@jbrowse/bandage-core 4.2.0 → 4.4.0

package/dist/cli/figure.js

@@ -16,8 +16,9 @@ import {
   loadGraph,
   openGbz,
   parseRegion,
-  refNameBinding
-} from "../chunks/chunk-FPBV6GNR.js";
+  refNameBinding,
+  walkRows
+} from "../chunks/chunk-YNLMROBC.js";
 
 // src/cli/figure.ts
 import { access, open, readFile, writeFile } from "node:fs/promises";
@@ -138,6 +139,8 @@ async function renderSpec(spec, base) {
   checkLayout(spec.layout);
   const resolve = (location) => isUrl(location) ? location : path.resolve(base, location);
   let source;
+  const mode = layoutModeByValue(spec.layout ?? "force");
+  const strip = !!spec.walkStrip && mode.drawsNodes;
   if (spec.gbz) {
     const { db, index } = spec.gbz.db === "hprc" ? HPRC_GBZ : spec.gbz;
     const indexLocation = index ? resolve(index) : await siblingIndex(resolve(db));
@@ -146,7 +149,8 @@ async function renderSpec(spec, base) {
         byteSource(resolve(db)),
         indexLocation ? byteSource(indexLocation) : void 0
       ),
-      spec.gbz
+      // walk rows measure whole walks, which a cut only follows when asked
+      mode.wholeWalks || strip ? { snarls: "overlapping", ...spec.gbz } : spec.gbz
     );
     source = { ...cut, name: `${cut.sample} ${spec.gbz.region}` };
   } else if (spec.gfa) {
@@ -161,7 +165,7 @@ async function renderSpec(spec, base) {
   const graph = loadGraph(source.text, source.name, {
     referencePath: spec.referencePath
   });
-  const layout = layoutModeByValue(spec.layout ?? "force").run(graph, source.region) ?? (await forceLayout(
+  const layout = mode.run(graph, source.region) ?? (await forceLayout(
     graph,
     {
       quality: spec.quality ?? 2,
@@ -170,8 +174,10 @@ async function renderSpec(spec, base) {
     },
     engine
   )).result;
+  const stripRows = strip ? walkRows(graph, source.region) : void 0;
   return figureSvg(graph, layout, {
     ...spec,
+    walkStrip: stripRows && { rows: stripRows },
     walks: spec.walks?.map((w) => typeof w === "string" ? { walk: w } : w),
     region: source.region,
     genes: spec.genes ? await readGenes(spec.genes, graph, resolve) : void 0,

package/dist/index.js

@@ -13,6 +13,7 @@ import {
   GENE_INK,
   HALO_FACTOR,
   HPRC_GBZ,
+  LABELLED_ROW_PX,
   LABEL_CHAR_PX,
   LABEL_PAD,
   LABEL_PX,
@@ -28,6 +29,7 @@ import {
   ROW_HEIGHT_PX,
   WALK_FIELDS,
   WALK_SCHEMES,
+  WALK_STRIP_CEILING_PX,
   WELL_KNOWN_SAMPLES,
   alongRow,
   assemblyWalk,
@@ -36,6 +38,7 @@ import {
   baseEdgeCurves,
   buildGeometry,
   clampZoom,
+  coalesceRuns,
   computeColorSchemeRange,
   computeReferenceRamp,
   contains,
@@ -105,7 +108,11 @@ import {
   runPaint,
   schemeCss,
   screenToLayout,
+  segmentAt,
   serializeEl,
+  stripGeneGaps,
+  stripMarks,
+  stripRowAt,
   svgCanvas,
   svgPath,
   translateCurves,
@@ -116,6 +123,7 @@ import {
   walkHighlight,
   walkKey,
   walkLift,
+  walkMarksTree,
   walkPosition,
   walkRowReadout,
   walkRows,
@@ -123,10 +131,12 @@ import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree,
+  walkStripFrame,
+  walkStripLabelsTree,
   wellKnownSample,
   yToXOf,
   zoomAbout
-} from "./chunks/chunk-FPBV6GNR.js";
+} from "./chunks/chunk-YNLMROBC.js";
 
 // src/index.ts
 import { getDpr } from "@jbrowse/render-core/canvas2dUtils";
@@ -243,14 +253,15 @@ var SpatialIndex = class {
   }
 };
 var EdgeSpatialIndex = class {
-  constructor(nodePositions, graph, drawPaths, axis, cellSize, deletions, version2 = 0) {
+  constructor(nodePositions, graph, drawPaths, axis, cellSize, deletions, version2 = 0, routes2) {
     this.cells = /* @__PURE__ */ new Map();
     this.edgeCurves = baseEdgeCurves(
       nodePositions,
       graph,
       axis,
       deletions,
-      version2
+      version2,
+      routes2
     );
     const boxes = [];
     let extentX = 0;
@@ -373,9 +384,9 @@ function getSpatialIndex(nodePositions, version2) {
   return index;
 }
 var edgeCache = /* @__PURE__ */ new WeakMap();
-function getEdgeSpatialIndex(nodePositions, graph, drawPaths, axis, version2, deletions) {
+function getEdgeSpatialIndex(nodePositions, graph, drawPaths, axis, version2, deletions, routes2) {
   const cached = edgeCache.get(nodePositions);
-  if (cached?.graph === graph && cached.drawPaths === drawPaths && cached.scaleX === axis.scaleX && cached.scaleY === axis.scaleY && cached.version === version2 && cached.deletions === deletions) {
+  if (cached?.graph === graph && cached.drawPaths === drawPaths && cached.scaleX === axis.scaleX && cached.scaleY === axis.scaleY && cached.version === version2 && cached.deletions === deletions && cached.routes === routes2) {
     return cached.index;
   }
   const index = new EdgeSpatialIndex(
@@ -385,7 +396,8 @@ function getEdgeSpatialIndex(nodePositions, graph, drawPaths, axis, version2, de
     axis,
     void 0,
     deletions,
-    version2
+    version2,
+    routes2
   );
   edgeCache.set(nodePositions, {
     graph,
@@ -394,7 +406,8 @@ function getEdgeSpatialIndex(nodePositions, graph, drawPaths, axis, version2, de
     scaleY: axis.scaleY,
     version: version2,
     index,
-    deletions
+    deletions,
+    routes: routes2
   });
   return index;
 }
@@ -424,7 +437,7 @@ function findHoveredNode(nodePositions, graphX, graphY, axis, version2 = 0, ink)
   }
   return hovered;
 }
-function findHoveredEdge(nodePositions, graph, graphX, graphY, axis, drawPaths, version2 = 0, deletions, hiddenEdges) {
+function findHoveredEdge(nodePositions, graph, graphX, graphY, axis, drawPaths, version2 = 0, deletions, hiddenEdges, deletionRoutes) {
   const yToX = yToXOf(axis);
   const edgeThreshold = 10 / axis.scaleX;
   const edgeIndex = getEdgeSpatialIndex(
@@ -433,7 +446,8 @@ function findHoveredEdge(nodePositions, graph, graphX, graphY, axis, drawPaths,
     drawPaths,
     axis,
     version2,
-    deletions
+    deletions,
+    deletionRoutes
   );
   const candidates = edgeIndex.query(
     graphX,
@@ -1783,6 +1797,7 @@ export {
   FORCE_LAYOUT_LABEL,
   HALO_FACTOR,
   HPRC_GBZ,
+  LABELLED_ROW_PX,
   LABEL_CHAR_PX,
   LABEL_PAD,
   LABEL_PX,
@@ -1802,6 +1817,7 @@ export {
   ON_REFERENCE as WALK_ON_REFERENCE,
   OUTSIDE_CUT as WALK_OUTSIDE_CUT,
   WALK_SCHEMES,
+  WALK_STRIP_CEILING_PX,
   WELL_KNOWN_SAMPLES,
   alongRow,
   assemblyWalk,
@@ -1814,6 +1830,7 @@ export {
   buildGeometry,
   clampZoom,
   classifyBubble,
+  coalesceRuns,
   computeReferenceRamp,
   connectorAt,
   contains,
@@ -1891,8 +1908,12 @@ export {
   runPaint,
   schemeCss,
   screenToLayout,
+  segmentAt,
   serializeEl,
   stripBlockAt,
+  stripGeneGaps,
+  stripMarks,
+  stripRowAt,
   svgCanvas,
   tubeMapConnectors,
   tubeMapFrame,
@@ -1907,6 +1928,7 @@ export {
   walkHighlight,
   walkKey,
   walkLift,
+  walkMarksTree,
   walkPosition,
   walkRowReadout,
   walkRows,
@@ -1914,6 +1936,8 @@ export {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree,
+  walkStripFrame,
+  walkStripLabelsTree,
   warpX,
   wellKnownSample,
   wheelZoomFactor,

package/dist/types/cli/figure.d.ts

@@ -3,7 +3,7 @@ import type { FigureOptions } from '../figure.js';
 import type { GbzSource } from '../gbzCut.js';
 import type { LayoutModeValue } from '../layoutModes.js';
 import type { WalkLayer } from '../walkEncoding.js';
-export interface FigureSpec extends Omit<FigureOptions, 'walks' | 'region' | 'genes' | 'spec'> {
+export interface FigureSpec extends Omit<FigureOptions, 'walks' | 'region' | 'genes' | 'spec' | 'walkStrip'> {
     gfa?: string;
     gbz?: GbzSource;
     region?: string;
@@ -12,6 +12,7 @@ export interface FigureSpec extends Omit<FigureOptions, 'walks' | 'region' | 'ge
     quality?: number;
     bubbleSpread?: BubbleSpread;
     walks?: (string | WalkLayer)[];
+    walkStrip?: boolean;
     genes?: {
         file: string;
         index?: string;

package/dist/types/deletionEdges.d.ts

@@ -1,4 +1,4 @@
-import type { Graph } from './types.js';
+import type { Graph, NodeSegment } from './types.js';
 import type { AxisScale } from './util/geometry.js';
 export interface DeletionEdge {
     edgeIndex: number;
@@ -20,5 +20,5 @@ export declare function bypassedPoints(nodePositions: Record<string, {
 export declare function deletionArcCurves(nodePositions: Record<string, {
     x: number;
     y: number;
-}[]>, deletion: DeletionEdge, axis: AxisScale): import("./util/geometry.js").BezierCurve[] | undefined;
+}[]>, deletion: DeletionEdge, axis: AxisScale, route?: NodeSegment[]): import("./util/geometry.js").BezierCurve[] | undefined;
 export declare function deletionEdges(graph: Graph): DeletionEdge[];

package/dist/types/figure.d.ts

@@ -2,6 +2,7 @@ import type { ColorScheme } from './colorSchemes.js';
 import type { FacetInput } from './facetGrid.js';
 import type { GeneModel } from './genes/genePins.js';
 import type { GeneGaps, RowGene, WalkRowsWithCalls } from './layout/walkRowDraw.js';
+import type { WalkRows } from './layout/walkRows.js';
 import type { NodeWidth } from './nodeWidths.js';
 import type { Graph, LayoutResult } from './types.js';
 import type { WalkLayer } from './walkEncoding.js';
@@ -30,5 +31,10 @@ export interface FigureOptions {
     walkRows?: WalkRowsWithCalls;
     rowGenes?: Map<string, RowGene[]>;
     rowGeneGaps?: GeneGaps;
+    walkStrip?: {
+        rows: WalkRows;
+        rowGenes?: Map<string, RowGene[]>;
+        rowGeneGaps?: GeneGaps;
+    };
 }
 export declare function figureSvg(graph: Graph, layout: LayoutResult, o?: FigureOptions): string;

package/dist/types/graphLabels.d.ts

@@ -1,4 +1,5 @@
 import type { DeletionEdge } from './deletionEdges.js';
+import type { DeletionRoutes } from './layout/deletionRoutes.js';
 import type { Box, TakeBox } from './overlayLabels.js';
 import type { AlleleDeletion, NodeSegment } from './types.js';
 import type { AxisScale } from './util/geometry.js';
@@ -23,6 +24,7 @@ interface SizeLabelArgs {
     nodePositions: Record<string, NodeSegment[]>;
     nodeLengths: Map<string, number>;
     deletions: DeletionEdge[];
+    deletionRoutes?: DeletionRoutes;
     alleleDeletions?: AlleleDeletion[];
     axis: AxisScale;
     translateX: number;
@@ -35,7 +37,7 @@ export interface SizeLabelCandidate {
     label: GraphLabel;
     box: Box;
 }
-export declare function sizeLabelCandidates({ nodePositions, nodeLengths, deletions, alleleDeletions, axis, translateX, translateY, width, height, version, }: SizeLabelArgs): {
+export declare function sizeLabelCandidates({ nodePositions, nodeLengths, deletions, deletionRoutes, alleleDeletions, axis, translateX, translateY, width, height, version, }: SizeLabelArgs): {
     deletions: SizeLabelCandidate[];
     nodes: SizeLabelCandidate[];
 };

package/dist/types/index.d.ts

@@ -56,8 +56,10 @@ export { bubbleSubgraph } from './bubbles/popBubble.js';
 export type { MinigraphBubble } from './bubbles/bubbleLine.js';
 export { walkRows } from './layout/walkRows.js';
 export type { WalkAxis, WalkRow, WalkRows, WalkRun } from './layout/walkRows.js';
-export { BAR_PX as WALK_BAR_PX, DISAGREES as WALK_DISAGREES, GAP_PX as WALK_GAP_PX, GENE_INK as WALK_GENE_INK, OFF_REFERENCE as WALK_OFF_REFERENCE, ON_REFERENCE as WALK_ON_REFERENCE, OUTSIDE_CUT as WALK_OUTSIDE_CUT, alongRow, placeRowGenes, readoutPlacement, rowGeneBoxes, rowSpan, runPaint, unitTicks, walkRowReadout, walkRowsKey, walkRowsKeyTree, walkRowsTree, } from './layout/walkRowDraw.js';
+export { BAR_PX as WALK_BAR_PX, DISAGREES as WALK_DISAGREES, GAP_PX as WALK_GAP_PX, GENE_INK as WALK_GENE_INK, OFF_REFERENCE as WALK_OFF_REFERENCE, ON_REFERENCE as WALK_ON_REFERENCE, OUTSIDE_CUT as WALK_OUTSIDE_CUT, alongRow, coalesceRuns, placeRowGenes, readoutPlacement, rowGeneBoxes, rowSpan, runPaint, unitTicks, walkRowReadout, walkRowsKey, walkRowsKeyTree, walkRowsTree, } from './layout/walkRowDraw.js';
 export type { GeneBox, GeneGaps, KeyEntry, KeySwatch, ReadoutCall, RowGene, WalkRowsFrame, WalkRowsWithCalls, } from './layout/walkRowDraw.js';
+export { LABELLED_ROW_PX, WALK_STRIP_CEILING_PX, segmentAt, stripGeneGaps, stripMarks, stripRowAt, walkMarksTree, walkStripFrame, walkStripLabelsTree, } from './layout/walkStrip.js';
+export type { StripFrame, StripMark } from './layout/walkStrip.js';
 export { el, serializeEl } from './el.js';
 export type { El, ElAttrs } from './el.js';
 export { RAMP_GRADIENT_CSS, rampHue, rampHueCss, rampStops, } from './referenceRampCss.js';

package/dist/types/labelLayout.d.ts

@@ -2,6 +2,7 @@ import type { BubbleHalo, RouteLabel } from './bubbles/bubbleHalos.js';
 import type { DeletionEdge } from './deletionEdges.js';
 import type { GenePin } from './genes/genePins.js';
 import type { GraphLabel } from './graphLabels.js';
+import type { DeletionRoutes } from './layout/deletionRoutes.js';
 import type { PlacedLabel } from './overlayLabels.js';
 import type { AlleleDeletion, NodeSegment } from './types.js';
 import type { AxisScale } from './util/geometry.js';
@@ -33,6 +34,7 @@ export interface LabelLayoutSource {
     nodeLengths: Map<string, number>;
     showDeletionEdges: boolean;
     deletions: DeletionEdge[];
+    deletionRoutes?: DeletionRoutes;
     alleleDeletions: AlleleDeletion[];
     positionsVersion: number;
 }

package/dist/types/layout/deletionRoutes.d.ts

@@ -0,0 +1,31 @@
+import type { BandageScaleOpts } from './drawnScale.js';
+import type { DeletionEdge } from '../deletionEdges.js';
+import type { Graph, GraphEdge, GraphNode, NodeSegment } from '../types.js';
+export type DeletionRoutes = Record<number, NodeSegment[]>;
+export declare function withDeletionRoutes(graph: Graph, deletions: DeletionEdge[]): {
+    graph: {
+        nodes: {
+            id: string;
+            name: string;
+            length: number;
+            depth: number;
+        }[];
+        edges: GraphEdge[];
+        name: string;
+        paths?: import("../types.js").GraphPath[];
+        anchorPaths?: import("../types.js").PathOrigin[];
+        pathVisits?: Map<string, import("../types.js").PathVisit[]>;
+        anchoredBy?: "tags" | "paths";
+        referencePath?: string;
+        reads?: import("../gaf/parseGaf.js").GafRecord[];
+    };
+    routes: Map<number, string>;
+    ids: Set<string>;
+};
+export declare function routeNodes(graph: Graph, deletions: DeletionEdge[], routes: Map<number, string>, drawnOf: (bp: number) => number, opts: BandageScaleOpts): GraphNode[];
+export declare function takeRoutes(positions: Record<string, NodeSegment[]>, routes: Map<number, string>): {
+    nodePositions: {
+        [x: string]: NodeSegment[];
+    };
+    deletionRoutes: DeletionRoutes;
+};

package/dist/types/layout/drawnScale.d.ts

@@ -25,4 +25,5 @@ export interface LayoutScaling {
     opts: BandageScaleOpts;
 }
 export declare function layoutScaling(graph: Graph, spread?: NodeLengthSpread): LayoutScaling;
+export declare function drawnLengthOf(graph: Graph, spread?: NodeLengthSpread): (bp: number) => number;
 export { MEAN_NODE_LENGTH };

package/dist/types/layout/mergeRuns.d.ts

@@ -3,7 +3,7 @@ export interface MergedRuns {
     graph: Graph;
     runs: Map<string, string[]>;
 }
-export declare function mergeRuns(graph: Graph): MergedRuns;
+export declare function mergeRuns(graph: Graph, alone?: ReadonlySet<string>): MergedRuns;
 export declare function splitRuns(positions: Record<string, NodeSegment[]>, runs: Map<string, string[]>, weightOf: (id: string) => number): Record<string, NodeSegment[]>;
 export declare function polylineSlice(line: NodeSegment[], from: number, to: number): NodeSegment[];
 export declare function polylineMidpoint(line: NodeSegment[]): NodeSegment;

package/dist/types/layout/walkRowDraw.d.ts

@@ -50,6 +50,7 @@ export interface RowGene {
     }[];
 }
 export declare function placeRowGenes(rows: WalkRow[], byRow: Map<string, GeneModel[]>): Map<string, RowGene[]>;
+export declare function boxesGenes(rowPx: number, barPx: number): boolean;
 export interface GeneBox {
     name: string;
     x: number;
@@ -66,7 +67,10 @@ export interface GeneBox {
         size: number;
     };
 }
-export declare function rowGeneBoxes(genes: RowGene[], X: (offset: number) => number, y: number): GeneBox[];
+export declare function rowGeneBoxes(genes: RowGene[], X: (offset: number) => number, y: number, { rowPx, barPx }?: {
+    rowPx?: number | undefined;
+    barPx?: number | undefined;
+}): GeneBox[];
 export type KeySwatch = {
     kind: 'bar';
     fill: string;
@@ -82,6 +86,7 @@ export interface KeyEntry {
     note?: true;
 }
 export interface GeneGaps {
+    crowded?: boolean;
     untracked: number;
     unplaced?: number;
     unread: number;
@@ -114,7 +119,11 @@ export interface WalkRowsFrame {
     translateY: number;
     width: number;
     height: number;
+    rowPx?: number;
+    barPx?: number;
+    readouts?: boolean;
 }
+export declare function coalesceRuns(runs: WalkRun[], pxPerBp: number): WalkRun[];
 export declare function walkRowsTree(bars: WalkRowsWithCalls, frame: WalkRowsFrame, o?: {
     ramp?: {
         start: number;

package/dist/types/layout/walkStrip.d.ts

@@ -0,0 +1,32 @@
+import type { GeneGaps, WalkRowsFrame } from './walkRowDraw.js';
+import type { WalkRow, WalkRows } from './walkRows.js';
+import type { Graph, GraphNode } from '../types.js';
+export declare const WALK_STRIP_CEILING_PX = 260;
+export declare const LABELLED_ROW_PX = 12;
+export interface StripMark {
+    row: string;
+    start: number;
+    bp: number;
+}
+export declare function stripMarks(graph: Graph, rows: WalkRow[], node: GraphNode): StripMark[];
+export declare function segmentAt(graph: Graph, row: WalkRow, offset: number, pxPerBp: number): string | undefined;
+export interface StripFrame extends WalkRowsFrame {
+    rowPx: number;
+    barPx: number;
+    readouts: boolean;
+    labelled: boolean;
+    boxesGenes: boolean;
+}
+export declare function walkStripFrame(bars: WalkRows, o: {
+    width: number;
+    maxHeight?: number;
+    labelPx?: number;
+}): StripFrame;
+export declare function stripRowAt(bars: WalkRows, frame: StripFrame, x: number, y: number): {
+    index: number;
+    row: WalkRow;
+    offset: number;
+} | undefined;
+export declare function walkMarksTree(bars: WalkRows, frame: StripFrame, marks: StripMark[]): import("../index.js").El;
+export declare function walkStripLabelsTree(bars: WalkRows, frame: StripFrame, bold?: ReadonlySet<string>): import("../index.js").El;
+export declare function stripGeneGaps(frame: StripFrame, gaps: GeneGaps | undefined): GeneGaps | undefined;

package/dist/types/pipeline.d.ts

@@ -32,23 +32,26 @@ export declare function engineRequest(graph: Graph, scaling: LayoutScaling, sett
 export declare function engineKey(graph: Graph, settings: EngineSettings): string;
 export declare function forceLayout(graph: Graph, settings: EngineSettings, engine: LayoutEngine): Promise<{
     result: {
-        nodePositions: Record<string, NodeSegment[]>;
-        rowLabels?: import("./types.js").RowLabel[];
-        sampleRows?: string[];
-        alleleDeletions?: import("./types.js").AlleleDeletion[];
-        referenceAxis?: boolean;
-        pixelRows?: boolean;
+        deletionRoutes?: import("./layout/deletionRoutes.js").DeletionRoutes | undefined;
         extent?: {
             minX?: number;
             minY?: number;
             maxX?: number;
             maxY?: number;
         };
+        nodePositions: {
+            [x: string]: NodeSegment[];
+        };
+        rowLabels?: import("./types.js").RowLabel[];
+        sampleRows?: string[];
+        alleleDeletions?: import("./types.js").AlleleDeletion[];
+        referenceAxis?: boolean;
+        pixelRows?: boolean;
         tubeMap?: import("./index.js").TubeMapDrawing;
     };
     duration: number;
 }>;
-export declare function layoutExtent(nodePositions: Record<string, NodeSegment[]>): Bounds;
+export declare function layoutExtent(nodePositions: Record<string | number, NodeSegment[]>): Bounds;
 export declare const FIT_PADDING = 40;
 export declare function clampZoom(zoom: number): number;
 export declare function fittedTranslateY(bounds: {

package/dist/types/renderer/GeometryBuilder.d.ts

@@ -1,4 +1,5 @@
 import type { ResolvedColorScheme } from '../colorSchemes.js';
+import type { DeletionRoutes } from '../layout/deletionRoutes.js';
 import type { NodeWidth } from '../nodeWidths.js';
 import type { Graph, GraphNode, NodeSegment } from '../types.js';
 import type { WalkLift } from '../walkHighlight.js';
@@ -27,6 +28,7 @@ export interface BuildOptions {
     };
     referenceRamp?: ReferenceRamp;
     deletions?: Map<number, string[]>;
+    deletionRoutes?: DeletionRoutes;
     hiddenEdges?: ReadonlySet<number>;
     version?: number;
 }

package/dist/types/types.d.ts

@@ -73,4 +73,5 @@ export interface LayoutResult {
         maxY?: number;
     };
     tubeMap?: TubeMapDrawing;
+    deletionRoutes?: Record<number, NodeSegment[]>;
 }

package/dist/types/util/SpatialIndex.d.ts

@@ -1,3 +1,4 @@
+import type { DeletionRoutes } from '../layout/deletionRoutes.js';
 import type { Graph, NodeSegment } from '../types.js';
 import type { AxisScale } from './geometry.js';
 interface CellEntry {
@@ -18,7 +19,7 @@ export declare class EdgeSpatialIndex {
     private cellSize;
     private cells;
     private edgeCurves;
-    constructor(nodePositions: Record<string, NodeSegment[]>, graph: Graph, drawPaths: boolean, axis: AxisScale, cellSize?: number | CellSize, deletions?: Map<number, string[]>, version?: number);
+    constructor(nodePositions: Record<string, NodeSegment[]>, graph: Graph, drawPaths: boolean, axis: AxisScale, cellSize?: number | CellSize, deletions?: Map<number, string[]>, version?: number, routes?: DeletionRoutes);
     getCurves(ei: number): import("./geometry.js").BezierCurve[] | undefined;
     query(x: number, y: number, radiusX: number, radiusY?: number): number[];
 }

package/dist/types/util/edgeCurves.d.ts

@@ -1,4 +1,5 @@
+import type { DeletionRoutes } from '../layout/deletionRoutes.js';
 import type { Graph, NodeSegment } from '../types.js';
 import type { AxisScale, BezierCurve } from './geometry.js';
 export type EdgeCurves = Map<number, BezierCurve[]>;
-export declare function baseEdgeCurves(nodePositions: Record<string, NodeSegment[]>, graph: Graph, axis: AxisScale, deletions: Map<number, string[]> | undefined, version: number): EdgeCurves;
+export declare function baseEdgeCurves(nodePositions: Record<string, NodeSegment[]>, graph: Graph, axis: AxisScale, deletions: Map<number, string[]> | undefined, version: number, routes?: DeletionRoutes): EdgeCurves;

package/dist/types/util/geometry.d.ts

@@ -43,4 +43,5 @@ export declare function pathRibbonOffsets(fromSegments: NodeSegment[], toSegment
 export type SelfLink = boolean | Side;
 export declare function selfLinkOf(edge: GraphEdge): SelfLink;
 export declare function computeEdgeCurves(fromSegments: NodeSegment[], toSegments: NodeSegment[], selfLink: SelfLink, offsetX: number, offsetY: number, axis: AxisScale, bypassed?: NodeSegment[], maxBowIn?: number): BezierCurve[];
+export declare function routedEdgeCurves(fromSegments: NodeSegment[], toSegments: NodeSegment[], route: NodeSegment[]): BezierCurve[];
 export {};

package/dist/types/util/hitDetection.d.ts

@@ -1,3 +1,4 @@
+import type { DeletionRoutes } from '../layout/deletionRoutes.js';
 import type { Graph, NodeSegment } from '../types.js';
 import type { AxisScale } from './geometry.js';
 export declare function distanceToSegment(px: number, py: number, x1: number, y1: number, x2: number, y2: number): number;
@@ -7,4 +8,4 @@ export interface NodeInk {
     maxHalfWidthPx: number;
 }
 export declare function findHoveredNode(nodePositions: Record<string, NodeSegment[]>, graphX: number, graphY: number, axis: AxisScale, version?: number, ink?: NodeInk): string | null;
-export declare function findHoveredEdge(nodePositions: Record<string, NodeSegment[]>, graph: Graph, graphX: number, graphY: number, axis: AxisScale, drawPaths: boolean, version?: number, deletions?: Map<number, string[]>, hiddenEdges?: ReadonlySet<number>): number | null;
+export declare function findHoveredEdge(nodePositions: Record<string, NodeSegment[]>, graph: Graph, graphX: number, graphY: number, axis: AxisScale, drawPaths: boolean, version?: number, deletions?: Map<number, string[]>, hiddenEdges?: ReadonlySet<number>, deletionRoutes?: DeletionRoutes): number | null;

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "4.2.0";
+export declare const version = "4.4.0";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "4.2.0",
+  "version": "4.4.0",
   "description": "Pangenome graph layout and drawing with no host: GFA in, the Bandage force-directed engine and reference-anchored layouts, a Canvas2D renderer, hit testing and labels out",
   "license": "GPL-3.0-or-later",
   "repository": {