@jbrowse/plugin-alignments 2.17.0 → 3.0.0

package/esm/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.js

@@ -1,10 +1,10 @@
-import React, { lazy } from 'react';
-import { Typography, Link } from '@mui/material';
-import { SimpleFeature, getSession, toLocale, } from '@jbrowse/core/util';
-// lazies
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { lazy } from 'react';
+import { SimpleFeature, getSession, toLocale } from '@jbrowse/core/util';
+import { Link, Typography } from '@mui/material';
 const BreakendMultiLevelOptionDialog = lazy(() => import('./BreakendMultiLevelOptionDialog'));
 const BreakendSingleLevelOptionDialog = lazy(() => import('./BreakendSingleLevelOptionDialog'));
-export default function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, viewType, }) {
+export default function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, }) {
     const session = getSession(model);
     const f1 = {
         uniqueId: feature.uniqueId,
@@ -20,47 +20,29 @@ export default function LaunchPairedEndBreakpointSplitViewPanel({ model, feature
         end: feature.next_pos + 1,
         strand: feature.strand,
     };
-    return (React.createElement("div", null,
-        React.createElement(Typography, null, "Launch split view"),
-        React.createElement("ul", null,
-            React.createElement("li", null,
-                f1.refName,
-                ":",
-                toLocale(f1.start),
-                " -> ",
-                f2.refName,
-                ":",
-                toLocale(f2.start),
-                ' ',
-                React.createElement(Link, { href: "#", onClick: event => {
-                        event.preventDefault();
-                        session.queueDialog(handleClose => [
-                            BreakendMultiLevelOptionDialog,
-                            {
-                                handleClose,
-                                model,
-                                feature: new SimpleFeature({ ...f1, mate: f2 }),
-                                // @ts-expect-error
-                                viewType,
-                                view: model.view,
-                                assemblyName: model.view.displayedRegions[0].assemblyName,
-                            },
-                        ]);
-                    } }, "(top/bottom)"),
-                ' ',
-                React.createElement(Link, { href: "#", onClick: event => {
-                        event.preventDefault();
-                        session.queueDialog(handleClose => [
-                            BreakendSingleLevelOptionDialog,
-                            {
-                                handleClose,
-                                model,
-                                feature: new SimpleFeature({ ...f1, mate: f2 }),
-                                // @ts-expect-error
-                                viewType,
-                                view: model.view,
-                                assemblyName: model.view.displayedRegions[0].assemblyName,
-                            },
-                        ]);
-                    } }, "(single row)")))));
+    return (_jsxs("div", { children: [_jsx(Typography, { children: "Launch split view" }), _jsx("ul", { children: _jsxs("li", { children: [f1.refName, ":", toLocale(f1.start), " -> ", f2.refName, ":", toLocale(f2.start), ' ', _jsx(Link, { href: "#", onClick: event => {
+                                event.preventDefault();
+                                session.queueDialog(handleClose => [
+                                    BreakendMultiLevelOptionDialog,
+                                    {
+                                        handleClose,
+                                        session,
+                                        feature: new SimpleFeature({ ...f1, mate: f2 }),
+                                        view: model.view,
+                                        assemblyName: model.view.displayedRegions[0].assemblyName,
+                                    },
+                                ]);
+                            }, children: "(top/bottom)" }), ' ', _jsx(Link, { href: "#", onClick: event => {
+                                event.preventDefault();
+                                session.queueDialog(handleClose => [
+                                    BreakendSingleLevelOptionDialog,
+                                    {
+                                        handleClose,
+                                        session,
+                                        feature: new SimpleFeature({ ...f1, mate: f2 }),
+                                        view: model.view,
+                                        assemblyName: model.view.displayedRegions[0].assemblyName,
+                                    },
+                                ]);
+                            }, children: "(single row)" })] }) })] }));
 }

package/esm/AlignmentsFeatureDetail/LaunchSupplementaryAlignmentBreakpointSplitViewPanel.d.ts

@@ -1,9 +1,6 @@
-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;
+}): import("react/jsx-runtime").JSX.Element | null;

package/esm/AlignmentsFeatureDetail/LaunchSupplementaryAlignmentBreakpointSplitViewPanel.js

@@ -1,18 +1,16 @@
-import React, { lazy, useEffect, useState } from 'react';
-import { Typography, Link } from '@mui/material';
-import { SimpleFeature, getSession, toLocale, } from '@jbrowse/core/util';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { lazy, useEffect, useState } from 'react';
 import { ErrorMessage } from '@jbrowse/core/ui';
+import { SimpleFeature, getSession, toLocale } from '@jbrowse/core/util';
+import { Link, Typography } from '@mui/material';
 import { getSAFeatures } from './getSAFeatures';
-// lazies
 const BreakendMultiLevelOptionDialog = lazy(() => import('./BreakendMultiLevelOptionDialog'));
 const BreakendSingleLevelOptionDialog = lazy(() => import('./BreakendSingleLevelOptionDialog'));
-export default function LaunchBreakpointSplitViewPanel({ model, feature, viewType, }) {
-    const session = getSession(model);
+export default function LaunchBreakpointSplitViewPanel({ model, feature, }) {
     const { view } = model;
     const [res, setRes] = useState();
     const [error, setError] = useState();
     useEffect(() => {
-        // eslint-disable-next-line @typescript-eslint/no-floating-promises
         ;
         (async () => {
             try {
@@ -34,51 +32,40 @@ export default function LaunchBreakpointSplitViewPanel({ model, feature, viewTyp
             ret.push([res[i], res[i + 1]]);
         }
     }
-    return ret.length ? (React.createElement("div", null,
-        React.createElement(Typography, null, "Launch split view"),
-        error ? React.createElement(ErrorMessage, { error: error }) : null,
-        React.createElement("ul", null, ret.map((arg, index) => {
-            const [f1, f2] = arg;
-            return (React.createElement("li", { key: `${JSON.stringify(arg)}-${index}` },
-                f1.refName,
-                ":",
-                toLocale(f1.strand === 1 ? f1.end : f1.start),
-                " ->",
-                ' ',
-                f2.refName,
-                ":",
-                toLocale(f2.strand === 1 ? f2.start : f2.end),
-                ' ',
-                React.createElement(Link, { href: "#", onClick: event => {
-                        event.preventDefault();
-                        session.queueDialog(handleClose => [
-                            BreakendMultiLevelOptionDialog,
-                            {
-                                handleClose,
-                                model,
-                                feature: new SimpleFeature({ ...f1, mate: f2 }),
-                                // @ts-expect-error
-                                viewType,
-                                view: model.view,
-                                assemblyName: model.view.displayedRegions[0].assemblyName,
-                            },
-                        ]);
-                    } }, "(top/bottom)"),
-                ' ',
-                React.createElement(Link, { href: "#", onClick: event => {
-                        event.preventDefault();
-                        session.queueDialog(handleClose => [
-                            BreakendSingleLevelOptionDialog,
-                            {
-                                handleClose,
-                                model,
-                                feature: new SimpleFeature({ ...f1, mate: f2 }),
-                                // @ts-expect-error
-                                viewType,
-                                view: model.view,
-                                assemblyName: model.view.displayedRegions[0].assemblyName,
-                            },
-                        ]);
-                    } }, "(single row)")));
-        })))) : null;
+    return ret.length ? (_jsxs("div", { children: [_jsx(Typography, { children: "Launch split view" }), error ? _jsx(ErrorMessage, { error: error }) : null, _jsx("ul", { children: ret.map((arg, index) => {
+                    const [f1, f2] = arg;
+                    return (_jsxs("li", { children: [f1.refName, ":", toLocale(f1.strand === 1 ? f1.end : f1.start), " ->", ' ', f2.refName, ":", toLocale(f2.strand === 1 ? f2.start : f2.end), ' ', _jsx(TopBottomSplitViewLink, { model: model, f1: f1, f2: f2 }), ' ', _jsx(SideBySideViewLink, { model: model, f1: f1, f2: f2 })] }, `${JSON.stringify(arg)}-${index}`));
+                }) })] })) : null;
+}
+function TopBottomSplitViewLink({ model, f1, f2, }) {
+    return (_jsx(Link, { href: "#", onClick: event => {
+            event.preventDefault();
+            const session = getSession(model);
+            session.queueDialog(handleClose => [
+                BreakendMultiLevelOptionDialog,
+                {
+                    handleClose,
+                    session,
+                    feature: new SimpleFeature({ ...f1, mate: f2 }),
+                    view: model.view,
+                    assemblyName: model.view.displayedRegions[0].assemblyName,
+                },
+            ]);
+        }, children: "(top/bottom)" }));
+}
+function SideBySideViewLink({ model, f1, f2, }) {
+    return (_jsx(Link, { href: "#", onClick: event => {
+            event.preventDefault();
+            const session = getSession(model);
+            session.queueDialog(handleClose => [
+                BreakendSingleLevelOptionDialog,
+                {
+                    handleClose,
+                    session,
+                    feature: new SimpleFeature({ ...f1, mate: f2 }),
+                    view: model.view,
+                    assemblyName: model.view.displayedRegions[0].assemblyName,
+                },
+            ]);
+        }, children: "(single row)" }));
 }

package/esm/AlignmentsFeatureDetail/LinkedPairedAlignments.d.ts

@@ -1,7 +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;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/esm/AlignmentsFeatureDetail/LinkedPairedAlignments.js

@@ -1,4 +1,4 @@
-import React from 'react';
+import { jsx as _jsx } from "react/jsx-runtime";
 import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
 import { getEnv, getSession } from '@jbrowse/core/util';
 import LaunchPairedEndBreakpointSplitViewPanel from './LaunchPairedEndBreakpointSplitViewPanel';
@@ -6,12 +6,11 @@ export default function SuppAlignments(props) {
     const { model, feature } = props;
     const session = getSession(model);
     const { pluginManager } = getEnv(session);
-    let viewType;
+    let hasBreakendSplitView = false;
     try {
-        viewType = pluginManager.getViewType('BreakpointSplitView');
+        hasBreakendSplitView = !!pluginManager.getViewType('BreakpointSplitView');
     }
     catch (e) {
-        // ignore
     }
-    return (React.createElement(BaseCard, { ...props, title: "Supplementary alignments" }, viewType ? (React.createElement(LaunchPairedEndBreakpointSplitViewPanel, { viewType: viewType, model: model, feature: feature })) : null));
+    return (_jsx(BaseCard, { ...props, title: "Paired alignments", children: hasBreakendSplitView ? (_jsx(LaunchPairedEndBreakpointSplitViewPanel, { model: model, feature: feature })) : null }));
 }

package/esm/AlignmentsFeatureDetail/PairLink.d.ts

@@ -1,6 +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;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/esm/AlignmentsFeatureDetail/PairLink.js

@@ -1,10 +1,9 @@
-import React from 'react';
+import { jsx as _jsx } from "react/jsx-runtime";
 import { Link } from '@mui/material';
 import { navToLoc } from './util';
 export default function PairLink({ locString, model, }) {
-    return (React.createElement(Link, { onClick: event => {
+    return (_jsx(Link, { onClick: event => {
             event.preventDefault();
-            // eslint-disable-next-line @typescript-eslint/no-floating-promises
             navToLoc(locString, model);
-        }, href: "#" }, locString));
+        }, href: "#", children: locString }));
 }

package/esm/AlignmentsFeatureDetail/SupplementaryAlignments.d.ts

@@ -1,8 +1,7 @@
-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;
     feature: SimpleFeatureSerialized;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/esm/AlignmentsFeatureDetail/SupplementaryAlignments.js

@@ -1,20 +1,17 @@
-import React from 'react';
-import { getEnv, getSession } from '@jbrowse/core/util';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
-import SupplementaryAlignmentsLocStrings from './SupplementaryAlignmentsLocStrings';
+import { getEnv, getSession } from '@jbrowse/core/util';
 import LaunchBreakpointSplitViewPanel from './LaunchSupplementaryAlignmentBreakpointSplitViewPanel';
+import SupplementaryAlignmentsLocStrings from './SupplementaryAlignmentsLocStrings';
 export default function SupplementaryAlignments(props) {
     const { model, tag, feature } = props;
     const session = getSession(model);
     const { pluginManager } = getEnv(session);
-    let viewType;
+    let hasBreakendSplitView = false;
     try {
-        viewType = pluginManager.getViewType('BreakpointSplitView');
+        hasBreakendSplitView = !!pluginManager.getViewType('BreakpointSplitView');
     }
     catch (e) {
-        // ignore
     }
-    return (React.createElement(BaseCard, { ...props, title: "Supplementary alignments" },
-        React.createElement(SupplementaryAlignmentsLocStrings, { model: model, tag: tag }),
-        viewType ? (React.createElement(LaunchBreakpointSplitViewPanel, { viewType: viewType, model: model, feature: feature })) : null));
+    return (_jsxs(BaseCard, { ...props, title: "Supplementary alignments", children: [_jsx(SupplementaryAlignmentsLocStrings, { model: model, tag: tag }), hasBreakendSplitView ? (_jsx(LaunchBreakpointSplitViewPanel, { model: model, feature: feature })) : null] }));
 }

package/esm/AlignmentsFeatureDetail/SupplementaryAlignmentsLocStrings.d.ts

@@ -1,6 +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;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/esm/AlignmentsFeatureDetail/SupplementaryAlignmentsLocStrings.js

@@ -1,33 +1,26 @@
-import React from 'react';
-import { Typography, Link } from '@mui/material';
-// locals
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { Link, Typography } from '@mui/material';
 import { getLengthOnRef } from '../MismatchParser';
 import { navToLoc } from './util';
 export default function SupplementaryAlignmentsLocStrings({ tag, model, }) {
-    return (React.createElement("div", null,
-        React.createElement(Typography, null, "List of supplementary alignment locations"),
-        React.createElement("ul", null, tag
-            .split(';')
-            .filter(SA => !!SA)
-            .map((SA, idx) => {
-            const [saRef, saStart, saStrand, saCigar] = SA.split(',');
-            const saLength = getLengthOnRef(saCigar);
-            const extra = Math.floor(saLength / 5);
-            const start = +saStart;
-            const end = +saStart + saLength;
-            const sp = start - extra;
-            const ep = end + extra;
-            const locString = `${saRef}:${Math.max(1, sp)}-${ep}`;
-            const displayStart = start.toLocaleString('en-US');
-            const displayEnd = end.toLocaleString('en-US');
-            const displayString = `${saRef}:${displayStart}-${displayEnd} (${saStrand}) [${saLength}bp]`;
-            return (
-            /* biome-ignore lint/suspicious/noArrayIndexKey: */
-            React.createElement("li", { key: `${locString}-${idx}` },
-                React.createElement(Link, { href: "#", onClick: async (event) => {
-                        event.preventDefault();
-                        // eslint-disable-next-line @typescript-eslint/no-floating-promises
-                        navToLoc(locString, model);
-                    } }, displayString)));
-        }))));
+    return (_jsxs("div", { children: [_jsx(Typography, { children: "List of supplementary alignment locations" }), _jsx("ul", { children: tag
+                    .split(';')
+                    .filter(SA => !!SA)
+                    .map((SA, idx) => {
+                    const [saRef, saStart, saStrand, saCigar] = SA.split(',');
+                    const saLength = getLengthOnRef(saCigar);
+                    const extra = Math.floor(saLength / 5);
+                    const start = +saStart;
+                    const end = +saStart + saLength;
+                    const sp = start - extra;
+                    const ep = end + extra;
+                    const locString = `${saRef}:${Math.max(1, sp)}-${ep}`;
+                    const displayStart = start.toLocaleString('en-US');
+                    const displayEnd = end.toLocaleString('en-US');
+                    const displayString = `${saRef}:${displayStart}-${displayEnd} (${saStrand}) [${saLength}bp]`;
+                    return (_jsx("li", { children: _jsx(Link, { href: "#", onClick: async (event) => {
+                                event.preventDefault();
+                                navToLoc(locString, model);
+                            }, children: displayString }) }, `${locString}-${idx}`));
+                }) })] }));
 }

package/esm/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/esm/AlignmentsFeatureDetail/getSAFeatures.js

@@ -1,5 +1,4 @@
 import { getSession } from '@jbrowse/core/util';
-// locals
 import { featurizeSA, getClip, getLengthSansClipping } from '../MismatchParser';
 export async function getSAFeatures({ view, feature, }) {
     var _a;
@@ -9,9 +8,6 @@ export async function getSAFeatures({ view, feature, }) {
     const SA = ((_a = feature.get('tags')) === null || _a === void 0 ? void 0 : _a.SA) || '';
     const readName = feature.get('name');
     const clipPos = 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/esm/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/esm/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/esm/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">;

package/esm/AlignmentsFeatureDetail/stateModelFactory.js

@@ -1,5 +1,5 @@
-import { types } from 'mobx-state-tree';
 import { stateModelFactory as baseModelFactory } from '@jbrowse/core/BaseFeatureWidget';
+import { types } from 'mobx-state-tree';
 export function stateModelFactory(pluginManager) {
     const baseModel = baseModelFactory(pluginManager);
     return types.compose(baseModel, types.model('AlignmentsFeatureWidget', {

package/esm/AlignmentsFeatureDetail/tagInfo.js

@@ -17,7 +17,7 @@ export const 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/esm/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/esm/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/esm/AlignmentsTrack/configSchemaF.js

@@ -1,15 +1,8 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration';
 import { createBaseTrackConfig } from '@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() { }
 export default function configSchemaFactory(pluginManager) {
     return ConfigurationSchema('AlignmentsTrack', {}, {
-        /**
-         * #baseConfiguration
-         */
         baseConfiguration: createBaseTrackConfig(pluginManager),
     });
 }

package/esm/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/esm/AlignmentsTrack/index.js

@@ -11,9 +11,6 @@ export default function register(pm) {
             stateModel: 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/esm/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 { FilterBy } from '../shared/types';
+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>;
@@ -23,7 +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[]>;