@jbrowse/bandage-core 4.0.25 → 4.0.26

package/dist/chunks/{chunk-B5ZHLU4N.js → chunk-75KVO2WV.js}

@@ -387,6 +387,18 @@ function anchorFromPaths(graph, preferred) {
 function anchorGraph(graph, preferred) {
   return graph.anchoredBy === "tags" ? graph : anchorFromPaths(graph, preferred);
 }
+function trimOrigins(origins, paths, stretches) {
+  const pieces = /* @__PURE__ */ new Map();
+  for (const path of paths) {
+    const origin = pathOrigin(path.name).name;
+    pieces.set(origin, (pieces.get(origin) ?? 0) + 1);
+  }
+  return origins.map((o) => {
+    const path = paths.find((p) => pathOrigin(p.name).name === o.name);
+    const stretch = path ? stretches.get(path.name) : void 0;
+    return stretch && pieces.get(o.name) === 1 ? { ...o, start: o.start + stretch.dropped, length: stretch.bp } : o;
+  });
+}
 
 // src/gfa/gfaConverter.ts
 function surveySegments(gfaGraph) {
@@ -4278,7 +4290,7 @@ function liftOf(walks, ramp) {
 function rangeText(contig, start, end) {
   const s = Math.round(start);
   const e = Math.round(end);
-  return `${contig ? `${contig}:` : ""}${s.toLocaleString()}-${e.toLocaleString()} (${formatBp(e - s)})`;
+  return `${contig ? `${contig}:` : ""}${s.toLocaleString("en-US")}-${e.toLocaleString("en-US")} (${formatBp(e - s)})`;
 }
 function walkKey(walk, reference) {
   const { field } = walk.encoding;
@@ -4299,7 +4311,7 @@ function walkPosition(walk, nodeId, length) {
     return void 0;
   }
   const start = Math.round(range.start + progress * walk.bp - length / 2);
-  return `${range.contig}:${start.toLocaleString()}-${(start + length).toLocaleString()}`;
+  return `${range.contig}:${start.toLocaleString("en-US")}-${(start + length).toLocaleString("en-US")}`;
 }
 
 // src/facetGrid.ts
@@ -4703,7 +4715,7 @@ function svgCanvas(width, height) {
 }
 
 // src/version.ts
-var version = "4.0.25";
+var version = "4.0.26";
 
 // src/viewport.ts
 function axisScaleOf(scale, pixelRows) {
@@ -4798,14 +4810,17 @@ function figureSvg(graph, layout, o = {}) {
   const width = o.width ?? 1200;
   const room = o.height ?? 800;
   const region = o.region;
-  const bounds = drawingBounds(layout, { region });
+  const rampDomain = o.colorDomain ?? region;
+  const bounds = drawingBounds(layout, {
+    region: o.fitToDrawing ? void 0 : region
+  });
   const pixelRows = layout.pixelRows ?? false;
   const nodeById = new Map(graph.nodes.map((node) => [node.id, node]));
   const colorScheme = resolveColorScheme(o.colorScheme ?? "auto", graph);
-  const referenceRamp = colorScheme === "reference-position" && !layout.tubeMap ? computeReferenceRamp(graph, region) : void 0;
+  const referenceRamp = colorScheme === "reference-position" && !layout.tubeMap ? computeReferenceRamp(graph, rampDomain) : void 0;
   const deletions = layout.tubeMap ? [] : deletionEdges(graph);
   const layers = o.walks ?? [];
-  const walkRamp = layers.some((l) => l.color?.field === "reference") ? referenceRamp ?? computeReferenceRamp(graph, region) : void 0;
+  const walkRamp = layers.some((l) => l.color?.field === "reference") ? referenceRamp ?? computeReferenceRamp(graph, rampDomain) : void 0;
   const lift = layers.length > 0 && !layout.tubeMap ? walkLift(graph, layers, walkRamp) : void 0;
   const by = o.facet ?? "none";
   const panels = by !== "none" && lift && lift.walks.length > 1 ? facetLifts(graph, lift, layers, walkRamp) : void 0;
@@ -5128,7 +5143,7 @@ function genesFromBed(text) {
       continue;
     }
     const refName = cols[0];
-    const name = cols[3] || `${refName}:${start + 1}-${end}`;
+    const name = cols[3] && cols[3] !== "." ? cols[3] : `${refName}:${start + 1}-${end}`;
     const sizes = cols[10]?.split(",").filter((s) => s !== "").map(Number);
     const starts = cols[11]?.split(",").filter((s) => s !== "").map(Number);
     const blocks = sizes?.length && sizes.length === starts?.length ? sizes.map((size, i) => ({
@@ -5435,6 +5450,7 @@ export {
   panSNSample,
   panSNHaplotype,
   panSNContig,
+  trimOrigins,
   loadGraph,
   engineRequest,
   engineKey,
@@ -5452,6 +5468,7 @@ export {
   walkRowsExtent,
   FORCE_LAYOUT_LABEL,
   LAYOUT_MODES,
+  LAYOUT_MODE_VALUES,
   modeUsesLayoutEngine,
   layoutModeByValue,
   COLOR_SCHEMES,

package/dist/cli/figure.js

@@ -1,6 +1,7 @@
 #!/usr/bin/env node
 import {
   HPRC_GBZ,
+  LAYOUT_MODE_VALUES,
   cutGbzRegion,
   featuresOnBackbone,
   figureSvg,
@@ -14,10 +15,10 @@ import {
   loadGraph,
   openGbz,
   parseRegion
-} from "../chunks/chunk-B5ZHLU4N.js";
+} from "../chunks/chunk-75KVO2WV.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";
@@ -36,7 +37,7 @@ function byteSource(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 +54,15 @@ function byteSource(location) {
     }
   };
 }
+async function fetchOk(location, init) {
+  const res = await fetch(location, init);
+  if (!res.ok) {
+    throw new Error(`HTTP ${res.status} reading ${location}`);
+  }
+  return res;
+}
 async function text(location) {
-  const bytes = isUrl(location) ? new Uint8Array(await (await fetch(location)).arrayBuffer()) : await readFile(location);
+  const bytes = isUrl(location) ? new Uint8Array(await (await fetchOk(location)).arrayBuffer()) : await readFile(location);
   const gzipped = bytes[0] === 31 && bytes[1] === 139;
   return new TextDecoder().decode(gzipped ? gunzipSync(bytes) : bytes);
 }
@@ -94,15 +102,43 @@ var engine = async (request) => {
   const result = bandage.computeLayout(request.graph, request.options);
   return { result, duration: performance.now() - start };
 };
+async function exists(location) {
+  try {
+    await (isUrl(location) ? fetchOk(location, { method: "HEAD" }) : access(location));
+    return true;
+  } catch {
+    return false;
+  }
+}
+async function siblingIndex(db) {
+  const sibling = db.replace(/\.gbz\.db$/i, ".haplotype-index.db");
+  return sibling !== db && await exists(sibling) ? sibling : void 0;
+}
+var UNDRAWABLE = /* @__PURE__ */ new Set(["walkrows", "tubemap", "tubemapref"]);
+function checkLayout(layout) {
+  if (layout === void 0) {
+    return;
+  }
+  if (!LAYOUT_MODE_VALUES.includes(layout)) {
+    throw new Error(
+      `unknown layout "${layout}": one of ${LAYOUT_MODE_VALUES.filter((v) => !UNDRAWABLE.has(v)).join(", ")}`
+    );
+  }
+  if (UNDRAWABLE.has(layout)) {
+    throw new Error(`a figure cannot draw the "${layout}" layout yet`);
+  }
+}
 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 +172,32 @@ 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 +208,9 @@ 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-75KVO2WV.js";
 
 // src/index.ts
 import { getDpr } from "@jbrowse/render-core/canvas2dUtils";
@@ -725,10 +726,11 @@ function shapeOf(d, color, alpha) {
   const commands = parsePath(d);
   return { commands, color, alpha, ...extentOf(commands) };
 }
-function layerOf(layout, type) {
+function layerOf(layout, type, tubes) {
   const { shapes } = layout;
+  const colorOf = (s) => tubes?.[s.id] ?? s.color;
   const rects = [...shapes.rectangles, ...shapes.verticalRectangles].filter((r) => r.type === type).map((r) => ({
-    color: r.color,
+    color: colorOf(r),
     alpha: r.alpha ?? 1,
     x0: r.xStart,
     x1: r.xEnd + 1,
@@ -736,22 +738,30 @@ 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, colorOf(c), c.alpha ?? 1)
   );
-  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, colorOf(c), 1));
   return { rects, shapes: [...curves, ...corners] };
 }
-function tubeMapPicture(layout) {
+function tubeMapPicture(layout, colors = {}) {
   const nodes = [];
   layout.nodes.forEach((node) => {
     if (node.order >= 0) {
       const commands = parsePath(nodeOutlinePath(node));
-      nodes.push({ name: node.name, commands, ...extentOf(commands) });
+      nodes.push({
+        name: node.name,
+        commands,
+        ...extentOf(commands),
+        color: colors.nodes?.get(node.name)
+      });
     }
   });
   return {
     bounds: layout.bounds,
-    layers: [layerOf(layout, "haplotype"), layerOf(layout, "read")],
+    layers: [
+      layerOf(layout, "haplotype", colors.tubes),
+      layerOf(layout, "read")
+    ],
     nodes,
     mismatches: tubeMapMismatches(layout).filter(
       (m) => m.kind !== "insertion" || !m.softClip
@@ -826,6 +836,7 @@ 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;
@@ -847,8 +858,10 @@ 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 : node.color;
+      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 +910,21 @@ 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 +1724,27 @@ 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 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 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)
+    });
+    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: graph.anchorPaths && trimOrigins(graph.anchorPaths, graph.paths ?? [], stretches),
     pathVisits: graph.pathVisits,
     anchoredBy: graph.anchoredBy,
     referencePath: graph.referencePath
@@ -1815,6 +1857,7 @@ export {
   tubeMapFrame,
   tubeMapGenes,
   tubeMapNodeAt,
+  tubeMapNodeColors,
   tubeMapPicture,
   tubeX,
   version,

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/index.d.ts

@@ -19,7 +19,8 @@ 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 { TubeMapFrame, TubeMapPicture } from './tubeMap/draw.js';
+export type { TubeMapColors, 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/pathAnchoring.d.ts

@@ -1,4 +1,4 @@
-import type { Graph, PathOrigin, PathVisit } from './types.js';
+import type { Graph, GraphPath, PathOrigin, PathVisit } from './types.js';
 export declare function pathOrigin(pathName: string): {
     name: string;
     start: number;
@@ -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(origins: PathOrigin[], paths: GraphPath[], stretches: Map<string, {
+    dropped: number;
+    bp: number;
+}>): PathOrigin[];

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

@@ -54,10 +54,15 @@ export interface TubeMapPicture {
         commands: Command[];
         x0: number;
         x1: number;
+        color?: string;
     }[];
     mismatches: TubeMapMismatch[];
 }
-export declare function tubeMapPicture(layout: TubeMapLayout): TubeMapPicture;
+export interface TubeMapColors {
+    tubes?: readonly string[];
+    nodes?: ReadonlyMap<string, string>;
+}
+export declare function tubeMapPicture(layout: TubeMapLayout, colors?: TubeMapColors): TubeMapPicture;
 export interface TubeMapFrame extends TubeMapTransform {
     width: number;
     highlightNode?: string | null;

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 = "4.0.26";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "4.0.25",
+  "version": "4.0.26",
   "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": {