@jbrowse/bandage-core 10.2.2 → 10.2.4

package/dist/chunks/{chunk-IW6CYVX2.js → chunk-AR4BUBMU.js}

@@ -1,6 +1,6 @@
 import {
   stableCoordinate
-} from "./chunk-CDLPYR5O.js";
+} from "./chunk-5I3K4R2G.js";
 import {
   pathOrigin,
   surveyPaths
@@ -95,7 +95,12 @@ function convertGFAToGraph(gfaGraph, name = "Imported GFA") {
     }
     return id;
   };
+  const declared = /* @__PURE__ */ new Set();
   for (const gfaNode of gfaGraph.nodes) {
+    if (declared.has(gfaNode.id)) {
+      continue;
+    }
+    declared.add(gfaNode.id);
     const depth = statedDepth(gfaNode) ?? Math.max(traversals.get(gfaNode.id) ?? 1, 1);
     nodes.push(makeNode(gfaNode, canonical.get(gfaNode.id) ?? "+", depth));
   }

package/dist/chunks/{chunk-IUDJKOLB.js → chunk-B6IW3IRE.js}

@@ -12,7 +12,7 @@ import {
 } from "./chunk-M6LK4GII.js";
 
 // src/tubeMap/draw.ts
-import { curvePaths, nodeOutlinePath } from "@jbrowse/tubemap-core";
+import { curvePaths, flattenPath, nodeOutlinePath } from "@jbrowse/tubemap-core";
 function parsePath(d) {
   const tokens = d.trim().split(/[\s,]+/);
   const commands = [];
@@ -61,7 +61,15 @@ function extentOf(commands) {
 }
 function shapeOf(d, color, id, haplotype, reference) {
   const commands = parsePath(d);
-  return { commands, color, id, haplotype, reference, ...extentOf(commands) };
+  return {
+    commands,
+    outline: flattenPath(d, 12),
+    color,
+    id,
+    haplotype,
+    reference,
+    ...extentOf(commands)
+  };
 }
 function trackColors(layout, pathColors) {
   return new Map(
@@ -302,36 +310,6 @@ function drawMismatches(ctx, marks, frame) {
     }
   }
 }
-function outline(commands, x, y) {
-  const points = [];
-  let cx = 0;
-  let cy = 0;
-  const STEPS = 12;
-  for (const c of commands) {
-    if (c.op === "C" || c.op === "Q") {
-      for (let i = 1; i <= STEPS; i++) {
-        const t = i / STEPS;
-        const u = 1 - t;
-        const [px, py] = c.op === "C" ? [
-          u * u * u * cx + 3 * u * u * t * c.x1 + 3 * u * t * t * c.x2 + t * t * t * c.x,
-          u * u * u * cy + 3 * u * u * t * c.y1 + 3 * u * t * t * c.y2 + t * t * t * c.y
-        ] : [
-          u * u * cx + 2 * u * t * c.x1 + t * t * c.x,
-          u * u * cy + 2 * u * t * c.y1 + t * t * c.y
-        ];
-        points.push([x(px), y(py)]);
-      }
-    }
-    if (c.op !== "Z") {
-      cx = "x" in c ? c.x : cx;
-      cy = "y" in c ? c.y : cy;
-      if (c.op !== "C" && c.op !== "Q") {
-        points.push([x(cx), y(cy)]);
-      }
-    }
-  }
-  return points;
-}
 function inside(points, sx, sy) {
   let hit = false;
   for (let i = 0, j = points.length - 1; i < points.length; j = i++) {
@@ -353,7 +331,11 @@ function tubeMapTrackAt(picture, { x, y }, sx, sy) {
         }
       }
       for (const s of shapes) {
-        if (s.reference === reference && x(s.x0) <= sx && sx <= x(s.x1) && inside(outline(s.commands, x, y), sx, sy)) {
+        if (s.reference === reference && x(s.x0) <= sx && sx <= x(s.x1) && inside(
+          s.outline.map(([px, py]) => [x(px), y(py)]),
+          sx,
+          sy
+        )) {
           return s.id;
         }
       }

package/dist/chunks/{chunk-JUIJI7RC.js → chunk-BAETMD3J.js}

@@ -2,10 +2,13 @@ import {
   alongRow,
   boxesGenes,
   rowPitch
-} from "./chunk-NRV7R36Q.js";
+} from "./chunk-EFQLEGWM.js";
 import {
   el
-} from "./chunk-NNODIW4U.js";
+} from "./chunk-H2H4Y3TV.js";
+import {
+  READOUT_ROOM
+} from "./chunk-54POIBVC.js";
 import {
   pathOrigin
 } from "./chunk-M6LK4GII.js";
@@ -24,7 +27,6 @@ var PAD_PX = 6;
 var WALK_STRIP_CEILING_PX = 260;
 var LABEL_FONT_PX = 11;
 var MIN_ROW_PX = 3;
-var READOUT_ROOM = 1.3;
 var MARK_INK = "#111";
 var TICK_PX = 3;
 function stripMarks(graph, rows, node) {
@@ -59,7 +61,10 @@ function spansOf(graph, name) {
     return byName.get(name);
   }
   const lengthOf = new Map(graph.nodes.map((n) => [n.id, n.length]));
-  const pieces = (graph.paths ?? []).filter((p) => p.name === name);
+  const origin = pathOrigin(name).name;
+  const pieces = (graph.paths ?? []).filter(
+    (p) => origin === graph.referencePath ? pathOrigin(p.name).name === origin : p.name === name
+  );
   let spans;
   if (pieces.every((p) => p.start !== void 0)) {
     spans = { ids: [], starts: [], ends: [] };

package/dist/chunks/{chunk-L5WF4ZPS.js → chunk-BS4UZ44I.js}

@@ -1,6 +1,6 @@
 import {
   clampZoom
-} from "./chunk-XTCNEKO5.js";
+} from "./chunk-2QLLQJ72.js";
 
 // src/viewport.ts
 function axisScaleOf(scale, pixelRows) {

package/dist/chunks/{chunk-HNQPEMYE.js → chunk-CM6LO6OC.js}

@@ -292,6 +292,5 @@ function orderedLayout(graph) {
 
 export {
   referenceOrder,
-  layerGraph,
   orderedLayout
 };

package/dist/chunks/{chunk-CLOP7UVD.js → chunk-CQHUZHET.js}

@@ -3,12 +3,20 @@ import {
 } from "./chunk-FX4RDMDN.js";
 import {
   referenceOrder
-} from "./chunk-HNQPEMYE.js";
+} from "./chunk-CM6LO6OC.js";
 import {
   isBackbone
 } from "./chunk-FYQWPEEY.js";
 
 // src/bubbles/bubblesFromGraph.ts
+function relax(best, to, cur, add) {
+  const prev = best.get(to);
+  best.set(to, {
+    min: Math.min(prev?.min ?? Infinity, cur.min + add),
+    max: Math.max(prev?.max ?? -Infinity, cur.max + add),
+    n: Math.min(SATURATED_PATH_COUNT, cur.n + (prev?.n ?? 0))
+  });
+}
 function bubblesFromGraph(graph) {
   if (!graph.nodes.some(isBackbone)) {
     return [];
@@ -61,13 +69,7 @@ function bubblesFromGraph(graph) {
         if (ti > i1) {
           continue;
         }
-        const add = t === end.id ? 0 : byId.get(t).length;
-        const prev = best.get(t);
-        best.set(t, {
-          min: Math.min(prev?.min ?? Infinity, cur.min + add),
-          max: Math.max(prev?.max ?? -Infinity, cur.max + add),
-          n: Math.min(SATURATED_PATH_COUNT, cur.n + (prev?.n ?? 0))
-        });
+        relax(best, t, cur, t === end.id ? 0 : byId.get(t).length);
       }
     }
     const walked = walkIndex && walkRoutes(graph, byId, walkIndex, start.id, end.id);
@@ -167,6 +169,7 @@ function walkRoutes(graph, byId, walkIndex, startId, endId) {
 }
 
 export {
+  relax,
   bubblesFromGraph,
   walkIndexOf,
   walkRoutes

package/dist/chunks/{chunk-R456ME6J.js → chunk-CU6P5RUG.js}

@@ -1,7 +1,7 @@
 import {
   encodedColor,
   resolveEncoding
-} from "./chunk-ALDGONEI.js";
+} from "./chunk-VQC7KELB.js";
 import {
   pathOrigin
 } from "./chunk-M6LK4GII.js";
@@ -28,10 +28,14 @@ function walkHighlight(graph, name) {
   const lengthOf = (id) => byId.get(id)?.length ?? 0;
   const bpOf = (path) => path.nodeIds.reduce((sum, id) => sum + lengthOf(id), 0);
   const bp = pieces.reduce((sum, piece) => sum + bpOf(piece), 0);
-  const range = first.start === void 0 ? void 0 : {
+  const extentOf = (ps) => {
+    const start = Math.min(...ps.map((p) => p.start ?? Infinity));
+    return Number.isFinite(start) ? { start, end: Math.max(...ps.map((p) => (p.start ?? 0) + bpOf(p))) } : void 0;
+  };
+  const extent = extentOf(pieces);
+  const range = extent && {
     contig: first.contig ?? panSNContig(pathOrigin(name).name),
-    start: first.start,
-    end: Math.max(...pieces.map((p) => (p.start ?? 0) + bpOf(p)))
+    ...extent
   };
   const span = range ? range.end - range.start : bp;
   const nodeIds = /* @__PURE__ */ new Set();
@@ -59,7 +63,14 @@ function walkHighlight(graph, name) {
     });
   }
   const reference = isReference(graph, name);
-  const referencePieces = reference ? [] : (graph.paths ?? []).filter((p) => isReference(graph, p.name));
+  const referenceSpan = () => {
+    const referencePieces = reference ? [] : (graph.paths ?? []).filter((p) => isReference(graph, p.name));
+    if (referencePieces.length === 0) {
+      return void 0;
+    }
+    const e = extentOf(referencePieces);
+    return e ? e.end - e.start : referencePieces.reduce((sum, piece) => sum + bpOf(piece), 0);
+  };
   return {
     name,
     reference,
@@ -69,7 +80,7 @@ function walkHighlight(graph, name) {
     progress,
     steps: pieces.reduce((sum, piece) => sum + piece.nodeIds.length, 0),
     bp,
-    referenceBp: referencePieces.length > 0 ? referencePieces.reduce((sum, piece) => sum + bpOf(piece), 0) : void 0
+    referenceBp: referenceSpan()
   };
 }
 function laneColors(graph, walk, encoding, ramp) {

package/dist/chunks/chunk-D5D36ZF6.js

@@ -0,0 +1,107 @@
+import {
+  layoutGeometryInputs
+} from "./chunk-LOCJN3BZ.js";
+import {
+  facetLifts,
+  walkLift
+} from "./chunk-CU6P5RUG.js";
+import {
+  buildGeometry,
+  computeReferenceRamp
+} from "./chunk-A4PFFC4Q.js";
+import {
+  walkRowsExtent
+} from "./chunk-54POIBVC.js";
+import {
+  pathLegend,
+  walkLabelsOf
+} from "./chunk-3XSM4OZU.js";
+import {
+  FIGURE_DEFAULTS
+} from "./chunk-HNCXR2VS.js";
+import {
+  drawingBounds
+} from "./chunk-2QLLQJ72.js";
+import {
+  referenceLabel
+} from "./chunk-RAKOB6IV.js";
+import {
+  resolveColorScheme
+} from "./chunk-JKJWSY4V.js";
+import {
+  deletionDrawing,
+  deletionEdges
+} from "./chunk-24WITXQY.js";
+import {
+  facetSettingOf
+} from "./chunk-XV4P5KEQ.js";
+
+// src/figureScene.ts
+function figureScene(graph, layout, o) {
+  const region = o.region;
+  const rampDomain = o.colorDomain ?? region;
+  const rows = o.walkRows;
+  const bounds = drawingBounds(layout, {
+    region: o.fitToDrawing ? void 0 : region,
+    extent: rows && layout.extent ? walkRowsExtent(rows, o.walkRowPitch) : void 0
+  });
+  const nodeById = new Map(graph.nodes.map((node) => [node.id, node]));
+  const colorScheme = resolveColorScheme(
+    o.colorScheme ?? FIGURE_DEFAULTS.colorScheme,
+    graph
+  );
+  const referenceRamp = colorScheme === "reference-position" && !layout.tubeMap ? computeReferenceRamp(graph, rampDomain) : void 0;
+  const drawnDeletions = deletionDrawing(
+    graph,
+    layout.tubeMap ? [] : deletionEdges(graph),
+    o.showDeletionEdges
+  );
+  const layers = o.walks ?? [];
+  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 facet = facetSettingOf(o.facet);
+  const panels = facet.field && lift && lift.walks.length > 1 ? facetLifts(graph, lift, layers, walkRamp) : void 0;
+  const labels = walkLabelsOf(
+    graph.paths?.length ? pathLegend(graph.paths) : []
+  );
+  const referenceName = o.referenceName ?? referenceLabel(graph, region);
+  const contigThickness = o.contigThickness ?? FIGURE_DEFAULTS.contigThickness;
+  const nodeWidth = o.nodeWidth ?? FIGURE_DEFAULTS.nodeWidth;
+  return {
+    bounds,
+    nodeById,
+    colorScheme,
+    referenceRamp,
+    drawnDeletions,
+    layers,
+    lift,
+    facet,
+    panels,
+    labelOf: (name) => labels.get(name) ?? name,
+    referenceName,
+    reference: lift?.referenceDomain && {
+      ...lift.referenceDomain,
+      name: referenceName
+    },
+    contigThickness,
+    nodeWidth,
+    geometry: (highlight, axis) => buildGeometry({
+      ...layoutGeometryInputs(layout, drawnDeletions, { drawsRows: !!rows }),
+      graph,
+      nodeById,
+      colorScheme,
+      contigThickness,
+      connectorThickness: o.connectorThickness ?? FIGURE_DEFAULTS.connectorThickness,
+      drawPaths: false,
+      nodeWidth,
+      linearLayout: o.linearLayout,
+      highlight,
+      axis,
+      referenceRamp
+    })
+  };
+}
+
+export {
+  figureScene
+};

package/dist/chunks/{chunk-AFP3NWSL.js → chunk-DY3JCAMX.js}

@@ -1,6 +1,6 @@
 import {
   ownStrand
-} from "./chunk-2CVHXFK7.js";
+} from "./chunk-7SRWJLSC.js";
 import {
   isBackbone
 } from "./chunk-FYQWPEEY.js";

package/dist/chunks/{chunk-NRV7R36Q.js → chunk-EFQLEGWM.js}

@@ -3,13 +3,13 @@ import {
   RAMP_GRADIENT_STOPS,
   rampHueCss,
   rampStops
-} from "./chunk-ZIUKZUPJ.js";
+} from "./chunk-XL472HHD.js";
 import {
   el
-} from "./chunk-NNODIW4U.js";
+} from "./chunk-H2H4Y3TV.js";
 import {
   REFERENCE_RAMP_ALT_CSS
-} from "./chunk-SBMJNRTV.js";
+} from "./chunk-A4PFFC4Q.js";
 import {
   LABEL_CHAR_PX
 } from "./chunk-AB35TJST.js";

package/dist/chunks/{chunk-BXEPA4KS.js → chunk-G6UIYQZR.js}

@@ -164,10 +164,13 @@ function genesFromBed(text) {
   }
   return mergeOverlappingByName(rows);
 }
-function genesFromText(text) {
+function sniffedFormat(text) {
   const first = text.split("\n", 1e3).find((l) => l.trim() !== "" && !/^(#|track|browser)/.test(l));
   const cols = first?.split("	") ?? [];
-  return /^\d+$/.test(cols[1] ?? "") && /^\d+$/.test(cols[2] ?? "") ? genesFromBed(text) : genesFromGff3Lines(text.split(/\r?\n/));
+  return /^\d+$/.test(cols[1] ?? "") && /^\d+$/.test(cols[2] ?? "") ? "bed" : "gff3";
+}
+function genesFromText(text, format = sniffedFormat(text)) {
+  return format === "bed" ? genesFromBed(text) : genesFromGff3Lines(text.split(/\r?\n/));
 }
 
 export {

package/dist/chunks/{chunk-ASSNZXCF.js → chunk-GINYTQ43.js}

@@ -1,79 +1,63 @@
 import {
   svgCanvas
-} from "./chunk-47DYCZOK.js";
+} from "./chunk-RUCH6ZFL.js";
 import {
   stripGeneGaps,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunk-JUIJI7RC.js";
-import {
-  Canvas2DRenderer
-} from "./chunk-WBCOREDZ.js";
+} from "./chunk-BAETMD3J.js";
 import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunk-NRV7R36Q.js";
+} from "./chunk-EFQLEGWM.js";
+import {
+  Canvas2DRenderer
+} from "./chunk-QLWI2PZ3.js";
 import {
   EXON_COLOR,
   exonOutlineTree,
   exonStretches
-} from "./chunk-3S3YVOJ7.js";
+} from "./chunk-JSUCGZ6K.js";
 import {
   genePins
-} from "./chunk-BUBZ32IC.js";
+} from "./chunk-RPRHR56C.js";
 import {
   geneLabelCandidates
-} from "./chunk-DRG4236Y.js";
+} from "./chunk-KC7T5RWG.js";
 import {
   nodesUnderBox
-} from "./chunk-FP4H7SFT.js";
+} from "./chunk-4HWM3FNK.js";
 import {
+  escapeAttr,
   serializeEl
-} from "./chunk-NNODIW4U.js";
-import {
-  layoutGeometryInputs
-} from "./chunk-LOCJN3BZ.js";
+} from "./chunk-H2H4Y3TV.js";
 import {
   version
-} from "./chunk-EYK7DJZV.js";
+} from "./chunk-2CHS5LMM.js";
 import {
   axisScaleOf
-} from "./chunk-L5WF4ZPS.js";
-import {
-  facetLifts,
-  walkLift
-} from "./chunk-R456ME6J.js";
-import {
-  encodingStops
-} from "./chunk-ALDGONEI.js";
+} from "./chunk-BS4UZ44I.js";
 import {
   rangeText,
   walkKey
-} from "./chunk-2LQ5BWT7.js";
+} from "./chunk-4ETPXDO6.js";
 import {
-  buildGeometry,
-  computeReferenceRamp
-} from "./chunk-SBMJNRTV.js";
+  figureScene
+} from "./chunk-D5D36ZF6.js";
 import {
-  walkRowLabels,
-  walkRowsExtent
-} from "./chunk-C7MZJSPT.js";
+  encodingStops
+} from "./chunk-VQC7KELB.js";
 import {
-  pathLegend,
-  walkLabelsOf
-} from "./chunk-TWRLC3KK.js";
+  walkRowLabels
+} from "./chunk-54POIBVC.js";
 import {
   nodeInk
-} from "./chunk-PBENCR5L.js";
+} from "./chunk-JBCZIBFC.js";
 import {
   FIT_PADDING,
-  drawingBounds,
   fitTransform
-} from "./chunk-XTCNEKO5.js";
-import {
-  referenceLabel
-} from "./chunk-RAKOB6IV.js";
+} from "./chunk-2QLLQJ72.js";
 import {
   LABEL_CHAR_PX,
   LABEL_PAD,
@@ -81,20 +65,12 @@ import {
   occupancy,
   placeLabels
 } from "./chunk-AB35TJST.js";
-import {
-  resolveColorScheme
-} from "./chunk-JKJWSY4V.js";
-import {
-  deletionDrawing,
-  deletionEdges
-} from "./chunk-N6FECAXP.js";
 import {
   FACET_GAP_PX,
   FACET_PAD_PX,
   FACET_TITLE_PX,
   facetCells,
-  facetGrid,
-  facetSettingOf
+  facetGrid
 } from "./chunk-XV4P5KEQ.js";
 
 // src/figure.ts
@@ -105,9 +81,6 @@ var KEY_GAP_PX = 16;
 var STRIP_KEY_PX = 22;
 var FADED = "rgb(160,160,160)";
 var GENE_INK = "#1c1c22";
-function esc(s) {
-  return s.replaceAll("&", "&amp;").replaceAll("<", "&lt;").replaceAll(">", "&gt;").replaceAll('"', "&quot;");
-}
 function keySvg(id, x, y, stops, label, after, under, opacity = 1) {
   const bar = stops.length > 1 ? BAR_PX : SWATCH_PX;
   const fill = stops.length > 1 ? `fill="url(#${id})"` : `fill="${stops[0].color}"${opacity < 1 ? ` fill-opacity="${opacity}"` : ""}`;
@@ -118,7 +91,7 @@ function keySvg(id, x, y, stops, label, after, under, opacity = 1) {
   );
   return {
     width,
-    markup: `${defs}<g transform="translate(${x} ${y})" ${FONT}><rect y="5" width="${bar}" height="8" rx="2" ${fill}/><text x="${bar + 5}" y="13"><tspan font-weight="bold">${esc(label)}</tspan>${esc(after)}</text>${under ? `<text y="28">${esc(under)}</text>` : ""}</g>`
+    markup: `${defs}<g transform="translate(${x} ${y})" ${FONT}><rect y="5" width="${bar}" height="8" rx="2" ${fill}/><text x="${bar + 5}" y="13"><tspan font-weight="bold">${escapeAttr(label)}</tspan>${escapeAttr(after)}</text>${under ? `<text y="28">${escapeAttr(under)}</text>` : ""}</g>`
   };
 }
 function exonKeySvg(x, y) {
@@ -146,47 +119,32 @@ function screenPath(d, t) {
   );
 }
 function chip(x, y, w, name, note) {
-  return `<rect x="${x - w / 2}" y="${y - LABEL_PX - LABEL_PAD + 2}" width="${w}" height="${LABEL_PX + LABEL_PAD * 2 - 2}" rx="3" fill="#fff" fill-opacity="0.85" stroke="${EXON_COLOR}"/><text x="${x}" y="${y}" font-family="Helvetica, Arial, sans-serif" font-size="${LABEL_PX}" fill="${GENE_INK}" text-anchor="middle"><tspan font-style="italic" font-weight="600">${esc(name)}</tspan>${note ? esc(note) : ""}</text>`;
+  return `<rect x="${x - w / 2}" y="${y - LABEL_PX - LABEL_PAD + 2}" width="${w}" height="${LABEL_PX + LABEL_PAD * 2 - 2}" rx="3" fill="#fff" fill-opacity="0.85" stroke="${EXON_COLOR}"/><text x="${x}" y="${y}" font-family="Helvetica, Arial, sans-serif" font-size="${LABEL_PX}" fill="${GENE_INK}" text-anchor="middle"><tspan font-style="italic" font-weight="600">${escapeAttr(name)}</tspan>${note ? escapeAttr(note) : ""}</text>`;
 }
 function figureSvg(graph, layout, o = {}) {
   const width = o.width ?? 1200;
   const room = o.height ?? 800;
-  const region = o.region;
-  const rampDomain = o.colorDomain ?? region;
   const rows = o.walkRows;
-  const bounds = drawingBounds(layout, {
-    region: o.fitToDrawing ? void 0 : region,
-    extent: rows && layout.extent ? walkRowsExtent(rows, o.walkRowPitch) : void 0
-  });
+  const {
+    bounds,
+    nodeById,
+    referenceRamp,
+    layers,
+    lift,
+    facet,
+    panels,
+    labelOf,
+    referenceName,
+    reference,
+    contigThickness,
+    nodeWidth,
+    geometry
+  } = figureScene(graph, layout, o);
   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, rampDomain) : void 0;
   const rampInterval = referenceRamp && {
     start: referenceRamp.start,
     end: referenceRamp.start + referenceRamp.span
   };
-  const drawnDeletions = deletionDrawing(
-    graph,
-    layout.tubeMap ? [] : deletionEdges(graph),
-    o.showDeletionEdges
-  );
-  const layers = o.walks ?? [];
-  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 facet = facetSettingOf(o.facet);
-  const panels = facet.field && lift && lift.walks.length > 1 ? facetLifts(graph, lift, layers, walkRamp) : void 0;
-  const labels = walkLabelsOf(
-    graph.paths?.length ? pathLegend(graph.paths) : []
-  );
-  const labelOf = (name) => labels.get(name) ?? name;
-  const referenceName = o.referenceName ?? referenceLabel(graph, region);
-  const reference = lift?.referenceDomain && {
-    ...lift.referenceDomain,
-    name: referenceName
-  };
-  const contigThickness = o.contigThickness ?? 6;
-  const nodeWidth = o.nodeWidth ?? "depth";
   const pins = o.genes?.length && !layout.tubeMap && !rows ? genePins(graph, o.genes, layout.nodePositions) : [];
   const ink = nodeInk(graph, nodeById, contigThickness, nodeWidth);
   let masks = 0;
@@ -239,7 +197,7 @@ function figureSvg(graph, layout, o = {}) {
       const sy = y * t.scaleY + t.translateY;
       if (sy >= 0 && sy <= h) {
         out.push(
-          `<text x="6" y="${sy + 4}" ${FONT} stroke="#fff" stroke-width="3" paint-order="stroke">${esc(label)}</text>`
+          `<text x="6" y="${sy + 4}" ${FONT} stroke="#fff" stroke-width="3" paint-order="stroke">${escapeAttr(label)}</text>`
         );
       }
     }
@@ -264,24 +222,7 @@ function figureSvg(graph, layout, o = {}) {
     const axis = axisScaleOf(fit.scale, pixelRows);
     const { canvas, markup } = svgCanvas(w, h);
     const renderer = new Canvas2DRenderer(canvas);
-    renderer.uploadGeometry(
-      buildGeometry({
-        ...layoutGeometryInputs(layout, drawnDeletions, {
-          drawsRows: !!rows
-        }),
-        graph,
-        nodeById,
-        colorScheme,
-        contigThickness,
-        connectorThickness: o.connectorThickness ?? 2,
-        drawPaths: false,
-        nodeWidth,
-        linearLayout: o.linearLayout,
-        highlight,
-        axis,
-        referenceRamp
-      })
-    );
+    renderer.uploadGeometry(geometry(highlight, axis));
     const t = {
       scaleX: axis.scaleX,
       scaleY: axis.scaleY,
@@ -420,7 +361,7 @@ function figureSvg(graph, layout, o = {}) {
     generator: `@jbrowse/bandage-core@${version}`,
     ...o.spec === void 0 ? {} : { spec: o.spec }
   });
-  return `<svg xmlns="http://www.w3.org/2000/svg" width="${width}" height="${height}" viewBox="0 0 ${width} ${height}"><metadata>${esc(metadata)}</metadata><rect width="${width}" height="${height}" fill="#fff"/>${parts.join("")}</svg>
+  return `<svg xmlns="http://www.w3.org/2000/svg" width="${width}" height="${height}" viewBox="0 0 ${width} ${height}"><metadata>${escapeAttr(metadata)}</metadata><rect width="${width}" height="${height}" fill="#fff"/>${parts.join("")}</svg>
 `;
 }
 

package/dist/chunks/{chunk-NNODIW4U.js → chunk-H2H4Y3TV.js}

@@ -22,5 +22,6 @@ function serializeEl(node) {
 
 export {
   el,
+  escapeAttr,
   serializeEl
 };

package/dist/chunks/{chunk-MVFDSFV2.js → chunk-HNCXR2VS.js}

@@ -1,6 +1,6 @@
 import {
   ENGINE_DEFAULTS
-} from "./chunk-XTCNEKO5.js";
+} from "./chunk-2QLLQJ72.js";
 
 // src/figureSettings.ts
 var FIGURE_DEFAULTS = {