@jbrowse/bandage-core 11.7.0 → 11.7.3

package/README.md

@@ -1,47 +1,60 @@
 # @jbrowse/bandage-core
 
-Pangenome graph layout and drawing with no host, the engine behind
+TypeScript library that lays out and draws pangenome graphs, used by
 [jbrowse-plugin-graphgenomeviewer](https://github.com/GMOD/jbrowse-plugin-graphgenomeviewer)
-and [BandageJS](https://github.com/cmdcolin/BandageJS).
+and [BandageJS](https://github.com/cmdcolin/BandageJS). It imports no React,
+MobX or JBrowse code. BandageJS's
+[`src/main.ts`](https://github.com/cmdcolin/BandageJS/blob/main/src/main.ts) is
+the worked example.
 
 ```
 npm install @jbrowse/bandage-core
 ```
 
-- GFA and rGFA text in (`loadGraph`), or the same graph as typed arrays a worker
-  can transfer (`GraphTables`)
-- A walk-file cut's W lines tag what lies past each fragment's start and end as
-  `ws:Z:`/`we:Z:`, such as `break,bp=19021` or
+## Reading a graph
+
+- `loadGraph` reads GFA or rGFA text. The caller decompresses a `.gfa.gz` first
+- `loadGraph` also takes `GraphTables`, the typed arrays that
+  [@jbrowse/graph-walks](https://github.com/GMOD/graph-walks) cuts from a
+  [gfa-to-tabix](https://github.com/GMOD/gfa-to-tabix) walk file
+  (`.walks.bed.gz` beside its `.tbi`) for a region on the reference. A worker
+  can transfer them without copying, and `graphTablesGFA` writes them as GFA
+- `openGbz` and `cutGbzRegion` cut a window from a
+  [gbz-base](https://github.com/jltsiren/gbz-base) database (`.gbz.db`) to GFA
+  text
+- In a walk-file cut, the `ws:Z:` and `we:Z:` tags on each W line record what
+  lies past the fragment's start and end, such as `break,bp=19021` or
   `elsewhere,trimmed=400,chunk=GRCh38#0#chr22:20316160`
-  (`src/gfa/walkStops.ts`). Walk rows split each gap by those stops into parts
-  that name their cause
-- Layouts: Bandage's FMMM engine as WASM from
-  [@jbrowse/graph-fmmm-layout](https://github.com/GMOD/graph-fmmm-layout)
-  (`loadBandage`, `forceLayout`), ordered, anchored, sample rows, walk rows,
-  tube map
-- A Canvas2D renderer (`buildGeometry`, `Canvas2DRenderer`), hit testing and
-  label placement
-- Bubbles, deletion edges, path colors, gbz-base windows cut to GFA
-- Walks lifted out of the drawing (`walkLift`), one facet panel per walk
-  (`facetLifts`, `facetGrid`) and each walk's key in words (`walkKey`)
-- Which assembly a backbone lies on (`graphBackbone`, `backboneAssembly`,
-  `assemblyWalk`), and the genes on it: `featuresOnBackbone` renames an
-  assembly's genes onto the backbone's refNames, and `genePins` pins only those
-
-- Figures: `figureSvg` draws a graph and its lifted walks to a standalone SVG,
-  and the `bandage-figure` CLI makes one from a JSON spec with no browser:
+  (`src/gfa/walkStops.ts`). Walk rows split each gap at those stops and label
+  each part with its cause
+
+## Laying out and drawing
+
+- `loadBandage` loads Bandage's FMMM engine, compiled to WASM in
+  [@jbrowse/graph-fmmm-layout](https://github.com/GMOD/graph-fmmm-layout), and
+  `forceLayout` runs it. The other layouts are ordered, anchored, sample rows,
+  walk rows and tube map
+- `buildGeometry` and `Canvas2DRenderer` draw to a canvas, with hit testing and
+  label placement. The library also finds bubbles and deletion edges and colors
+  paths
+- `walkLift` lifts a walk out of the drawing, `facetLifts` and `facetGrid` draw
+  one panel per walk, and `walkKey` describes each walk in words
+- `graphBackbone`, `backboneAssembly` and `assemblyWalk` find which assembly a
+  backbone lies on. `featuresOnBackbone` renames that assembly's genes onto the
+  backbone's refNames, and `genePins` pins only those
+
+## Figures and the coarse tier
+
+- `figureSvg` draws a graph and its lifted walks to a standalone SVG. The
+  `bandage-figure` CLI makes one from a JSON spec with no browser:
   `npx -p @jbrowse/bandage-core bandage-figure spec.json -o figure.svg`. See
   [docs/figures.md](docs/figures.md)
-- Coarse tier: the `bandage-fold` CLI folds every variant under a size into the
-  reference, so a graph track draws a whole chromosome. See
-  [docs/coarse-tier.md](docs/coarse-tier.md)
-- Figure data: `figureData` returns what `figureSvg` would paint as columnar
-  tables, for another graphics system to draw;
+- `figureData` returns what `figureSvg` would draw as columnar tables, for
+  another graphics system to draw;
   [ggbandage](https://github.com/GMOD/ggbandage) draws them in ggplot2
-
-Nothing here imports React, MobX or a JBrowse host. BandageJS's
-[`src/main.ts`](https://github.com/cmdcolin/BandageJS/blob/main/src/main.ts) is
-the worked example.
+- The `bandage-fold` CLI folds every variant under a size into the reference, so
+  a graph track can draw a whole chromosome. See
+  [docs/coarse-tier.md](docs/coarse-tier.md)
 
 ## Developing
 
@@ -51,27 +64,32 @@ pnpm test          # unit tests
 pnpm build         # dist/ with declarations
 ```
 
-The FMMM engine and its wasm build live in
+The FMMM engine and its wasm build are in
 [graph-fmmm-layout](https://github.com/GMOD/graph-fmmm-layout).
 
-CI also packs the core and runs
+CI also packs the core and runs the typecheck and tests of
 [BandageJS](https://github.com/cmdcolin/BandageJS) and
 [jbrowse-plugin-graphgenomeviewer](https://github.com/GMOD/jbrowse-plugin-graphgenomeviewer)
-against it. An API change lands with the consumer's side on a `core-next` branch
-in that repo, which CI tests in place of `main` until the release.
+against it. For an API change, push the consumer's matching change to a
+`core-next` branch in that consumer's repo, which CI tests in place of `main`
+until the release.
 
 Release with `pnpm version patch`: it lints, tests, stamps `src/version.ts`,
 writes the changelog with git-cliff and pushes the `v*` tag. `publish.yml` then
 runs CI, consumers included, and publishes to npm with trusted publishing only
-if it passes. When a consumer fails, land its side on `core-next` and rerun the
+if it passes. When a consumer fails, push its side to `core-next` and rerun the
 failed jobs.
 
 ## See also
 
 - [jbrowse-plugin-graphgenomeviewer](https://github.com/GMOD/jbrowse-plugin-graphgenomeviewer) -
   JBrowse 2 plugin that browses these graphs by locus
-- [BandageJS](https://github.com/cmdcolin/BandageJS) - standalone page for GFA
-  and gbz-base graphs
+- [BandageJS](https://github.com/cmdcolin/BandageJS) - browser viewer for GFA
+  files, walk files and gbz-base databases
+- [gfa-to-tabix](https://github.com/GMOD/gfa-to-tabix) - indexes a GFA by
+  reference position, writing the `.walks.bed.gz` walk files
+- [@jbrowse/graph-walks](https://github.com/GMOD/graph-walks) - range-request
+  reader for walk files
 - [@jbrowse/graph-fmmm-layout](https://github.com/GMOD/graph-fmmm-layout) -
   Bandage's FMMM layout as wasm
 - [@jbrowse/graph-stress-layout](https://github.com/GMOD/graph-stress-layout) -
@@ -83,7 +101,7 @@ failed jobs.
 - [@jbrowse/tubemap-core](https://github.com/GMOD/tubemap-core) -
   sequenceTubeMap's layout, without the DOM
 
-Tutorials on [jbrowse.org](https://jbrowse.org/jb2/docs/tutorials/)
+Tutorials on [jbrowse.org](https://jbrowse.org/jb2/docs/tutorials/):
 
 - [HPRC part 1: graph alleles and haplotypes](https://jbrowse.org/jb2/docs/tutorials/pangenome_hprc/)
 - [HPRC part 3: repeat lengths](https://jbrowse.org/jb2/docs/tutorials/pangenome_hprc_repeats/)

package/dist/bubbles/bubbleHalos.js

@@ -1,14 +1,15 @@
 import {
   bubbleHalos,
   coversGraph
-} from "../chunks/chunk-KZMSSPS6.js";
-import "../chunks/chunk-SNF2MIEF.js";
+} from "../chunks/chunk-BLDUBB7X.js";
+import "../chunks/chunk-AWJJSA7D.js";
 import "../chunks/chunk-FX4RDMDN.js";
-import "../chunks/chunk-T3H5ELLA.js";
+import "../chunks/chunk-N73RA4DR.js";
 import "../chunks/chunk-HMXCN6PG.js";
 import "../chunks/chunk-AB35TJST.js";
 import "../chunks/chunk-2VMKQKVO.js";
-import "../chunks/chunk-DV5B5UU7.js";
+import "../chunks/chunk-P276TWPM.js";
+import "../chunks/chunk-TLWXLNLY.js";
 import "../chunks/chunk-3YBP46PB.js";
 import "../chunks/chunk-VACK24HF.js";
 import "../chunks/chunk-CPMHA4W5.js";

package/dist/bubbles/classifyBubble.js

@@ -3,13 +3,14 @@ import {
   BUBBLE_KIND_NAMES,
   bubbleSegmentIds,
   classifyBubble
-} from "../chunks/chunk-SNF2MIEF.js";
+} from "../chunks/chunk-AWJJSA7D.js";
 import "../chunks/chunk-FX4RDMDN.js";
-import "../chunks/chunk-T3H5ELLA.js";
+import "../chunks/chunk-N73RA4DR.js";
 import "../chunks/chunk-HMXCN6PG.js";
 import "../chunks/chunk-AB35TJST.js";
 import "../chunks/chunk-2VMKQKVO.js";
-import "../chunks/chunk-DV5B5UU7.js";
+import "../chunks/chunk-P276TWPM.js";
+import "../chunks/chunk-TLWXLNLY.js";
 import "../chunks/chunk-3YBP46PB.js";
 import "../chunks/chunk-VACK24HF.js";
 import "../chunks/chunk-CPMHA4W5.js";

package/dist/bubbles/superbubbles.js

@@ -1,19 +1,20 @@
 import {
   graphBubbles,
   superbubblesFromGraph
-} from "../chunks/chunk-C6E6HXP5.js";
-import "../chunks/chunk-KZMSSPS6.js";
+} from "../chunks/chunk-KMLATBNT.js";
+import "../chunks/chunk-BLDUBB7X.js";
 import "../chunks/chunk-RFG42VIO.js";
-import "../chunks/chunk-SNF2MIEF.js";
+import "../chunks/chunk-AWJJSA7D.js";
 import "../chunks/chunk-FX4RDMDN.js";
 import "../chunks/chunk-MHZTTLBU.js";
 import "../chunks/chunk-UAFATXYA.js";
 import "../chunks/chunk-VX656OAZ.js";
-import "../chunks/chunk-T3H5ELLA.js";
+import "../chunks/chunk-N73RA4DR.js";
 import "../chunks/chunk-HMXCN6PG.js";
 import "../chunks/chunk-AB35TJST.js";
 import "../chunks/chunk-2VMKQKVO.js";
-import "../chunks/chunk-DV5B5UU7.js";
+import "../chunks/chunk-P276TWPM.js";
+import "../chunks/chunk-TLWXLNLY.js";
 import "../chunks/chunk-3YBP46PB.js";
 import "../chunks/chunk-VACK24HF.js";
 import "../chunks/chunk-CPMHA4W5.js";

package/dist/chunks/{chunk-YEYQFNFQ.js → chunk-2T3V6Z3M.js}

@@ -1,7 +1,7 @@
 import {
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-JGHZ3N34.js";
+} from "./chunk-VXKL2ZLR.js";
 import {
   abgrToCssRgba
 } from "./chunk-G2FD7S3C.js";

package/dist/chunks/{chunk-6YRSOL4K.js → chunk-2US43KNG.js}

@@ -1,6 +1,6 @@
 import {
   baseEdgeCurves
-} from "./chunk-OYCQVJYY.js";
+} from "./chunk-33KUO34R.js";
 import {
   curveBounds,
   pathRibbonOffsets

package/dist/chunks/{chunk-OYCQVJYY.js → chunk-33KUO34R.js}

@@ -3,7 +3,7 @@ import {
 } from "./chunk-HMXCN6PG.js";
 import {
   edgeCurvesOf
-} from "./chunk-DV5B5UU7.js";
+} from "./chunk-P276TWPM.js";
 
 // src/util/edgeCurves.ts
 var cache = weakMemo();

package/dist/chunks/{chunk-KJDERUQF.js → chunk-4KOYS5WR.js}

@@ -9,7 +9,7 @@ import {
 } from "./chunk-RJWPJCIB.js";
 
 // src/foldVariants.ts
-function foldVariants(graph, belowBp) {
+function foldVariants(graph, belowBp, { cut = false } = {}) {
   if (!(belowBp > 0) || graph.paths?.length || !graph.nodes.some((node) => isBackbone(node))) {
     return graph;
   }
@@ -41,17 +41,52 @@ function foldVariants(graph, belowBp) {
       }
     }
   }
-  const keptEdges = edges.filter((edge, k) => {
-    const a = index.get(edge.from);
-    const b = index.get(edge.to);
-    if (a === void 0 || b === void 0) {
-      return false;
-    }
-    const skip = skipped(nodes[a], sides[k].from, nodes[b], sides[k].to);
-    return kept[a] && kept[b] && !(skip > 0 && skip < belowBp);
+  const ends = edges.map((edge) => [index.get(edge.from), index.get(edge.to)]);
+  const keeps = edges.map((_, k) => {
+    const [a, b] = ends[k];
+    return a !== void 0 && b !== void 0 && !!kept[a] && !!kept[b];
   });
+  const smallSkips = edges.flatMap((_, k) => {
+    const [a, b] = ends[k];
+    if (!keeps[k]) {
+      return [];
+    }
+    const bp = skipped(nodes[a], sides[k].from, nodes[b], sides[k].to);
+    return bp > 0 && bp < belowBp ? [{ k, bp }] : [];
+  }).sort((x, y) => x.bp - y.bp).map(({ k }) => k);
+  for (const k of smallSkips) {
+    keeps[k] = false;
+  }
+  const bridging = new Set(
+    cut ? bridges(nodes.length, ends, keeps, smallSkips) : []
+  );
+  const keptEdges = edges.flatMap(
+    (edge, k) => bridging.has(k) ? [{ ...edge, foldBridge: true }] : keeps[k] ? [edge] : []
+  );
   return mergeAlleleRuns({ ...graph, nodes, edges: keptEdges }, kept, allele);
 }
+function bridges(count, ends, keeps, smallSkips) {
+  const parent = Array.from({ length: count }, (_, i) => i);
+  const find = (i) => {
+    while (parent[i] !== i) {
+      parent[i] = parent[parent[i]];
+      i = parent[i];
+    }
+    return i;
+  };
+  const join = (k) => {
+    const [a, b] = ends[k];
+    const [ra, rb] = [find(a), find(b)];
+    parent[ra] = rb;
+    return ra !== rb;
+  };
+  keeps.forEach((keep, k) => {
+    if (keep) {
+      join(k);
+    }
+  });
+  return smallSkips.filter(join);
+}
 function readForward({ nodes, edges }) {
   const reversed = new Set(
     nodes.filter((node) => node.stable?.strand === "-").map((node) => node.id)

package/dist/chunks/{chunk-NTKWT6XL.js → chunk-4SN7R4UF.js}

@@ -1,6 +1,6 @@
 import {
   ENGINE_DEFAULTS
-} from "./chunk-YER6TUXV.js";
+} from "./chunk-XKPXOIWD.js";
 
 // src/figureSettings.ts
 var FIGURE_DEFAULTS = {

package/dist/chunks/{chunk-SIA75TEG.js → chunk-63XWYNID.js}

@@ -8,7 +8,7 @@ import {
 import {
   pathCssColor,
   pathGreyCssColor
-} from "./chunk-BW2NMXRV.js";
+} from "./chunk-GD6RUZU5.js";
 import {
   pathOrigin
 } from "./chunk-3YBP46PB.js";

package/dist/chunks/{chunk-2XEAITWM.js → chunk-6RB5ZQ34.js}

@@ -1,7 +1,7 @@
 import {
   REFERENCE_RAMP_ALT_COLOR,
   hslToRgb
-} from "./chunk-JGHZ3N34.js";
+} from "./chunk-VXKL2ZLR.js";
 import {
   packAbgr
 } from "./chunk-G2FD7S3C.js";

package/dist/chunks/{chunk-ZHZRAYEM.js → chunk-AJQRKN3X.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "11.7.0";
+var version = "11.7.3";
 
 export {
   version

package/dist/chunks/{chunk-SNF2MIEF.js → chunk-AWJJSA7D.js}

@@ -3,7 +3,7 @@ import {
 } from "./chunk-FX4RDMDN.js";
 import {
   formatBp
-} from "./chunk-T3H5ELLA.js";
+} from "./chunk-N73RA4DR.js";
 
 // src/bubbles/classifyBubble.ts
 var REPEAT_GROWTH = 10;

package/dist/chunks/{chunk-KZMSSPS6.js → chunk-BLDUBB7X.js}

@@ -1,7 +1,7 @@
 import {
   bubbleSegmentIds,
   classifyBubble
-} from "./chunk-SNF2MIEF.js";
+} from "./chunk-AWJJSA7D.js";
 import {
   svgPath
 } from "./chunk-VACK24HF.js";

package/dist/chunks/{chunk-IJCSW6MV.js → chunk-CL6ELLVF.js}

@@ -1,6 +1,6 @@
 import {
   pathSteps
-} from "./chunk-SIA75TEG.js";
+} from "./chunk-63XWYNID.js";
 import {
   pathOrigin
 } from "./chunk-3YBP46PB.js";

package/dist/chunks/{chunk-A7Q7RTWX.js → chunk-EPOPGV5G.js}

@@ -3,7 +3,7 @@ import {
 } from "./chunk-H2H4Y3TV.js";
 import {
   REFERENCE_RAMP_ALT_CSS
-} from "./chunk-JGHZ3N34.js";
+} from "./chunk-VXKL2ZLR.js";
 import {
   RAMP_GRADIENT_CSS,
   RAMP_GRADIENT_STOPS,

package/dist/chunks/{chunk-5ZQKQ24Z.js → chunk-F4CDC72I.js}

@@ -1,6 +1,6 @@
 import {
   clampZoom
-} from "./chunk-YER6TUXV.js";
+} from "./chunk-XKPXOIWD.js";
 
 // src/viewport.ts
 function axisScaleOf(scale, pixelRows) {

package/dist/chunks/{chunk-BW2NMXRV.js → chunk-GD6RUZU5.js}

@@ -1,6 +1,6 @@
 import {
   groupDigits
-} from "./chunk-T3H5ELLA.js";
+} from "./chunk-N73RA4DR.js";
 import {
   pathOrigin
 } from "./chunk-3YBP46PB.js";

package/dist/chunks/{chunk-GZ36HNPJ.js → chunk-IHM43Y7B.js}

@@ -1,6 +1,6 @@
 import {
   tubeSpan
-} from "./chunk-VO6FKNZE.js";
+} from "./chunk-W5YRBEWQ.js";
 
 // src/tubeMap/genes.ts
 function tubeMapGenes(byRefName, genes) {

package/dist/chunks/{chunk-DTEXQ65J.js → chunk-K4KVAMEF.js}

@@ -1,7 +1,7 @@
 import {
   engineKey,
   forceLayout
-} from "./chunk-YER6TUXV.js";
+} from "./chunk-XKPXOIWD.js";
 
 // src/layout/forceCache.ts
 var DEFAULT_SIZE = 4;

package/dist/chunks/{chunk-C6E6HXP5.js → chunk-KMLATBNT.js}

@@ -1,6 +1,6 @@
 import {
   coversGraph
-} from "./chunk-KZMSSPS6.js";
+} from "./chunk-BLDUBB7X.js";
 import {
   bubblesFromGraph,
   derivedBubble,
@@ -10,7 +10,7 @@ import {
 } from "./chunk-RFG42VIO.js";
 import {
   bubbleSegmentIds
-} from "./chunk-SNF2MIEF.js";
+} from "./chunk-AWJJSA7D.js";
 import {
   bubbleSubgraph
 } from "./chunk-MHZTTLBU.js";

package/dist/chunks/{chunk-56L6R6D2.js → chunk-LH436HS2.js}

@@ -1,7 +1,7 @@
 import {
   EdgeSpatialIndex,
   SpatialIndex
-} from "./chunk-6YRSOL4K.js";
+} from "./chunk-2US43KNG.js";
 import {
   weakMemo
 } from "./chunk-HMXCN6PG.js";

package/dist/chunks/{chunk-T3H5ELLA.js → chunk-N73RA4DR.js}

@@ -10,7 +10,7 @@ import {
 } from "./chunk-2VMKQKVO.js";
 import {
   edgeCurvesOf
-} from "./chunk-DV5B5UU7.js";
+} from "./chunk-P276TWPM.js";
 import {
   curveBounds,
   curveMidpoint,

package/dist/chunks/{chunk-DV5B5UU7.js → chunk-P276TWPM.js}

@@ -1,3 +1,6 @@
+import {
+  unclipped
+} from "./chunk-TLWXLNLY.js";
 import {
   referenceVisitStarts
 } from "./chunk-3YBP46PB.js";
@@ -117,7 +120,8 @@ function switchesCopy(copies, start, bp) {
   const near = [copies[i - 1], copies[i]].filter((c) => c !== void 0).sort((a, b) => Math.abs(a.at - start) - Math.abs(b.at - start))[0];
   return near !== void 0 && Math.abs(near.at - start) <= near.copy && Math.abs(bp - near.copy) <= near.copy * COPY_SWITCH_SHARE;
 }
-function deletionEdges(graph) {
+function deletionEdges(cut) {
+  const graph = unclipped(cut);
   const byId = new Map(graph.nodes.map((n) => [n.id, n]));
   const backbone = backboneBySequence(graph);
   const startsOf = referenceVisitStarts(graph);
@@ -127,7 +131,7 @@ function deletionEdges(graph) {
     const edge = graph.edges[edgeIndex];
     const from = byId.get(edge.from);
     const to = byId.get(edge.to);
-    if (from !== void 0 && to !== void 0 && isBackbone(from) && isBackbone(to) && from.stable.refName === to.stable.refName) {
+    if (!edge.foldBridge && from !== void 0 && to !== void 0 && isBackbone(from) && isBackbone(to) && from.stable.refName === to.stable.refName) {
       const span = skippedSpan(edge, from, to, startsOf);
       const refName = from.stable.refName;
       const bp = span ? span.end - span.start : 0;

package/dist/chunks/{chunk-HELOUO6K.js → chunk-PKGPSTRW.js}

@@ -3,7 +3,7 @@ import {
   boxesGenes,
   rowPitch,
   rowSpan
-} from "./chunk-A7Q7RTWX.js";
+} from "./chunk-EPOPGV5G.js";
 import {
   el
 } from "./chunk-H2H4Y3TV.js";

package/dist/chunks/{chunk-KA4F3N55.js → chunk-QJC63NFR.js}

@@ -1,10 +1,10 @@
 import {
   nodesUnderBox
-} from "./chunk-56L6R6D2.js";
+} from "./chunk-LH436HS2.js";
 import {
   graphLabels,
   rowLabelBox
-} from "./chunk-T3H5ELLA.js";
+} from "./chunk-N73RA4DR.js";
 import {
   LABEL_CHAR_PX,
   LABEL_PAD,

package/dist/chunks/{chunk-QCOVHLJO.js → chunk-QLLKALSH.js}

@@ -2,7 +2,7 @@ import {
   LIFT_BACKDROP_CSS,
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-JGHZ3N34.js";
+} from "./chunk-VXKL2ZLR.js";
 import {
   abgrToCssRgba
 } from "./chunk-G2FD7S3C.js";

package/dist/chunks/{chunk-HERVZPWA.js → chunk-QXBQDHKL.js}

@@ -2,7 +2,7 @@ import {
   stripGeneGaps,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunk-HELOUO6K.js";
+} from "./chunk-PKGPSTRW.js";
 import {
   Canvas2DRenderer
 } from "./chunk-4DMSPNYV.js";
@@ -13,7 +13,7 @@ import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunk-A7Q7RTWX.js";
+} from "./chunk-EPOPGV5G.js";
 import {
   EXON_COLOR,
   exonOutlineTree,
@@ -21,10 +21,10 @@ import {
 } from "./chunk-JSUCGZ6K.js";
 import {
   geneLabelCandidates
-} from "./chunk-KA4F3N55.js";
+} from "./chunk-QJC63NFR.js";
 import {
   nodesUnderBox
-} from "./chunk-56L6R6D2.js";
+} from "./chunk-LH436HS2.js";
 import {
   escapeAttr,
   serializeEl
@@ -34,19 +34,19 @@ import {
 } from "./chunk-BFUS3ENH.js";
 import {
   version
-} from "./chunk-ZHZRAYEM.js";
+} from "./chunk-AJQRKN3X.js";
 import {
   axisScaleOf
-} from "./chunk-5ZQKQ24Z.js";
+} from "./chunk-F4CDC72I.js";
 import {
   figureScene
-} from "./chunk-WWIUC4N4.js";
+} from "./chunk-UTDMFVC7.js";
 import {
   encodingStops
-} from "./chunk-2XEAITWM.js";
+} from "./chunk-6RB5ZQ34.js";
 import {
   rangeText
-} from "./chunk-SVPR7IZO.js";
+} from "./chunk-SG7VQB4F.js";
 import {
   walkRowLabels
 } from "./chunk-SENPGW4O.js";
@@ -55,11 +55,11 @@ import {
 } from "./chunk-ZANALBSX.js";
 import {
   FIGURE_DEFAULTS
-} from "./chunk-NTKWT6XL.js";
+} from "./chunk-4SN7R4UF.js";
 import {
   FIT_PADDING,
   fitTransform
-} from "./chunk-YER6TUXV.js";
+} from "./chunk-XKPXOIWD.js";
 import {
   LABEL_CHAR_PX,
   LABEL_PAD,

package/dist/chunks/{chunk-SVPR7IZO.js → chunk-SG7VQB4F.js}

@@ -5,7 +5,7 @@ import {
 import {
   formatBp,
   groupDigits
-} from "./chunk-T3H5ELLA.js";
+} from "./chunk-N73RA4DR.js";
 
 // src/walkKey.ts
 function rangeText(contig, start, end) {

package/dist/chunks/{chunk-EH5JZETS.js → chunk-T3MEG5D3.js}

@@ -3,7 +3,7 @@ import {
 } from "./chunk-CO6RGQAD.js";
 import {
   layoutModeByValue
-} from "./chunk-DD5EZG3T.js";
+} from "./chunk-VNF236GG.js";
 import {
   parseRegion
 } from "./chunk-FNDNSDKW.js";
@@ -12,16 +12,16 @@ import {
 } from "./chunk-BFUS3ENH.js";
 import {
   version
-} from "./chunk-ZHZRAYEM.js";
+} from "./chunk-AJQRKN3X.js";
 import {
   axisScaleOf
-} from "./chunk-5ZQKQ24Z.js";
+} from "./chunk-F4CDC72I.js";
 import {
   figureScene
-} from "./chunk-WWIUC4N4.js";
+} from "./chunk-UTDMFVC7.js";
 import {
   encodingStops
-} from "./chunk-2XEAITWM.js";
+} from "./chunk-6RB5ZQ34.js";
 import {
   abgrAlpha,
   abgrBlue,
@@ -30,13 +30,13 @@ import {
 } from "./chunk-G2FD7S3C.js";
 import {
   FIGURE_DEFAULTS
-} from "./chunk-NTKWT6XL.js";
+} from "./chunk-4SN7R4UF.js";
 import {
   engineSettingsOf,
   fitTransform,
   forceLayout,
   loadGraph
-} from "./chunk-YER6TUXV.js";
+} from "./chunk-XKPXOIWD.js";
 import {
   referenceVisitStarts
 } from "./chunk-3YBP46PB.js";