@jbrowse/bandage-core 4.4.0 → 4.4.1

package/dist/chunks/{chunk-YNLMROBC.js → chunk-JJU4D2SE.js}

@@ -5583,8 +5583,11 @@ function walkStripLabelsTree(bars, frame, bold = /* @__PURE__ */ new Set()) {
     )
   );
 }
-function stripGeneGaps(frame, gaps) {
-  return gaps && !frame.boxesGenes ? { ...gaps, crowded: true } : gaps;
+function stripGeneGaps(frame, gaps, rowGenes) {
+  if (rowGenes ? !rowGenes.size : !gaps) {
+    return void 0;
+  }
+  return frame.boxesGenes ? gaps : { untracked: 0, unread: 0, ...gaps, crowded: true };
 }
 
 // src/renderer/svgCanvas.ts
@@ -5700,7 +5703,7 @@ function svgCanvas(width, height) {
 }
 
 // src/version.ts
-var version = "4.4.0";
+var version = "4.4.1";
 
 // src/viewport.ts
 function axisScaleOf(scale, pixelRows) {
@@ -5806,6 +5809,10 @@ function figureSvg(graph, layout, o = {}) {
   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, rampDomain) : void 0;
+  const rampInterval = referenceRamp && {
+    start: referenceRamp.start,
+    end: referenceRamp.start + referenceRamp.span
+  };
   const deletions = layout.tubeMap ? [] : deletionEdges(graph);
   const layers = o.walks ?? [];
   const walkRamp = layers.some((l) => l.color?.field === "reference") ? referenceRamp ?? computeReferenceRamp(graph, rampDomain) : void 0;
@@ -5872,10 +5879,7 @@ function figureSvg(graph, layout, o = {}) {
             rows,
             { ...t, width: w, height: h },
             {
-              ramp: referenceRamp && {
-                start: referenceRamp.start,
-                end: referenceRamp.start + referenceRamp.span
-              },
+              ramp: rampInterval,
               rowGenes: o.rowGenes
             }
           )
@@ -5998,10 +6002,7 @@ function figureSvg(graph, layout, o = {}) {
     if (rows) {
       const key = walkRowsKeyTree(
         walkRowsKey(rows, {
-          ramp: referenceRamp && {
-            start: referenceRamp.start,
-            end: referenceRamp.start + referenceRamp.span
-          },
+          ramp: rampInterval,
           genes: o.rowGenes?.size ? o.rowGeneGaps : void 0
         }),
         x,
@@ -6042,11 +6043,8 @@ function figureSvg(graph, layout, o = {}) {
     const frame = walkStripFrame(strip.rows, { width });
     const key = walkRowsKeyTree(
       walkRowsKey(strip.rows, {
-        ramp: referenceRamp && {
-          start: referenceRamp.start,
-          end: referenceRamp.start + referenceRamp.span
-        },
-        genes: strip.rowGenes?.size ? stripGeneGaps(frame, strip.rowGeneGaps) : void 0
+        ramp: rampInterval,
+        genes: stripGeneGaps(frame, strip.rowGeneGaps, strip.rowGenes)
       }),
       6,
       height + frame.height
@@ -6055,10 +6053,7 @@ function figureSvg(graph, layout, o = {}) {
       `<line x1="0" x2="${width}" y1="${height + 0.5}" y2="${height + 0.5}" stroke="#ddd"/>`,
       `<svg y="${height}" width="${width}" height="${frame.height}">${serializeEl(
         walkRowsTree(strip.rows, frame, {
-          ramp: referenceRamp && {
-            start: referenceRamp.start,
-            end: referenceRamp.start + referenceRamp.span
-          },
+          ramp: rampInterval,
           rowGenes: strip.rowGenes,
           idPrefix: "strip"
         })

package/dist/cli/figure.js

@@ -18,7 +18,7 @@ import {
   parseRegion,
   refNameBinding,
   walkRows
-} from "../chunks/chunk-YNLMROBC.js";
+} from "../chunks/chunk-JJU4D2SE.js";
 
 // src/cli/figure.ts
 import { access, open, readFile, writeFile } from "node:fs/promises";
@@ -139,8 +139,6 @@ async function renderSpec(spec, base) {
   checkLayout(spec.layout);
   const resolve = (location) => isUrl(location) ? location : path.resolve(base, location);
   let source;
-  const mode = layoutModeByValue(spec.layout ?? "force");
-  const strip = !!spec.walkStrip && mode.drawsNodes;
   if (spec.gbz) {
     const { db, index } = spec.gbz.db === "hprc" ? HPRC_GBZ : spec.gbz;
     const indexLocation = index ? resolve(index) : await siblingIndex(resolve(db));
@@ -149,8 +147,8 @@ async function renderSpec(spec, base) {
         byteSource(resolve(db)),
         indexLocation ? byteSource(indexLocation) : void 0
       ),
-      // walk rows measure whole walks, which a cut only follows when asked
-      mode.wholeWalks || strip ? { snarls: "overlapping", ...spec.gbz } : spec.gbz
+      // the strip measures whole walks, which a cut only follows when asked
+      spec.walkStrip ? { snarls: "overlapping", ...spec.gbz } : spec.gbz
     );
     source = { ...cut, name: `${cut.sample} ${spec.gbz.region}` };
   } else if (spec.gfa) {
@@ -165,7 +163,7 @@ async function renderSpec(spec, base) {
   const graph = loadGraph(source.text, source.name, {
     referencePath: spec.referencePath
   });
-  const layout = mode.run(graph, source.region) ?? (await forceLayout(
+  const layout = layoutModeByValue(spec.layout ?? "force").run(graph, source.region) ?? (await forceLayout(
     graph,
     {
       quality: spec.quality ?? 2,
@@ -174,7 +172,7 @@ async function renderSpec(spec, base) {
     },
     engine
   )).result;
-  const stripRows = strip ? walkRows(graph, source.region) : void 0;
+  const stripRows = spec.walkStrip ? walkRows(graph, source.region) : void 0;
   return figureSvg(graph, layout, {
     ...spec,
     walkStrip: stripRows && { rows: stripRows },

package/dist/index.js

@@ -136,7 +136,7 @@ import {
   wellKnownSample,
   yToXOf,
   zoomAbout
-} from "./chunks/chunk-YNLMROBC.js";
+} from "./chunks/chunk-JJU4D2SE.js";
 
 // src/index.ts
 import { getDpr } from "@jbrowse/render-core/canvas2dUtils";

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

@@ -1,4 +1,4 @@
-import type { GeneGaps, WalkRowsFrame } from './walkRowDraw.js';
+import type { GeneGaps, RowGene, WalkRowsFrame } from './walkRowDraw.js';
 import type { WalkRow, WalkRows } from './walkRows.js';
 import type { Graph, GraphNode } from '../types.js';
 export declare const WALK_STRIP_CEILING_PX = 260;
@@ -29,4 +29,4 @@ export declare function stripRowAt(bars: WalkRows, frame: StripFrame, x: number,
 } | undefined;
 export declare function walkMarksTree(bars: WalkRows, frame: StripFrame, marks: StripMark[]): import("../index.js").El;
 export declare function walkStripLabelsTree(bars: WalkRows, frame: StripFrame, bold?: ReadonlySet<string>): import("../index.js").El;
-export declare function stripGeneGaps(frame: StripFrame, gaps: GeneGaps | undefined): GeneGaps | undefined;
+export declare function stripGeneGaps(frame: StripFrame, gaps: GeneGaps | undefined, rowGenes?: Map<string, RowGene[]>): GeneGaps | undefined;

package/dist/types/version.d.ts

@@ -1 +1 @@
-export declare const version = "4.4.0";
+export declare const version = "4.4.1";

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/bandage-core",
-  "version": "4.4.0",
+  "version": "4.4.1",
   "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": {