${locString}-${idx}` },
+            return (react_1.default.createElement("li", { key: `${locString}-${idx}` },
                 react_1.default.createElement(material_1.Link, { href: "#", onClick: async (event) => {
                         event.preventDefault();
-                        // eslint-disable-next-line @typescript-eslint/no-floating-promises
                         (0, util_1.navToLoc)(locString, model);
                     } }, displayString)));
         }))));

package/dist/AlignmentsFeatureDetail/getSAFeatures.d.ts

@@ -1,5 +1,5 @@
-import { Feature } from '@jbrowse/core/util';
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+import type { Feature } from '@jbrowse/core/util';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 export interface ReducedFeature {
     refName: string;
     start: number;

package/dist/AlignmentsFeatureDetail/getSAFeatures.js

@@ -2,19 +2,15 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.getSAFeatures = getSAFeatures;
 const util_1 = require("@jbrowse/core/util");
-// locals
 const MismatchParser_1 = require("../MismatchParser");
-const util_2 = require("../util");
 async function getSAFeatures({ view, feature, }) {
+    var _a;
     const { assemblyManager } = (0, util_1.getSession)(view);
     const cigar = feature.get('CIGAR');
     const origStrand = feature.get('strand');
-    const SA = (0, util_2.getTag)(feature, 'SA') || '';
+    const SA = ((_a = feature.get('tags')) === null || _a === void 0 ? void 0 : _a.SA) || '';
     const readName = feature.get('name');
     const clipPos = (0, MismatchParser_1.getClip)(cigar, 1);
-    // get the canonical refname for the read because if the read.get('refName')
-    // is chr1 and the actual fasta refName is 1 then no tracks can be opened on
-    // the top panel of the linear read vs ref
     const assembly = await assemblyManager.waitForAssembly(view.assemblyNames[0]);
     if (!assembly) {
         throw new Error('assembly not found');

package/dist/AlignmentsFeatureDetail/index.d.ts

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

package/dist/AlignmentsFeatureDetail/launchBreakpointSplitView.d.ts

@@ -1,5 +1,5 @@
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
-import { ReducedFeature } from './getSAFeatures';
+import type { ReducedFeature } from './getSAFeatures';
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 export declare function getBreakpointSplitView({ f1, f2, view, }: {
     f1: ReducedFeature;
     f2: ReducedFeature;

package/dist/AlignmentsFeatureDetail/stateModelFactory.d.ts

@@ -1,5 +1,5 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-import { Instance } from 'mobx-state-tree';
+import type PluginManager from '@jbrowse/core/PluginManager';
+import type { Instance } from 'mobx-state-tree';
 export declare function stateModelFactory(pluginManager: PluginManager): import("mobx-state-tree").IModelType<{
     id: import("mobx-state-tree").IOptionalIType<import("mobx-state-tree").ISimpleType<string>, [undefined]>;
     type: import("mobx-state-tree").ISimpleType<"BaseFeatureWidget">;
@@ -92,8 +92,8 @@ export declare function stateModelFactory(pluginManager: PluginManager): import(
     trackId: string | undefined;
     trackType: string | undefined;
     maxDepth: number | undefined;
-    formattedFields: any;
     sequenceFeatureDetails: import("mobx-state-tree").ModelSnapshotType<{}>;
+    formattedFields: any;
     finalizedFeatureData: any;
 } & import("mobx-state-tree")._NotCustomized>;
 export type AlignmentFeatureWidgetStateModel = ReturnType<typeof stateModelFactory>;

package/dist/AlignmentsFeatureDetail/stateModelFactory.js

@@ -1,8 +1,8 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.stateModelFactory = stateModelFactory;
-const mobx_state_tree_1 = require("mobx-state-tree");
 const BaseFeatureWidget_1 = require("@jbrowse/core/BaseFeatureWidget");
+const mobx_state_tree_1 = require("mobx-state-tree");
 function stateModelFactory(pluginManager) {
     const baseModel = (0, BaseFeatureWidget_1.stateModelFactory)(pluginManager);
     return mobx_state_tree_1.types.compose(baseModel, mobx_state_tree_1.types.model('AlignmentsFeatureWidget', {

package/dist/AlignmentsFeatureDetail/tagInfo.js

@@ -20,7 +20,7 @@ exports.tags = {
     E2: 'The 2nd most likely base calls',
     FI: 'The index of segment in the template',
     FS: 'Segment suffix',
-    FZ: 'Flow signal intensities',
+    FZ: 'Flow stopToken intensities',
     GC: 'Reserved for backwards compatibility reasons',
     GQ: 'Reserved for backwards compatibility reasons',
     GS: 'Reserved for backwards compatibility reasons',

package/dist/AlignmentsFeatureDetail/util.d.ts

@@ -1,4 +1,4 @@
-import { IAnyStateTreeNode } from 'mobx-state-tree';
+import type { IAnyStateTreeNode } from 'mobx-state-tree';
 export declare function getTag(tag: string, feat: {
     tags?: Record<string, unknown>;
     [key: string]: unknown;

package/dist/AlignmentsTrack/configSchemaF.d.ts

@@ -1,4 +1,4 @@
-import PluginManager from '@jbrowse/core/PluginManager';
+import type PluginManager from '@jbrowse/core/PluginManager';
 export default function configSchemaFactory(pluginManager: PluginManager): import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
     name: {
         description: string;

package/dist/AlignmentsTrack/configSchemaF.js

@@ -3,16 +3,9 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = configSchemaFactory;
 const configuration_1 = require("@jbrowse/core/configuration");
 const pluggableElementTypes_1 = require("@jbrowse/core/pluggableElementTypes");
-/**
- * #config AlignmentsTrack
- * has very little config; most config and state logic is on the display
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
+function x() { }
 function configSchemaFactory(pluginManager) {
     return (0, configuration_1.ConfigurationSchema)('AlignmentsTrack', {}, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: (0, pluggableElementTypes_1.createBaseTrackConfig)(pluginManager),
     });
 }

package/dist/AlignmentsTrack/index.d.ts

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

package/dist/AlignmentsTrack/index.js

@@ -17,9 +17,6 @@ function register(pm) {
             stateModel: (0, models_1.createBaseTrackModel)(pm, 'AlignmentsTrack', configSchema),
         });
         const linearAlignmentsDisplay = pm.getDisplayType('LinearAlignmentsDisplay');
-        // Add LinearAlignmentsDisplay here so that it has priority over the other
-        // linear displays (defaults to order the displays are added, but we have
-        // to add the Pileup and SNPCoverage displays first).
         track.addDisplayType(linearAlignmentsDisplay);
         return track;
     });

package/dist/BamAdapter/BamAdapter.d.ts

@@ -1,8 +1,9 @@
 import { BamFile } from '@gmod/bam';
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Region } from '@jbrowse/core/util/types';
-import { Feature } from '@jbrowse/core/util';
-import { IFilter } from '../shared';
+import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { FilterBy } from '../shared/types';
+import type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import type { Feature } from '@jbrowse/core/util';
+import type { Region } from '@jbrowse/core/util/types';
 interface Header {
     idToName: string[];
     nameToId: Record<string, number>;
@@ -10,6 +11,7 @@ interface Header {
 export default class BamAdapter extends BaseFeatureDataAdapter {
     private samHeader?;
     private setupP?;
+    private ultraLongFeatureCache;
     private configureP?;
     protected configurePre(): Promise<{
         bam: BamFile;
@@ -22,7 +24,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
         bam: BamFile;
         sequenceAdapter?: BaseFeatureDataAdapter;
     }>;
-    getHeader(opts?: BaseOptions): Promise<string | undefined>;
+    getHeader(_opts?: BaseOptions): Promise<string | undefined>;
     private setupPre;
     setup(opts?: BaseOptions): Promise<Header>;
     getRefNames(opts?: BaseOptions): Promise<string[]>;
@@ -30,7 +32,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
     getFeatures(region: Region & {
         originalRefName?: string;
     }, opts?: BaseOptions & {
-        filterBy: IFilter;
+        filterBy: FilterBy;
     }): import("rxjs").Observable<Feature>;
     getMultiRegionFeatureDensityStats(regions: Region[], opts?: BaseOptions): Promise<import("@jbrowse/core/data_adapters/BaseAdapter").FeatureDensityStats | {
         bytes: number;