@jbrowse/bandage-core 8.2.0 → 9.1.0

package/dist/index.js

@@ -1,41 +1,48 @@
 import {
   wheelZoomFactor
 } from "./chunks/chunk-TDQLINVI.js";
+import {
+  connectorAt,
+  drawLitConnector,
+  drawTubeMapConnectors,
+  tubeMapConnectors
+} from "./chunks/chunk-2ZT7ZF7A.js";
 import {
   drawTubeMap,
-  tubeMapPicture
-} from "./chunks/chunk-KCRL5JB2.js";
+  drawTubeMapHighlight,
+  tubeMapMismatchAt,
+  tubeMapPicture,
+  tubeMapTrackAt
+} from "./chunks/chunk-75HR3756.js";
 import {
   tubeMapFrame,
   tubeMapNodeAt
 } from "./chunks/chunk-VZQ4FKLR.js";
+import {
+  referenceKnots,
+  warpX
+} from "./chunks/chunk-KQFOCDFY.js";
 import {
   drawTubeMapGenes,
   tubeMapGenes
-} from "./chunks/chunk-OWFPAIJI.js";
-import "./chunks/chunk-733L2TS6.js";
+} from "./chunks/chunk-WEDZ76AK.js";
+import "./chunks/chunk-XXT2JCAC.js";
 import {
   tubeMapNodeColors
 } from "./chunks/chunk-FFFQNQUI.js";
-import {
-  referenceKnots,
-  warpX
-} from "./chunks/chunk-KQFOCDFY.js";
 import {
   drawTubeMapRuler,
   referenceBoxes,
   rulerBoxes,
   tubeX
-} from "./chunks/chunk-DRA7733Q.js";
-import {
-  connectorAt,
-  drawTubeMapConnectors,
-  referenceNodes,
-  tubeMapConnectors
-} from "./chunks/chunk-GQ2AOHU4.js";
+} from "./chunks/chunk-BPRXQ2SS.js";
 import {
   createForceLayoutCache
-} from "./chunks/chunk-SKKYLBRA.js";
+} from "./chunks/chunk-RRZMMYBG.js";
+import {
+  graphBubbles,
+  superbubblesFromGraph
+} from "./chunks/chunk-FUVI4WQP.js";
 import {
   bubbleSubgraph
 } from "./chunks/chunk-VHW7FDHU.js";
@@ -47,17 +54,17 @@ import {
 } from "./chunks/chunk-BXEPA4KS.js";
 import {
   bubbleHalos
-} from "./chunks/chunk-ISEI2FH3.js";
+} from "./chunks/chunk-2AWUWGAD.js";
 import {
   bubblesFromGraph
-} from "./chunks/chunk-4S47XRYA.js";
+} from "./chunks/chunk-GOZYKNQ2.js";
 import {
   BUBBLE_KIND_COLORS,
   BUBBLE_KIND_NAMES,
   bubbleSegmentIds,
   classifyBubble
-} from "./chunks/chunk-WOO7QYKB.js";
-import "./chunks/chunk-MFKORG3F.js";
+} from "./chunks/chunk-XKWD2RY3.js";
+import "./chunks/chunk-FX4RDMDN.js";
 import {
   REFERENCE_STRIP_ZONE_PX,
   drawReferenceStrip,
@@ -69,9 +76,9 @@ import {
   LAYOUT_MODES,
   layoutModeByValue,
   modeUsesLayoutEngine
-} from "./chunks/chunk-CF62U3QS.js";
-import "./chunks/chunk-W2I4DOL4.js";
-import "./chunks/chunk-TEDQJPMI.js";
+} from "./chunks/chunk-WNUZP3WQ.js";
+import "./chunks/chunk-INJ2UVOT.js";
+import "./chunks/chunk-CWFNEKST.js";
 import "./chunks/chunk-LOEA5IHZ.js";
 import "./chunks/chunk-L3O7AWLI.js";
 import "./chunks/chunk-TZFWUT2C.js";
@@ -112,7 +119,7 @@ import {
 } from "./chunks/chunk-7XHHVYG7.js";
 import {
   figureSvg
-} from "./chunks/chunk-DE4UFDUZ.js";
+} from "./chunks/chunk-3TGUKQWQ.js";
 import {
   layoutGeometryInputs
 } from "./chunks/chunk-LOCJN3BZ.js";
@@ -160,7 +167,7 @@ import {
 } from "./chunks/chunk-MIW3HYPE.js";
 import {
   Canvas2DRenderer
-} from "./chunks/chunk-2WNBVB55.js";
+} from "./chunks/chunk-WBCOREDZ.js";
 import {
   getDpr
 } from "./chunks/chunk-4BYTEJGW.js";
@@ -204,7 +211,7 @@ import {
 import "./chunks/chunk-G2FD7S3C.js";
 import {
   version
-} from "./chunks/chunk-3FXPFVKJ.js";
+} from "./chunks/chunk-UID3QBWH.js";
 import {
   axisScaleOf,
   contains,
@@ -212,7 +219,7 @@ import {
   screenToLayout,
   viewportOf,
   zoomAbout
-} from "./chunks/chunk-TL4B342F.js";
+} from "./chunks/chunk-MXDQGA7A.js";
 import {
   walkRowLabels,
   walkRowsExtent
@@ -283,7 +290,7 @@ import {
 import {
   FIGURE_DEFAULTS,
   figureSpecSettings
-} from "./chunks/chunk-6VBDMZBZ.js";
+} from "./chunks/chunk-XLCTQHBE.js";
 import {
   ENGINE_DEFAULTS,
   FIT_PADDING,
@@ -296,16 +303,16 @@ import {
   forceLayout,
   layoutExtent,
   loadGraph
-} from "./chunks/chunk-5OIVTEF7.js";
+} from "./chunks/chunk-OOXIMURX.js";
 import "./chunks/chunk-PUG7LXDF.js";
 import "./chunks/chunk-IGVV37VI.js";
-import "./chunks/chunk-OCMBULGN.js";
-import "./chunks/chunk-QYBZZI5H.js";
-import "./chunks/chunk-CDLPYR5O.js";
 import {
   graphFromTables,
   graphTablesGFA
 } from "./chunks/chunk-OA7RIMZ2.js";
+import "./chunks/chunk-OCMBULGN.js";
+import "./chunks/chunk-QYBZZI5H.js";
+import "./chunks/chunk-CDLPYR5O.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-ST2IBUAN.js";
 import {
@@ -393,10 +400,12 @@ export {
   cutsWholeWalks,
   deletionDrawing,
   deletionEdges,
+  drawLitConnector,
   drawReferenceStrip,
   drawTubeMap,
   drawTubeMapConnectors,
   drawTubeMapGenes,
+  drawTubeMapHighlight,
   drawTubeMapRuler,
   drawingBounds,
   edgeHoverText,
@@ -429,6 +438,7 @@ export {
   genesOnRow,
   getDpr,
   graphBackbone,
+  graphBubbles,
   graphFromTables,
   graphTablesGFA,
   haplotypeWanted,
@@ -463,7 +473,6 @@ export {
   referenceBoxes,
   referenceKnots,
   referenceLabel,
-  referenceNodes,
   referencePathQuery,
   referenceSamplesOf,
   referenceStripBlocks,
@@ -485,13 +494,16 @@ export {
   stripGeneGaps,
   stripMarks,
   stripRowAt,
+  superbubblesFromGraph,
   svgCanvas,
   tubeMapConnectors,
   tubeMapFrame,
   tubeMapGenes,
+  tubeMapMismatchAt,
   tubeMapNodeAt,
   tubeMapNodeColors,
   tubeMapPicture,
+  tubeMapTrackAt,
   tubeX,
   unitTicks,
   version,

package/dist/layout/forceCache.js

@@ -1,13 +1,13 @@
 import {
   createForceLayoutCache
-} from "../chunks/chunk-SKKYLBRA.js";
-import "../chunks/chunk-5OIVTEF7.js";
+} from "../chunks/chunk-RRZMMYBG.js";
+import "../chunks/chunk-OOXIMURX.js";
 import "../chunks/chunk-PUG7LXDF.js";
 import "../chunks/chunk-IGVV37VI.js";
+import "../chunks/chunk-OA7RIMZ2.js";
 import "../chunks/chunk-OCMBULGN.js";
 import "../chunks/chunk-QYBZZI5H.js";
 import "../chunks/chunk-CDLPYR5O.js";
-import "../chunks/chunk-OA7RIMZ2.js";
 import "../chunks/chunk-ES2N6V56.js";
 import "../chunks/chunk-ST2IBUAN.js";
 import "../chunks/chunk-BPLIXMH7.js";

package/dist/layout/tubeMapLayout.js

@@ -1,12 +1,15 @@
 import {
+  boxGraph,
+  hasTubeMapBackbone,
   hasTubeMapPaths,
+  mergedRuns,
+  pathSteps,
   tubeMapLayout,
   tubeMapReferenceLayout,
   tubeMapTracks,
-  tubeWidth,
-  visitStrands
-} from "../chunks/chunk-W2I4DOL4.js";
-import "../chunks/chunk-TEDQJPMI.js";
+  tubeWidth
+} from "../chunks/chunk-INJ2UVOT.js";
+import "../chunks/chunk-CWFNEKST.js";
 import "../chunks/chunk-C44YRP5F.js";
 import "../chunks/chunk-7GBL7SJY.js";
 import "../chunks/chunk-3ZZSX5HN.js";
@@ -19,10 +22,13 @@ import "../chunks/chunk-2CVHXFK7.js";
 import "../chunks/chunk-CPMHA4W5.js";
 import "../chunks/chunk-FYQWPEEY.js";
 export {
+  boxGraph,
+  hasTubeMapBackbone,
   hasTubeMapPaths,
+  mergedRuns,
+  pathSteps,
   tubeMapLayout,
   tubeMapReferenceLayout,
   tubeMapTracks,
-  tubeWidth,
-  visitStrands
+  tubeWidth
 };

package/dist/layoutModes.js

@@ -4,9 +4,9 @@ import {
   LAYOUT_MODE_VALUES,
   layoutModeByValue,
   modeUsesLayoutEngine
-} from "./chunks/chunk-CF62U3QS.js";
-import "./chunks/chunk-W2I4DOL4.js";
-import "./chunks/chunk-TEDQJPMI.js";
+} from "./chunks/chunk-WNUZP3WQ.js";
+import "./chunks/chunk-INJ2UVOT.js";
+import "./chunks/chunk-CWFNEKST.js";
 import "./chunks/chunk-LOEA5IHZ.js";
 import "./chunks/chunk-L3O7AWLI.js";
 import "./chunks/chunk-TZFWUT2C.js";

package/dist/pipeline.js

@@ -11,13 +11,13 @@ import {
   forceLayout,
   layoutExtent,
   loadGraph
-} from "./chunks/chunk-5OIVTEF7.js";
+} from "./chunks/chunk-OOXIMURX.js";
 import "./chunks/chunk-PUG7LXDF.js";
 import "./chunks/chunk-IGVV37VI.js";
+import "./chunks/chunk-OA7RIMZ2.js";
 import "./chunks/chunk-OCMBULGN.js";
 import "./chunks/chunk-QYBZZI5H.js";
 import "./chunks/chunk-CDLPYR5O.js";
-import "./chunks/chunk-OA7RIMZ2.js";
 import "./chunks/chunk-ES2N6V56.js";
 import "./chunks/chunk-ST2IBUAN.js";
 import "./chunks/chunk-BPLIXMH7.js";

package/dist/renderer/Canvas2DRenderer.js

@@ -1,7 +1,7 @@
 import {
   Canvas2DRenderer,
   arrowheadOutline
-} from "../chunks/chunk-2WNBVB55.js";
+} from "../chunks/chunk-WBCOREDZ.js";
 import "../chunks/chunk-4BYTEJGW.js";
 import "../chunks/chunk-G2FD7S3C.js";
 export {

package/dist/renderer/recordingCanvas.js

@@ -4,6 +4,7 @@ function recordingCanvas() {
   const fills = [];
   const lineWidths = [];
   const points = [];
+  let clears = 0;
   const at = (x, y) => {
     points.push({ x, y });
   };
@@ -27,6 +28,9 @@ function recordingCanvas() {
     },
     fillRect: () => {
     },
+    clearRect: () => {
+      clears++;
+    },
     stroke: () => {
       strokes.push(ctx.strokeStyle);
       lineWidths.push(ctx.lineWidth);
@@ -37,7 +41,14 @@ function recordingCanvas() {
   };
   const canvas = document.createElement("canvas");
   canvas.getContext = () => ctx;
-  return { canvas, strokes, fills, lineWidths, points };
+  return {
+    canvas,
+    strokes,
+    fills,
+    lineWidths,
+    points,
+    clears: () => clears
+  };
 }
 export {
   recordingCanvas

package/dist/tubeMap/axis.js

@@ -6,7 +6,7 @@ import {
   rulerMarks,
   tubeSpan,
   tubeX
-} from "../chunks/chunk-DRA7733Q.js";
+} from "../chunks/chunk-BPRXQ2SS.js";
 import "../chunks/chunk-3ZZSX5HN.js";
 import "../chunks/chunk-AB35TJST.js";
 import "../chunks/chunk-TAMCZHLW.js";

package/dist/tubeMap/coarsen.js

@@ -1,9 +1,7 @@
 import {
-  visitStrands
-} from "../chunks/chunk-W2I4DOL4.js";
-import {
-  canonicalStrand
-} from "../chunks/chunk-TEDQJPMI.js";
+  pathSteps
+} from "../chunks/chunk-INJ2UVOT.js";
+import "../chunks/chunk-CWFNEKST.js";
 import "../chunks/chunk-C44YRP5F.js";
 import "../chunks/chunk-7GBL7SJY.js";
 import "../chunks/chunk-3ZZSX5HN.js";
@@ -21,20 +19,11 @@ import {
 } from "../chunks/chunk-FYQWPEEY.js";
 
 // src/tubeMap/coarsen.ts
-function readWalk(path, nodeById, strands) {
-  const visitName = pathOrigin(path.name).name;
-  const seen = /* @__PURE__ */ new Map();
+function readWalk(path, steps) {
   const runs = [];
   const open = () => ({ a: -Infinity, b: Infinity, detour: [], bp: 0 });
   const gaps = [open()];
-  for (const id of path.nodeIds) {
-    const node = nodeById.get(id);
-    if (!node) {
-      continue;
-    }
-    const k = seen.get(node.name) ?? 0;
-    seen.set(node.name, k + 1);
-    const strand = strands.get(`${visitName}	${node.name}`)?.[k] ?? canonicalStrand(node);
+  for (const { node, strand } of steps) {
     const gap = gaps.at(-1);
     const last = runs.at(-1);
     if (isBackbone(node)) {
@@ -119,13 +108,13 @@ function findCuts(walks, sigma, cuts) {
       }
     }
   }
+  const spans = walks.flatMap(({ runs, gaps }) => [
+    ...gaps.filter((g) => isSmall(g, sigma)).map((g) => [g.a, g.b]),
+    ...runs.filter((r) => r.inverted && r.end - r.start < sigma).map((r) => [r.start, r.end])
+  ]);
   for (let changed = true; changed; ) {
     changed = false;
     const sorted = [...cuts.keys()].sort((x, y) => x - y);
-    const spans = walks.flatMap(({ runs, gaps }) => [
-      ...gaps.filter((g) => isSmall(g, sigma)).map((g) => [g.a, g.b]),
-      ...runs.filter((r) => r.inverted && r.end - r.start < sigma).map((r) => [r.start, r.end])
-    ]);
     for (const [a, b] of spans) {
       if (strictlyInside(sorted, a, b)) {
         changed ||= !cuts.has(a) || !cuts.has(b);
@@ -179,9 +168,8 @@ function coarsenTubeMap(graph, sigma) {
   if (backbone.length === 0 || paths.length === 0) {
     return void 0;
   }
-  const nodeById = new Map(graph.nodes.map((n) => [n.id, n]));
-  const strands = visitStrands(graph);
-  const walks = paths.map((p) => readWalk(p, nodeById, strands));
+  const stepsOf = pathSteps(graph);
+  const walks = paths.map((p, i) => readWalk(p, stepsOf[i]));
   const cuts = findCuts(walks, sigma, referenceGaps(backbone));
   const sortedCuts = [...cuts.keys()].sort((x, y) => x - y);
   const merged = mergeReference(backbone, cuts);

package/dist/tubeMap/connectors.js

@@ -1,13 +1,12 @@
 import {
   connectorAt,
+  drawLitConnector,
   drawTubeMapConnectors,
-  referenceNodes,
   tubeMapConnectors
-} from "../chunks/chunk-GQ2AOHU4.js";
-import "../chunks/chunk-FYQWPEEY.js";
+} from "../chunks/chunk-2ZT7ZF7A.js";
 export {
   connectorAt,
+  drawLitConnector,
   drawTubeMapConnectors,
-  referenceNodes,
   tubeMapConnectors
 };

package/dist/tubeMap/deviations.js

@@ -1,20 +1,15 @@
 import {
-  isBackbone
-} from "../chunks/chunk-FYQWPEEY.js";
+  referenceBoxes
+} from "../chunks/chunk-BPRXQ2SS.js";
+import "../chunks/chunk-3ZZSX5HN.js";
+import "../chunks/chunk-AB35TJST.js";
+import "../chunks/chunk-TAMCZHLW.js";
+import "../chunks/chunk-N6FECAXP.js";
+import "../chunks/chunk-2CVHXFK7.js";
+import "../chunks/chunk-CPMHA4W5.js";
+import "../chunks/chunk-FYQWPEEY.js";
 
 // src/tubeMap/deviations.ts
-function boxesOf(graph, layout) {
-  const nodeById = new Map(graph.nodes.map((n) => [n.id, n]));
-  const boxes = [];
-  layout.nodes.forEach((node, index) => {
-    const g = nodeById.get(node.name);
-    if (node.order >= 0 && g && isBackbone(g)) {
-      const bp0 = g.stable.start;
-      boxes.push({ bp0, bp1: bp0 + node.sequenceLength, index, node });
-    }
-  });
-  return boxes.sort((a, b) => a.bp0 - b.bp0);
-}
 function boxAt(boxes, bp, visited) {
   let lo = 0;
   let hi = boxes.length - 1;
@@ -30,8 +25,9 @@ function boxAt(boxes, bp, visited) {
     (box) => box && visited.has(box.index) && box.bp0 <= bp && bp <= box.bp1
   );
 }
-function deviationMarks(graph, layout, deviations) {
-  const boxes = boxesOf(graph, layout);
+function deviationMarks(drawing, deviations) {
+  const { layout } = drawing;
+  const boxes = [...referenceBoxes(drawing).values()].flat().sort((a, b) => a.bp0 - b.bp0);
   const marks = [];
   for (const track of layout.tracks) {
     const devs = track.name ? deviations.get(track.name) : void 0;
@@ -45,12 +41,12 @@ function deviationMarks(graph, layout, deviations) {
       for (const d of devs) {
         const box = boxAt(boxes, d.start, visited);
         if (box) {
-          const { node, bp0, bp1 } = box;
-          const at = (bp) => node.x + (Math.min(bp, bp1) - bp0) / (bp1 - bp0) * node.pixelWidth;
+          const { bp0, bp1, x0, x1, index } = box;
+          const at = (bp) => x0 + (Math.min(bp, bp1) - bp0) / (bp1 - bp0) * (x1 - x0);
           marks.push({
             x0: at(d.start),
             x1: at(d.end),
-            y: visited.get(box.index),
+            y: visited.get(index),
             height: track.width
           });
         }

package/dist/tubeMap/draw.js

@@ -1,19 +1,25 @@
 import {
   drawTubeMap,
+  drawTubeMapHighlight,
   mismatchOnScreen,
   mismatchesLegible,
   parsePath,
   trackColors,
-  tubeMapPicture
-} from "../chunks/chunk-KCRL5JB2.js";
-import "../chunks/chunk-733L2TS6.js";
-import "../chunks/chunk-TEDQJPMI.js";
+  tubeMapMismatchAt,
+  tubeMapPicture,
+  tubeMapTrackAt
+} from "../chunks/chunk-75HR3756.js";
+import "../chunks/chunk-XXT2JCAC.js";
+import "../chunks/chunk-CWFNEKST.js";
 import "../chunks/chunk-C44YRP5F.js";
 export {
   drawTubeMap,
+  drawTubeMapHighlight,
   mismatchOnScreen,
   mismatchesLegible,
   parsePath,
   trackColors,
-  tubeMapPicture
+  tubeMapMismatchAt,
+  tubeMapPicture,
+  tubeMapTrackAt
 };

package/dist/tubeMap/genes.js

@@ -3,8 +3,8 @@ import {
   drawTubeMapGenes,
   tubeMapGeneRows,
   tubeMapGenes
-} from "../chunks/chunk-OWFPAIJI.js";
-import "../chunks/chunk-DRA7733Q.js";
+} from "../chunks/chunk-WEDZ76AK.js";
+import "../chunks/chunk-BPRXQ2SS.js";
 import "../chunks/chunk-3ZZSX5HN.js";
 import "../chunks/chunk-AB35TJST.js";
 import "../chunks/chunk-TAMCZHLW.js";

package/dist/tubeMap/mismatches.js

@@ -1,6 +1,6 @@
 import {
   tubeMapMismatches
-} from "../chunks/chunk-733L2TS6.js";
+} from "../chunks/chunk-XXT2JCAC.js";
 export {
   tubeMapMismatches
 };

package/dist/tubeMap/reads.js

@@ -5,7 +5,7 @@ import {
   readColor,
   stepName,
   tubeMapReads
-} from "../chunks/chunk-TEDQJPMI.js";
+} from "../chunks/chunk-CWFNEKST.js";
 import "../chunks/chunk-C44YRP5F.js";
 export {
   FORWARD_READ_COLORS,

package/dist/types/bubbles/bubbleHalos.d.ts

@@ -17,4 +17,6 @@ export interface RouteLabel {
     at: NodeSegment;
     text: string;
 }
+export declare const WHOLE_FRACTION = 0.9;
+export declare function coversGraph(members: number, nodes: number): boolean;
 export declare function bubbleHalos(graph: Graph, bubbles: MinigraphBubble[], positions: Record<string, NodeSegment[]>, walkLabel?: (name: string) => string, repeats?: readonly RepeatSpan[]): BubbleHalo[];

package/dist/types/bubbles/bubbleLine.d.ts

@@ -12,6 +12,8 @@ export interface MinigraphBubble {
     longestAllele: string | undefined;
     partial?: boolean;
     routes?: BubbleRoute[];
+    key?: string;
+    offReference?: true;
 }
 export interface BubbleRoute {
     steps: string[];
@@ -20,6 +22,7 @@ export interface BubbleRoute {
 }
 export declare function parseBubbleLine(line: string): MinigraphBubble;
 export declare function sameBubble(a: MinigraphBubble, b: MinigraphBubble): boolean;
+export declare function bubbleKey(b: MinigraphBubble): string;
 export declare function bubbleLabel(bubble: MinigraphBubble): string;
 export declare const SATURATED_PATH_COUNT = 2147483647;
 export declare function bubbleDescription(bubble: MinigraphBubble): string;

package/dist/types/bubbles/bubblesFromGraph.d.ts

@@ -1,3 +1,13 @@
-import type { MinigraphBubble } from './bubbleLine.js';
-import type { Graph } from '../types.js';
+import type { BubbleRoute, MinigraphBubble } from './bubbleLine.js';
+import type { Graph, GraphNode } from '../types.js';
+export interface Routes {
+    min: number;
+    max: number;
+    n: number;
+}
 export declare function bubblesFromGraph(graph: Graph): MinigraphBubble[];
+export declare function walkIndexOf(graph: Graph): Map<string, number>[] | undefined;
+export declare function walkRoutes(graph: Graph, byId: Map<string, GraphNode>, walkIndex: Map<string, number>[], startId: string, endId: string): (Routes & {
+    left: number;
+    routes: BubbleRoute[];
+}) | undefined;

package/dist/types/bubbles/superbubbles.d.ts

@@ -0,0 +1,5 @@
+import type { MinigraphBubble } from './bubbleLine.js';
+import type { Graph } from '../types.js';
+export declare const MAX_SUPERBUBBLES = 50;
+export declare function superbubblesFromGraph(graph: Graph, span?: MinigraphBubble): MinigraphBubble[];
+export declare function graphBubbles(graph: Graph, span?: MinigraphBubble): MinigraphBubble[];

package/dist/types/index.d.ts

@@ -31,18 +31,18 @@ export type { AxisScale } from './util/geometry.js';
 export { wheelZoomFactor } from './util/wheelZoom.js';
 export { REFERENCE_STRIP_ZONE_PX, drawReferenceStrip, referenceStripBlocks, stripBlockAt, } from './referenceStrip.js';
 export type { StripBlock } from './referenceStrip.js';
-export { drawTubeMap, tubeMapPicture } from './tubeMap/draw.js';
+export { drawTubeMap, drawTubeMapHighlight, tubeMapMismatchAt, tubeMapPicture, tubeMapTrackAt, } from './tubeMap/draw.js';
 export type { TubeMapFrame, TubeMapPicture } from './tubeMap/draw.js';
 export { tubeMapNodeColors } from './tubeMap/nodeColors.js';
 export { referenceKnots, warpX } from './tubeMap/warp.js';
 export { tubeMapFrame, tubeMapNodeAt } from './tubeMap/frame.js';
 export type { TubeMapTransform, TubeMapView } from './tubeMap/frame.js';
 export { drawTubeMapRuler, referenceBoxes, rulerBoxes, tubeX, } from './tubeMap/axis.js';
-export type { Box as TubeMapBox, ReferenceBoxes } from './tubeMap/axis.js';
+export type { Box as TubeMapBox, ReferenceBox, ReferenceBoxes, } from './tubeMap/axis.js';
 export { drawTubeMapGenes, tubeMapGenes } from './tubeMap/genes.js';
 export type { TubeMapGene } from './tubeMap/genes.js';
-export { connectorAt, drawTubeMapConnectors, referenceNodes, tubeMapConnectors, } from './tubeMap/connectors.js';
-export type { Connector, ReferenceNode } from './tubeMap/connectors.js';
+export { connectorAt, drawLitConnector, drawTubeMapConnectors, tubeMapConnectors, } from './tubeMap/connectors.js';
+export type { Connector } from './tubeMap/connectors.js';
 export type { TubeMapColumn, TubeMapDrawing } from './layout/tubeMapLayout.js';
 export { deletionDrawing, deletionEdges } from './deletionEdges.js';
 export type { DeletionDrawing, DeletionEdge } from './deletionEdges.js';
@@ -62,6 +62,7 @@ export { WALK_FIELDS, WALK_SCHEMES, encodingStops, encodingSwatchCss, resolveEnc
 export type { WalkEncoding, WalkField, WalkLayer, WalkScheme, } from './walkEncoding.js';
 export { pathColorsLegible, pathLegend, walkLabelsOf } from './pathColors.js';
 export { bubblesFromGraph } from './bubbles/bubblesFromGraph.js';
+export { graphBubbles, superbubblesFromGraph } from './bubbles/superbubbles.js';
 export { bubbleHalos } from './bubbles/bubbleHalos.js';
 export type { BubbleHalo } from './bubbles/bubbleHalos.js';
 export { BUBBLE_KIND_COLORS, BUBBLE_KIND_NAMES, bubbleSegmentIds, classifyBubble, } from './bubbles/classifyBubble.js';

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

@@ -1,5 +1,5 @@
 import type { Coarsened } from '../tubeMap/coarsen.js';
-import type { Graph, LayoutResult } from '../types.js';
+import type { Graph, GraphNode, LayoutResult } from '../types.js';
 import type { InputTrack, TubeMapLayout } from '@jbrowse/tubemap-core';
 export interface TubeMapColumn {
     order: number;
@@ -14,10 +14,23 @@ export interface TubeMapDrawing {
     yOffset: number;
     columns?: TubeMapColumn[];
     coarse?: Coarsened;
+    graph: Graph;
+    members: Map<string, string[]>;
 }
-export declare function visitStrands(graph: Graph): Map<string, ("+" | "-")[]>;
+export interface PathStep {
+    node: GraphNode;
+    strand: '+' | '-';
+}
+export declare function pathSteps(graph: Graph): PathStep[][];
 export declare function tubeMapTracks(graph: Graph): InputTrack[];
 export declare function hasTubeMapPaths(graph: Graph): boolean;
 export declare function tubeWidth(trackCount: number): number;
+export interface MergedRuns {
+    members: Map<string, string[]>;
+    flipped: Set<string>;
+}
+export declare function mergedRuns(graph: Graph, layout: TubeMapLayout, walks: readonly InputTrack[]): MergedRuns;
+export declare function boxGraph(graph: Graph, { members, flipped }: MergedRuns): Graph;
 export declare function tubeMapLayout(graph: Graph): LayoutResult | undefined;
+export declare function hasTubeMapBackbone(graph: Graph): boolean;
 export declare function tubeMapReferenceLayout(graph: Graph): LayoutResult | undefined;