@jbrowse/bandage-core 10.2.7 → 10.3.1

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-PNMJFFNB.js";
+import "../chunks/chunk-B5X2RLJG.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-2Q22S52W.js";
+import "../chunks/chunk-RFG42VIO.js";
+import "../chunks/chunk-PNMJFFNB.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-B5X2RLJG.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-ABUIN5AK.js → chunk-2Q22S52W.js}

@@ -1,24 +1,28 @@
 import {
   bubblesFromGraph,
+  derivedBubble,
   relax,
   walkIndexOf,
   walkRoutes
-} from "./chunk-CQHUZHET.js";
+} from "./chunk-RFG42VIO.js";
 import {
   bubbleSubgraph
-} from "./chunk-T6V4KI2L.js";
+} from "./chunk-PNMJFFNB.js";
 import {
   coversGraph
-} from "./chunk-JA2HJIYS.js";
+} from "./chunk-E4ZM4OOJ.js";
 import {
   bubbleSegmentIds
-} from "./chunk-URZ3CH2R.js";
+} from "./chunk-A4JDEUAI.js";
 import {
   strandSides
-} from "./chunk-7SRWJLSC.js";
+} from "./chunk-UBQSRCWR.js";
+import {
+  pushTo
+} from "./chunk-BSOZW3FC.js";
 import {
   isBackbone
-} from "./chunk-FYQWPEEY.js";
+} from "./chunk-RJWPJCIB.js";
 
 // src/bubbles/superbubbles.ts
 function slotGraph(graph, index) {
@@ -207,8 +211,7 @@ function superbubblesFromGraph(graph, span) {
   const holders = /* @__PURE__ */ new Map();
   members.forEach((vs, i) => {
     for (const v of vs) {
-      ;
-      (holders.get(v) ?? holders.set(v, []).get(v)).push(i);
+      pushTo(holders, v, i);
     }
   });
   const nested = (f, i) => holders.get(f.inside[0] >> 1).some(
@@ -226,24 +229,26 @@ function superbubblesFromGraph(graph, span) {
   return outermost.map((f) => {
     const source = nodes[f.source >> 1];
     const sink = nodes[f.sink >> 1];
-    const walked = walkIndex && walkRoutes(graph, byId, walkIndex, source.id, sink.id);
-    const crossed = walked?.n ? walked : void 0;
-    const routes = crossed ?? routesThrough(nodes, offset, next, f);
+    const walked = walkRoutes(
+      graph,
+      byId,
+      walkIndex,
+      source.id,
+      sink.id,
+      () => routesThrough(nodes, offset, next, f)
+    );
     const placedOn = onReference(source, sink);
     return {
-      refName: placedOn ? source.stable.refName : span.refName,
-      start: placedOn ? source.stable.start + source.length : span.start,
-      end: placedOn ? sink.stable.start : span.end,
-      segmentCount: f.inside.length + 2,
-      pathCount: routes.n,
-      inversion: false,
-      shortestAlleleLength: routes.min,
-      longestAlleleLength: routes.max,
-      segments: nodesOf(f).map((v) => nodes[v].name).join(","),
-      shortestAllele: void 0,
-      longestAllele: void 0,
-      partial: walked !== void 0 && walked.left > 0,
-      routes: crossed?.routes,
+      ...derivedBubble(
+        {
+          refName: placedOn ? source.stable.refName : span.refName,
+          start: placedOn ? source.stable.start + source.length : span.start,
+          end: placedOn ? sink.stable.start : span.end
+        },
+        nodesOf(f).map((v) => nodes[v]),
+        walked,
+        walked.walksLeave
+      ),
       key: `${source.name}>${sink.name}`,
       ...placedOn ? {} : { offReference: true }
     };

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-3XSM4OZU.js → chunk-3GP3KT5L.js}

@@ -1,12 +1,12 @@
 import {
   pathOrigin
-} from "./chunk-M6LK4GII.js";
-import {
-  isGenericSample
-} from "./chunk-BPLIXMH7.js";
+} from "./chunk-B5X2RLJG.js";
 import {
   groupDigits
-} from "./chunk-PTABFYQ7.js";
+} from "./chunk-PFRQBCGC.js";
+import {
+  isGenericSample
+} from "./chunk-4XWZNPQ2.js";
 
 // src/pathColors.ts
 function nameHue(name) {

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-JLSJMCDJ.js → chunk-3UST3ZQE.js}

@@ -2,13 +2,13 @@ import {
   LIFT_BACKDROP_CSS,
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-A4PFFC4Q.js";
+} from "./chunk-SWCULW6S.js";
 import {
   abgrToCssRgba
 } from "./chunk-G2FD7S3C.js";
 import {
   isBackbone
-} from "./chunk-FYQWPEEY.js";
+} from "./chunk-RJWPJCIB.js";
 
 // src/referenceStrip.ts
 var REFERENCE_STRIP_PX = 12;
@@ -21,7 +21,7 @@ function referenceStripBlocks(graph, {
   referenceRamp,
   walks
 }) {
-  const range = { ...computeColorSchemeRange(graph), referenceRamp };
+  const range = computeColorSchemeRange(graph, referenceRamp);
   const out = [];
   graph.nodes.forEach((node, index) => {
     if (isBackbone(node)) {

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

package/dist/chunks/{chunk-4DRQTBBE.js → chunk-6EOB6ANX.js}

@@ -1,6 +1,6 @@
 import {
   tubeSpan
-} from "./chunk-XMW266WS.js";
+} from "./chunk-HSVFCA2J.js";
 
 // src/tubeMap/genes.ts
 function tubeMapGenes(byRefName, genes) {

package/dist/chunks/{chunk-L2HDM2R3.js → chunk-A2TJ5UX6.js}

@@ -1,6 +1,6 @@
 import {
   walkRows
-} from "./chunk-LKW2TP4N.js";
+} from "./chunk-OOIOX36I.js";
 import {
   ROW_HEIGHT_PX
 } from "./chunk-CPMHA4W5.js";
@@ -8,20 +8,19 @@ import {
   backboneNodes,
   backbonePositions,
   overlapsWindow
-} from "./chunk-FYQWPEEY.js";
+} from "./chunk-RJWPJCIB.js";
 
 // src/layout/walkRowLayout.ts
 var READOUT_ROOM = 1.3;
+function longestBar(walks) {
+  return Math.max(walks.reference.bp, ...walks.rows.map((r) => r.bp));
+}
 function walkRowsExtent(walks, pitch = {
   rowPx: ROW_HEIGHT_PX,
   readouts: true
 }) {
-  let longest = walks.reference.bp;
-  for (const row of walks.rows) {
-    longest = Math.max(longest, row.bp);
-  }
   return {
-    maxX: walks.origin + longest * (pitch.readouts ? READOUT_ROOM : 1),
+    maxX: walks.origin + longestBar(walks) * (pitch.readouts ? READOUT_ROOM : 1),
     maxY: walks.rows.length * pitch.rowPx
   };
 }
@@ -58,6 +57,7 @@ function walkRowLayout(graph, region) {
 
 export {
   READOUT_ROOM,
+  longestBar,
   walkRowsExtent,
   walkRowLabels,
   walkRowLayout

package/dist/chunks/{chunk-URZ3CH2R.js → chunk-A4JDEUAI.js}

@@ -3,7 +3,7 @@ import {
 } from "./chunk-FX4RDMDN.js";
 import {
   formatBp
-} from "./chunk-PTABFYQ7.js";
+} from "./chunk-PFRQBCGC.js";
 
 // src/bubbles/classifyBubble.ts
 var REPEAT_GROWTH = 10;

package/dist/chunks/{chunk-CWFNEKST.js → chunk-A7H753BA.js}

@@ -34,13 +34,13 @@ function mismatchesByStep(record, lengths) {
   const startOf = (k) => starts[known[k]];
   const endOf = (k) => startOf(k) + lengths[known[k]];
   let first = 0;
-  const stepAt = (pos2, atEnd = false) => {
+  const stepAt = (pos2) => {
     while (first < known.length && endOf(first) < pos2) {
       first++;
     }
     for (let k = first; k < known.length && startOf(k) <= pos2; k++) {
       const end = endOf(k);
-      if (pos2 < end || atEnd && pos2 === end) {
+      if (pos2 < end) {
         return { s: known[k], local: pos2 - startOf(k), room: end - pos2 };
       }
     }
@@ -74,7 +74,7 @@ function mismatchesByStep(record, lengths) {
       }
       pos += 1;
     } else if (op.op === "insertion") {
-      const at = stepAt(pos, pos === record.pathEnd);
+      const at = pos > record.pathStart && pos < record.pathEnd ? stepAt(pos) : void 0;
       if (at) {
         add(at.s, { type: "insertion", pos: at.local, seq: op.seq });
       }

package/dist/chunks/{chunk-CG35S2S2.js → chunk-AQCOIE5R.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "10.2.7";
+var version = "10.3.1";
 
 export {
   version

package/dist/chunks/{chunk-TKIJ5535.js → chunk-AZ4EEF6Q.js}

@@ -1,25 +1,25 @@
 import {
   sampleRowLayout
-} from "./chunk-LOEA5IHZ.js";
+} from "./chunk-GJU6BJJA.js";
 import {
   hasTubeMapBackbone,
   hasTubeMapPaths,
   tubeMapLayout,
   tubeMapReferenceLayout
-} from "./chunk-XI3ZUTWF.js";
+} from "./chunk-FW2R7UDZ.js";
 import {
   anchoredLayout
-} from "./chunk-L3O7AWLI.js";
+} from "./chunk-GJLZ2MKE.js";
 import {
   orderedLayout
-} from "./chunk-CM6LO6OC.js";
+} from "./chunk-UAFATXYA.js";
 import {
   walkRowLayout
-} from "./chunk-L2HDM2R3.js";
+} from "./chunk-A2TJ5UX6.js";
 import {
   isBackbone,
   isOffReference
-} from "./chunk-FYQWPEEY.js";
+} from "./chunk-RJWPJCIB.js";
 
 // src/layoutModes.ts
 var FORCE_LAYOUT_LABEL = "Force-directed layout";

package/dist/chunks/{chunk-M6LK4GII.js → chunk-B5X2RLJG.js}

@@ -1,12 +1,15 @@
 import {
   PathVisitsBuilder
-} from "./chunk-RAEABQNW.js";
+} from "./chunk-ZPZ7GNBT.js";
 import {
-  panSNSample
-} from "./chunk-BPLIXMH7.js";
+  groupBy
+} from "./chunk-BSOZW3FC.js";
 import {
   REFERENCE_RANK
-} from "./chunk-FYQWPEEY.js";
+} from "./chunk-RJWPJCIB.js";
+import {
+  panSNSample
+} from "./chunk-4XWZNPQ2.js";
 
 // src/pathAnchoring.ts
 var RANGE_SUFFIX = /:(\d+)-\d+$/;
@@ -118,7 +121,15 @@ function anchorFromPaths(graph, preferred) {
   };
 }
 function anchorGraph(graph, preferred) {
-  return graph.anchoredBy === "tags" ? graph : anchorFromPaths(graph, preferred);
+  if (graph.anchoredBy !== "tags") {
+    return anchorFromPaths(graph, preferred);
+  }
+  const referencePath = taggedReferencePath(graph);
+  return referencePath ? { ...graph, referencePath } : graph;
+}
+function taggedReferencePath(graph) {
+  const refName = graph.nodes.find((n) => n.stable?.rank === 0)?.stable?.refName;
+  return refName !== void 0 && graph.anchorPaths?.some((p) => p.name === refName) ? refName : void 0;
 }
 function trimOrigins(graph, kept) {
   if (!graph.anchorPaths) {
@@ -132,11 +143,7 @@ function trimOrigins(graph, kept) {
     }
     return sum;
   };
-  const byOrigin = /* @__PURE__ */ new Map();
-  for (const path of graph.paths ?? []) {
-    const origin = pathOrigin(path.name).name;
-    byOrigin.set(origin, [...byOrigin.get(origin) ?? [], path]);
-  }
+  const byOrigin = groupBy(graph.paths ?? [], (p) => pathOrigin(p.name).name);
   return graph.anchorPaths.map((o) => {
     const pieces = byOrigin.get(o.name);
     const path = pieces?.length === 1 ? pieces[0] : void 0;

package/dist/chunks/{chunk-A7CFWFQS.js → chunk-BKEZLETL.js}

@@ -1,6 +1,6 @@
 import {
   clampZoom
-} from "./chunk-QXUEF3AJ.js";
+} from "./chunk-KMBE2Q42.js";
 
 // src/viewport.ts
 function axisScaleOf(scale, pixelRows) {