@jbrowse/bandage-core 10.2.6 → 10.3.0

package/dist/alleleProjection/projectAlleles.js

@@ -1,9 +1,13 @@
 import {
-  parsePanSN,
   projectAlleles
-} from "../chunks/chunk-RVS2QCOX.js";
-import "../chunks/chunk-ES2N6V56.js";
-import "../chunks/chunk-FYQWPEEY.js";
+} from "../chunks/chunk-3GLG3ZLE.js";
+import "../chunks/chunk-VX656OAZ.js";
+import "../chunks/chunk-BSOZW3FC.js";
+import "../chunks/chunk-RJWPJCIB.js";
+import "../chunks/chunk-HOAIOEI7.js";
+import {
+  parsePanSN
+} from "../chunks/chunk-4XWZNPQ2.js";
 export {
   parsePanSN,
   projectAlleles

package/dist/anchoredNodes.js

@@ -9,7 +9,8 @@ import {
   isOffReference,
   overlapsWindow,
   referenceSpan
-} from "./chunks/chunk-FYQWPEEY.js";
+} from "./chunks/chunk-RJWPJCIB.js";
+import "./chunks/chunk-HOAIOEI7.js";
 export {
   REFERENCE_RANK,
   backboneNodes,

package/dist/bubbleSpreads.js

@@ -2,8 +2,8 @@ import {
   BUBBLE_SPREADS,
   BUBBLE_SPREAD_VALUES,
   spreadFor
-} from "./chunks/chunk-UVBGRJQX.js";
-import "./chunks/chunk-6JEWNXCQ.js";
+} from "./chunks/chunk-HKYXWZQS.js";
+import "./chunks/chunk-34BOZKIE.js";
 export {
   BUBBLE_SPREADS,
   BUBBLE_SPREAD_VALUES,

package/dist/bubbles/bubbleHalos.js

@@ -1,21 +1,20 @@
 import {
-  SMALL_VARIANT_BP,
-  WHOLE_FRACTION,
   bubbleHalos,
   coversGraph
-} from "../chunks/chunk-JA2HJIYS.js";
-import "../chunks/chunk-URZ3CH2R.js";
+} from "../chunks/chunk-E4ZM4OOJ.js";
+import "../chunks/chunk-A4JDEUAI.js";
 import "../chunks/chunk-FX4RDMDN.js";
-import "../chunks/chunk-PTABFYQ7.js";
+import "../chunks/chunk-PFRQBCGC.js";
+import "../chunks/chunk-HMXCN6PG.js";
 import "../chunks/chunk-AB35TJST.js";
-import "../chunks/chunk-N73TI3VG.js";
-import "../chunks/chunk-24WITXQY.js";
-import "../chunks/chunk-7SRWJLSC.js";
+import "../chunks/chunk-BZFOFC4D.js";
+import "../chunks/chunk-CGMSKIEO.js";
+import "../chunks/chunk-UBQSRCWR.js";
 import "../chunks/chunk-CPMHA4W5.js";
-import "../chunks/chunk-FYQWPEEY.js";
+import "../chunks/chunk-BSOZW3FC.js";
+import "../chunks/chunk-RJWPJCIB.js";
+import "../chunks/chunk-HOAIOEI7.js";
 export {
-  SMALL_VARIANT_BP,
-  WHOLE_FRACTION,
   bubbleHalos,
   coversGraph
 };

package/dist/bubbles/bubblesFromGraph.js

@@ -1,15 +1,20 @@
 import {
   bubblesFromGraph,
+  derivedBubble,
   relax,
   walkIndexOf,
   walkRoutes
-} from "../chunks/chunk-CQHUZHET.js";
+} from "../chunks/chunk-RFG42VIO.js";
 import "../chunks/chunk-FX4RDMDN.js";
-import "../chunks/chunk-CM6LO6OC.js";
+import "../chunks/chunk-UAFATXYA.js";
+import "../chunks/chunk-VX656OAZ.js";
 import "../chunks/chunk-CPMHA4W5.js";
-import "../chunks/chunk-FYQWPEEY.js";
+import "../chunks/chunk-BSOZW3FC.js";
+import "../chunks/chunk-RJWPJCIB.js";
+import "../chunks/chunk-HOAIOEI7.js";
 export {
   bubblesFromGraph,
+  derivedBubble,
   relax,
   walkIndexOf,
   walkRoutes

package/dist/bubbles/classifyBubble.js

@@ -3,15 +3,18 @@ import {
   BUBBLE_KIND_NAMES,
   bubbleSegmentIds,
   classifyBubble
-} from "../chunks/chunk-URZ3CH2R.js";
+} from "../chunks/chunk-A4JDEUAI.js";
 import "../chunks/chunk-FX4RDMDN.js";
-import "../chunks/chunk-PTABFYQ7.js";
+import "../chunks/chunk-PFRQBCGC.js";
+import "../chunks/chunk-HMXCN6PG.js";
 import "../chunks/chunk-AB35TJST.js";
-import "../chunks/chunk-N73TI3VG.js";
-import "../chunks/chunk-24WITXQY.js";
-import "../chunks/chunk-7SRWJLSC.js";
+import "../chunks/chunk-BZFOFC4D.js";
+import "../chunks/chunk-CGMSKIEO.js";
+import "../chunks/chunk-UBQSRCWR.js";
 import "../chunks/chunk-CPMHA4W5.js";
-import "../chunks/chunk-FYQWPEEY.js";
+import "../chunks/chunk-BSOZW3FC.js";
+import "../chunks/chunk-RJWPJCIB.js";
+import "../chunks/chunk-HOAIOEI7.js";
 export {
   BUBBLE_KIND_COLORS,
   BUBBLE_KIND_NAMES,

package/dist/bubbles/popBubble.js

@@ -1,10 +1,12 @@
 import {
   bubbleSubgraph
-} from "../chunks/chunk-T6V4KI2L.js";
-import "../chunks/chunk-M6LK4GII.js";
-import "../chunks/chunk-RAEABQNW.js";
-import "../chunks/chunk-BPLIXMH7.js";
-import "../chunks/chunk-FYQWPEEY.js";
+} from "../chunks/chunk-PPDE4IVT.js";
+import "../chunks/chunk-LGJBB5BP.js";
+import "../chunks/chunk-ZPZ7GNBT.js";
+import "../chunks/chunk-BSOZW3FC.js";
+import "../chunks/chunk-RJWPJCIB.js";
+import "../chunks/chunk-HOAIOEI7.js";
+import "../chunks/chunk-4XWZNPQ2.js";
 export {
   bubbleSubgraph
 };

package/dist/bubbles/superbubbles.js

@@ -1,23 +1,27 @@
 import {
   graphBubbles,
   superbubblesFromGraph
-} from "../chunks/chunk-ABUIN5AK.js";
-import "../chunks/chunk-CQHUZHET.js";
-import "../chunks/chunk-T6V4KI2L.js";
-import "../chunks/chunk-JA2HJIYS.js";
-import "../chunks/chunk-URZ3CH2R.js";
+} from "../chunks/chunk-EHXBZ5JZ.js";
+import "../chunks/chunk-RFG42VIO.js";
+import "../chunks/chunk-PPDE4IVT.js";
+import "../chunks/chunk-E4ZM4OOJ.js";
+import "../chunks/chunk-A4JDEUAI.js";
 import "../chunks/chunk-FX4RDMDN.js";
-import "../chunks/chunk-CM6LO6OC.js";
-import "../chunks/chunk-M6LK4GII.js";
-import "../chunks/chunk-RAEABQNW.js";
-import "../chunks/chunk-BPLIXMH7.js";
-import "../chunks/chunk-PTABFYQ7.js";
+import "../chunks/chunk-UAFATXYA.js";
+import "../chunks/chunk-LGJBB5BP.js";
+import "../chunks/chunk-VX656OAZ.js";
+import "../chunks/chunk-ZPZ7GNBT.js";
+import "../chunks/chunk-PFRQBCGC.js";
+import "../chunks/chunk-HMXCN6PG.js";
 import "../chunks/chunk-AB35TJST.js";
-import "../chunks/chunk-N73TI3VG.js";
-import "../chunks/chunk-24WITXQY.js";
-import "../chunks/chunk-7SRWJLSC.js";
+import "../chunks/chunk-BZFOFC4D.js";
+import "../chunks/chunk-CGMSKIEO.js";
+import "../chunks/chunk-UBQSRCWR.js";
 import "../chunks/chunk-CPMHA4W5.js";
-import "../chunks/chunk-FYQWPEEY.js";
+import "../chunks/chunk-BSOZW3FC.js";
+import "../chunks/chunk-RJWPJCIB.js";
+import "../chunks/chunk-HOAIOEI7.js";
+import "../chunks/chunk-4XWZNPQ2.js";
 export {
   graphBubbles,
   superbubblesFromGraph

package/dist/chunks/{chunk-RAKOB6IV.js → chunk-234NFZS4.js}

@@ -1,12 +1,15 @@
+import {
+  addTo
+} from "./chunk-BSOZW3FC.js";
+import {
+  isBackbone
+} from "./chunk-RJWPJCIB.js";
 import {
   isGenericSample,
   panSNContig,
   panSNHaplotype,
   panSNSample
-} from "./chunk-BPLIXMH7.js";
-import {
-  isBackbone
-} from "./chunk-FYQWPEEY.js";
+} from "./chunk-4XWZNPQ2.js";
 
 // src/reference.ts
 var WELL_KNOWN_SAMPLES = /* @__PURE__ */ new Map([
@@ -37,8 +40,7 @@ function graphHaplotypes(graph) {
   for (const refName of refNames) {
     const sample = sampleOf(refName);
     if (sample !== void 0) {
-      const haplotypes = bySample.get(sample) ?? bySample.set(sample, /* @__PURE__ */ new Set()).get(sample);
-      haplotypes.add(haplotypeOf(refName));
+      addTo(bySample, sample, haplotypeOf(refName));
     }
   }
   return bySample;

package/dist/chunks/{chunk-A4PFFC4Q.js → chunk-2XEQR54X.js}

@@ -3,29 +3,38 @@ import {
   fadeAbgr,
   packAbgr
 } from "./chunk-G2FD7S3C.js";
+import {
+  REFERENCE_RAMP_LIGHTNESS,
+  REFERENCE_RAMP_SATURATION,
+  rampHueAt
+} from "./chunk-GQZVR5DW.js";
 import {
   baseEdgeCurves
-} from "./chunk-ZY2AFL4Y.js";
+} from "./chunk-WA5WNP6V.js";
 import {
   PATH_LIGHTNESS,
   PATH_SATURATION,
   nameHue,
   pathHueAt
-} from "./chunk-3XSM4OZU.js";
+} from "./chunk-IYALCKNB.js";
 import {
   meanDepth,
   nodeWidthPx
-} from "./chunk-JBCZIBFC.js";
+} from "./chunk-CRCD3ODN.js";
 import {
   referenceMidpoints
-} from "./chunk-ES2N6V56.js";
+} from "./chunk-VX656OAZ.js";
 import {
   dashCurves,
   pathRibbonOffsets,
+  polylinePx,
   strandSides,
   translateCurves,
   yToXOf
-} from "./chunk-7SRWJLSC.js";
+} from "./chunk-UBQSRCWR.js";
+import {
+  pushTo
+} from "./chunk-BSOZW3FC.js";
 
 // src/renderer/GeometryBuilder.ts
 var EDGE_DEFAULT_COLOR = packAbgr(119, 119, 119, 217);
@@ -119,7 +128,7 @@ function arrowheadFor({
   const lengthPx = walkPx[n - 1];
   const abutting = lengthPx < ABUTTING_PX;
   const inset = Math.min(nodeHalfWidth, lengthPx);
-  const fit = abutting ? Math.min(1, polylinePx(fromSegments, scale, yToX) / length) : 1;
+  const fit = abutting ? Math.min(1, polylinePx(fromSegments, scale, scale * yToX) / length) : 1;
   if (abutting ? fit < MIN_ARROW_FIT : lengthPx < MIN_LINK_HEADS * length) {
     return void 0;
   }
@@ -137,16 +146,6 @@ function arrowheadFor({
     color
   };
 }
-function polylinePx(segments, scale, yToX) {
-  let length = 0;
-  for (let i = 1; i < segments.length; i++) {
-    length += Math.hypot(
-      segments[i].x - segments[i - 1].x,
-      (segments[i].y - segments[i - 1].y) * yToX
-    );
-  }
-  return length * scale;
-}
 function leavesStart(edge, segments, first, stranded, yToX) {
   if (stranded) {
     return strandSides(edge).from === "start";
@@ -163,58 +162,28 @@ function intoDirection(last, toSegments) {
   const atStart = Math.hypot(last.x1 - first.x, last.y1 - first.y) <= Math.hypot(last.x1 - final.x, last.y1 - final.y);
   return atStart ? { from: first, to: toSegments[1] } : { from: final, to: toSegments[toSegments.length - 2] };
 }
+function normal(a, b) {
+  if (!a || !b) {
+    return void 0;
+  }
+  const dx = b.x - a.x;
+  const dy = b.y - a.y;
+  const len = Math.hypot(dx, dy);
+  return len > 0 ? { nx: -dy / len, ny: dx / len } : void 0;
+}
 function pointNormalsOf(rawPoints, yToX = 1) {
   const points = yToX === 1 ? rawPoints : rawPoints.map((p) => ({ x: p.x, y: p.y * yToX }));
-  const pointNormals = [];
-  for (let i = 0; i < points.length; i++) {
-    let nx = 0;
-    let ny = 0;
-    if (i === 0) {
-      const dx = points[1].x - points[0].x;
-      const dy = points[1].y - points[0].y;
-      const len = Math.hypot(dx, dy);
-      if (len > 0) {
-        nx = -dy / len;
-        ny = dx / len;
-      }
-    } else if (i === points.length - 1) {
-      const dx = points[i].x - points[i - 1].x;
-      const dy = points[i].y - points[i - 1].y;
-      const len = Math.hypot(dx, dy);
-      if (len > 0) {
-        nx = -dy / len;
-        ny = dx / len;
-      }
-    } else {
-      const dx1 = points[i].x - points[i - 1].x;
-      const dy1 = points[i].y - points[i - 1].y;
-      const len1 = Math.hypot(dx1, dy1);
-      const dx2 = points[i + 1].x - points[i].x;
-      const dy2 = points[i + 1].y - points[i].y;
-      const len2 = Math.hypot(dx2, dy2);
-      if (len1 > 0 && len2 > 0) {
-        const nx1 = -dy1 / len1;
-        const ny1 = dx1 / len1;
-        const nx2 = -dy2 / len2;
-        const ny2 = dx2 / len2;
-        nx = (nx1 + nx2) / 2;
-        ny = (ny1 + ny2) / 2;
-        const dot = nx1 * nx + ny1 * ny;
-        if (dot > 0.1) {
-          nx /= dot;
-          ny /= dot;
-        }
-      } else if (len1 > 0) {
-        nx = -dy1 / len1;
-        ny = dx1 / len1;
-      } else if (len2 > 0) {
-        nx = -dy2 / len2;
-        ny = dx2 / len2;
-      }
+  return points.map((p, i) => {
+    const before = normal(points[i - 1], p);
+    const after = normal(p, points[i + 1]);
+    if (before && after) {
+      const nx = (before.nx + after.nx) / 2;
+      const ny = (before.ny + after.ny) / 2;
+      const dot = before.nx * nx + before.ny * ny;
+      return dot > 0.1 ? { nx: nx / dot, ny: ny / dot } : { nx, ny };
     }
-    pointNormals.push({ nx, ny });
-  }
-  return pointNormals;
+    return before ?? after ?? { nx: 0, ny: 0 };
+  });
 }
 function offsetPolyline(points, normals, distance, yToX = 1) {
   return points.map((p, i) => ({
@@ -222,14 +191,6 @@ function offsetPolyline(points, normals, distance, yToX = 1) {
     y: p.y + normals[i].ny * distance / yToX
   }));
 }
-function packNorm(r, g, b, a) {
-  return packAbgr(
-    Math.round(r * 255),
-    Math.round(g * 255),
-    Math.round(b * 255),
-    Math.round(a * 255)
-  );
-}
 function hslToRgb(h, s, l) {
   const c = (1 - Math.abs(2 * l - 1)) * s;
   const x = c * (1 - Math.abs(h / 60 % 2 - 1));
@@ -258,6 +219,15 @@ function hslToRgb(h, s, l) {
   }
   return [r + m, g + m, b + m];
 }
+function packHsl(h, s, l, a = 1) {
+  const [r, g, b] = hslToRgb(h, s, l);
+  return packAbgr(
+    Math.round(r * 255),
+    Math.round(g * 255),
+    Math.round(b * 255),
+    Math.round(a * 255)
+  );
+}
 var DEPTH_GRADIENT = [
   [68, 1, 84],
   [59, 82, 139],
@@ -287,12 +257,8 @@ function sampleGradient(stops, t) {
   );
 }
 function hashColor(str, alpha) {
-  const [r, g, b] = hslToRgb(nameHue(str), PATH_SATURATION, PATH_LIGHTNESS);
-  return packNorm(r, g, b, alpha);
+  return packHsl(nameHue(str), PATH_SATURATION, PATH_LIGHTNESS, alpha);
 }
-var REFERENCE_RAMP_MAX_HUE = 300;
-var REFERENCE_RAMP_SATURATION = 0.7;
-var REFERENCE_RAMP_LIGHTNESS = 0.5;
 var REFERENCE_RAMP_ALT_RGB = [60, 65, 72];
 var REFERENCE_RAMP_ALT_COLOR = packAbgr(...REFERENCE_RAMP_ALT_RGB, 255);
 var REFERENCE_RAMP_ALT_CSS = `rgb(${REFERENCE_RAMP_ALT_RGB.join(", ")})`;
@@ -317,7 +283,7 @@ function computeReferenceRamp(graph, domain) {
     midpoints
   };
 }
-function computeColorSchemeRange(graph) {
+function computeColorSchemeRange(graph, referenceRamp) {
   let minDepth = Infinity;
   let maxDepth = -Infinity;
   let minLength = Infinity;
@@ -346,7 +312,8 @@ function computeColorSchemeRange(graph) {
     minLength,
     maxLength,
     maxRank,
-    nodeCount: graph.nodes.length
+    nodeCount: graph.nodes.length,
+    referenceRamp
   };
 }
 function getNodeColor(node, nodeIndex, colorScheme, range) {
@@ -384,20 +351,17 @@ function getNodeColor(node, nodeIndex, colorScheme, range) {
       if (node.stable !== void 0 && node.stable.rank > 0) {
         return REFERENCE_RAMP_ALT_COLOR;
       }
-      const frac = Math.max(0, Math.min(1, (mid - ramp.start) / ramp.span));
-      const [r, g, b] = hslToRgb(
-        frac * REFERENCE_RAMP_MAX_HUE,
+      return packHsl(
+        rampHueAt((mid - ramp.start) / ramp.span),
         REFERENCE_RAMP_SATURATION,
         REFERENCE_RAMP_LIGHTNESS
       );
-      return packNorm(r, g, b, 1);
     }
     case "grey":
       return packAbgr(160, 160, 160, 255);
     case "rainbow": {
       const hue = range.nodeCount > 1 ? nodeIndex / range.nodeCount * 360 : 0;
-      const [r, g, b] = hslToRgb(hue, 0.75, 0.5);
-      return packNorm(r, g, b, 1);
+      return packHsl(hue, 0.75, 0.5);
     }
     default:
       return packAbgr(52, 152, 219, 255);
@@ -447,12 +411,14 @@ function pathPaletteOf(graph) {
     const pathIndexByName = /* @__PURE__ */ new Map();
     const paths = graph.paths ?? [];
     for (let i = 0; i < paths.length; i++) {
-      const [r, g, b] = hslToRgb(
-        pathHueAt(i, paths.length),
-        PATH_SATURATION,
-        PATH_LIGHTNESS
+      pathColorByIndex.push(
+        packHsl(
+          pathHueAt(i, paths.length),
+          PATH_SATURATION,
+          PATH_LIGHTNESS,
+          0.85
+        )
       );
-      pathColorByIndex.push(packNorm(r, g, b, 0.85));
       if (!pathIndexByName.has(paths[i].name)) {
         pathIndexByName.set(paths[i].name, i);
       }
@@ -470,12 +436,7 @@ function pathSlotsOf(graph) {
     slots = /* @__PURE__ */ new Map();
     for (const [pathIdx, path] of (graph.paths ?? []).entries()) {
       for (const nodeId of new Set(path.nodeIds)) {
-        const visits = slots.get(nodeId);
-        if (visits) {
-          visits.push(pathIdx);
-        } else {
-          slots.set(nodeId, [pathIdx]);
-        }
+        pushTo(slots, nodeId, pathIdx);
       }
     }
     slotsCache.set(graph, slots);
@@ -505,6 +466,7 @@ function buildGeometry(options) {
   } = options;
   const depthNorm = nodeWidth === "depth" ? meanDepth(graph) : 0;
   const scale = axis.scaleX;
+  const worldPerScreenPx = 1 / Math.max(scale, MIN_SCALE_FOR_OFFSET);
   const yToX = yToXOf(axis);
   const sharedCurves = baseEdgeCurves(
     nodePositions,
@@ -521,7 +483,7 @@ function buildGeometry(options) {
   const arrowRuns = /* @__PURE__ */ new Map();
   const edgeCurves = [];
   const edgeCurveRuns = /* @__PURE__ */ new Map();
-  const colorRange = { ...computeColorSchemeRange(graph), referenceRamp };
+  const colorRange = computeColorSchemeRange(graph, referenceRamp);
   const nodeIndexMap = /* @__PURE__ */ new Map();
   if (colorScheme === "rainbow") {
     for (let i = 0; i < graph.nodes.length; i++) {
@@ -594,7 +556,6 @@ function buildGeometry(options) {
         nx: 0,
         ny: 0
       };
-      const worldPerScreenPx = 1 / Math.max(scale, MIN_SCALE_FOR_OFFSET);
       laneWalks.forEach((walk, lane) => {
         if (!walk.edgeIndexes.has(ei)) {
           return;
@@ -677,7 +638,6 @@ function buildGeometry(options) {
     if (drawable && lanes) {
       const laneWidth = Math.max(width / lanes.length, MIN_WALK_LANE_PX);
       const normals = pointNormalsOf(segments, yToX);
-      const worldPerScreenPx = 1 / Math.max(scale, MIN_SCALE_FOR_OFFSET);
       lanes.forEach((walk, lane) => {
         const laneColor = walk.colors.get(nodeId);
         if (laneColor === void 0) {
@@ -692,7 +652,6 @@ function buildGeometry(options) {
       });
     } else if (drawable && slots?.length && slotWidth >= MIN_PATH_STRIPE_PX) {
       const normals = pointNormalsOf(segments, yToX);
-      const worldPerScreenPx = 1 / Math.max(scale, MIN_SCALE_FOR_OFFSET);
       for (const slot of slots) {
         const offset = (slot - (pathCount - 1) / 2) * slotWidth * worldPerScreenPx;
         const stripe = pathColorByIndex[slot] ?? EDGE_PATH_FALLBACK_COLOR;
@@ -726,7 +685,6 @@ export {
   FADED_ALPHA,
   LIFT_BACKDROP_CSS,
   hslToRgb,
-  REFERENCE_RAMP_MAX_HUE,
   REFERENCE_RAMP_ALT_COLOR,
   REFERENCE_RAMP_ALT_CSS,
   computeReferenceRamp,

package/dist/chunks/{chunk-6JEWNXCQ.js → chunk-34BOZKIE.js}

@@ -82,9 +82,7 @@ export {
   drawnNodeLength,
   bandageAutoScale,
   PROPORTIONAL_LENGTH,
-  isProportional,
   drawnLengthFor,
-  PROPORTIONAL_SPREAD,
   layoutScaling,
   drawnLengthOf
 };

package/dist/chunks/{chunk-RVS2QCOX.js → chunk-3GLG3ZLE.js}

@@ -1,20 +1,12 @@
 import {
   buildNeighbors
-} from "./chunk-ES2N6V56.js";
+} from "./chunk-VX656OAZ.js";
 import {
   REFERENCE_RANK,
   isAnchored
-} from "./chunk-FYQWPEEY.js";
+} from "./chunk-RJWPJCIB.js";
 
 // src/alleleProjection/projectAlleles.ts
-function parsePanSN(refName) {
-  const parts = refName.split("#");
-  const haplotype = parts.length >= 2 ? Number(parts[1]) : Number.NaN;
-  return {
-    sample: parts[0] ?? refName,
-    haplotype: Number.isFinite(haplotype) ? haplotype : void 0
-  };
-}
 function collectRun(seed, byId, adj, claimed) {
   const members = [];
   const anchors = [];
@@ -130,6 +122,5 @@ function projectAlleles(graph) {
 }
 
 export {
-  parsePanSN,
   projectAlleles
 };

package/dist/chunks/{chunk-PUG7LXDF.js → chunk-3PZSBNLI.js}

@@ -1,6 +1,6 @@
 import {
   isBackbone
-} from "./chunk-FYQWPEEY.js";
+} from "./chunk-RJWPJCIB.js";
 
 // src/layout/orientToReference.ts
 function orientToReference(graph, positions) {
@@ -21,6 +21,9 @@ function orientToReference(graph, positions) {
     };
   });
   const weight = points.reduce((sum, p) => sum + p.w, 0);
+  if (weight === 0) {
+    return positions;
+  }
   const cx = points.reduce((sum, p) => sum + p.x * p.w, 0) / weight;
   const cy = points.reduce((sum, p) => sum + p.y * p.w, 0) / weight;
   const cr = points.reduce((sum, p) => sum + p.r * p.w, 0) / weight;

package/dist/chunks/{chunk-KBEP7VYK.js → chunk-3VCKBSML.js}

@@ -1,10 +1,10 @@
 import {
   baseEdgeCurves
-} from "./chunk-ZY2AFL4Y.js";
+} from "./chunk-WA5WNP6V.js";
 import {
   curveBounds,
   pathRibbonOffsets
-} from "./chunk-7SRWJLSC.js";
+} from "./chunk-UBQSRCWR.js";
 
 // src/util/SpatialIndex.ts
 var FALLBACK_CELL_SIZE = 50;
@@ -118,7 +118,7 @@ var SpatialIndex = class {
   }
 };
 var EdgeSpatialIndex = class {
-  constructor(nodePositions, graph, drawPaths, axis, cellSize, deletions, version = 0, routes, stranded = false) {
+  constructor(nodePositions, graph, drawPaths, axis, deletions, version = 0, routes, stranded = false) {
     this.cells = /* @__PURE__ */ new Map();
     this.edgeCurves = baseEdgeCurves(
       nodePositions,
@@ -162,7 +162,7 @@ var EdgeSpatialIndex = class {
         boxes.push({ ei, minX, minY, maxX, maxY });
       }
     }
-    this.cellSize = resolveCellSize(cellSize, boxes, extentX, extentY);
+    this.cellSize = cellSizeFrom(boxes, extentX, extentY);
     for (const b of boxes) {
       addToGrid(this.cells, this.cellSize, b.minX, b.minY, b.maxX, b.maxY, b.ei);
     }

package/dist/chunks/{chunk-BPLIXMH7.js → chunk-4XWZNPQ2.js}

@@ -15,6 +15,18 @@ function panSNContig(refName) {
   const parts = refName.split(SEP);
   return parts.length >= 3 ? parts.slice(2).join(SEP) : parts.length === 2 ? parts[1] : refName;
 }
+function panSNFields(name) {
+  const [sample = "", haplotype = "", ...contig] = name.split(SEP);
+  return contig.length > 0 ? { sample, haplotype: +haplotype, contig: contig.join(SEP) } : void 0;
+}
+function parsePanSN(refName) {
+  const parts = refName.split(SEP);
+  const haplotype = parts.length >= 2 ? Number(parts[1]) : Number.NaN;
+  return {
+    sample: parts[0],
+    haplotype: Number.isFinite(haplotype) ? haplotype : void 0
+  };
+}
 function panSNMatchesPrefix(refName, prefix) {
   return prefix !== void 0 && (refName === prefix || refName.startsWith(prefix + SEP));
 }
@@ -46,6 +58,8 @@ export {
   isGenericSample,
   panSNHaplotype,
   panSNContig,
+  panSNFields,
+  parsePanSN,
   panSNMatchesPrefix,
   resolvePanSNPrefix,
   assemblyByPanSNPrefix