@jbrowse/bandage-core 4.0.26 → 4.0.27

package/dist/cli/figure.js

@@ -1,7 +1,7 @@
 #!/usr/bin/env node
 import {
   HPRC_GBZ,
-  LAYOUT_MODE_VALUES,
+  LAYOUT_MODES,
   cutGbzRegion,
   featuresOnBackbone,
   figureSvg,
@@ -10,12 +10,14 @@ import {
   genesFromGff3Lines,
   genesFromText,
   graphBackbone,
+  haplotypeIndexBeside,
   layoutModeByValue,
   loadBandage,
   loadGraph,
   openGbz,
-  parseRegion
-} from "../chunks/chunk-75KVO2WV.js";
+  parseRegion,
+  refNameBinding
+} from "../chunks/chunk-VNCGWA2N.js";
 
 // src/cli/figure.ts
 import { access, open, readFile, writeFile } from "node:fs/promises";
@@ -28,12 +30,9 @@ 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 ${location}`);
-        }
         return new Uint8Array(await res.arrayBuffer());
       },
       async stat() {
@@ -71,30 +70,48 @@ async function readGenes(genes, graph, resolve) {
   if (!backbone) {
     return [];
   }
-  const file = resolve(genes.file);
+  const bind = refNameBinding(
+    backbone.contigs.map((c) => c.refName),
+    genes.refNames
+  );
   const format = genes.format ?? (/\.bed(\.gz)?$/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();
@@ -111,22 +128,18 @@ async function exists(location) {
   }
 }
 async function siblingIndex(db) {
-  const sibling = db.replace(/\.gbz\.db$/i, ".haplotype-index.db");
-  return sibling !== db && await exists(sibling) ? sibling : void 0;
+  const sibling = haplotypeIndexBeside(db);
+  return sibling && await exists(sibling) ? sibling : void 0;
 }
-var UNDRAWABLE = /* @__PURE__ */ new Set(["walkrows", "tubemap", "tubemapref"]);
+var DRAWABLE = LAYOUT_MODES.filter((m) => m.drawsNodes).map(
+  (m) => m.value
+);
 function checkLayout(layout) {
-  if (layout === void 0) {
-    return;
-  }
-  if (!LAYOUT_MODE_VALUES.includes(layout)) {
+  if (layout !== void 0 && !DRAWABLE.includes(layout)) {
     throw new Error(
-      `unknown layout "${layout}": one of ${LAYOUT_MODE_VALUES.filter((v) => !UNDRAWABLE.has(v)).join(", ")}`
+      `a figure draws no "${layout}" layout: one of ${DRAWABLE.join(", ")}`
     );
   }
-  if (UNDRAWABLE.has(layout)) {
-    throw new Error(`a figure cannot draw the "${layout}" layout yet`);
-  }
 }
 async function renderSpec(spec, base) {
   checkLayout(spec.layout);

package/dist/index.js

@@ -102,7 +102,7 @@ import {
   wellKnownSample,
   yToXOf,
   zoomAbout
-} from "./chunks/chunk-75KVO2WV.js";
+} from "./chunks/chunk-VNCGWA2N.js";
 
 // src/index.ts
 import { getDpr } from "@jbrowse/render-core/canvas2dUtils";
@@ -722,15 +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, tubes) {
+function layerOf(layout, type) {
   const { shapes } = layout;
-  const colorOf = (s) => tubes?.[s.id] ?? s.color;
+  const trackOf = (s) => type === "haplotype" ? s.id : void 0;
   const rects = [...shapes.rectangles, ...shapes.verticalRectangles].filter((r) => r.type === type).map((r) => ({
-    color: colorOf(r),
+    color: r.color,
+    track: trackOf(r),
     alpha: r.alpha ?? 1,
     x0: r.xStart,
     x1: r.xEnd + 1,
@@ -738,30 +739,22 @@ function layerOf(layout, type, tubes) {
     y1: r.yEnd + 1
   }));
   const curves = curvePaths(shapes.curves, type).map(
-    (c) => shapeOf(c.path, colorOf(c), 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, colorOf(c), 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, colors = {}) {
+function tubeMapPicture(layout) {
   const nodes = [];
   layout.nodes.forEach((node) => {
     if (node.order >= 0) {
       const commands = parsePath(nodeOutlinePath(node));
-      nodes.push({
-        name: node.name,
-        commands,
-        ...extentOf(commands),
-        color: colors.nodes?.get(node.name)
-      });
+      nodes.push({ name: node.name, commands, ...extentOf(commands) });
     }
   });
   return {
     bounds: layout.bounds,
-    layers: [
-      layerOf(layout, "haplotype", colors.tubes),
-      layerOf(layout, "read")
-    ],
+    layers: [layerOf(layout, "haplotype"), layerOf(layout, "read")],
     nodes,
     mismatches: tubeMapMismatches(layout).filter(
       (m) => m.kind !== "insertion" || !m.softClip
@@ -807,11 +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);
@@ -821,7 +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) {
@@ -840,13 +833,14 @@ 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);
     });
   }
@@ -858,7 +852,7 @@ function drawTubeMap(ctx, picture, frame) {
       const lit = node.name === frame.highlightNode;
       ctx.beginPath();
       trace(ctx, node.commands, x, y);
-      const tint = lit ? void 0 : node.color;
+      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;
@@ -1724,19 +1718,14 @@ 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 lengthOf = new Map(graph.nodes.map((n) => [n.id, n.length]));
-  const bpOf = (steps) => steps.reduce((sum, id) => sum + (lengthOf.get(id) ?? 0), 0);
-  const stretches = /* @__PURE__ */ new Map();
+  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));
-    stretches.set(p.name, {
-      dropped: bpOf(p.nodeIds.slice(0, first)),
-      bp: bpOf(nodeIds)
-    });
+    kept.set(p.name, { first, nodeIds });
     return [{ ...p, nodeIds }];
   });
   return {
@@ -1744,7 +1733,7 @@ function bubbleSubgraph(graph, segmentIds) {
     nodes,
     edges: graph.edges.filter((e) => ids.has(e.from) && ids.has(e.to)),
     ...paths?.length ? { paths } : {},
-    anchorPaths: graph.anchorPaths && trimOrigins(graph.anchorPaths, graph.paths ?? [], stretches),
+    anchorPaths: trimOrigins(graph, kept),
     pathVisits: graph.pathVisits,
     anchoredBy: graph.anchoredBy,
     referencePath: graph.referencePath

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/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

@@ -19,7 +19,7 @@ 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 type { TubeMapColors, TubeMapFrame, 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';

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

@@ -1,4 +1,4 @@
-import type { Graph, GraphPath, PathOrigin, PathVisit } from './types.js';
+import type { Graph, PathOrigin, PathVisit } from './types.js';
 export declare function pathOrigin(pathName: string): {
     name: string;
     start: number;
@@ -18,7 +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(origins: PathOrigin[], paths: GraphPath[], stretches: Map<string, {
-    dropped: number;
-    bp: number;
-}>): PathOrigin[];
+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;
@@ -54,19 +55,16 @@ export interface TubeMapPicture {
         commands: Command[];
         x0: number;
         x1: number;
-        color?: string;
     }[];
     mismatches: TubeMapMismatch[];
 }
-export interface TubeMapColors {
-    tubes?: readonly string[];
-    nodes?: ReadonlyMap<string, string>;
-}
-export declare function tubeMapPicture(layout: TubeMapLayout, colors?: TubeMapColors): TubeMapPicture;
+export declare function tubeMapPicture(layout: TubeMapLayout): TubeMapPicture;
 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/version.d.ts

@@ -1 +1 @@
-export declare const version = "4.0.26";
+export declare const version = "4.0.27";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "4.0.26",
+  "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": {