@jbrowse/plugin-breakpoint-split-view 2.6.1

package/esm/BreakpointSplitView/components/Breakends.js

@@ -0,0 +1,92 @@
+import React, { useState, useMemo } from 'react';
+import { getSession } from '@jbrowse/core/util';
+import { observer } from 'mobx-react';
+import { getSnapshot } from 'mobx-state-tree';
+// locals
+import { findMatchingAlt, getMatchedBreakendFeatures } from './util';
+import { yPos, getPxFromCoordinate, useNextFrame } from '../util';
+const [LEFT] = [0, 1, 2, 3];
+const Breakends = observer(function ({ model, trackId, parentRef: ref, getTrackYPosOverride, }) {
+    const { views } = model;
+    const session = getSession(model);
+    const { assemblyManager } = session;
+    const totalFeatures = model.getTrackFeatures(trackId);
+    const layoutMatches = useMemo(() => model.getMatchedFeaturesInLayout(trackId, getMatchedBreakendFeatures(totalFeatures)), [totalFeatures, trackId, model]);
+    const [mouseoverElt, setMouseoverElt] = useState();
+    const snap = getSnapshot(model);
+    useNextFrame(snap);
+    const assembly = assemblyManager.get(views[0].assemblyNames[0]);
+    if (!assembly) {
+        return null;
+    }
+    let yoff = 0;
+    if (ref.current) {
+        const rect = ref.current.getBoundingClientRect();
+        yoff = rect.top;
+    }
+    return (React.createElement("g", { stroke: "green", strokeWidth: 5, fill: "none", "data-testid": layoutMatches.length ? `${trackId}-loaded` : trackId }, layoutMatches.map(chunk => {
+        const ret = [];
+        // we follow a path in the list of chunks, not from top to bottom, just
+        // in series following x1,y1 -> x2,y2
+        for (let i = 0; i < chunk.length - 1; i += 1) {
+            const { layout: c1, feature: f1, level: level1 } = chunk[i];
+            const { layout: c2, feature: f2, level: level2 } = chunk[i + 1];
+            const id = f1.id();
+            const relevantAlt = findMatchingAlt(f1, f2);
+            if (!c1 || !c2) {
+                return null;
+            }
+            const f1origref = f1.get('refName');
+            const f2origref = f2.get('refName');
+            const f1ref = assembly.getCanonicalRefName(f1origref);
+            const f2ref = assembly.getCanonicalRefName(f2origref);
+            if (!f1ref || !f2ref) {
+                throw new Error(`unable to find ref for ${f1ref || f2ref}`);
+            }
+            const x1 = getPxFromCoordinate(views[level1], f1ref, c1[LEFT]);
+            const x2 = getPxFromCoordinate(views[level2], f2ref, c2[LEFT]);
+            const reversed1 = views[level1].pxToBp(x1).reversed;
+            const reversed2 = views[level2].pxToBp(x2).reversed;
+            const tracks = views.map(v => v.getTrack(trackId));
+            const y1 = yPos(trackId, level1, views, tracks, c1, getTrackYPosOverride) -
+                yoff;
+            const y2 = yPos(trackId, level2, views, tracks, c2, getTrackYPosOverride) -
+                yoff;
+            if (!relevantAlt) {
+                console.warn('the relevant ALT allele was not found, cannot render');
+            }
+            else {
+                const path = [
+                    'M',
+                    x1 -
+                        20 *
+                            (relevantAlt.Join === 'left' ? -1 : 1) *
+                            (reversed1 ? -1 : 1),
+                    y1,
+                    'L',
+                    x1,
+                    y1,
+                    'L',
+                    x2,
+                    y2,
+                    'L',
+                    x2 -
+                        20 *
+                            (relevantAlt.MateDirection === 'left' ? 1 : -1) *
+                            (reversed2 ? -1 : 1),
+                    y2,
+                ].join(' ');
+                ret.push(React.createElement("path", { d: path, key: JSON.stringify(path), strokeWidth: id === mouseoverElt ? 10 : 5, onClick: () => {
+                        var _a, _b, _c;
+                        const featureWidget = (_a = session.addWidget) === null || _a === void 0 ? void 0 : _a.call(session, 'VariantFeatureWidget', 'variantFeature', {
+                            featureData: (_b = totalFeatures.get(id)) === null || _b === void 0 ? void 0 : _b.toJSON(),
+                        });
+                        (_c = session.showWidget) === null || _c === void 0 ? void 0 : _c.call(session, featureWidget);
+                    }, onMouseOver: () => setMouseoverElt(id), onMouseOut: () => setMouseoverElt(undefined) }));
+            }
+        }
+        return ret;
+    })));
+});
+export default Breakends;
+//# sourceMappingURL=Breakends.js.map

package/esm/BreakpointSplitView/components/Breakends.js.map

@@ -0,0 +1 @@
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package/esm/BreakpointSplitView/components/BreakpointSplitView.d.ts

@@ -0,0 +1,6 @@
+import React from 'react';
+import { BreakpointViewModel } from '../model';
+declare const BreakpointSplitView: ({ model, }: {
+    model: BreakpointViewModel;
+}) => React.JSX.Element;
+export default BreakpointSplitView;

package/esm/BreakpointSplitView/components/BreakpointSplitView.js

@@ -0,0 +1,61 @@
+import React, { useRef } from 'react';
+import { observer } from 'mobx-react';
+import { getEnv } from 'mobx-state-tree';
+import { makeStyles } from 'tss-react/mui';
+import Overlay from './Overlay';
+const useStyles = makeStyles()(theme => ({
+    viewDivider: {
+        background: theme.palette.secondary.main,
+        height: 3,
+    },
+    container: {
+        display: 'grid',
+    },
+    overlay: {
+        display: 'flex',
+        width: '100%',
+        gridArea: '1/1',
+        '& path': {
+            cursor: 'crosshair',
+            fill: 'none',
+        },
+    },
+    content: {
+        gridArea: '1/1',
+    },
+}));
+const BreakpointSplitView = observer(function ({ model, }) {
+    const { classes } = useStyles();
+    const { views } = model;
+    const { pluginManager } = getEnv(model);
+    const ref = useRef(null);
+    return (React.createElement("div", null,
+        React.createElement("div", { className: classes.container },
+            React.createElement("div", { className: classes.content },
+                React.createElement("div", { style: { position: 'relative' } }, views.map((view, idx) => {
+                    const { ReactComponent } = pluginManager.getViewType(view.type);
+                    const viewComponent = (React.createElement(ReactComponent, { key: view.id, model: view }));
+                    if (idx === views.length - 1) {
+                        return viewComponent;
+                    }
+                    return [
+                        viewComponent,
+                        React.createElement("div", { key: `${view.id}-divider`, className: classes.viewDivider }),
+                    ];
+                }))),
+            React.createElement("div", { className: classes.overlay },
+                React.createElement("svg", { ref: ref, style: {
+                        width: '100%',
+                        zIndex: 10,
+                        pointerEvents: model.interactToggled ? undefined : 'none',
+                    } }, model.matchedTracks.map(track => (
+                // note: we must pass ref down, because the child component
+                // needs to getBoundingClientRect on the this components SVG,
+                // and we cannot rely on using getBoundingClientRect in this
+                // component to make sure this works because if it gets
+                // shifted around by another element, this will not re-render
+                // necessarily
+                React.createElement(Overlay, { parentRef: ref, key: track.configuration.trackId, model: model, trackId: track.configuration.trackId }))))))));
+});
+export default BreakpointSplitView;
+//# sourceMappingURL=BreakpointSplitView.js.map

package/esm/BreakpointSplitView/components/BreakpointSplitView.js.map

@@ -0,0 +1 @@
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package/esm/BreakpointSplitView/components/ExportSvgDialog.d.ts

@@ -0,0 +1,8 @@
+import React from 'react';
+import { ExportSvgOptions } from '../model';
+export default function ExportSvgDlg({ model, handleClose, }: {
+    model: {
+        exportSvg(opts: ExportSvgOptions): Promise<void>;
+    };
+    handleClose: () => void;
+}): React.JSX.Element;

package/esm/BreakpointSplitView/components/ExportSvgDialog.js

@@ -0,0 +1,58 @@
+import React, { useState } from 'react';
+import { Button, Checkbox, CircularProgress, DialogActions, DialogContent, FormControlLabel, MenuItem, TextField, Typography, } from '@mui/material';
+import { Dialog, ErrorMessage } from '@jbrowse/core/ui';
+import { getSession, useLocalStorage } from '@jbrowse/core/util';
+function LoadingMessage() {
+    return (React.createElement("div", null,
+        React.createElement(CircularProgress, { size: 20, style: { marginRight: 20 } }),
+        React.createElement(Typography, { display: "inline" }, "Creating SVG")));
+}
+function useSvgLocal(key, val) {
+    return useLocalStorage('svg-' + key, val);
+}
+export default function ExportSvgDlg({ model, handleClose, }) {
+    const session = getSession(model);
+    const offscreenCanvas = typeof OffscreenCanvas !== 'undefined';
+    const [rasterizeLayers, setRasterizeLayers] = useState(offscreenCanvas);
+    const [loading, setLoading] = useState(false);
+    const [error, setError] = useState();
+    const [filename, setFilename] = useSvgLocal('file', 'jbrowse.svg');
+    const [trackLabels, setTrackLabels] = useSvgLocal('tracklabels', 'offset');
+    const [themeName, setThemeName] = useSvgLocal('theme', session.themeName || 'default');
+    return (React.createElement(Dialog, { open: true, onClose: handleClose, title: "Export SVG" },
+        React.createElement(DialogContent, null,
+            error ? (React.createElement(ErrorMessage, { error: error })) : loading ? (React.createElement(LoadingMessage, null)) : null,
+            React.createElement(TextField, { helperText: "filename", value: filename, onChange: event => setFilename(event.target.value) }),
+            React.createElement("br", null),
+            React.createElement(TextField, { select: true, label: "Track label positioning", variant: "outlined", style: { width: 150 }, value: trackLabels, onChange: event => setTrackLabels(event.target.value) },
+                React.createElement(MenuItem, { value: "offset" }, "Offset"),
+                React.createElement(MenuItem, { value: "overlay" }, "Overlay"),
+                React.createElement(MenuItem, { value: "left" }, "Left"),
+                React.createElement(MenuItem, { value: "none" }, "None")),
+            React.createElement("br", null),
+            session.allThemes ? (React.createElement(TextField, { select: true, label: "Theme", variant: "outlined", value: themeName, onChange: event => setThemeName(event.target.value) }, Object.entries(session.allThemes()).map(([key, val]) => (React.createElement(MenuItem, { key: key, value: key }, 
+            // @ts-expect-error
+            val.name || '(Unknown name)'))))) : null,
+            offscreenCanvas ? (React.createElement(FormControlLabel, { control: React.createElement(Checkbox, { checked: rasterizeLayers, onChange: () => setRasterizeLayers(val => !val) }), label: "Rasterize canvas based tracks? File may be much larger if this is turned off" })) : (React.createElement(Typography, null, "Note: rasterizing layers not yet supported in this browser, so SVG size may be large"))),
+        React.createElement(DialogActions, null,
+            React.createElement(Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel"),
+            React.createElement(Button, { variant: "contained", color: "primary", type: "submit", onClick: async () => {
+                    setLoading(true);
+                    setError(undefined);
+                    try {
+                        await model.exportSvg({
+                            rasterizeLayers,
+                            filename,
+                            trackLabels,
+                            themeName,
+                        });
+                        handleClose();
+                    }
+                    catch (e) {
+                        console.error(e);
+                        setError(e);
+                        setLoading(false);
+                    }
+                } }, "Submit"))));
+}
+//# sourceMappingURL=ExportSvgDialog.js.map

package/esm/BreakpointSplitView/components/ExportSvgDialog.js.map

@@ -0,0 +1 @@
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package/esm/BreakpointSplitView/components/Overlay.d.ts

@@ -0,0 +1,9 @@
+import React from 'react';
+import { BreakpointViewModel } from '../model';
+declare const _default: (props: {
+    parentRef: React.RefObject<SVGSVGElement>;
+    model: BreakpointViewModel;
+    trackId: string;
+    getTrackYPosOverride?: ((trackId: string, level: number) => number) | undefined;
+}) => React.JSX.Element | null;
+export default _default;

package/esm/BreakpointSplitView/components/Overlay.js

@@ -0,0 +1,18 @@
+import React from 'react';
+import { observer } from 'mobx-react';
+import AlignmentConnections from './AlignmentConnections';
+import Breakends from './Breakends';
+import Translocations from './Translocations';
+export default observer(function (props) {
+    var _a, _b;
+    const { model, trackId } = props;
+    const tracks = model.getMatchedTracks(trackId);
+    if (((_a = tracks[0]) === null || _a === void 0 ? void 0 : _a.type) === 'AlignmentsTrack') {
+        return React.createElement(AlignmentConnections, { ...props });
+    }
+    if (((_b = tracks[0]) === null || _b === void 0 ? void 0 : _b.type) === 'VariantTrack') {
+        return model.hasTranslocations(trackId) ? (React.createElement(Translocations, { ...props })) : (React.createElement(Breakends, { ...props }));
+    }
+    return null;
+});
+//# sourceMappingURL=Overlay.js.map

package/esm/BreakpointSplitView/components/Overlay.js.map

@@ -0,0 +1 @@
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package/esm/BreakpointSplitView/components/Translocations.d.ts

@@ -0,0 +1,9 @@
+import React from 'react';
+import { BreakpointViewModel } from '../model';
+declare const Translocations: ({ model, trackId, parentRef: ref, getTrackYPosOverride, }: {
+    model: BreakpointViewModel;
+    trackId: string;
+    parentRef: React.RefObject<SVGSVGElement>;
+    getTrackYPosOverride?: ((trackId: string, level: number) => number) | undefined;
+}) => React.JSX.Element | null;
+export default Translocations;

package/esm/BreakpointSplitView/components/Translocations.js

@@ -0,0 +1,88 @@
+import React, { useState, useMemo } from 'react';
+import { getSession } from '@jbrowse/core/util';
+import { observer } from 'mobx-react';
+import { getSnapshot } from 'mobx-state-tree';
+// locals
+import { getMatchedTranslocationFeatures } from './util';
+import { yPos, getPxFromCoordinate, useNextFrame } from '../util';
+const [LEFT] = [0, 1, 2, 3];
+const Translocations = observer(function ({ model, trackId, parentRef: ref, getTrackYPosOverride, }) {
+    const { views } = model;
+    const session = getSession(model);
+    const { assemblyManager } = session;
+    const totalFeatures = model.getTrackFeatures(trackId);
+    const layoutMatches = useMemo(() => model.getMatchedFeaturesInLayout(trackId, getMatchedTranslocationFeatures(totalFeatures)), [totalFeatures, trackId, model]);
+    const [mouseoverElt, setMouseoverElt] = useState();
+    const snap = getSnapshot(model);
+    useNextFrame(snap);
+    const assembly = assemblyManager.get(views[0].assemblyNames[0]);
+    if (!assembly) {
+        return null;
+    }
+    let yOffset = 0;
+    if (ref.current) {
+        const rect = ref.current.getBoundingClientRect();
+        yOffset = rect.top;
+    }
+    // we hardcode the TRA to go to the "other view" and if there is none, we
+    // just return null here note: would need to do processing of the INFO
+    // CHR2/END and see which view could contain those coordinates to really do
+    // it properly
+    if (views.length < 2) {
+        return null;
+    }
+    return (React.createElement("g", { fill: "none", stroke: "green", strokeWidth: 5, "data-testid": layoutMatches.length ? `${trackId}-loaded` : trackId }, layoutMatches.map(chunk => {
+        // we follow a path in the list of chunks, not from top to bottom,
+        // just in series following x1,y1 -> x2,y2
+        const ret = [];
+        for (let i = 0; i < chunk.length; i += 1) {
+            const { layout: c1, feature: f1, level: level1 } = chunk[i];
+            const level2 = level1 === 0 ? 1 : 0;
+            const id = f1.id();
+            if (!c1) {
+                return null;
+            }
+            const info = f1.get('INFO');
+            const chr2 = info.CHR2[0];
+            const end2 = info.END[0];
+            const [myDirection, mateDirection] = info.STRANDS[0].split('');
+            const r = getPxFromCoordinate(views[level2], chr2, end2);
+            if (r) {
+                const c2 = [r, 0, r + 1, 0];
+                const x1 = getPxFromCoordinate(views[level1], f1.get('refName'), c1[LEFT]);
+                const x2 = r;
+                const reversed1 = views[level1].pxToBp(x1).reversed;
+                const reversed2 = views[level2].pxToBp(x2).reversed;
+                const tracks = views.map(v => v.getTrack(trackId));
+                const y1 = yPos(trackId, level1, views, tracks, c1, getTrackYPosOverride) -
+                    yOffset;
+                const y2 = yPos(trackId, level2, views, tracks, c2, getTrackYPosOverride) -
+                    yOffset;
+                const path = [
+                    'M',
+                    x1 - 20 * (myDirection === '+' ? 1 : -1) * (reversed1 ? -1 : 1),
+                    y1,
+                    'L',
+                    x1,
+                    y1,
+                    'L',
+                    x2,
+                    y2,
+                    'L',
+                    x2 - 20 * (mateDirection === '+' ? 1 : -1) * (reversed2 ? -1 : 1),
+                    y2,
+                ].join(' ');
+                ret.push(React.createElement("path", { d: path, key: JSON.stringify(path), strokeWidth: id === mouseoverElt ? 10 : 5, onClick: () => {
+                        var _a, _b;
+                        const featureWidget = (_a = session.addWidget) === null || _a === void 0 ? void 0 : _a.call(session, 'VariantFeatureWidget', 'variantFeature', {
+                            featureData: (totalFeatures.get(id) || { toJSON: () => { } }).toJSON(),
+                        });
+                        (_b = session.showWidget) === null || _b === void 0 ? void 0 : _b.call(session, featureWidget);
+                    }, onMouseOver: () => setMouseoverElt(id), onMouseOut: () => setMouseoverElt(undefined) }));
+            }
+        }
+        return ret;
+    })));
+});
+export default Translocations;
+//# sourceMappingURL=Translocations.js.map

package/esm/BreakpointSplitView/components/Translocations.js.map

@@ -0,0 +1 @@
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package/esm/BreakpointSplitView/components/util.d.ts

@@ -0,0 +1,7 @@
+import { Feature } from '@jbrowse/core/util';
+export declare function getBadlyPairedAlignments(features: Map<string, Feature>): Feature[][];
+export declare function getMatchedAlignmentFeatures(features: Map<string, Feature>): Feature[][];
+export declare function hasPairedReads(features: Map<string, Feature>): boolean;
+export declare function findMatchingAlt(feat1: Feature, feat2: Feature): import("@gmod/vcf").Breakend | undefined;
+export declare function getMatchedBreakendFeatures(feats: Map<string, Feature>): Feature[][];
+export declare function getMatchedTranslocationFeatures(feats: Map<string, Feature>): Feature[][];

package/esm/BreakpointSplitView/components/util.js

@@ -0,0 +1,107 @@
+import { notEmpty } from '@jbrowse/core/util';
+import { parseBreakend } from '@gmod/vcf';
+// this finds candidate alignment features, aimed at plotting split reads from
+// BAM/CRAM files
+export function getBadlyPairedAlignments(features) {
+    const candidates = new Map();
+    const alreadySeen = new Set();
+    // this finds candidate features that share the same name
+    for (const feature of features.values()) {
+        const flags = feature.get('flags');
+        const id = feature.id();
+        const unmapped = flags & 4;
+        const correctlyPaired = flags & 2;
+        if (!alreadySeen.has(id) && !correctlyPaired && !unmapped) {
+            const n = feature.get('name');
+            let val = candidates.get(n);
+            if (!val) {
+                val = [];
+                candidates.set(n, val);
+            }
+            val.push(feature);
+        }
+        alreadySeen.add(feature.id());
+    }
+    return [...candidates.values()].filter(v => v.length > 1);
+}
+function getTag(f, tag) {
+    const tags = f.get('tags');
+    return tags ? tags[tag] : f.get(tag);
+}
+// this finds candidate alignment features, aimed at plotting split reads from
+// BAM/CRAM files
+export function getMatchedAlignmentFeatures(features) {
+    const candidates = new Map();
+    const alreadySeen = new Set();
+    // this finds candidate features that share the same name
+    for (const feature of features.values()) {
+        const id = feature.id();
+        const unmapped = feature.get('flags') & 4;
+        const hasSA = !!getTag(feature, 'SA');
+        if (!alreadySeen.has(id) && !unmapped && hasSA) {
+            const n = feature.get('name');
+            let val = candidates.get(n);
+            if (!val) {
+                val = [];
+                candidates.set(n, val);
+            }
+            val.push(feature);
+        }
+        alreadySeen.add(feature.id());
+    }
+    return [...candidates.values()].filter(v => v.length > 1);
+}
+export function hasPairedReads(features) {
+    for (const f of features.values()) {
+        if (f.get('flags') & 1) {
+            return true;
+        }
+    }
+    return false;
+}
+export function findMatchingAlt(feat1, feat2) {
+    const alts = feat1.get('ALT');
+    if (alts) {
+        return new Map(alts === null || alts === void 0 ? void 0 : alts.map(alt => parseBreakend(alt)).filter(notEmpty).map(bnd => [bnd.MatePosition, bnd])).get(`${feat2.get('refName')}:${feat2.get('start') + 1}`);
+    }
+    return undefined;
+}
+// Returns paired BND features across multiple views by inspecting the ALT
+// field to get exact coordinate matches
+export function getMatchedBreakendFeatures(feats) {
+    const candidates = new Map();
+    const alreadySeen = new Set();
+    for (const f of feats.values()) {
+        if (!alreadySeen.has(f.id()) && f.get('type') === 'breakend') {
+            const alts = f.get('ALT');
+            alts === null || alts === void 0 ? void 0 : alts.forEach(a => {
+                const cur = `${f.get('refName')}:${f.get('start') + 1}`;
+                const bnd = parseBreakend(a);
+                if (bnd) {
+                    const val = candidates.get(cur);
+                    if (!val) {
+                        candidates.set(bnd.MatePosition || 'none', [f]);
+                    }
+                    else {
+                        val.push(f);
+                    }
+                }
+            });
+        }
+        alreadySeen.add(f.id());
+    }
+    return [...candidates.values()].filter(v => v.length > 1);
+}
+// Getting "matched" TRA means just return all TRA
+export function getMatchedTranslocationFeatures(feats) {
+    const ret = [];
+    const alreadySeen = new Set();
+    for (const f of feats.values()) {
+        if (!alreadySeen.has(f.id()) && f.get('ALT')[0] === '<TRA>') {
+            ret.push([f]);
+        }
+        alreadySeen.add(f.id());
+    }
+    return ret;
+}
+//# sourceMappingURL=util.js.map

package/esm/BreakpointSplitView/components/util.js.map

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package/esm/BreakpointSplitView/index.d.ts

@@ -0,0 +1,3 @@
+import PluginManager from '@jbrowse/core/PluginManager';
+declare const _default: (pluginManager: PluginManager) => void;
+export default _default;

package/esm/BreakpointSplitView/index.js

@@ -0,0 +1,15 @@
+import { lazy } from 'react';
+// locals
+import BreakpointSplitView from './BreakpointSplitView';
+import stateModelFactory from './model';
+export default (pluginManager) => {
+    pluginManager.addViewType(() => {
+        return new BreakpointSplitView({
+            name: 'BreakpointSplitView',
+            displayName: 'Breakpoint split view',
+            stateModel: stateModelFactory(pluginManager),
+            ReactComponent: lazy(() => import('./components/BreakpointSplitView')),
+        });
+    });
+};
+//# sourceMappingURL=index.js.map

package/esm/BreakpointSplitView/index.js.map

@@ -0,0 +1 @@
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