@jbrowse/sv-core 2.17.0 → 3.0.0

package/esm/navToMultiLevelBreak.js

@@ -0,0 +1,74 @@
+import { when } from '@jbrowse/core/util';
+import { getBreakendCoveringRegions, makeTitle, stripIds } from './util';
+export 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 } = getBreakendCoveringRegions({
+        feature,
+        assembly: assembly,
+    });
+    let view = session.views.find(f => f.id === stableViewId);
+    if (!view) {
+        view = session.addView('BreakpointSplitView', {
+            id: stableViewId,
+            type: 'BreakpointSplitView',
+            displayName: makeTitle(feature),
+            views: [
+                {
+                    type: 'LinearGenomeView',
+                    hideHeader: true,
+                    tracks: stripIds(viewTracks),
+                },
+                {
+                    type: 'LinearGenomeView',
+                    hideHeader: true,
+                    tracks: stripIds(mirror ? [...viewTracks].reverse() : viewTracks),
+                },
+            ],
+        });
+    }
+    view.setDisplayName(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 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/esm/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/esm/navToSingleLevelBreak.js

@@ -0,0 +1,131 @@
+import { gatherOverlaps, getSession, when } from '@jbrowse/core/util';
+import { getSnapshot } from 'mobx-state-tree';
+import { getBreakendCoveringRegions, makeTitle, stripIds } from './util';
+export 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 = 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: gatherOverlaps([
+                        {
+                            ...topRegion,
+                            end: coverage.pos + windowSize,
+                            assemblyName,
+                        },
+                        {
+                            ...bottomRegion,
+                            start: coverage.matePos - windowSize,
+                            assemblyName,
+                        },
+                    ]),
+                },
+            ],
+            displayName: makeTitle(feature),
+        },
+    };
+}
+export 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 = 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: gatherOverlaps([
+                        { ...topRegion, assemblyName },
+                        { ...bottomRegion, assemblyName },
+                    ]),
+                },
+            ],
+            displayName: makeTitle(feature),
+        },
+    };
+}
+export 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 ? stripIds(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 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 {
+        getSession(lgv).notify('Unable to navigate to breakpoint');
+    }
+}

package/esm/types.d.ts

@@ -0,0 +1,13 @@
+import type { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view';
+export interface Display {
+    id: string;
+    [key: string]: unknown;
+}
+export interface Track {
+    id: string;
+    displays: Display[];
+    [key: string]: unknown;
+}
+export interface BreakpointSplitView {
+    views: LinearGenomeViewModel[];
+}

package/esm/types.js

@@ -0,0 +1 @@
+export {};

package/esm/util.d.ts

@@ -0,0 +1,18 @@
+import type { Track } from './types';
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly';
+import type { Feature } from '@jbrowse/core/util';
+export declare function getBreakendCoveringRegions({ feature, assembly, }: {
+    feature: Feature;
+    assembly: Assembly;
+}): {
+    pos: number;
+    refName: string;
+    mateRefName: string;
+    matePos: any;
+};
+export declare function stripIds(arr: Track[]): {
+    displays: {
+        [key: string]: unknown;
+    }[];
+}[];
+export declare function makeTitle(f: Feature): string;

package/esm/util.js

@@ -0,0 +1,53 @@
+import { parseBreakend } from '@gmod/vcf';
+export function getBreakendCoveringRegions({ feature, assembly, }) {
+    var _a;
+    const alt = (_a = feature.get('ALT')) === null || _a === void 0 ? void 0 : _a[0];
+    const bnd = alt ? parseBreakend(alt) : undefined;
+    const startPos = feature.get('start');
+    const refName = feature.get('refName');
+    const f = (ref) => assembly.getCanonicalRefName(ref) || ref;
+    if (alt === '<TRA>') {
+        const INFO = feature.get('INFO');
+        return {
+            pos: startPos,
+            refName: f(refName),
+            mateRefName: f(INFO.CHR2[0]),
+            matePos: INFO.END[0] - 1,
+        };
+    }
+    else if (bnd === null || bnd === void 0 ? void 0 : bnd.MatePosition) {
+        const matePosition = bnd.MatePosition.split(':');
+        return {
+            pos: startPos,
+            refName: f(refName),
+            mateRefName: f(matePosition[0]),
+            matePos: +matePosition[1] - 1,
+        };
+    }
+    else if (feature.get('mate')) {
+        const mate = feature.get('mate');
+        return {
+            pos: startPos,
+            refName: f(refName),
+            mateRefName: f(mate.refName),
+            matePos: mate.start,
+        };
+    }
+    else {
+        return {
+            pos: startPos,
+            refName: f(refName),
+            mateRefName: f(refName),
+            matePos: feature.get('end'),
+        };
+    }
+}
+export function stripIds(arr) {
+    return arr.map(({ id, displays, ...rest }) => ({
+        ...rest,
+        displays: displays.map(({ id, ...rest }) => rest),
+    }));
+}
+export function makeTitle(f) {
+    return `${f.get('name') || f.get('id') || 'breakend'} split detail`;
+}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/sv-core",
-  "version": "2.17.0",
+  "version": "3.0.0",
   "description": "JBrowse 2 code shared between sv type code",
   "keywords": [
     "jbrowse",
@@ -41,7 +41,9 @@
     "useSrc": "node ../../scripts/useSrc.js"
   },
   "dependencies": {
-    "@jbrowse/plugin-linear-genome-view": "^2.17.0",
+    "@gmod/vcf": "^6.0.0",
+    "@jbrowse/core": "^3.0.0",
+    "@jbrowse/plugin-linear-genome-view": "^3.0.0",
     "@mui/icons-material": "^6.0.0",
     "@mui/material": "^6.0.0"
   },
@@ -57,5 +59,5 @@
   "publishConfig": {
     "access": "public"
   },
-  "gitHead": "eed30b5e671f8f7823652d7cecc51aa89226de46"
+  "gitHead": "2c6897f1fa732b1db5b094d1dca197e333e95319"
 }