@jbrowse/bandage-core 5.0.1 → 5.2.0

package/dist/cli/figure.js

@@ -21,7 +21,7 @@ import {
   placeRowGenes,
   refNameBinding,
   walkRows
-} from "../chunks/chunk-RS23442A.js";
+} from "../chunks/chunk-ZMVFSZI5.js";
 
 // src/cli/figure.ts
 import { access, open, readFile, writeFile } from "node:fs/promises";
@@ -171,7 +171,9 @@ async function renderSpec(spec, base) {
     {
       quality: spec.quality ?? 2,
       linearLayout: false,
-      bubbleSpread: spec.bubbleSpread ?? "auto"
+      bubbleSpread: spec.bubbleSpread ?? "auto",
+      spacing: spec.spacing,
+      componentSeparation: spec.componentSeparation
     },
     engine
   )).result;

package/dist/index.js

@@ -4,6 +4,7 @@ import {
   COLOR_SCHEMES,
   Canvas2DRenderer,
   DISAGREES,
+  EXON_COLOR,
   FACET_GAP_PX,
   FACET_PAD_PX,
   FACET_TITLE_PX,
@@ -35,14 +36,12 @@ import {
   assemblyWalk,
   axisScaleOf,
   backboneAssembly,
-  baseEdgeCurves,
   buildGeometry,
   clampZoom,
   coalesceRuns,
   computeColorSchemeRange,
   computeReferenceRamp,
   contains,
-  curveBounds,
   cutGbzRegion,
   cutWindowGFA,
   deletionEdges,
@@ -52,6 +51,8 @@ import {
   encodingSwatchCss,
   engineKey,
   engineRequest,
+  exonOutlineTree,
+  exonStretches,
   facetCells,
   facetGrid,
   facetLifts,
@@ -59,6 +60,8 @@ import {
   featuresOnBackbone,
   figureSvg,
   filterSamples,
+  findHoveredEdge,
+  findHoveredNode,
   fitTransform,
   forceLayout,
   formatBp,
@@ -91,7 +94,6 @@ import {
   parseRegion,
   pathColorsLegible,
   pathLegend,
-  pathRibbonOffsets,
   placeRowGenes,
   rampHue,
   rampHueCss,
@@ -99,6 +101,7 @@ import {
   rangeText,
   readoutPlacement,
   refNameBinding,
+  referenceLabel,
   referenceOrder,
   referencePathQuery,
   referenceSamplesOf,
@@ -117,7 +120,6 @@ import {
   stripRowAt,
   svgCanvas,
   svgPath,
-  translateCurves,
   trimOrigins,
   unitTicks,
   version,
@@ -136,368 +138,12 @@ import {
   walkStripFrame,
   walkStripLabelsTree,
   wellKnownSample,
-  yToXOf,
   zoomAbout
-} from "./chunks/chunk-RS23442A.js";
+} from "./chunks/chunk-ZMVFSZI5.js";
 
 // src/index.ts
 import { getDpr } from "@jbrowse/render-core/canvas2dUtils";
 
-// src/util/SpatialIndex.ts
-var FALLBACK_CELL_SIZE = 50;
-function meanExtentCellSize(extentTotal, count) {
-  return count > 0 ? Math.max(1, extentTotal / count) : FALLBACK_CELL_SIZE;
-}
-function rowPitchOf(boxes) {
-  const distinct = /* @__PURE__ */ new Set();
-  let min = Infinity;
-  let max = -Infinity;
-  for (const box of boxes) {
-    distinct.add(box.minY);
-    min = Math.min(min, box.minY);
-    max = Math.max(max, box.minY);
-  }
-  return distinct.size > 1 ? (max - min) / (distinct.size - 1) : void 0;
-}
-function cellSizeFrom(boxes, extentX, extentY) {
-  const x = meanExtentCellSize(extentX, boxes.length);
-  return {
-    x,
-    y: extentY > 0 ? meanExtentCellSize(extentY, boxes.length) : rowPitchOf(boxes) ?? x
-  };
-}
-function resolveCellSize(given, boxes, extentX, extentY) {
-  return given === void 0 ? cellSizeFrom(boxes, extentX, extentY) : typeof given === "number" ? { x: given, y: given } : given;
-}
-function getOrCreateCell(cells, cx, cy) {
-  let row = cells.get(cx);
-  if (!row) {
-    row = /* @__PURE__ */ new Map();
-    cells.set(cx, row);
-  }
-  let cell = row.get(cy);
-  if (!cell) {
-    cell = [];
-    row.set(cy, cell);
-  }
-  return cell;
-}
-function addToGrid(cells, cellSize, minX, minY, maxX, maxY, entry) {
-  const cx0 = Math.floor(minX / cellSize.x);
-  const cx1 = Math.floor(maxX / cellSize.x);
-  const cy0 = Math.floor(minY / cellSize.y);
-  const cy1 = Math.floor(maxY / cellSize.y);
-  for (let cx = cx0; cx <= cx1; cx++) {
-    for (let cy = cy0; cy <= cy1; cy++) {
-      getOrCreateCell(cells, cx, cy).push(entry);
-    }
-  }
-}
-function queryGrid(cells, cellSize, x, y, radiusX, radiusY) {
-  const cx0 = Math.floor((x - radiusX) / cellSize.x);
-  const cx1 = Math.floor((x + radiusX) / cellSize.x);
-  const cy0 = Math.floor((y - radiusY) / cellSize.y);
-  const cy1 = Math.floor((y + radiusY) / cellSize.y);
-  const results = [];
-  const seen = /* @__PURE__ */ new Set();
-  for (let cx = cx0; cx <= cx1; cx++) {
-    const row = cells.get(cx);
-    if (row) {
-      for (let cy = cy0; cy <= cy1; cy++) {
-        const cell = row.get(cy);
-        if (cell) {
-          for (const entry of cell) {
-            if (!seen.has(entry)) {
-              seen.add(entry);
-              results.push(entry);
-            }
-          }
-        }
-      }
-    }
-  }
-  return results;
-}
-var SpatialIndex = class {
-  constructor(nodePositions, cellSize) {
-    this.cells = /* @__PURE__ */ new Map();
-    const boxes = [];
-    let extentX = 0;
-    let extentY = 0;
-    for (const [nodeId, segments] of Object.entries(nodePositions)) {
-      for (let i = 0; i < segments.length - 1; i++) {
-        const seg = segments[i];
-        const next = segments[i + 1];
-        const minX = Math.min(seg.x, next.x);
-        const minY = Math.min(seg.y, next.y);
-        const maxX = Math.max(seg.x, next.x);
-        const maxY = Math.max(seg.y, next.y);
-        extentX += maxX - minX;
-        extentY += maxY - minY;
-        boxes.push({ entry: { nodeId, segmentIdx: i }, minX, minY, maxX, maxY });
-      }
-    }
-    this.cellSize = resolveCellSize(cellSize, boxes, extentX, extentY);
-    for (const b of boxes) {
-      addToGrid(
-        this.cells,
-        this.cellSize,
-        b.minX,
-        b.minY,
-        b.maxX,
-        b.maxY,
-        b.entry
-      );
-    }
-  }
-  query(x, y, radiusX, radiusY = radiusX) {
-    return queryGrid(this.cells, this.cellSize, x, y, radiusX, radiusY);
-  }
-};
-var EdgeSpatialIndex = class {
-  constructor(nodePositions, graph, drawPaths, axis, cellSize, deletions, version2 = 0, routes2) {
-    this.cells = /* @__PURE__ */ new Map();
-    this.edgeCurves = baseEdgeCurves(
-      nodePositions,
-      graph,
-      axis,
-      deletions,
-      version2,
-      routes2
-    );
-    const boxes = [];
-    let extentX = 0;
-    let extentY = 0;
-    for (let ei = 0; ei < graph.edges.length; ei++) {
-      const edge = graph.edges[ei];
-      const fromSegments = nodePositions[edge.from];
-      const toSegments = nodePositions[edge.to];
-      const curves = this.edgeCurves.get(ei);
-      if (fromSegments?.length && toSegments?.length && curves) {
-        let { minX, minY, maxX, maxY } = curveBounds(curves);
-        const numPaths = edge.pathIds?.length ?? 0;
-        if (drawPaths && numPaths > 0) {
-          let padX = 0;
-          let padY = 0;
-          for (const o of pathRibbonOffsets(
-            fromSegments,
-            toSegments,
-            numPaths,
-            axis
-          )) {
-            padX = Math.max(padX, Math.abs(o.x));
-            padY = Math.max(padY, Math.abs(o.y));
-          }
-          minX -= padX;
-          minY -= padY;
-          maxX += padX;
-          maxY += padY;
-        }
-        extentX += maxX - minX;
-        extentY += maxY - minY;
-        boxes.push({ ei, minX, minY, maxX, maxY });
-      }
-    }
-    this.cellSize = resolveCellSize(cellSize, boxes, extentX, extentY);
-    for (const b of boxes) {
-      addToGrid(this.cells, this.cellSize, b.minX, b.minY, b.maxX, b.maxY, b.ei);
-    }
-  }
-  getCurves(ei) {
-    return this.edgeCurves.get(ei);
-  }
-  query(x, y, radiusX, radiusY = radiusX) {
-    return queryGrid(this.cells, this.cellSize, x, y, radiusX, radiusY);
-  }
-};
-
-// src/util/hitDetection.ts
-function distanceToSegment(px, py, x1, y1, x2, y2) {
-  const dx = x2 - x1;
-  const dy = y2 - y1;
-  const lenSq = dx * dx + dy * dy;
-  if (lenSq === 0) {
-    return Math.hypot(px - x1, py - y1);
-  }
-  const t = Math.max(0, Math.min(1, ((px - x1) * dx + (py - y1) * dy) / lenSq));
-  return Math.hypot(px - (x1 + t * dx), py - (y1 + t * dy));
-}
-function distanceToCubicBezier(px, py, x1, y1, cx1, cy1, cx2, cy2, x2, y2) {
-  let minDist = Infinity;
-  const samples = 20;
-  let lastX = x1;
-  let lastY = y1;
-  for (let i = 1; i <= samples; i++) {
-    const t = i / samples;
-    const u = 1 - t;
-    const bx = u * u * u * x1 + 3 * u * u * t * cx1 + 3 * u * t * t * cx2 + t * t * t * x2;
-    const by = u * u * u * y1 + 3 * u * u * t * cy1 + 3 * u * t * t * cy2 + t * t * t * y2;
-    minDist = Math.min(minDist, distanceToSegment(px, py, lastX, lastY, bx, by));
-    lastX = bx;
-    lastY = by;
-  }
-  return minDist;
-}
-function distanceToBezierCurve(px, py, c) {
-  return distanceToCubicBezier(
-    px,
-    py,
-    c.x0,
-    c.y0,
-    c.cx0,
-    c.cy0,
-    c.cx1,
-    c.cy1,
-    c.x1,
-    c.y1
-  );
-}
-function distanceToEdgeCurves(px, py, curves, yToX = 1) {
-  let minDist = Infinity;
-  for (const c of curves) {
-    const d = distanceToBezierCurve(
-      px,
-      py,
-      yToX === 1 ? c : {
-        x0: c.x0,
-        y0: c.y0 * yToX,
-        cx0: c.cx0,
-        cy0: c.cy0 * yToX,
-        cx1: c.cx1,
-        cy1: c.cy1 * yToX,
-        x1: c.x1,
-        y1: c.y1 * yToX
-      }
-    );
-    if (d < minDist) {
-      minDist = d;
-    }
-  }
-  return minDist;
-}
-var nodeCache = /* @__PURE__ */ new WeakMap();
-function getSpatialIndex(nodePositions, version2) {
-  const cached = nodeCache.get(nodePositions);
-  if (cached?.version === version2) {
-    return cached.index;
-  }
-  const index = new SpatialIndex(nodePositions);
-  nodeCache.set(nodePositions, { version: version2, index });
-  return index;
-}
-var edgeCache = /* @__PURE__ */ new WeakMap();
-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 && cached.routes === routes2) {
-    return cached.index;
-  }
-  const index = new EdgeSpatialIndex(
-    nodePositions,
-    graph,
-    drawPaths,
-    axis,
-    void 0,
-    deletions,
-    version2,
-    routes2
-  );
-  edgeCache.set(nodePositions, {
-    graph,
-    drawPaths,
-    scaleX: axis.scaleX,
-    scaleY: axis.scaleY,
-    version: version2,
-    index,
-    deletions,
-    routes: routes2
-  });
-  return index;
-}
-var MIN_NODE_REACH_PX = 5;
-function findHoveredNode(nodePositions, graphX, graphY, axis, version2 = 0, ink) {
-  const yToX = yToXOf(axis);
-  const index = getSpatialIndex(nodePositions, version2);
-  const reach = (px) => Math.max(MIN_NODE_REACH_PX, px) / axis.scaleX;
-  const queryReach = reach(ink?.maxHalfWidthPx ?? 0);
-  const candidates = index.query(graphX, graphY, queryReach, queryReach / yToX);
-  let hovered = null;
-  let best = Infinity;
-  for (const { nodeId, segmentIdx } of candidates) {
-    const segments = nodePositions[nodeId];
-    const dist = distanceToSegment(
-      graphX,
-      graphY * yToX,
-      segments[segmentIdx].x,
-      segments[segmentIdx].y * yToX,
-      segments[segmentIdx + 1].x,
-      segments[segmentIdx + 1].y * yToX
-    );
-    if (dist < best && dist < reach(ink?.halfWidthPx(nodeId) ?? 0)) {
-      best = dist;
-      hovered = nodeId;
-    }
-  }
-  return hovered;
-}
-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(
-    nodePositions,
-    graph,
-    drawPaths,
-    axis,
-    version2,
-    deletions,
-    deletionRoutes
-  );
-  const candidates = edgeIndex.query(
-    graphX,
-    graphY,
-    edgeThreshold,
-    edgeThreshold / yToX
-  );
-  let hovered = null;
-  let best = edgeThreshold;
-  for (const edgeIdx of candidates) {
-    const edge = graph.edges[edgeIdx];
-    const fromSegments = nodePositions[edge.from];
-    const toSegments = nodePositions[edge.to];
-    if (!fromSegments?.length || !toSegments?.length || hiddenEdges?.has(edgeIdx)) {
-      continue;
-    }
-    const numPaths = edge.pathIds?.length ?? 0;
-    const baseCurves = edgeIndex.getCurves(edgeIdx);
-    if (!baseCurves) {
-      continue;
-    }
-    let dist;
-    if (!drawPaths || numPaths === 0) {
-      dist = distanceToEdgeCurves(graphX, graphY * yToX, baseCurves, yToX);
-    } else {
-      let minDist = Infinity;
-      for (const offset of pathRibbonOffsets(
-        fromSegments,
-        toSegments,
-        numPaths,
-        axis
-      )) {
-        const curves = offset.x === 0 && offset.y === 0 ? baseCurves : translateCurves(baseCurves, offset.x, offset.y);
-        const d = distanceToEdgeCurves(graphX, graphY * yToX, curves, yToX);
-        if (d < minDist) {
-          minDist = d;
-        }
-      }
-      dist = minDist;
-    }
-    if (dist < best) {
-      best = dist;
-      hovered = edgeIdx;
-    }
-  }
-  return hovered;
-}
-
 // src/util/wheelZoom.ts
 var ZOOM_PER_NOTCH = 1.1;
 var NOTCH_PX = 100;
@@ -1792,6 +1438,7 @@ export {
   BUBBLE_SPREADS,
   COLOR_SCHEMES,
   Canvas2DRenderer,
+  EXON_COLOR,
   FACET_GAP_PX,
   FACET_PAD_PX,
   FACET_TITLE_PX,
@@ -1850,6 +1497,8 @@ export {
   encodingSwatchCss,
   engineKey,
   engineRequest,
+  exonOutlineTree,
+  exonStretches,
   facetCells,
   facetGrid,
   facetLifts,
@@ -1899,6 +1548,7 @@ export {
   refNameBinding,
   referenceBoxes,
   referenceKnots,
+  referenceLabel,
   referenceNodes,
   referencePathQuery,
   referenceSamplesOf,

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

@@ -11,6 +11,8 @@ export interface FigureSpec extends Omit<FigureOptions, 'walks' | 'region' | 'ge
     layout?: LayoutModeValue;
     quality?: number;
     bubbleSpread?: BubbleSpread;
+    spacing?: number;
+    componentSeparation?: number;
     walks?: (string | WalkLayer)[];
     walkStrip?: boolean;
     walkRowSamples?: string[];

package/dist/types/colorSchemes.d.ts

@@ -16,7 +16,7 @@ export declare const COLOR_SCHEMES: readonly [{
     readonly label: "Depth";
 }, {
     readonly value: "node-length";
-    readonly label: "Node Length";
+    readonly label: "Node length";
 }, {
     readonly value: "stable-rank";
     readonly label: "Stable rank";

package/dist/types/deletionEdges.d.ts

@@ -4,6 +4,8 @@ export interface DeletionEdge {
     edgeIndex: number;
     from: string;
     to: string;
+    fromStrand?: '+' | '-';
+    toStrand?: '+' | '-';
     refName: string;
     start: number;
     end: number;
@@ -20,5 +22,5 @@ export declare function bypassedPoints(nodePositions: Record<string, {
 export declare function deletionArcCurves(nodePositions: Record<string, {
     x: number;
     y: number;
-}[]>, deletion: DeletionEdge, axis: AxisScale, route?: NodeSegment[]): import("./util/geometry.js").BezierCurve[] | undefined;
+}[]>, deletion: DeletionEdge, axis: AxisScale, route?: NodeSegment[], stranded?: boolean): import("./util/geometry.js").BezierCurve[] | undefined;
 export declare function deletionEdges(graph: Graph): DeletionEdge[];

package/dist/types/figure.d.ts

@@ -21,6 +21,7 @@ export interface FigureOptions {
         start: number;
         end: number;
     };
+    referenceName?: string;
     colorDomain?: {
         start: number;
         end: number;

package/dist/types/gbzWindow.d.ts

@@ -4,7 +4,9 @@ export declare class NoReferenceSampleError extends Error {
     constructor(anchor: string, referenceSamples: string[]);
 }
 export declare class NodeLimitError extends Error {
+    readonly fitsBp: number;
     name: string;
+    readonly regionTooLarge = true;
     constructor(limit: number, windowBp: number, fitsBp: number);
 }
 export declare function haplotypePrefix(name: Pick<PathName, 'sample' | 'haplotype'>): string;

package/dist/types/genes/exonOutline.d.ts

@@ -0,0 +1,18 @@
+import type { El } from '../el.js';
+import type { GenePin } from './genePins.js';
+export declare const EXON_COLOR = "#daa520";
+export interface ExonStretch {
+    key: string;
+    d: string;
+    inner: number;
+}
+export declare function exonStretches(pins: GenePin[], halfWidthPx: (nodeId: string) => number, lift?: {
+    nodeIds: ReadonlySet<string>;
+    walks: readonly unknown[];
+}, pathOf?: (d: string) => string): ExonStretch[];
+export declare function exonOutlineTree(stretches: ExonStretch[], o: {
+    id: string;
+    width: number;
+    height: number;
+    transform?: string;
+}): El | undefined;

package/dist/types/genes/genePins.d.ts

@@ -17,6 +17,7 @@ export interface GenePin {
         nodeId: string;
         d: string;
     }[];
+    nodeIds: ReadonlySet<string>;
     at: NodeSegment;
     covered: number;
 }

package/dist/types/graphLabels.d.ts

@@ -25,6 +25,7 @@ interface SizeLabelArgs {
     nodeLengths: Map<string, number>;
     deletions: DeletionEdge[];
     deletionRoutes?: DeletionRoutes;
+    stranded?: boolean;
     alleleDeletions?: AlleleDeletion[];
     axis: AxisScale;
     translateX: number;
@@ -37,7 +38,7 @@ export interface SizeLabelCandidate {
     label: GraphLabel;
     box: Box;
 }
-export declare function sizeLabelCandidates({ nodePositions, nodeLengths, deletions, deletionRoutes, alleleDeletions, axis, translateX, translateY, width, height, version, }: SizeLabelArgs): {
+export declare function sizeLabelCandidates({ nodePositions, nodeLengths, deletions, deletionRoutes, stranded, alleleDeletions, axis, translateX, translateY, width, height, version, }: SizeLabelArgs): {
     deletions: SizeLabelCandidate[];
     nodes: SizeLabelCandidate[];
 };

package/dist/types/index.d.ts

@@ -68,9 +68,11 @@ export { ROW_HEIGHT_PX } from './layout/rowSpacing.js';
 export { HALO_FACTOR, LEGEND_INSET_PX, geneCoverageNote, layoutLabels, } from './labelLayout.js';
 export type { LabelLayout, LabelLayoutSource } from './labelLayout.js';
 export { formatBp } from './graphLabels.js';
+export { EXON_COLOR, exonOutlineTree, exonStretches } from './genes/exonOutline.js';
+export type { ExonStretch } from './genes/exonOutline.js';
 export { genePins } from './genes/genePins.js';
 export type { GeneModel, GenePin } from './genes/genePins.js';
-export { WELL_KNOWN_SAMPLES, assemblyWalk, backboneAssembly, featuresOnBackbone, graphBackbone, refNameBinding, wellKnownSample, } from './reference.js';
+export { WELL_KNOWN_SAMPLES, assemblyWalk, backboneAssembly, featuresOnBackbone, graphBackbone, refNameBinding, referenceLabel, wellKnownSample, } from './reference.js';
 export type { AssemblyNames, Backbone, BackboneContig } from './reference.js';
 export { LABEL_CHAR_PX, LABEL_PAD, LABEL_PX } from './overlayLabels.js';
 export type { Graph, GraphEdge, GraphNode, LayoutResult, NodeSegment, } from './types.js';

package/dist/types/labelLayout.d.ts

@@ -3,7 +3,7 @@ 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 { Box, PlacedLabel } from './overlayLabels.js';
 import type { AlleleDeletion, NodeSegment } from './types.js';
 import type { AxisScale } from './util/geometry.js';
 export declare const HALO_FACTOR = 3.4;
@@ -35,6 +35,7 @@ export interface LabelLayoutSource {
     showDeletionEdges: boolean;
     deletions: DeletionEdge[];
     deletionRoutes?: DeletionRoutes;
+    stranded?: boolean;
     alleleDeletions: AlleleDeletion[];
     positionsVersion: number;
 }
@@ -54,12 +55,13 @@ export declare function geneLabelCandidates(pins: GenePin[], screen: (p: {
 }) => {
     x: number;
     y: number;
-}, contigThickness: number): {
+}, contigThickness: number, nodesUnder: (box: Box) => ReadonlySet<string>): {
     item: GenePin;
     x: number;
     y: number;
     text: string;
     fallback: string | undefined;
     stack: number;
+    fits: (box: Box) => boolean;
 }[];
 export declare function layoutLabels(m: LabelLayoutSource): LabelLayout;

package/dist/types/overlayLabels.d.ts

@@ -14,6 +14,7 @@ export interface LabelCandidate<T> {
     text: string;
     stack?: number;
     fallback?: string;
+    fits?: (box: Box) => boolean;
 }
 export interface PlacedLabel<T> extends LabelCandidate<T> {
     w: number;

package/dist/types/pipeline.d.ts

@@ -27,6 +27,8 @@ export interface EngineSettings {
     quality: number;
     linearLayout: boolean;
     bubbleSpread: BubbleSpread;
+    spacing?: number;
+    componentSeparation?: number;
 }
 export declare function engineRequest(graph: Graph, scaling: LayoutScaling, settings: EngineSettings): EngineRequest;
 export declare function engineKey(graph: Graph, settings: EngineSettings): string;
@@ -42,6 +44,7 @@ export declare function forceLayout(graph: Graph, settings: EngineSettings, engi
         nodePositions: {
             [x: string]: NodeSegment[];
         };
+        stranded: boolean;
         rowLabels?: import("./types.js").RowLabel[];
         sampleRows?: string[];
         alleleDeletions?: import("./types.js").AlleleDeletion[];

package/dist/types/reference.d.ts

@@ -17,6 +17,9 @@ export interface AssemblyNames {
 export declare const WELL_KNOWN_SAMPLES: ReadonlyMap<string, string>;
 export declare function wellKnownSample(assemblyName: string): string | undefined;
 export declare function graphBackbone(graph: Graph): Backbone | undefined;
+export declare function referenceLabel(graph: Graph, region?: {
+    refName: string;
+}): string | undefined;
 export declare function backboneAssembly<T extends AssemblyNames>(backbone: Backbone | undefined, assemblies: T[]): T | undefined;
 export declare function assemblyWalk(graph: Graph, assembly: AssemblyNames): PathOrigin | undefined;
 export declare function contigNames(contig: string): string[];

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

@@ -29,6 +29,7 @@ export interface BuildOptions {
     referenceRamp?: ReferenceRamp;
     deletions?: Map<number, string[]>;
     deletionRoutes?: DeletionRoutes;
+    stranded?: boolean;
     hiddenEdges?: ReadonlySet<number>;
     version?: number;
 }

package/dist/types/types.d.ts

@@ -74,4 +74,5 @@ export interface LayoutResult {
     };
     tubeMap?: TubeMapDrawing;
     deletionRoutes?: Record<number, NodeSegment[]>;
+    stranded?: boolean;
 }

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

@@ -19,7 +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, routes?: DeletionRoutes);
+    constructor(nodePositions: Record<string, NodeSegment[]>, graph: Graph, drawPaths: boolean, axis: AxisScale, cellSize?: number | CellSize, deletions?: Map<number, string[]>, version?: number, routes?: DeletionRoutes, stranded?: boolean);
     getCurves(ei: number): import("./geometry.js").BezierCurve[] | undefined;
     query(x: number, y: number, radiusX: number, radiusY?: number): number[];
 }