@jbrowse/bandage-core 4.0.25 → 4.0.27

package/dist/cli/figure.js

@@ -1,6 +1,7 @@
 #!/usr/bin/env node
 import {
   HPRC_GBZ,
+  LAYOUT_MODES,
   cutGbzRegion,
   featuresOnBackbone,
   figureSvg,
@@ -9,15 +10,17 @@ import {
   genesFromGff3Lines,
   genesFromText,
   graphBackbone,
+  haplotypeIndexBeside,
   layoutModeByValue,
   loadBandage,
   loadGraph,
   openGbz,
-  parseRegion
-} from "../chunks/chunk-B5ZHLU4N.js";
+  parseRegion,
+  refNameBinding
+} from "../chunks/chunk-VNCGWA2N.js";
 
 // src/cli/figure.ts
-import { open, readFile, writeFile } from "node:fs/promises";
+import { access, open, readFile, writeFile } from "node:fs/promises";
 import path from "node:path";
 import { parseArgs } from "node:util";
 import { gunzipSync } from "node:zlib";
@@ -27,16 +30,13 @@ function byteSource(location) {
   if (isUrl(location)) {
     return {
       async read(length, position) {
-        const res = await fetch(location, {
+        const res = await fetchOk(location, {
           headers: { range: `bytes=${position}-${position + length - 1}` }
         });
-        if (!res.ok) {
-          throw new Error(`HTTP ${res.status} reading ${location}`);
-        }
         return new Uint8Array(await res.arrayBuffer());
       },
       async stat() {
-        const res = await fetch(location, { method: "HEAD" });
+        const res = await fetchOk(location, { method: "HEAD" });
         return { size: Number(res.headers.get("content-length")) };
       }
     };
@@ -53,8 +53,15 @@ function byteSource(location) {
     }
   };
 }
+async function fetchOk(location, init) {
+  const res = await fetch(location, init);
+  if (!res.ok) {
+    throw new Error(`HTTP ${res.status} reading ${location}`);
+  }
+  return res;
+}
 async function text(location) {
-  const bytes = isUrl(location) ? new Uint8Array(await (await fetch(location)).arrayBuffer()) : await readFile(location);
+  const bytes = isUrl(location) ? new Uint8Array(await (await fetchOk(location)).arrayBuffer()) : await readFile(location);
   const gzipped = bytes[0] === 31 && bytes[1] === 139;
   return new TextDecoder().decode(gzipped ? gunzipSync(bytes) : bytes);
 }
@@ -63,30 +70,48 @@ async function readGenes(genes, graph, resolve) {
   if (!backbone) {
     return [];
   }
-  const file = resolve(genes.file);
+  const bind = refNameBinding(
+    backbone.contigs.map((c) => c.refName),
+    genes.refNames
+  );
   const format = genes.format ?? (/\.bed(\.gz)?$/i.test(genes.file) ? "bed" : "gff3");
-  if (!genes.index) {
-    return featuresOnBackbone(genesFromText(await text(file)), backbone);
+  const { names, features } = genes.index ? await indexedGenes(
+    resolve(genes.file),
+    resolve(genes.index),
+    format,
+    backbone.contigs,
+    bind
+  ) : namedBy(genesFromText(await text(resolve(genes.file))));
+  if (!names.some((name) => bind(name) !== void 0)) {
+    const shown = names.slice(0, 4).join(", ");
+    console.warn(
+      `bandage-figure: no sequence in ${genes.file} names ${backbone.contigs.map((c) => c.contig).join(", ")}` + (names.length ? `; it has ${shown}${names.length > 4 ? ", \u2026" : ""}` : "") + `. Give the file's name under genes.refNames, as { "chr6": "NC_000006.12" }`
+    );
   }
-  const index = resolve(genes.index);
+  return featuresOnBackbone(features, backbone, genes.refNames);
+}
+function namedBy(features) {
+  return { names: [...new Set(features.map((f) => f.refName))], features };
+}
+async function indexedGenes(file, index, format, contigs, bind) {
   const csi = index.endsWith(".csi");
   const tabix = new TabixIndexedFile(
     isUrl(file) ? { url: file, ...csi ? { csiUrl: index } : { tbiUrl: index } } : { path: file, ...csi ? { csiPath: index } : { tbiPath: index } }
   );
-  const indexed = new Set(await tabix.getReferenceSequenceNames());
+  const names = await tabix.getReferenceSequenceNames();
   const lines = [];
-  for (const contig of backbone.contigs) {
-    const refName = [contig.contig, contig.refName].find((n) => indexed.has(n));
-    if (refName !== void 0) {
-      await tabix.getLines(refName, contig.start, contig.end, {
+  for (const contig of contigs) {
+    const name = names.find((n) => bind(n) === contig.refName);
+    if (name !== void 0) {
+      await tabix.getLines(name, contig.start, contig.end, {
         lineCallback: (line) => lines.push(line)
       });
     }
   }
-  return featuresOnBackbone(
-    format === "gff3" ? genesFromGff3Lines(lines) : genesFromBed(lines.join("\n")),
-    backbone
-  );
+  return {
+    names,
+    features: format === "gff3" ? genesFromGff3Lines(lines) : genesFromBed(lines.join("\n"))
+  };
 }
 var engine = async (request) => {
   const bandage = await loadBandage();
@@ -94,15 +119,39 @@ var engine = async (request) => {
   const result = bandage.computeLayout(request.graph, request.options);
   return { result, duration: performance.now() - start };
 };
+async function exists(location) {
+  try {
+    await (isUrl(location) ? fetchOk(location, { method: "HEAD" }) : access(location));
+    return true;
+  } catch {
+    return false;
+  }
+}
+async function siblingIndex(db) {
+  const sibling = haplotypeIndexBeside(db);
+  return sibling && await exists(sibling) ? sibling : void 0;
+}
+var DRAWABLE = LAYOUT_MODES.filter((m) => m.drawsNodes).map(
+  (m) => m.value
+);
+function checkLayout(layout) {
+  if (layout !== void 0 && !DRAWABLE.includes(layout)) {
+    throw new Error(
+      `a figure draws no "${layout}" layout: one of ${DRAWABLE.join(", ")}`
+    );
+  }
+}
 async function renderSpec(spec, base) {
+  checkLayout(spec.layout);
   const resolve = (location) => isUrl(location) ? location : path.resolve(base, location);
   let source;
   if (spec.gbz) {
     const { db, index } = spec.gbz.db === "hprc" ? HPRC_GBZ : spec.gbz;
+    const indexLocation = index ? resolve(index) : await siblingIndex(resolve(db));
     const cut = await cutGbzRegion(
       await openGbz(
         byteSource(resolve(db)),
-        index ? byteSource(resolve(index)) : void 0
+        indexLocation ? byteSource(indexLocation) : void 0
       ),
       spec.gbz
     );
@@ -136,14 +185,32 @@ async function renderSpec(spec, base) {
     spec
   });
 }
+var USAGE = "usage: bandage-figure <spec.json> [-o figure.svg]";
+function args() {
+  try {
+    return parseArgs({
+      allowPositionals: true,
+      options: {
+        out: { type: "string", short: "o" },
+        help: { type: "boolean", short: "h" }
+      }
+    });
+  } catch (e) {
+    console.error(`${e instanceof Error ? e.message : String(e)}
+${USAGE}`);
+    process.exit(2);
+  }
+}
 async function main() {
-  const { positionals, values } = parseArgs({
-    allowPositionals: true,
-    options: { out: { type: "string", short: "o" } }
-  });
+  const { positionals, values } = args();
+  if (values.help) {
+    process.stdout.write(`${USAGE}
+`);
+    return;
+  }
   const file = positionals[0];
   if (!file) {
-    console.error("usage: bandage-figure <spec.json> [-o figure.svg]");
+    console.error(USAGE);
     process.exit(2);
   }
   const spec = JSON.parse(await readFile(file, "utf8"));
@@ -154,4 +221,9 @@ async function main() {
     process.stdout.write(svg);
   }
 }
-await main();
+try {
+  await main();
+} catch (e) {
+  console.error(`bandage-figure: ${e instanceof Error ? e.message : String(e)}`);
+  process.exit(1);
+}

package/dist/index.js

@@ -90,6 +90,7 @@ import {
   svgCanvas,
   svgPath,
   translateCurves,
+  trimOrigins,
   version,
   viewportOf,
   walkHighlight,
@@ -101,7 +102,7 @@ import {
   wellKnownSample,
   yToXOf,
   zoomAbout
-} from "./chunks/chunk-B5ZHLU4N.js";
+} from "./chunks/chunk-VNCGWA2N.js";
 
 // src/index.ts
 import { getDpr } from "@jbrowse/render-core/canvas2dUtils";
@@ -721,14 +722,16 @@ function extentOf(commands) {
   }
   return { x0, x1 };
 }
-function shapeOf(d, color, alpha) {
+function shapeOf(d, color, alpha, track) {
   const commands = parsePath(d);
-  return { commands, color, alpha, ...extentOf(commands) };
+  return { commands, color, track, alpha, ...extentOf(commands) };
 }
 function layerOf(layout, type) {
   const { shapes } = layout;
+  const trackOf = (s) => type === "haplotype" ? s.id : void 0;
   const rects = [...shapes.rectangles, ...shapes.verticalRectangles].filter((r) => r.type === type).map((r) => ({
     color: r.color,
+    track: trackOf(r),
     alpha: r.alpha ?? 1,
     x0: r.xStart,
     x1: r.xEnd + 1,
@@ -736,9 +739,9 @@ function layerOf(layout, type) {
     y1: r.yEnd + 1
   }));
   const curves = curvePaths(shapes.curves, type).map(
-    (c) => shapeOf(c.path, c.color, c.alpha ?? 1)
+    (c) => shapeOf(c.path, c.color, c.alpha ?? 1, trackOf(c))
   );
-  const corners = shapes.corners.filter((c) => c.type === type).map((c) => shapeOf(c.path, c.color, 1));
+  const corners = shapes.corners.filter((c) => c.type === type).map((c) => shapeOf(c.path, c.color, 1, trackOf(c)));
   return { rects, shapes: [...curves, ...corners] };
 }
 function tubeMapPicture(layout) {
@@ -797,11 +800,11 @@ function trace(ctx, commands, x, y) {
     }
   }
 }
-function fillByColor(ctx, items, visible, addTo) {
+function fillByColor(ctx, items, visible, colorOf, addTo) {
   const byColor = /* @__PURE__ */ new Map();
   for (const item of items) {
     if (visible(item)) {
-      const key = `${item.color}|${item.alpha}`;
+      const key = `${colorOf(item)}|${item.alpha}`;
       const list = byColor.get(key);
       if (list) {
         list.push(item);
@@ -811,7 +814,7 @@ function fillByColor(ctx, items, visible, addTo) {
     }
   }
   for (const list of byColor.values()) {
-    ctx.fillStyle = list[0].color;
+    ctx.fillStyle = colorOf(list[0]);
     ctx.globalAlpha = list[0].alpha;
     ctx.beginPath();
     for (const item of list) {
@@ -826,16 +829,18 @@ var MIN_OUTLINE_ALPHA = 0.15;
 function outlineAlpha(screenWidth) {
   return Math.max(MIN_OUTLINE_ALPHA, Math.min(1, screenWidth / FULL_OUTLINE_PX));
 }
+var NODE_TINT_ALPHA = 0.55;
 function drawTubeMap(ctx, picture, frame) {
   const { x, y, width } = frame;
   const visible = (item) => x(item.x1) >= 0 && x(item.x0) <= width;
+  const colorOf = (item) => item.track !== void 0 && frame.tubeColors?.[item.track] || item.color;
   for (const layer of picture.layers) {
-    fillByColor(ctx, layer.rects, visible, (r) => {
+    fillByColor(ctx, layer.rects, visible, colorOf, (r) => {
       const left = x(r.x0);
       const top = y(r.y0);
       ctx.rect(left, top, x(r.x1) - left, y(r.y1) - top);
     });
-    fillByColor(ctx, layer.shapes, visible, (s) => {
+    fillByColor(ctx, layer.shapes, visible, colorOf, (s) => {
       trace(ctx, s.commands, x, y);
     });
   }
@@ -847,8 +852,10 @@ function drawTubeMap(ctx, picture, frame) {
       const lit = node.name === frame.highlightNode;
       ctx.beginPath();
       trace(ctx, node.commands, x, y);
-      ctx.fillStyle = lit ? "rgba(255,192,203,0.5)" : fill;
+      const tint = lit ? void 0 : frame.nodeColors?.get(node.name);
+      ctx.fillStyle = lit ? "rgba(255,192,203,0.5)" : tint ?? fill;
       ctx.strokeStyle = lit ? "#ff0000" : stroke;
+      ctx.globalAlpha = tint ? NODE_TINT_ALPHA : 1;
       ctx.fill();
       ctx.globalAlpha = lit ? 1 : outlineAlpha(x(node.x1) - x(node.x0));
       ctx.stroke();
@@ -897,6 +904,21 @@ function drawMismatches(ctx, marks, frame) {
   }
 }
 
+// src/tubeMap/nodeColors.ts
+import { abgrToCssRgba as abgrToCssRgba2 } from "@jbrowse/core/util/colorBits";
+function tubeMapNodeColors(graph, colorScheme, referenceRamp) {
+  if (colorScheme === "uniform" || colorScheme === "grey") {
+    return void 0;
+  }
+  const range = { ...computeColorSchemeRange(graph), referenceRamp };
+  return new Map(
+    graph.nodes.map((node, index) => [
+      node.id,
+      abgrToCssRgba2(getNodeColor(node, index, colorScheme, range))
+    ])
+  );
+}
+
 // src/tubeMap/warp.ts
 var MAX_GAP_PX = 24;
 var isReal = (c) => c.bp1 > c.bp0;
@@ -1696,13 +1718,22 @@ function bubbleSubgraph(graph, segmentIds) {
   const keep = new Set(segmentIds);
   const nodes = graph.nodes.filter((n) => keep.has(n.name));
   const ids = new Set(nodes.map((n) => n.id));
-  const paths = graph.paths?.map((p) => ({ ...p, nodeIds: p.nodeIds.filter((id) => ids.has(id)) })).filter((p) => p.nodeIds.length > 0);
+  const kept = /* @__PURE__ */ new Map();
+  const paths = graph.paths?.flatMap((p) => {
+    const first = p.nodeIds.findIndex((id) => ids.has(id));
+    if (first < 0) {
+      return [];
+    }
+    const nodeIds = p.nodeIds.filter((id) => ids.has(id));
+    kept.set(p.name, { first, nodeIds });
+    return [{ ...p, nodeIds }];
+  });
   return {
     name: graph.name,
     nodes,
     edges: graph.edges.filter((e) => ids.has(e.from) && ids.has(e.to)),
     ...paths?.length ? { paths } : {},
-    anchorPaths: graph.anchorPaths,
+    anchorPaths: trimOrigins(graph, kept),
     pathVisits: graph.pathVisits,
     anchoredBy: graph.anchoredBy,
     referencePath: graph.referencePath
@@ -1815,6 +1846,7 @@ export {
   tubeMapFrame,
   tubeMapGenes,
   tubeMapNodeAt,
+  tubeMapNodeColors,
   tubeMapPicture,
   tubeX,
   version,

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

@@ -16,5 +16,6 @@ export interface FigureSpec extends Omit<FigureOptions, 'walks' | 'region' | 'ge
         file: string;
         index?: string;
         format?: 'gff3' | 'bed';
+        refNames?: Record<string, string>;
     };
 }

package/dist/types/figure.d.ts

@@ -20,6 +20,11 @@ export interface FigureOptions {
         start: number;
         end: number;
     };
+    colorDomain?: {
+        start: number;
+        end: number;
+    };
+    fitToDrawing?: boolean;
     genes?: GeneModel[];
     spec?: unknown;
 }

package/dist/types/gbzCut.d.ts

@@ -13,6 +13,7 @@ export declare const HPRC_GBZ: {
     db: string;
     index: string;
 };
+export declare function haplotypeIndexBeside(db: string): string | undefined;
 export declare function parseRegion(text: string): {
     refName: string;
     start: number;

package/dist/types/graphLabels.d.ts

@@ -17,6 +17,7 @@ export interface GraphLabel {
     kind: 'node' | 'deletion';
     leader?: Leader;
 }
+export declare function groupDigits(n: number): string;
 export declare function formatBp(bp: number): string;
 interface SizeLabelArgs {
     nodePositions: Record<string, NodeSegment[]>;

package/dist/types/index.d.ts

@@ -20,6 +20,7 @@ export { REFERENCE_STRIP_ZONE_PX, drawReferenceStrip, referenceStripBlocks, stri
 export type { StripBlock } from './referenceStrip.js';
 export { drawTubeMap, tubeMapPicture } 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';

package/dist/types/layoutModes.d.ts

@@ -17,6 +17,7 @@ export interface LayoutMode {
     cutMargins: boolean;
     wholeWalks: boolean;
     drawsLocally: (graph: Graph) => boolean;
+    drawsNodes: boolean;
 }
 export declare const LAYOUT_MODES: readonly [{
     readonly value: "auto";
@@ -27,6 +28,7 @@ export declare const LAYOUT_MODES: readonly [{
     readonly wholeWalks: false;
     readonly available: (graph: Graph) => boolean;
     readonly drawsLocally: (graph: Graph) => boolean;
+    readonly drawsNodes: true;
 }, {
     readonly value: "samplerows";
     readonly label: "Sample rows";
@@ -36,6 +38,7 @@ export declare const LAYOUT_MODES: readonly [{
     readonly wholeWalks: false;
     readonly available: (graph: Graph) => boolean;
     readonly drawsLocally: (graph: Graph) => boolean;
+    readonly drawsNodes: true;
 }, {
     readonly value: "walkrows";
     readonly label: "Walk rows";
@@ -45,6 +48,7 @@ export declare const LAYOUT_MODES: readonly [{
     readonly wholeWalks: true;
     readonly available: (graph: Graph) => boolean;
     readonly drawsLocally: (graph: Graph) => boolean;
+    readonly drawsNodes: false;
 }, {
     readonly value: "ordered";
     readonly label: "Ordered";
@@ -54,6 +58,7 @@ export declare const LAYOUT_MODES: readonly [{
     readonly wholeWalks: false;
     readonly available: (graph: Graph) => boolean;
     readonly drawsLocally: (graph: Graph) => boolean;
+    readonly drawsNodes: true;
 }, {
     readonly value: "tubemap";
     readonly label: "Tube map";
@@ -63,6 +68,7 @@ export declare const LAYOUT_MODES: readonly [{
     readonly wholeWalks: false;
     readonly available: typeof hasTubeMapPaths;
     readonly drawsLocally: typeof hasTubeMapPaths;
+    readonly drawsNodes: false;
 }, {
     readonly value: "tubemapref";
     readonly label: "Tube map on reference";
@@ -72,6 +78,7 @@ export declare const LAYOUT_MODES: readonly [{
     readonly wholeWalks: false;
     readonly available: (graph: Graph) => boolean;
     readonly drawsLocally: (graph: Graph) => boolean;
+    readonly drawsNodes: false;
 }, {
     readonly value: "force";
     readonly label: "Force-directed layout";
@@ -81,6 +88,7 @@ export declare const LAYOUT_MODES: readonly [{
     readonly wholeWalks: false;
     readonly available: () => true;
     readonly drawsLocally: () => false;
+    readonly drawsNodes: true;
 }];
 export type LayoutModeValue = (typeof LAYOUT_MODES)[number]['value'];
 export declare const LAYOUT_MODE_VALUES: ("auto" | "ordered" | "samplerows" | "walkrows" | "tubemap" | "tubemapref" | "force")[];
@@ -94,6 +102,7 @@ export declare function layoutModeByValue(value: string): {
     readonly wholeWalks: false;
     readonly available: (graph: Graph) => boolean;
     readonly drawsLocally: (graph: Graph) => boolean;
+    readonly drawsNodes: true;
 } | {
     readonly value: "samplerows";
     readonly label: "Sample rows";
@@ -103,6 +112,7 @@ export declare function layoutModeByValue(value: string): {
     readonly wholeWalks: false;
     readonly available: (graph: Graph) => boolean;
     readonly drawsLocally: (graph: Graph) => boolean;
+    readonly drawsNodes: true;
 } | {
     readonly value: "walkrows";
     readonly label: "Walk rows";
@@ -112,6 +122,7 @@ export declare function layoutModeByValue(value: string): {
     readonly wholeWalks: true;
     readonly available: (graph: Graph) => boolean;
     readonly drawsLocally: (graph: Graph) => boolean;
+    readonly drawsNodes: false;
 } | {
     readonly value: "ordered";
     readonly label: "Ordered";
@@ -121,6 +132,7 @@ export declare function layoutModeByValue(value: string): {
     readonly wholeWalks: false;
     readonly available: (graph: Graph) => boolean;
     readonly drawsLocally: (graph: Graph) => boolean;
+    readonly drawsNodes: true;
 } | {
     readonly value: "tubemap";
     readonly label: "Tube map";
@@ -130,6 +142,7 @@ export declare function layoutModeByValue(value: string): {
     readonly wholeWalks: false;
     readonly available: typeof hasTubeMapPaths;
     readonly drawsLocally: typeof hasTubeMapPaths;
+    readonly drawsNodes: false;
 } | {
     readonly value: "tubemapref";
     readonly label: "Tube map on reference";
@@ -139,6 +152,7 @@ export declare function layoutModeByValue(value: string): {
     readonly wholeWalks: false;
     readonly available: (graph: Graph) => boolean;
     readonly drawsLocally: (graph: Graph) => boolean;
+    readonly drawsNodes: false;
 } | {
     readonly value: "force";
     readonly label: "Force-directed layout";
@@ -148,4 +162,5 @@ export declare function layoutModeByValue(value: string): {
     readonly wholeWalks: false;
     readonly available: () => true;
     readonly drawsLocally: () => false;
+    readonly drawsNodes: true;
 };

package/dist/types/pathAnchoring.d.ts

@@ -18,3 +18,7 @@ export declare function surveyPaths(paths: PathSteps[], lengthOf: (segmentId: st
 export declare function chooseReferencePath(anchorPaths: PathOrigin[], preferred: string | undefined): PathOrigin | undefined;
 export declare function anchorFromPaths(graph: Graph, preferred: string | undefined): Graph;
 export declare function anchorGraph(graph: Graph, preferred: string | undefined): Graph;
+export declare function trimOrigins(graph: Graph, kept: Map<string, {
+    first: number;
+    nodeIds: string[];
+}>): PathOrigin[] | undefined;

package/dist/types/reference.d.ts

@@ -19,7 +19,8 @@ export declare function wellKnownSample(assemblyName: string): string | undefine
 export declare function graphBackbone(graph: Graph): Backbone | 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 refNameBinding(refNames: Iterable<string>): (name: string) => string | undefined;
+export declare function contigNames(contig: string): string[];
+export declare function refNameBinding(refNames: Iterable<string>, aliases?: Record<string, string>): (name: string) => string | undefined;
 export declare function featuresOnBackbone<T extends {
     refName: string;
-}>(features: readonly T[], backbone: Backbone): T[];
+}>(features: readonly T[], backbone: Backbone, aliases?: Record<string, string>): T[];

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

@@ -31,6 +31,7 @@ type Command = {
 export declare function parsePath(d: string): Command[];
 interface Filled {
     color: string;
+    track?: number;
     alpha: number;
     x0: number;
     x1: number;
@@ -62,6 +63,8 @@ export interface TubeMapFrame extends TubeMapTransform {
     width: number;
     highlightNode?: string | null;
     darkMode?: boolean;
+    tubeColors?: readonly string[];
+    nodeColors?: ReadonlyMap<string, string>;
 }
 export declare function drawTubeMap(ctx: CanvasRenderingContext2D, picture: TubeMapPicture, frame: TubeMapFrame): void;
 export declare function mismatchesLegible(yScale: number): boolean;

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

@@ -0,0 +1,4 @@
+import type { ResolvedColorScheme } from '../colorSchemes.js';
+import type { ReferenceRamp } from '../renderer/GeometryBuilder.js';
+import type { Graph } from '../types.js';
+export declare function tubeMapNodeColors(graph: Graph, colorScheme: ResolvedColorScheme, referenceRamp?: ReferenceRamp): Map<string, string> | undefined;

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "4.0.25";
+export declare const version = "4.0.27";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "4.0.25",
+  "version": "4.0.27",
   "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": {