@jbrowse/bandage-core 8.2.0 → 9.0.0

package/dist/cli/figure.js

@@ -7,9 +7,9 @@ import {
 import {
   LAYOUT_MODES,
   layoutModeByValue
-} 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";
@@ -35,7 +35,7 @@ import "../chunks/chunk-LYJ4US66.js";
 import "../chunks/chunk-7XHHVYG7.js";
 import {
   figureSvg
-} from "../chunks/chunk-DE4UFDUZ.js";
+} from "../chunks/chunk-TLQ7F2ZT.js";
 import "../chunks/chunk-LOCJN3BZ.js";
 import "../chunks/chunk-47DYCZOK.js";
 import "../chunks/chunk-WDTXW7T2.js";
@@ -53,7 +53,7 @@ import "../chunks/chunk-2LQ5BWT7.js";
 import "../chunks/chunk-6ZNQJ5ZD.js";
 import "../chunks/chunk-HBEKUQO4.js";
 import "../chunks/chunk-G2FD7S3C.js";
-import "../chunks/chunk-3FXPFVKJ.js";
+import "../chunks/chunk-AMS3MAFP.js";
 import "../chunks/chunk-TL4B342F.js";
 import "../chunks/chunk-3C5UXR2U.js";
 import {

package/dist/figure.js

@@ -1,6 +1,6 @@
 import {
   figureSvg
-} from "./chunks/chunk-DE4UFDUZ.js";
+} from "./chunks/chunk-TLQ7F2ZT.js";
 import "./chunks/chunk-LOCJN3BZ.js";
 import "./chunks/chunk-47DYCZOK.js";
 import "./chunks/chunk-WDTXW7T2.js";
@@ -15,7 +15,7 @@ import "./chunks/chunk-2LQ5BWT7.js";
 import "./chunks/chunk-6ZNQJ5ZD.js";
 import "./chunks/chunk-HBEKUQO4.js";
 import "./chunks/chunk-G2FD7S3C.js";
-import "./chunks/chunk-3FXPFVKJ.js";
+import "./chunks/chunk-AMS3MAFP.js";
 import "./chunks/chunk-TL4B342F.js";
 import "./chunks/chunk-3C5UXR2U.js";
 import "./chunks/chunk-MAUEPAMG.js";

package/dist/index.js

@@ -3,8 +3,10 @@ import {
 } from "./chunks/chunk-TDQLINVI.js";
 import {
   drawTubeMap,
-  tubeMapPicture
-} from "./chunks/chunk-KCRL5JB2.js";
+  tubeMapMismatchAt,
+  tubeMapPicture,
+  tubeMapTrackAt
+} from "./chunks/chunk-LLP3FXPM.js";
 import {
   tubeMapFrame,
   tubeMapNodeAt
@@ -12,8 +14,8 @@ import {
 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";
@@ -26,13 +28,12 @@ import {
   referenceBoxes,
   rulerBoxes,
   tubeX
-} from "./chunks/chunk-DRA7733Q.js";
+} from "./chunks/chunk-BPRXQ2SS.js";
 import {
   connectorAt,
   drawTubeMapConnectors,
-  referenceNodes,
   tubeMapConnectors
-} from "./chunks/chunk-GQ2AOHU4.js";
+} from "./chunks/chunk-YOYLCLIG.js";
 import {
   createForceLayoutCache
 } from "./chunks/chunk-SKKYLBRA.js";
@@ -69,9 +70,9 @@ 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 +113,7 @@ import {
 } from "./chunks/chunk-7XHHVYG7.js";
 import {
   figureSvg
-} from "./chunks/chunk-DE4UFDUZ.js";
+} from "./chunks/chunk-TLQ7F2ZT.js";
 import {
   layoutGeometryInputs
 } from "./chunks/chunk-LOCJN3BZ.js";
@@ -204,7 +205,7 @@ import {
 import "./chunks/chunk-G2FD7S3C.js";
 import {
   version
-} from "./chunks/chunk-3FXPFVKJ.js";
+} from "./chunks/chunk-AMS3MAFP.js";
 import {
   axisScaleOf,
   contains,
@@ -463,7 +464,6 @@ export {
   referenceBoxes,
   referenceKnots,
   referenceLabel,
-  referenceNodes,
   referencePathQuery,
   referenceSamplesOf,
   referenceStripBlocks,
@@ -489,9 +489,11 @@ export {
   tubeMapConnectors,
   tubeMapFrame,
   tubeMapGenes,
+  tubeMapMismatchAt,
   tubeMapNodeAt,
   tubeMapNodeColors,
   tubeMapPicture,
+  tubeMapTrackAt,
   tubeX,
   unitTicks,
   version,

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/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 +1,10 @@
 import {
   connectorAt,
   drawTubeMapConnectors,
-  referenceNodes,
   tubeMapConnectors
-} from "../chunks/chunk-GQ2AOHU4.js";
-import "../chunks/chunk-FYQWPEEY.js";
+} from "../chunks/chunk-YOYLCLIG.js";
 export {
   connectorAt,
   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

@@ -4,10 +4,12 @@ import {
   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-LLP3FXPM.js";
+import "../chunks/chunk-XXT2JCAC.js";
+import "../chunks/chunk-CWFNEKST.js";
 import "../chunks/chunk-C44YRP5F.js";
 export {
   drawTubeMap,
@@ -15,5 +17,7 @@ export {
   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/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, 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, 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';

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;

package/dist/types/layoutModes.d.ts

@@ -1,7 +1,7 @@
 import { anchoredLayout } from './layout/anchoredLayout.js';
 import { orderedLayout } from './layout/orderedLayout.js';
 import { sampleRowLayout } from './layout/sampleRowLayout.js';
-import { hasTubeMapPaths, tubeMapLayout, tubeMapReferenceLayout } from './layout/tubeMapLayout.js';
+import { hasTubeMapBackbone, hasTubeMapPaths, tubeMapLayout, tubeMapReferenceLayout } from './layout/tubeMapLayout.js';
 import { walkRowLayout } from './layout/walkRowLayout.js';
 import type { Graph, LayoutResult } from './types.js';
 export declare const FORCE_LAYOUT_LABEL = "Force-directed layout";
@@ -76,8 +76,8 @@ export declare const LAYOUT_MODES: readonly [{
     readonly run: typeof tubeMapReferenceLayout;
     readonly cutMargins: true;
     readonly wholeWalks: false;
-    readonly available: (graph: Graph) => boolean;
-    readonly drawsLocally: (graph: Graph) => boolean;
+    readonly available: typeof hasTubeMapBackbone;
+    readonly drawsLocally: typeof hasTubeMapBackbone;
     readonly drawsNodes: false;
 }, {
     readonly value: "force";
@@ -150,8 +150,8 @@ export declare function layoutModeByValue(value: string): {
     readonly run: typeof tubeMapReferenceLayout;
     readonly cutMargins: true;
     readonly wholeWalks: false;
-    readonly available: (graph: Graph) => boolean;
-    readonly drawsLocally: (graph: Graph) => boolean;
+    readonly available: typeof hasTubeMapBackbone;
+    readonly drawsLocally: typeof hasTubeMapBackbone;
     readonly drawsNodes: false;
 } | {
     readonly value: "force";

package/dist/types/tubeMap/axis.d.ts

@@ -1,13 +1,16 @@
 import type { TubeMapFrame } from './draw.js';
-import type { Graph } from '../types.js';
-import type { TubeMapLayout } from '@jbrowse/tubemap-core';
+import type { TubeMapDrawing } from '../layout/tubeMapLayout.js';
 export interface Box {
     bp0: number;
     bp1: number;
     x0: number;
     x1: number;
 }
-export declare function referenceBoxes(graph: Graph, layout: TubeMapLayout): Map<string, Box[]>;
+export interface ReferenceBox extends Box {
+    name: string;
+    index: number;
+}
+export declare function referenceBoxes({ graph, layout, }: Pick<TubeMapDrawing, 'graph' | 'layout'>): Map<string, ReferenceBox[]>;
 export type ReferenceBoxes = ReturnType<typeof referenceBoxes>;
 export declare function tubeX(boxes: readonly Box[], bp: number, isEnd?: boolean): number;
 export declare function tubeSpan(boxes: readonly Box[], start: number, end: number): {

package/dist/types/tubeMap/connectors.d.ts

@@ -1,12 +1,4 @@
-import type { Graph } from '../types.js';
-import type { TubeMapLayout } from '@jbrowse/tubemap-core';
-export interface ReferenceNode {
-    node: string;
-    bp0: number;
-    bp1: number;
-    x0: number;
-    x1: number;
-}
+import type { ReferenceBox } from './axis.js';
 export interface Connector {
     node: string;
     top0: number;
@@ -14,8 +6,7 @@ export interface Connector {
     bottom0: number;
     bottom1: number;
 }
-export declare function referenceNodes(graph: Graph, layout: TubeMapLayout): ReferenceNode[];
-export declare function tubeMapConnectors(nodes: readonly ReferenceNode[], bpToScreen: (bp: number) => number, tubeToScreen: (tx: number) => number, width: number): Connector[];
+export declare function tubeMapConnectors(boxes: readonly ReferenceBox[], bpToScreen: (bp: number) => number, tubeToScreen: (tx: number) => number, width: number): Connector[];
 export declare function connectorAt(connectors: readonly Connector[], zoneBottom: number, sx: number, sy: number): string | undefined;
 export declare function drawTubeMapConnectors(ctx: CanvasRenderingContext2D, connectors: readonly Connector[], bottom: number, { highlightNode, darkMode, }: {
     highlightNode?: string | null;

package/dist/types/tubeMap/deviations.d.ts

@@ -1,13 +1,12 @@
 import type { Deviation } from './coarsen.js';
 import type { TubeMapFrame } from './draw.js';
-import type { Graph } from '../types.js';
-import type { TubeMapLayout } from '@jbrowse/tubemap-core';
+import type { TubeMapDrawing } from '../layout/tubeMapLayout.js';
 export interface DeviationMark {
     x0: number;
     x1: number;
     y: number;
     height: number;
 }
-export declare function deviationMarks(graph: Graph, layout: TubeMapLayout, deviations: Map<string, Deviation[]>): DeviationMark[];
+export declare function deviationMarks(drawing: Pick<TubeMapDrawing, 'graph' | 'layout'>, deviations: Map<string, Deviation[]>): DeviationMark[];
 export declare function deviationInk(darkMode?: boolean): "rgba(255,255,255,0.9)" | "rgba(0,0,0,0.8)";
 export declare function drawDeviationMarks(ctx: CanvasRenderingContext2D, marks: readonly DeviationMark[], { x, y, width, darkMode }: TubeMapFrame): void;

package/dist/types/tubeMap/draw.d.ts

@@ -32,7 +32,8 @@ type Command = {
 export declare function parsePath(d: string): Command[];
 interface Filled {
     color: string;
-    track?: number;
+    id: number;
+    haplotype: boolean;
     x0: number;
     x1: number;
 }
@@ -70,4 +71,6 @@ export interface TubeMapFrame extends TubeMapTransform {
 export declare function drawTubeMap(ctx: CanvasRenderingContext2D, picture: TubeMapPicture, frame: TubeMapFrame): void;
 export declare function mismatchesLegible(yScale: number): boolean;
 export declare function mismatchOnScreen(m: TubeMapMismatch, { x, width }: Pick<TubeMapFrame, 'x' | 'width'>): boolean;
+export declare function tubeMapTrackAt(picture: TubeMapPicture, { x, y }: TubeMapTransform, sx: number, sy: number): number | undefined;
+export declare function tubeMapMismatchAt(picture: TubeMapPicture, frame: TubeMapTransform, sx: number, sy: number): TubeMapMismatch | undefined;
 export {};

package/dist/types/tubeMap/mismatches.d.ts

@@ -3,7 +3,6 @@ interface MarkBase {
     readId: number;
     y: number;
     height: number;
-    nodeY: number;
 }
 export type TubeMapMismatch = (MarkBase & {
     kind: 'insertion';
@@ -14,6 +13,7 @@ export type TubeMapMismatch = (MarkBase & {
     kind: 'deletion';
     x0: number;
     x1: number;
+    length: number;
 }) | (MarkBase & {
     kind: 'substitution';
     x0: number;

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "8.2.0";
+export declare const version = "9.0.0";

package/dist/version.js

@@ -1,6 +1,6 @@
 import {
   version
-} from "./chunks/chunk-3FXPFVKJ.js";
+} from "./chunks/chunk-AMS3MAFP.js";
 export {
   version
 };

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "8.2.0",
+  "version": "9.0.0",
   "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": {