@jbrowse/plugin-alignments 2.18.0 → 3.0.1

package/dist/shared/renderSvgUtil.js

@@ -15,19 +15,26 @@ var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (
 }) : function(o, v) {
     o["default"] = v;
 });
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.renderSvg = renderSvg;
-const react_1 = __importDefault(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
 const util_1 = require("@jbrowse/core/util");
 function getId(id) {
     const isJest = typeof jest === 'undefined';
@@ -47,17 +54,13 @@ async function renderSvg(self, opts, cb) {
         }
         ctx.scale(2, 2);
         cb(self, ctx, width, height);
-        return (react_1.default.createElement("image", { width: width, height: height, xlinkHref: canvas.toDataURL('image/png') }));
+        return ((0, jsx_runtime_1.jsx)("image", { width: width, height: height, xlinkHref: canvas.toDataURL('image/png') }));
     }
     else {
         const C2S = await Promise.resolve().then(() => __importStar(require('canvas2svg')));
         const ctx = new C2S.default(width, height);
         cb(self, ctx, width, height);
         const clipid = getId(self.id);
-        return (react_1.default.createElement(react_1.default.Fragment, null,
-            react_1.default.createElement("defs", null,
-                react_1.default.createElement("clipPath", { id: clipid },
-                    react_1.default.createElement("rect", { x: 0, y: 0, width: width, height: height }))),
-            react_1.default.createElement("g", { dangerouslySetInnerHTML: { __html: ctx.getSvg().innerHTML }, clipPath: `url(#${clipid})` })));
+        return ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)("defs", { children: (0, jsx_runtime_1.jsx)("clipPath", { id: clipid, children: (0, jsx_runtime_1.jsx)("rect", { x: 0, y: 0, width: width, height: height }) }) }), (0, jsx_runtime_1.jsx)("g", { dangerouslySetInnerHTML: { __html: ctx.getSvg().innerHTML }, clipPath: `url(#${clipid})` })] }));
     }
 }

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.d.ts

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

package/esm/AlignmentsFeatureDetail/AlignmentsFeatureDetail.js

@@ -1,4 +1,5 @@
-import React, { lazy } from 'react';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
+import { lazy } from 'react';
 import FeatureDetails from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/FeatureDetails';
 import { Paper } from '@mui/material';
 import { observer } from 'mobx-react';
@@ -15,10 +16,6 @@ const AlignmentsFeatureDetails = observer(function (props) {
     const feat = structuredClone(featureData);
     const SA = getTag('SA', feat);
     const { flags } = feat;
-    return (React.createElement(Paper, { "data-testid": "alignment-side-drawer" },
-        React.createElement(FeatureDetails, { ...props, descriptions: { tags }, feature: feat, formatter: (value, key) => key === 'next_segment_position' ? (React.createElement(PairLink, { model: model, locString: value })) : (React.createElement(Formatter, { value: value })) }),
-        SA !== undefined ? (React.createElement(SupplementaryAlignments, { model: model, tag: SA, feature: feat })) : null,
-        flags & 1 ? (React.createElement(LinkedPairedAlignments, { model: model, feature: feat })) : null,
-        flags !== undefined ? React.createElement(Flags, { feature: feat, ...props }) : null));
+    return (_jsxs(Paper, { "data-testid": "alignment-side-drawer", children: [_jsx(FeatureDetails, { ...props, descriptions: { tags }, feature: feat, formatter: (value, key) => key === 'next_segment_position' ? (_jsx(PairLink, { model: model, locString: value })) : (_jsx(Formatter, { value: value })) }), SA !== undefined ? (_jsx(SupplementaryAlignments, { model: model, tag: SA, feature: feat })) : null, flags & 1 ? (_jsx(LinkedPairedAlignments, { model: model, feature: feat })) : null, flags !== undefined ? _jsx(Flags, { feature: feat, ...props }) : null] }));
 });
 export default AlignmentsFeatureDetails;

package/esm/AlignmentsFeatureDetail/Flags.d.ts

@@ -1,6 +1,5 @@
-import React from 'react';
 export default function AlignmentFlags(props: {
     feature: {
         flags: number;
     };
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/esm/AlignmentsFeatureDetail/Flags.js

@@ -1,4 +1,4 @@
-import React from 'react';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
 import SimpleField from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/SimpleField';
 import { Checkbox, FormControlLabel, FormGroup } from '@mui/material';
@@ -28,11 +28,9 @@ export default function AlignmentFlags(props) {
     const { classes } = useStyles();
     const { feature } = props;
     const { flags } = feature;
-    return (React.createElement(BaseCard, { ...props, title: "Flags" },
-        React.createElement(SimpleField, { name: "Flag", value: flags }),
-        React.createElement(FormGroup, null, flagNames.map((name, idx) => {
-            const val = flags & (1 << idx);
-            const key = `${name}_${val}`;
-            return (React.createElement(FormControlLabel, { key: key, control: React.createElement(Checkbox, { className: classes.compact, checked: Boolean(val), name: name, readOnly: true }), label: name }));
-        }))));
+    return (_jsxs(BaseCard, { ...props, title: "Flags", children: [_jsx(SimpleField, { name: "Flag", value: flags }), _jsx(FormGroup, { children: flagNames.map((name, idx) => {
+                    const val = flags & (1 << idx);
+                    const key = `${name}_${val}`;
+                    return (_jsx(FormControlLabel, { control: _jsx(Checkbox, { className: classes.compact, checked: Boolean(val), name: name, readOnly: true }), label: name }, key));
+                }) })] }));
 }

package/esm/AlignmentsFeatureDetail/Formatter.d.ts

@@ -1,4 +1,3 @@
-import React from 'react';
 export default function Formatter({ value }: {
     value: unknown;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/esm/AlignmentsFeatureDetail/Formatter.js

@@ -1,19 +1,17 @@
-import React, { useState } from 'react';
+import { jsx as _jsx, Fragment as _Fragment, jsxs as _jsxs } from "react/jsx-runtime";
+import { useState } from 'react';
 import copy from 'copy-to-clipboard';
 export default function Formatter({ value }) {
     const [show, setShow] = useState(false);
     const [copied, setCopied] = useState(false);
     const display = String(value);
-    return display.length > 100 ? (React.createElement(React.Fragment, null,
-        React.createElement("button", { type: "button", onClick: () => {
-                copy(display);
-                setCopied(true);
-                setTimeout(() => {
-                    setCopied(false);
-                }, 700);
-            } }, copied ? 'Copied to clipboard' : 'Copy'),
-        React.createElement("button", { type: "button", onClick: () => {
-                setShow(val => !val);
-            } }, show ? 'Show less' : 'Show more'),
-        React.createElement("div", null, show ? display : `${display.slice(0, 100)}...`))) : (React.createElement("div", null, display));
+    return display.length > 100 ? (_jsxs(_Fragment, { children: [_jsx("button", { type: "button", onClick: () => {
+                    copy(display);
+                    setCopied(true);
+                    setTimeout(() => {
+                        setCopied(false);
+                    }, 700);
+                }, children: copied ? 'Copied to clipboard' : 'Copy' }), _jsx("button", { type: "button", onClick: () => {
+                    setShow(val => !val);
+                }, children: show ? 'Show less' : 'Show more' }), _jsx("div", { children: show ? display : `${display.slice(0, 100)}...` })] })) : (_jsx("div", { children: display }));
 }

package/esm/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.d.ts

@@ -1,7 +1,6 @@
-import React from 'react';
 import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
 import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
 export default function LaunchPairedEndBreakpointSplitViewPanel({ model, feature, }: {
     model: AlignmentFeatureWidgetModel;
     feature: SimpleFeatureSerialized;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/esm/AlignmentsFeatureDetail/LaunchPairedEndBreakpointSplitViewPanel.js

@@ -1,4 +1,5 @@
-import React, { lazy } from 'react';
+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'));
@@ -19,43 +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,
-                                session,
-                                feature: new SimpleFeature({ ...f1, mate: f2 }),
-                                view: model.view,
-                                assemblyName: model.view.displayedRegions[0].assemblyName,
-                            },
-                        ]);
-                    } }, "(top/bottom)"),
-                ' ',
-                React.createElement(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,
-                            },
-                        ]);
-                    } }, "(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

@@ -1,7 +1,6 @@
-import React from 'react';
 import type { AlignmentFeatureWidgetModel } from './stateModelFactory';
 import type { SimpleFeatureSerialized } from '@jbrowse/core/util';
 export default function LaunchBreakpointSplitViewPanel({ model, feature, }: {
     model: AlignmentFeatureWidgetModel;
     feature: SimpleFeatureSerialized;
-}): React.JSX.Element | null;
+}): import("react/jsx-runtime").JSX.Element | null;

package/esm/AlignmentsFeatureDetail/LaunchSupplementaryAlignmentBreakpointSplitViewPanel.js

@@ -1,4 +1,5 @@
-import React, { lazy, useEffect, useState } from 'react';
+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';
@@ -31,28 +32,13 @@ export default function LaunchBreakpointSplitViewPanel({ model, feature, }) {
             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(TopBottomSplitViewLink, { model: model, f1: f1, f2: f2 }),
-                ' ',
-                React.createElement(SideBySideViewLink, { model: model, f1: f1, f2: f2 })));
-        })))) : 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 (React.createElement(Link, { href: "#", onClick: event => {
+    return (_jsx(Link, { href: "#", onClick: event => {
             event.preventDefault();
             const session = getSession(model);
             session.queueDialog(handleClose => [
@@ -65,10 +51,10 @@ function TopBottomSplitViewLink({ model, f1, f2, }) {
                     assemblyName: model.view.displayedRegions[0].assemblyName,
                 },
             ]);
-        } }, "(top/bottom)"));
+        }, children: "(top/bottom)" }));
 }
 function SideBySideViewLink({ model, f1, f2, }) {
-    return (React.createElement(Link, { href: "#", onClick: event => {
+    return (_jsx(Link, { href: "#", onClick: event => {
             event.preventDefault();
             const session = getSession(model);
             session.queueDialog(handleClose => [
@@ -81,5 +67,5 @@ function SideBySideViewLink({ model, f1, f2, }) {
                     assemblyName: model.view.displayedRegions[0].assemblyName,
                 },
             ]);
-        } }, "(single row)"));
+        }, children: "(single row)" }));
 }

package/esm/AlignmentsFeatureDetail/LinkedPairedAlignments.d.ts

@@ -1,7 +1,6 @@
-import React from 'react';
 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';
@@ -12,5 +12,5 @@ export default function SuppAlignments(props) {
     }
     catch (e) {
     }
-    return (React.createElement(BaseCard, { ...props, title: "Paired alignments" }, hasBreakendSplitView ? (React.createElement(LaunchPairedEndBreakpointSplitViewPanel, { 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 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

@@ -1,9 +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();
             navToLoc(locString, model);
-        }, href: "#" }, locString));
+        }, href: "#", children: locString }));
 }

package/esm/AlignmentsFeatureDetail/SupplementaryAlignments.d.ts

@@ -1,8 +1,7 @@
-import React from 'react';
 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

@@ -1,4 +1,4 @@
-import React from 'react';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import BaseCard from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail/BaseCard';
 import { getEnv, getSession } from '@jbrowse/core/util';
 import LaunchBreakpointSplitViewPanel from './LaunchSupplementaryAlignmentBreakpointSplitViewPanel';
@@ -13,7 +13,5 @@ export default function SupplementaryAlignments(props) {
     }
     catch (e) {
     }
-    return (React.createElement(BaseCard, { ...props, title: "Supplementary alignments" },
-        React.createElement(SupplementaryAlignmentsLocStrings, { model: model, tag: tag }),
-        hasBreakendSplitView ? (React.createElement(LaunchBreakpointSplitViewPanel, { 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 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

@@ -1,29 +1,26 @@
-import React from 'react';
+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 (React.createElement("li", { key: `${locString}-${idx}` },
-                React.createElement(Link, { href: "#", onClick: async (event) => {
-                        event.preventDefault();
-                        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/CramAdapter/CramAdapter.js

@@ -24,7 +24,9 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
         const pm = this.pluginManager;
         const cram = new IndexedCramFile({
             cramFilehandle: openLocation(cramLocation, pm),
-            index: new CraiIndex({ filehandle: openLocation(craiLocation, pm) }),
+            index: new CraiIndex({
+                filehandle: openLocation(craiLocation, pm),
+            }),
             seqFetch: (...args) => this.seqFetch(...args),
             checkSequenceMD5: false,
         });
@@ -110,7 +112,10 @@ export default class CramAdapter extends BaseFeatureDataAdapter {
                 .map(rgLine => { var _a; return (_a = rgLine.data.find(item => item.tag === 'ID')) === null || _a === void 0 ? void 0 : _a.value; });
             const data = { idToName, nameToId, readGroups };
             this.samHeader = data;
-            return { samHeader: data, ...conf };
+            return {
+                samHeader: data,
+                ...conf,
+            };
         });
     }
     async setup(opts) {

package/esm/CramAdapter/CramTestAdapters.d.ts

@@ -1,7 +1,7 @@
 import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter';
 import SimpleFeature from '@jbrowse/core/util/simpleFeature';
 import { Observable } from 'rxjs';
-import type { GenericFilehandle } from 'generic-filehandle';
+import type { GenericFilehandle } from 'generic-filehandle2';
 export declare function parseSmallFasta(text: string): {
     id: string;
     description: string;

package/esm/CramAdapter/CramTestAdapters.js

@@ -21,7 +21,8 @@ export function parseSmallFasta(text) {
 export class FetchableSmallFasta {
     constructor(filehandle) {
         this.data = filehandle.readFile().then(buffer => {
-            const text = buffer.toString('utf8');
+            const decoder = new TextDecoder('utf8');
+            const text = decoder.decode(buffer);
             return parseSmallFasta(text);
         });
     }

package/esm/GuessAlignmentsTypes/index.js

@@ -1,45 +1,30 @@
+import { testAdapter } from '@jbrowse/core/util';
 import { getFileName, makeIndex, makeIndexType, } from '@jbrowse/core/util/tracks';
 export default function GuessAlignmentsTypesF(pluginManager) {
     pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
         return (file, index, adapterHint) => {
-            const regexGuess = /\.cram$/i;
-            const adapterName = 'CramAdapter';
-            const fileName = getFileName(file);
-            const obj = {
-                type: adapterName,
-                cramLocation: file,
-                craiLocation: index || makeIndex(file, '.crai'),
-            };
-            if (regexGuess.test(fileName) && !adapterHint) {
-                return obj;
-            }
-            if (adapterHint === adapterName) {
-                return obj;
-            }
-            return adapterGuesser(file, index, adapterHint);
-        };
-    });
-    pluginManager.addToExtensionPoint('Core-guessAdapterForLocation', (adapterGuesser) => {
-        return (file, index, adapterHint) => {
-            const regexGuess = /\.bam$/i;
-            const adapterName = 'BamAdapter';
             const fileName = getFileName(file);
             const indexName = index && getFileName(index);
-            const obj = {
-                type: adapterName,
-                bamLocation: file,
-                index: {
-                    location: index || makeIndex(file, '.bai'),
-                    indexType: makeIndexType(indexName, 'CSI', 'BAI'),
-                },
-            };
-            if (regexGuess.test(fileName) && !adapterHint) {
-                return obj;
+            if (testAdapter(fileName, /\.bam$/i, adapterHint, 'BamAdapter')) {
+                return {
+                    type: 'BamAdapter',
+                    bamLocation: file,
+                    index: {
+                        location: index || makeIndex(file, '.bai'),
+                        indexType: makeIndexType(indexName, 'CSI', 'BAI'),
+                    },
+                };
+            }
+            else if (testAdapter(fileName, /\.cram$/i, adapterHint, 'CramAdapter')) {
+                return {
+                    type: 'CramAdapter',
+                    cramLocation: file,
+                    craiLocation: index || makeIndex(file, '.crai'),
+                };
             }
-            if (adapterHint === adapterName) {
-                return obj;
+            else {
+                return adapterGuesser(file, index, adapterHint);
             }
-            return adapterGuesser(file, index, adapterHint);
         };
     });
     pluginManager.addToExtensionPoint('Core-guessTrackTypeForLocation', (trackTypeGuesser) => {

package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.d.ts

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

package/esm/LinearAlignmentsDisplay/components/AlignmentsDisplay.js

@@ -1,4 +1,4 @@
-import React from 'react';
+import { jsx as _jsx, jsxs as _jsxs } from "react/jsx-runtime";
 import { getConf } from '@jbrowse/core/configuration';
 import { ResizeHandle } from '@jbrowse/core/ui';
 import { observer } from 'mobx-react';
@@ -18,17 +18,12 @@ const AlignmentsDisplay = observer(function AlignmentsDisplay({ model, }) {
         return null;
     }
     const top = (_a = SNPCoverageDisplay.height) !== null && _a !== void 0 ? _a : 100;
-    return (React.createElement("div", { "data-testid": `display-${getConf(model, 'displayId')}`, style: { position: 'relative' } },
-        React.createElement("div", { "data-testid": "Blockset-snpcoverage" },
-            React.createElement(SNPCoverageDisplay.RenderingComponent, { model: SNPCoverageDisplay })),
-        React.createElement(ResizeHandle, { onDrag: delta => {
-                SNPCoverageDisplay.setHeight(SNPCoverageDisplay.height + delta);
-                return delta;
-            }, className: classes.resizeHandle, style: { top: top - 4 } }),
-        React.createElement("div", { "data-testid": "Blockset-pileup", style: {
-                position: 'absolute',
-                top,
-            } },
-            React.createElement(PileupDisplay.RenderingComponent, { model: PileupDisplay }))));
+    return (_jsxs("div", { "data-testid": `display-${getConf(model, 'displayId')}`, style: { position: 'relative' }, children: [_jsx("div", { "data-testid": "Blockset-snpcoverage", children: _jsx(SNPCoverageDisplay.RenderingComponent, { model: SNPCoverageDisplay }) }), _jsx(ResizeHandle, { onDrag: delta => {
+                    SNPCoverageDisplay.setHeight(SNPCoverageDisplay.height + delta);
+                    return delta;
+                }, className: classes.resizeHandle, style: { top: top - 4 } }), _jsx("div", { "data-testid": "Blockset-pileup", style: {
+                    position: 'absolute',
+                    top,
+                }, children: _jsx(PileupDisplay.RenderingComponent, { model: PileupDisplay }) })] }));
 });
 export default AlignmentsDisplay;