@jbrowse/sv-core 2.18.0 → 3.0.1

package/dist/BreakendMultiLevelOptionDialog.d.ts

@@ -1,4 +1,3 @@
-import React from 'react';
 import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 declare const BreakendMultiLevelOptionDialog: ({ session, handleClose, feature, assemblyName, stableViewId, view, }: {
@@ -8,5 +7,5 @@ declare const BreakendMultiLevelOptionDialog: ({ session, handleClose, feature,
     view?: LinearGenomeViewModel;
     assemblyName: string;
     stableViewId?: string;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default BreakendMultiLevelOptionDialog;

package/dist/BreakendMultiLevelOptionDialog.js

@@ -1,148 +1,46 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : 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 };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const ui_1 = require("@jbrowse/core/ui");
 const material_1 = require("@mui/material");
-const mobx_1 = require("mobx");
 const mobx_react_1 = require("mobx-react");
 const mobx_state_tree_1 = require("mobx-state-tree");
 const Checkbox2_1 = __importDefault(require("./Checkbox2"));
-const util_1 = require("./util");
-function stripIds(arr) {
-    return arr.map(({ id, displays, ...rest }) => ({
-        ...rest,
-        displays: displays.map(({ id, ...rest }) => rest),
-    }));
-}
+const navToMultiLevelBreak_1 = require("./navToMultiLevelBreak");
 const BreakendMultiLevelOptionDialog = (0, mobx_react_1.observer)(function ({ session, handleClose, feature, assemblyName, stableViewId, view, }) {
     const [copyTracks, setCopyTracks] = (0, react_1.useState)(true);
     const [mirror, setMirror] = (0, react_1.useState)(true);
-    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Multi-level breakpoint split view options" },
-        react_1.default.createElement(material_1.DialogContent, null,
-            react_1.default.createElement("div", null, "Launch multi-level breakpoint split view"),
-            view ? (react_1.default.createElement(react_1.default.Fragment, null,
-                react_1.default.createElement(Checkbox2_1.default, { checked: copyTracks, label: "Copy tracks into the new view", onChange: event => {
-                        setCopyTracks(event.target.checked);
-                    } }),
-                copyTracks ? (react_1.default.createElement(Checkbox2_1.default, { checked: mirror, disabled: !copyTracks, label: "Mirror the copied tracks (only available if copying tracks and using two level)", onChange: event => {
-                        setMirror(event.target.checked);
-                    } })) : null)) : null),
-        react_1.default.createElement(material_1.DialogActions, null,
-            react_1.default.createElement(material_1.Button, { onClick: () => {
-                    ;
-                    (async () => {
-                        try {
-                            const { assemblyManager } = session;
-                            const assembly = await assemblyManager.waitForAssembly(assemblyName);
-                            if (!assembly) {
-                                throw new Error(`assembly ${assemblyName} not found`);
-                            }
-                            const { refName, pos, mateRefName, matePos } = (0, util_1.getBreakendCoveringRegions)({
-                                feature,
-                                assembly: assembly,
-                            });
-                            const viewTracks = view
-                                ? (0, mobx_state_tree_1.getSnapshot)(view.tracks)
-                                : [];
-                            let viewInStack = session.views.find(f => f.id === stableViewId);
-                            const displayName = `${feature.get('name') || feature.get('id') || 'breakend'} split detail`;
-                            if (!viewInStack) {
-                                viewInStack = session.addView('BreakpointSplitView', {
-                                    id: stableViewId,
-                                    type: 'BreakpointSplitView',
-                                    displayName,
-                                    views: [
-                                        {
-                                            type: 'LinearGenomeView',
-                                            hideHeader: true,
-                                            tracks: stripIds(viewTracks),
-                                        },
-                                        {
-                                            type: 'LinearGenomeView',
-                                            hideHeader: true,
-                                            tracks: stripIds(mirror ? [...viewTracks].reverse() : viewTracks),
-                                        },
-                                    ],
-                                });
-                            }
-                            viewInStack.setDisplayName(displayName);
-                            const r1 = assembly.regions.find(r => r.refName === refName);
-                            const r2 = assembly.regions.find(r => r.refName === mateRefName);
-                            if (!r1 || !r2) {
-                                throw new Error("can't find regions");
-                            }
-                            await Promise.all([
-                                viewInStack.views[0].navToLocations([
-                                    {
-                                        refName,
-                                        start: r1.start,
-                                        end: pos,
-                                        assemblyName,
-                                    },
-                                    {
-                                        refName,
-                                        start: pos + 1,
-                                        end: r1.end,
-                                        assemblyName,
-                                    },
-                                ]),
-                                viewInStack.views[1].navToLocations([
-                                    {
-                                        refName: mateRefName,
-                                        start: r2.start,
-                                        end: matePos,
-                                        assemblyName,
-                                    },
-                                    {
-                                        refName: mateRefName,
-                                        start: matePos + 1,
-                                        end: r2.end,
+    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { open: true, onClose: handleClose, title: "Multi-level breakpoint split view options", children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [(0, jsx_runtime_1.jsx)("div", { children: "Launch multi-level breakpoint split view" }), view ? ((0, jsx_runtime_1.jsxs)(jsx_runtime_1.Fragment, { children: [(0, jsx_runtime_1.jsx)(Checkbox2_1.default, { checked: copyTracks, label: "Copy tracks into the new view", onChange: event => {
+                                    setCopyTracks(event.target.checked);
+                                } }), copyTracks ? ((0, jsx_runtime_1.jsx)(Checkbox2_1.default, { checked: mirror, disabled: !copyTracks, label: "Mirror the copied tracks (only available if copying tracks and using two level)", onChange: event => {
+                                    setMirror(event.target.checked);
+                                } })) : null] })) : null] }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { onClick: () => {
+                            ;
+                            (async () => {
+                                try {
+                                    await (0, navToMultiLevelBreak_1.navToMultiLevelBreak)({
+                                        stableViewId,
+                                        session,
+                                        tracks: copyTracks && view
+                                            ? (0, mobx_state_tree_1.getSnapshot)(view.tracks)
+                                            : [],
+                                        mirror,
+                                        feature,
                                         assemblyName,
-                                    },
-                                ]),
-                            ]);
-                            await (0, mobx_1.when)(() => viewInStack.views[1].initialized &&
-                                viewInStack.views[0].initialized);
-                            viewInStack.views[1].zoomTo(10);
-                            viewInStack.views[0].zoomTo(10);
-                            viewInStack.views[1].centerAt(matePos, mateRefName);
-                            viewInStack.views[0].centerAt(pos, refName);
-                        }
-                        catch (e) {
-                            console.error(e);
-                            session.notifyError(`${e}`, e);
-                        }
-                    })();
-                    handleClose();
-                }, variant: "contained", color: "primary", autoFocus: true }, "OK"),
-            react_1.default.createElement(material_1.Button, { color: "secondary", variant: "contained", onClick: () => {
-                    handleClose();
-                } }, "Cancel"))));
+                                    });
+                                }
+                                catch (e) {
+                                    console.error(e);
+                                    session.notifyError(`${e}`, e);
+                                }
+                            })();
+                            handleClose();
+                        }, variant: "contained", color: "primary", autoFocus: true, children: "OK" }), (0, jsx_runtime_1.jsx)(material_1.Button, { color: "secondary", variant: "contained", onClick: () => {
+                            handleClose();
+                        }, children: "Cancel" })] })] }));
 });
 exports.default = BreakendMultiLevelOptionDialog;

package/dist/BreakendSingleLevelOptionDialog.d.ts

@@ -1,4 +1,3 @@
-import React from 'react';
 import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
 import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
 declare const BreakendSingleLevelOptionDialog: ({ session, handleClose, feature, stableViewId, assemblyName, view, }: {
@@ -8,5 +7,5 @@ declare const BreakendSingleLevelOptionDialog: ({ session, handleClose, feature,
     feature: Feature;
     view?: LinearGenomeViewModel;
     assemblyName: string;
-}) => React.JSX.Element;
+}) => import("react/jsx-runtime").JSX.Element;
 export default BreakendSingleLevelOptionDialog;

package/dist/BreakendSingleLevelOptionDialog.js

@@ -1,77 +1,53 @@
 "use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    var desc = Object.getOwnPropertyDescriptor(m, k);
-    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
-      desc = { enumerable: true, get: function() { return m[k]; } };
-    }
-    Object.defineProperty(o, k2, desc);
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : 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 };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const react_1 = __importStar(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
+const react_1 = require("react");
 const ui_1 = require("@jbrowse/core/ui");
 const util_1 = require("@jbrowse/core/util");
 const material_1 = require("@mui/material");
 const mobx_react_1 = require("mobx-react");
 const Checkbox2_1 = __importDefault(require("./Checkbox2"));
-const util_2 = require("./util");
+const navToSingleLevelBreak_1 = require("./navToSingleLevelBreak");
 const BreakendSingleLevelOptionDialog = (0, mobx_react_1.observer)(function ({ session, handleClose, feature, stableViewId, assemblyName, view, }) {
     const [copyTracks, setCopyTracks] = (0, react_1.useState)(true);
+    const [focusOnBreakends, setFocusOnBreakends] = (0, react_1.useState)(true);
     const [windowSize, setWindowSize] = (0, util_1.useLocalStorage)('breakpointWindowSize', '5000');
-    return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Single-level breakpoint split view options" },
-        react_1.default.createElement(material_1.DialogContent, null,
-            view ? (react_1.default.createElement(Checkbox2_1.default, { checked: copyTracks, label: "Copy tracks into the new view", onChange: event => {
-                    setCopyTracks(event.target.checked);
-                } })) : null,
-            react_1.default.createElement(material_1.TextField, { label: "Window size (bp)", value: windowSize, onChange: event => {
-                    setWindowSize(event.target.value);
-                } })),
-        react_1.default.createElement(material_1.DialogActions, null,
-            react_1.default.createElement(material_1.Button, { onClick: () => {
-                    ;
-                    (async () => {
-                        try {
-                            const { assemblyManager } = session;
-                            const assembly = await assemblyManager.waitForAssembly(assemblyName);
-                            if (!assembly) {
-                                throw new Error(`assembly ${assemblyName} not found`);
-                            }
-                            await (0, util_2.navToSingleLevelBreak)({
-                                feature,
-                                assemblyName,
-                                session,
-                                stableViewId,
-                                tracks: view === null || view === void 0 ? void 0 : view.tracks,
-                                windowSize: +windowSize || 0,
-                            });
-                        }
-                        catch (e) {
-                            console.error(e);
-                            session.notifyError(`${e}`, e);
-                        }
-                    })();
-                    handleClose();
-                }, variant: "contained", color: "primary", autoFocus: true }, "OK"),
-            react_1.default.createElement(material_1.Button, { color: "secondary", variant: "contained", onClick: () => {
-                    handleClose();
-                } }, "Cancel"))));
+    return ((0, jsx_runtime_1.jsxs)(ui_1.Dialog, { open: true, onClose: handleClose, title: "Single-level breakpoint split view options", children: [(0, jsx_runtime_1.jsxs)(material_1.DialogContent, { children: [view ? ((0, jsx_runtime_1.jsx)(Checkbox2_1.default, { checked: copyTracks, label: "Copy tracks into the new view", onChange: event => {
+                            setCopyTracks(event.target.checked);
+                        } })) : null, (0, jsx_runtime_1.jsx)(Checkbox2_1.default, { checked: copyTracks, label: "Focus on breakends", onChange: event => {
+                            setFocusOnBreakends(event.target.checked);
+                        } }), (0, jsx_runtime_1.jsx)(material_1.TextField, { label: "Window size (bp)", value: windowSize, onChange: event => {
+                            setWindowSize(event.target.value);
+                        } })] }), (0, jsx_runtime_1.jsxs)(material_1.DialogActions, { children: [(0, jsx_runtime_1.jsx)(material_1.Button, { onClick: () => {
+                            ;
+                            (async () => {
+                                try {
+                                    const { assemblyManager } = session;
+                                    const assembly = await assemblyManager.waitForAssembly(assemblyName);
+                                    if (!assembly) {
+                                        throw new Error(`assembly ${assemblyName} not found`);
+                                    }
+                                    await (0, navToSingleLevelBreak_1.navToSingleLevelBreak)({
+                                        feature,
+                                        assemblyName,
+                                        focusOnBreakends,
+                                        session,
+                                        stableViewId,
+                                        tracks: view === null || view === void 0 ? void 0 : view.tracks,
+                                        windowSize: +windowSize || 0,
+                                    });
+                                }
+                                catch (e) {
+                                    console.error(e);
+                                    session.notifyError(`${e}`, e);
+                                }
+                            })();
+                            handleClose();
+                        }, variant: "contained", color: "primary", autoFocus: true, children: "OK" }), (0, jsx_runtime_1.jsx)(material_1.Button, { color: "secondary", variant: "contained", onClick: () => {
+                            handleClose();
+                        }, children: "Cancel" })] })] }));
 });
 exports.default = BreakendSingleLevelOptionDialog;

package/dist/Checkbox2.d.ts

@@ -1,7 +1,6 @@
-import React from 'react';
 export default function Checkbox2({ checked, disabled, label, onChange, }: {
     checked: boolean;
     disabled?: boolean;
     label: string;
     onChange: (event: React.ChangeEvent<HTMLInputElement>) => void;
-}): React.JSX.Element;
+}): import("react/jsx-runtime").JSX.Element;

package/dist/Checkbox2.js

@@ -1,10 +1,7 @@
 "use strict";
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.default = Checkbox2;
-const react_1 = __importDefault(require("react"));
+const jsx_runtime_1 = require("react/jsx-runtime");
 const material_1 = require("@mui/material");
 const mui_1 = require("tss-react/mui");
 const useStyles = (0, mui_1.makeStyles)()({
@@ -14,5 +11,5 @@ const useStyles = (0, mui_1.makeStyles)()({
 });
 function Checkbox2({ checked, disabled, label, onChange, }) {
     const { classes } = useStyles();
-    return (react_1.default.createElement(material_1.FormControlLabel, { disabled: disabled, className: classes.block, control: react_1.default.createElement(material_1.Checkbox, { checked: checked, onChange: onChange }), label: label }));
+    return ((0, jsx_runtime_1.jsx)(material_1.FormControlLabel, { disabled: disabled, className: classes.block, control: (0, jsx_runtime_1.jsx)(material_1.Checkbox, { checked: checked, onChange: onChange }), label: label }));
 }

package/dist/index.d.ts

@@ -1,3 +1,5 @@
 export { default as BreakendMultiLevelOptionDialog } from './BreakendMultiLevelOptionDialog';
 export { default as BreakendSingleLevelOptionDialog } from './BreakendSingleLevelOptionDialog';
 export * from './util';
+export * from './navToSingleLevelBreak';
+export * from './navToMultiLevelBreak';

package/dist/index.js

@@ -23,3 +23,5 @@ Object.defineProperty(exports, "BreakendMultiLevelOptionDialog", { enumerable: t
 var BreakendSingleLevelOptionDialog_1 = require("./BreakendSingleLevelOptionDialog");
 Object.defineProperty(exports, "BreakendSingleLevelOptionDialog", { enumerable: true, get: function () { return __importDefault(BreakendSingleLevelOptionDialog_1).default; } });
 __exportStar(require("./util"), exports);
+__exportStar(require("./navToSingleLevelBreak"), exports);
+__exportStar(require("./navToMultiLevelBreak"), exports);

package/dist/navToMultiLevelBreak.d.ts

@@ -0,0 +1,11 @@
+import type { Track } from './types';
+import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
+export declare function navToMultiLevelBreak({ stableViewId, feature, assemblyName, session, mirror, tracks: viewTracks, }: {
+    stableViewId?: string;
+    feature: Feature;
+    assemblyName: string;
+    windowSize?: number;
+    session: AbstractSessionModel;
+    mirror?: boolean;
+    tracks?: Track[];
+}): Promise<void>;

package/dist/navToMultiLevelBreak.js

@@ -0,0 +1,77 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.navToMultiLevelBreak = navToMultiLevelBreak;
+const util_1 = require("@jbrowse/core/util");
+const util_2 = require("./util");
+async function navToMultiLevelBreak({ stableViewId, feature, assemblyName, session, mirror, tracks: viewTracks = [], }) {
+    const { assemblyManager } = session;
+    const assembly = await assemblyManager.waitForAssembly(assemblyName);
+    if (!assembly) {
+        throw new Error(`assembly ${assemblyName} not found`);
+    }
+    const { refName, pos, mateRefName, matePos } = (0, util_2.getBreakendCoveringRegions)({
+        feature,
+        assembly: assembly,
+    });
+    let view = session.views.find(f => f.id === stableViewId);
+    if (!view) {
+        view = session.addView('BreakpointSplitView', {
+            id: stableViewId,
+            type: 'BreakpointSplitView',
+            displayName: (0, util_2.makeTitle)(feature),
+            views: [
+                {
+                    type: 'LinearGenomeView',
+                    hideHeader: true,
+                    tracks: (0, util_2.stripIds)(viewTracks),
+                },
+                {
+                    type: 'LinearGenomeView',
+                    hideHeader: true,
+                    tracks: (0, util_2.stripIds)(mirror ? [...viewTracks].reverse() : viewTracks),
+                },
+            ],
+        });
+    }
+    view.setDisplayName((0, util_2.makeTitle)(feature));
+    const r1 = assembly.regions.find(r => r.refName === refName);
+    const r2 = assembly.regions.find(r => r.refName === mateRefName);
+    if (!r1 || !r2) {
+        throw new Error("can't find regions");
+    }
+    await Promise.all([
+        view.views[0].navToLocations([
+            {
+                refName,
+                start: r1.start,
+                end: pos,
+                assemblyName,
+            },
+            {
+                refName,
+                start: pos + 1,
+                end: r1.end,
+                assemblyName,
+            },
+        ]),
+        view.views[1].navToLocations([
+            {
+                refName: mateRefName,
+                start: r2.start,
+                end: matePos,
+                assemblyName,
+            },
+            {
+                refName: mateRefName,
+                start: matePos + 1,
+                end: r2.end,
+                assemblyName,
+            },
+        ]),
+    ]);
+    await (0, util_1.when)(() => view.views[1].initialized && view.views[0].initialized);
+    view.views[1].zoomTo(10);
+    view.views[0].zoomTo(10);
+    view.views[1].centerAt(matePos, mateRefName);
+    view.views[0].centerAt(pos, refName);
+}

package/dist/navToSingleLevelBreak.d.ts

@@ -0,0 +1,61 @@
+import type { AbstractSessionModel, Feature } from '@jbrowse/core/util';
+export declare function singleLevelFocusedSnapshotFromBreakendFeature({ feature, session, assemblyName, windowSize, }: {
+    feature: Feature;
+    session: AbstractSessionModel;
+    assemblyName: string;
+    windowSize?: number;
+}): {
+    coverage: {
+        pos: number;
+        refName: string;
+        mateRefName: string;
+        matePos: any;
+    };
+    snap: {
+        type: string;
+        views: {
+            type: string;
+            displayedRegions: {
+                end: number;
+                assemblyName: string;
+                start: number;
+                refName: string;
+            }[];
+        }[];
+        displayName: string;
+    };
+};
+export declare function singleLevelEncompassingSnapshotFromBreakendFeature({ feature, session, assemblyName, }: {
+    feature: Feature;
+    session: AbstractSessionModel;
+    assemblyName: string;
+}): {
+    coverage: {
+        pos: number;
+        refName: string;
+        mateRefName: string;
+        matePos: any;
+    };
+    snap: {
+        type: string;
+        views: {
+            type: string;
+            displayedRegions: {
+                assemblyName: string;
+                start: number;
+                end: number;
+                refName: string;
+            }[];
+        }[];
+        displayName: string;
+    };
+};
+export declare function navToSingleLevelBreak({ stableViewId, feature, assemblyName, session, tracks, windowSize, focusOnBreakends, }: {
+    stableViewId?: string;
+    feature: Feature;
+    assemblyName: string;
+    windowSize?: number;
+    session: AbstractSessionModel;
+    tracks?: any;
+    focusOnBreakends?: boolean;
+}): Promise<void>;

package/dist/navToSingleLevelBreak.js

@@ -0,0 +1,136 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.singleLevelFocusedSnapshotFromBreakendFeature = singleLevelFocusedSnapshotFromBreakendFeature;
+exports.singleLevelEncompassingSnapshotFromBreakendFeature = singleLevelEncompassingSnapshotFromBreakendFeature;
+exports.navToSingleLevelBreak = navToSingleLevelBreak;
+const util_1 = require("@jbrowse/core/util");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const util_2 = require("./util");
+function singleLevelFocusedSnapshotFromBreakendFeature({ feature, session, assemblyName, windowSize = 0, }) {
+    const { assemblyManager } = session;
+    const assembly = assemblyManager.get(assemblyName);
+    if (!assembly) {
+        throw new Error(`assembly ${assemblyName} not found`);
+    }
+    if (!assembly.regions) {
+        throw new Error(`assembly ${assemblyName} regions not loaded`);
+    }
+    const coverage = (0, util_2.getBreakendCoveringRegions)({
+        feature,
+        assembly,
+    });
+    const { refName, mateRefName } = coverage;
+    const topRegion = assembly.regions.find(f => f.refName === refName);
+    const bottomRegion = assembly.regions.find(f => f.refName === mateRefName);
+    return {
+        coverage,
+        snap: {
+            type: 'BreakpointSplitView',
+            views: [
+                {
+                    type: 'LinearGenomeView',
+                    displayedRegions: (0, util_1.gatherOverlaps)([
+                        {
+                            ...topRegion,
+                            end: coverage.pos + windowSize,
+                            assemblyName,
+                        },
+                        {
+                            ...bottomRegion,
+                            start: coverage.matePos - windowSize,
+                            assemblyName,
+                        },
+                    ]),
+                },
+            ],
+            displayName: (0, util_2.makeTitle)(feature),
+        },
+    };
+}
+function singleLevelEncompassingSnapshotFromBreakendFeature({ feature, session, assemblyName, }) {
+    const { assemblyManager } = session;
+    const assembly = assemblyManager.get(assemblyName);
+    if (!assembly) {
+        throw new Error(`assembly ${assemblyName} not found`);
+    }
+    if (!assembly.regions) {
+        throw new Error(`assembly ${assemblyName} regions not loaded`);
+    }
+    const coverage = (0, util_2.getBreakendCoveringRegions)({
+        feature,
+        assembly,
+    });
+    const { refName, mateRefName } = coverage;
+    const topRegion = assembly.regions.find(f => f.refName === refName);
+    const bottomRegion = assembly.regions.find(f => f.refName === mateRefName);
+    return {
+        coverage,
+        snap: {
+            type: 'BreakpointSplitView',
+            views: [
+                {
+                    type: 'LinearGenomeView',
+                    displayedRegions: (0, util_1.gatherOverlaps)([
+                        { ...topRegion, assemblyName },
+                        { ...bottomRegion, assemblyName },
+                    ]),
+                },
+            ],
+            displayName: (0, util_2.makeTitle)(feature),
+        },
+    };
+}
+async function navToSingleLevelBreak({ stableViewId, feature, assemblyName, session, tracks, windowSize = 0, focusOnBreakends, }) {
+    var _a;
+    const { snap, coverage } = focusOnBreakends
+        ? singleLevelFocusedSnapshotFromBreakendFeature({
+            feature,
+            assemblyName,
+            session,
+            windowSize,
+        })
+        : singleLevelEncompassingSnapshotFromBreakendFeature({
+            feature,
+            assemblyName,
+            session,
+        });
+    const { refName, pos: startPos, mateRefName, matePos: endPos } = coverage;
+    let view = session.views.find(f => f.id === stableViewId);
+    if (!view) {
+        view = session.addView('BreakpointSplitView', {
+            ...snap,
+            views: [
+                {
+                    ...snap.views[0],
+                    tracks: tracks ? (0, util_2.stripIds)((0, mobx_state_tree_1.getSnapshot)(tracks)) : [],
+                },
+            ],
+        });
+    }
+    else {
+        (_a = view.views[0]) === null || _a === void 0 ? void 0 : _a.setDisplayedRegions(snap.views[0].displayedRegions);
+        view.setDisplayName(snap.displayName);
+    }
+    const lgv = view.views[0];
+    await (0, util_1.when)(() => lgv.initialized);
+    const l0 = lgv.bpToPx({
+        coord: Math.max(0, startPos - windowSize),
+        refName,
+    });
+    const r0 = lgv.bpToPx({
+        coord: endPos + windowSize,
+        refName: mateRefName,
+    });
+    if (l0 && r0) {
+        lgv.moveTo({
+            ...l0,
+            offset: l0.offsetPx,
+        }, {
+            ...r0,
+            offset: r0.offsetPx,
+        });
+    }
+    else {
+        (0, util_1.getSession)(lgv).notify('Unable to navigate to breakpoint');
+    }
+}