@jbrowse/bandage-core 11.15.0 → 11.17.0

package/dist/bubbles/bubbleHalos.js

@@ -1,14 +1,14 @@
 import {
   bubbleHalos,
   coversGraph
-} from "../chunks/chunk-SZYFZNCO.js";
-import "../chunks/chunk-NWEVR2OQ.js";
+} from "../chunks/chunk-RATN62M3.js";
+import "../chunks/chunk-HYVIQS4D.js";
 import "../chunks/chunk-FX4RDMDN.js";
-import "../chunks/chunk-AURNOR27.js";
+import "../chunks/chunk-ENBFQH7Y.js";
 import "../chunks/chunk-HMXCN6PG.js";
 import "../chunks/chunk-AB35TJST.js";
 import "../chunks/chunk-HNNP5QUN.js";
-import "../chunks/chunk-3GORESBG.js";
+import "../chunks/chunk-OMQWCVOJ.js";
 import "../chunks/chunk-TLWXLNLY.js";
 import "../chunks/chunk-3YBP46PB.js";
 import "../chunks/chunk-JJV2GT2Z.js";

package/dist/bubbles/classifyBubble.js

@@ -3,13 +3,13 @@ import {
   BUBBLE_KIND_NAMES,
   bubbleSegmentIds,
   classifyBubble
-} from "../chunks/chunk-NWEVR2OQ.js";
+} from "../chunks/chunk-HYVIQS4D.js";
 import "../chunks/chunk-FX4RDMDN.js";
-import "../chunks/chunk-AURNOR27.js";
+import "../chunks/chunk-ENBFQH7Y.js";
 import "../chunks/chunk-HMXCN6PG.js";
 import "../chunks/chunk-AB35TJST.js";
 import "../chunks/chunk-HNNP5QUN.js";
-import "../chunks/chunk-3GORESBG.js";
+import "../chunks/chunk-OMQWCVOJ.js";
 import "../chunks/chunk-TLWXLNLY.js";
 import "../chunks/chunk-3YBP46PB.js";
 import "../chunks/chunk-JJV2GT2Z.js";

package/dist/bubbles/superbubbles.js

@@ -1,19 +1,19 @@
 import {
   graphBubbles,
   superbubblesFromGraph
-} from "../chunks/chunk-DOCI5O5R.js";
-import "../chunks/chunk-SZYFZNCO.js";
+} from "../chunks/chunk-G3R7LUOS.js";
+import "../chunks/chunk-RATN62M3.js";
 import "../chunks/chunk-V6WSDZPL.js";
-import "../chunks/chunk-NWEVR2OQ.js";
+import "../chunks/chunk-HYVIQS4D.js";
 import "../chunks/chunk-FX4RDMDN.js";
 import "../chunks/chunk-MHZTTLBU.js";
 import "../chunks/chunk-Q7OFBTBW.js";
 import "../chunks/chunk-L4DBSRA2.js";
-import "../chunks/chunk-AURNOR27.js";
+import "../chunks/chunk-ENBFQH7Y.js";
 import "../chunks/chunk-HMXCN6PG.js";
 import "../chunks/chunk-AB35TJST.js";
 import "../chunks/chunk-HNNP5QUN.js";
-import "../chunks/chunk-3GORESBG.js";
+import "../chunks/chunk-OMQWCVOJ.js";
 import "../chunks/chunk-TLWXLNLY.js";
 import "../chunks/chunk-3YBP46PB.js";
 import "../chunks/chunk-JJV2GT2Z.js";

package/dist/chunks/{chunk-BDS5VZYZ.js → chunk-2BSGQKF3.js}

@@ -8,7 +8,7 @@ import {
 import {
   pathCssColor,
   pathGreyCssColor
-} from "./chunk-VQ353UDK.js";
+} from "./chunk-EHEIS3TE.js";
 import {
   pathOrigin
 } from "./chunk-3YBP46PB.js";

package/dist/chunks/{chunk-H2TSYHOA.js → chunk-42MMT5QM.js}

@@ -1,5 +1,5 @@
 // src/version.ts
-var version = "11.15.0";
+var version = "11.17.0";
 
 export {
   version

package/dist/chunks/{chunk-XBX3HSC7.js → chunk-47R7GMU3.js}

@@ -4,27 +4,27 @@ import {
 import {
   facetLifts,
   walkLift
-} from "./chunk-MB4UWYDG.js";
+} from "./chunk-PL6X2IJC.js";
 import {
   buildGeometry,
   computeReferenceRamp
-} from "./chunk-JUYPCLF4.js";
+} from "./chunk-DTBQNR7P.js";
 import {
   walkKey
-} from "./chunk-IZKM4NY7.js";
+} from "./chunk-OKH32P3Z.js";
 import {
   walkRowsExtent
 } from "./chunk-VCUOYVLC.js";
 import {
   pathLegend,
   walkLabelsOf
-} from "./chunk-VQ353UDK.js";
+} from "./chunk-EHEIS3TE.js";
 import {
   FIGURE_DEFAULTS
-} from "./chunk-5SW3PTHO.js";
+} from "./chunk-XESCKKKT.js";
 import {
   drawingBounds
-} from "./chunk-2AVTTUP2.js";
+} from "./chunk-5LTWXDXK.js";
 import {
   referenceLabel
 } from "./chunk-5ORP7EFJ.js";
@@ -34,7 +34,7 @@ import {
 import {
   deletionDrawing,
   deletionEdges
-} from "./chunk-3GORESBG.js";
+} from "./chunk-OMQWCVOJ.js";
 import {
   facetCells,
   facetSettingOf

package/dist/chunks/{chunk-TEFNVUGD.js → chunk-54CX2MCH.js}

@@ -6,7 +6,7 @@ import {
   hasTubeMapPaths,
   tubeMapLayout,
   tubeMapReferenceLayout
-} from "./chunk-BDS5VZYZ.js";
+} from "./chunk-2BSGQKF3.js";
 import {
   anchoredLayout
 } from "./chunk-CNWAVRLF.js";

package/dist/chunks/{chunk-2AVTTUP2.js → chunk-5LTWXDXK.js}

@@ -14,7 +14,7 @@ import {
 } from "./chunk-VPE4AYP7.js";
 import {
   convertGFAToGraph
-} from "./chunk-TUMJNAOL.js";
+} from "./chunk-MSVYSCAH.js";
 import {
   parseGFA
 } from "./chunk-CFXXFHRK.js";
@@ -39,7 +39,7 @@ import {
 import {
   deletionDrawing,
   deletionEdges
-} from "./chunk-3GORESBG.js";
+} from "./chunk-OMQWCVOJ.js";
 import {
   anchorGraph
 } from "./chunk-3YBP46PB.js";

package/dist/chunks/{chunk-S6E3PMH7.js → chunk-7KVA7TFI.js}

@@ -1,6 +1,6 @@
 import {
   pathSteps
-} from "./chunk-BDS5VZYZ.js";
+} from "./chunk-2BSGQKF3.js";
 import {
   pathOrigin
 } from "./chunk-3YBP46PB.js";

package/dist/chunks/{chunk-P2GJBFNA.js → chunk-AGUBPT45.js}

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

package/dist/chunks/{chunk-EOB4Y3EM.js → chunk-BDMISSNR.js}

@@ -1,7 +1,7 @@
 import {
   REFERENCE_RAMP_ALT_COLOR,
   hslToRgb
-} from "./chunk-JUYPCLF4.js";
+} from "./chunk-DTBQNR7P.js";
 import {
   packAbgr
 } from "./chunk-G2FD7S3C.js";

package/dist/chunks/{chunk-EIMRD6L7.js → chunk-CIMRLDRO.js}

@@ -1,7 +1,7 @@
 import {
   engineKey,
   forceLayout
-} from "./chunk-2AVTTUP2.js";
+} from "./chunk-5LTWXDXK.js";
 
 // src/layout/forceCache.ts
 var DEFAULT_SIZE = 4;

package/dist/chunks/{chunk-JUYPCLF4.js → chunk-DTBQNR7P.js}

@@ -21,18 +21,18 @@ import {
 } from "./chunk-GQZVR5DW.js";
 import {
   baseEdgeCurves
-} from "./chunk-P2GJBFNA.js";
+} from "./chunk-AGUBPT45.js";
 import {
   PATH_LIGHTNESS,
   PATH_SATURATION,
   nameHue,
   pathHueAt
-} from "./chunk-VQ353UDK.js";
+} from "./chunk-EHEIS3TE.js";
 import {
-  meanDepth,
   nodeWidthPx,
-  walkLaneWidthPx
-} from "./chunk-ZANALBSX.js";
+  walkLaneWidthPx,
+  widthNorm
+} from "./chunk-XWH4LB56.js";
 import {
   referenceMidpoints
 } from "./chunk-L4DBSRA2.js";
@@ -515,7 +515,7 @@ function buildGeometry(options) {
     hiddenEdges,
     version = 0
   } = options;
-  const depthNorm = nodeWidth === "depth" ? meanDepth(graph) : 0;
+  const widthScale = widthNorm(graph, nodeWidth);
   const busiest = edgeWidth === "walks" ? busiestEdge(graph) : 0;
   const scale = axis.scaleX;
   const worldPerScreenPx = 1 / Math.max(scale, MIN_SCALE_FOR_OFFSET);
@@ -618,7 +618,7 @@ function buildGeometry(options) {
     if (width === void 0) {
       const node = nodeById.get(id);
       width = walkLaneWidthPx(
-        node ? nodeWidthPx(node, contigThickness, nodeWidth, depthNorm) : contigThickness,
+        node ? nodeWidthPx(node, contigThickness, nodeWidth, widthScale) : contigThickness,
         liftedWalks.length
       );
       laneWidths.set(id, width);
@@ -697,7 +697,7 @@ function buildGeometry(options) {
     const plainEdgeColor = isDeletion ? EDGE_DELETION_COLOR : EDGE_DEFAULT_COLOR;
     const edgeColor = !highlight || onWalk ? plainEdgeColor : fadeAbgr(plainEdgeColor, FADED_ALPHA);
     const toNode = nodeById.get(edge.to);
-    const intoHalfWidth = (toNode ? nodeWidthPx(toNode, contigThickness, nodeWidth, depthNorm) : contigThickness) / 2;
+    const intoHalfWidth = (toNode ? nodeWidthPx(toNode, contigThickness, nodeWidth, widthScale) : contigThickness) / 2;
     const inView = (curves) => !viewportBounds || isBezierInBounds(curves, viewportBounds);
     const dashesOf = (curves) => dashSpans(curves, DELETION_DASH_PX / scale, yToX, viewportBounds);
     const stroke = (curves, thickness, color) => {
@@ -882,7 +882,7 @@ function buildGeometry(options) {
       colorRange
     );
     const color = faded ? fadeAbgr(own, FADED_ALPHA) : own;
-    const width = nodeWidthPx(node, contigThickness, nodeWidth, depthNorm);
+    const width = nodeWidthPx(node, contigThickness, nodeWidth, widthScale);
     const nodeThickness = width / 2;
     const start = nodeStrokes.length;
     const slots = nodePathSlots.get(nodeId);

package/dist/chunks/{chunk-VQ353UDK.js → chunk-EHEIS3TE.js}

@@ -1,6 +1,6 @@
 import {
   groupDigits
-} from "./chunk-AURNOR27.js";
+} from "./chunk-ENBFQH7Y.js";
 import {
   pathOrigin
 } from "./chunk-3YBP46PB.js";

package/dist/chunks/{chunk-AURNOR27.js → chunk-ENBFQH7Y.js}

@@ -10,7 +10,7 @@ import {
 } from "./chunk-HNNP5QUN.js";
 import {
   edgeCurvesOf
-} from "./chunk-3GORESBG.js";
+} from "./chunk-OMQWCVOJ.js";
 import {
   curveBounds,
   curveMidpoint,

package/dist/chunks/{chunk-RVIRKMQI.js → chunk-FKMZG7HI.js}

@@ -3,7 +3,7 @@ import {
 } from "./chunk-CO6RGQAD.js";
 import {
   layoutModeByValue
-} from "./chunk-TEFNVUGD.js";
+} from "./chunk-54CX2MCH.js";
 import {
   parseRegion
 } from "./chunk-FNDNSDKW.js";
@@ -12,19 +12,19 @@ import {
 } from "./chunk-HEYIAMTC.js";
 import {
   version
-} from "./chunk-H2TSYHOA.js";
+} from "./chunk-42MMT5QM.js";
 import {
   axisScaleOf
-} from "./chunk-OKPSS5PG.js";
+} from "./chunk-ZZUSCQVT.js";
 import {
   figureScene
-} from "./chunk-XBX3HSC7.js";
+} from "./chunk-47R7GMU3.js";
 import {
   fadedKey
-} from "./chunk-MB4UWYDG.js";
+} from "./chunk-PL6X2IJC.js";
 import {
   encodingStops
-} from "./chunk-EOB4Y3EM.js";
+} from "./chunk-BDMISSNR.js";
 import {
   laneSlideAt,
   passesKey,
@@ -36,18 +36,27 @@ import {
   abgrGreen,
   abgrRed
 } from "./chunk-G2FD7S3C.js";
+import {
+  frequencyKey,
+  haplotypeCount,
+  nodeFrequency,
+  withFrequencies
+} from "./chunk-XWH4LB56.js";
 import {
   FIGURE_DEFAULTS
-} from "./chunk-5SW3PTHO.js";
+} from "./chunk-XESCKKKT.js";
 import {
   engineSettingsOf,
   fitTransform,
   forceLayout,
   loadGraph
-} from "./chunk-2AVTTUP2.js";
+} from "./chunk-5LTWXDXK.js";
 import {
   referencePositions
 } from "./chunk-L4DBSRA2.js";
+import {
+  deletionKey
+} from "./chunk-OMQWCVOJ.js";
 import {
   referenceVisitStarts
 } from "./chunk-3YBP46PB.js";
@@ -305,6 +314,7 @@ function figureData(graph, layout, o = {}) {
   }
   const startsOf = referenceVisitStarts(graph);
   const positions = referencePositions(graph);
+  const haplotypes = haplotypeCount(graph);
   return {
     meta: {
       generator: `@jbrowse/bandage-core@${version}`,
@@ -321,12 +331,15 @@ function figureData(graph, layout, o = {}) {
         end: referenceRamp.start + referenceRamp.span
       } : null,
       deletions: drawnDeletions.shown.length,
+      deletionKey: drawnDeletions.shown.length ? deletionKey(referenceName) : null,
       // what the key for the drawing a lift fades says
       fadedKey: lift ? fadedKey(
         graph,
         lift,
         lift.walks.length === 1 ? labelOf(lift.walks[0].name) : "these walks"
-      ) : null
+      ) : null,
+      // the widths a key shows where nodes are as wide as their frequency
+      frequencyKey: o.nodeWidth === "frequency" ? frequencyKey(o.contigThickness ?? FIGURE_DEFAULTS.contigThickness) : null
     },
     panels: {
       panel: panels.map((p) => p.name),
@@ -346,6 +359,7 @@ function figureData(graph, layout, o = {}) {
       name: graph.nodes.map((n) => n.name),
       length: graph.nodes.map((n) => n.length),
       depth: graph.nodes.map((n) => n.depth),
+      frequency: graph.nodes.map((n) => nodeFrequency(n, haplotypes) ?? null),
       backbone: graph.nodes.map((n) => isBackbone(n)),
       referenceVisits: graph.nodes.map(
         (n) => isBackbone(n) ? startsOf(n).length : 0
@@ -359,7 +373,10 @@ function figureData(graph, layout, o = {}) {
   };
 }
 async function laidOutGraph(text, name, region, spec) {
-  const graph = loadGraph(text, name, { referencePath: spec.referencePath });
+  const graph = withFrequencies(
+    loadGraph(text, name, { referencePath: spec.referencePath }),
+    spec.frequencies
+  );
   const layout = layoutModeByValue(spec.layout ?? "force").run(graph, region) ?? (await forceLayout(graph, engineSettingsOf(spec), layoutEngine)).result;
   return { graph, layout };
 }

package/dist/chunks/{chunk-DOCI5O5R.js → chunk-G3R7LUOS.js}

@@ -1,6 +1,6 @@
 import {
   coversGraph
-} from "./chunk-SZYFZNCO.js";
+} from "./chunk-RATN62M3.js";
 import {
   bubblesFromGraph,
   derivedBubble,
@@ -10,7 +10,7 @@ import {
 } from "./chunk-V6WSDZPL.js";
 import {
   bubbleSegmentIds
-} from "./chunk-NWEVR2OQ.js";
+} from "./chunk-HYVIQS4D.js";
 import {
   bubbleSubgraph
 } from "./chunk-MHZTTLBU.js";

package/dist/chunks/{chunk-ZHCQOC67.js → chunk-GZ2F2CDT.js}

@@ -1,7 +1,7 @@
 import {
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-JUYPCLF4.js";
+} from "./chunk-DTBQNR7P.js";
 import {
   abgrToCssRgba
 } from "./chunk-G2FD7S3C.js";

package/dist/chunks/{chunk-NWEVR2OQ.js → chunk-HYVIQS4D.js}

@@ -3,7 +3,7 @@ import {
 } from "./chunk-FX4RDMDN.js";
 import {
   formatBp
-} from "./chunk-AURNOR27.js";
+} from "./chunk-ENBFQH7Y.js";
 
 // src/bubbles/classifyBubble.ts
 var REPEAT_GROWTH = 10;

package/dist/chunks/{chunk-N65FW7LX.js → chunk-IWPINV4U.js}

@@ -5,7 +5,7 @@ import {
   stripGeneGaps,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunk-QL673EK5.js";
+} from "./chunk-STUG7I25.js";
 import {
   Canvas2DRenderer
 } from "./chunk-4DMSPNYV.js";
@@ -13,7 +13,7 @@ import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunk-OYBYCF2O.js";
+} from "./chunk-PIPNW3VY.js";
 import {
   EXON_COLOR,
   exonOutlineTree,
@@ -21,28 +21,28 @@ import {
 } from "./chunk-JSUCGZ6K.js";
 import {
   geneLabelCandidates
-} from "./chunk-TQ26XEFL.js";
+} from "./chunk-U6TXPLFJ.js";
 import {
   nodesUnderBox
-} from "./chunk-4JDO7ZLN.js";
+} from "./chunk-QWLCHMNS.js";
 import {
   genePins
 } from "./chunk-HEYIAMTC.js";
 import {
   version
-} from "./chunk-H2TSYHOA.js";
+} from "./chunk-42MMT5QM.js";
 import {
   axisScaleOf
-} from "./chunk-OKPSS5PG.js";
+} from "./chunk-ZZUSCQVT.js";
 import {
   figureScene
-} from "./chunk-XBX3HSC7.js";
+} from "./chunk-47R7GMU3.js";
 import {
   fadedKey
-} from "./chunk-MB4UWYDG.js";
+} from "./chunk-PL6X2IJC.js";
 import {
   encodingStops
-} from "./chunk-EOB4Y3EM.js";
+} from "./chunk-BDMISSNR.js";
 import {
   THREAD_PX,
   passesKey,
@@ -50,20 +50,20 @@ import {
 } from "./chunk-YUIKEUKY.js";
 import {
   rangeText
-} from "./chunk-IZKM4NY7.js";
+} from "./chunk-OKH32P3Z.js";
 import {
   walkRowLabels
 } from "./chunk-VCUOYVLC.js";
 import {
   nodeInk
-} from "./chunk-ZANALBSX.js";
+} from "./chunk-XWH4LB56.js";
 import {
   FIGURE_DEFAULTS
-} from "./chunk-5SW3PTHO.js";
+} from "./chunk-XESCKKKT.js";
 import {
   FIT_PADDING,
   fitTransform
-} from "./chunk-2AVTTUP2.js";
+} from "./chunk-5LTWXDXK.js";
 import {
   LABEL_CHAR_PX,
   LABEL_PAD,
@@ -71,6 +71,9 @@ import {
   occupancy,
   placeLabels
 } from "./chunk-AB35TJST.js";
+import {
+  deletionKey
+} from "./chunk-OMQWCVOJ.js";
 import {
   escapeAttr,
   serializeEl
@@ -91,6 +94,7 @@ var KEY_LINE_PX = 16;
 var KEY_TALL_PX = 32;
 var STRIP_KEY_PX = 22;
 var FADED = "rgb(160,160,160)";
+var DELETION_INK = "rgb(24,24,28)";
 var GENE_INK = "#1c1c22";
 function keySvg(id, x, y, stops, label, after, under, opacity = 1) {
   const bar = stops.length > 1 ? BAR_PX : SWATCH_PX;
@@ -113,6 +117,13 @@ function exonKeySvg(x, y) {
     markup: `<g transform="translate(${x} ${y})" ${FONT}><rect x="1" y="4" width="${SWATCH_PX - 2}" height="10" rx="4" fill="none" stroke="${EXON_COLOR}" stroke-width="2"/><text x="${SWATCH_PX + 5}" y="13">exon</text></g>`
   };
 }
+function deletionKeySvg(x, y, note, color) {
+  return {
+    width: SWATCH_PX + 5 + note.length * LABEL_CHAR_PX,
+    height: KEY_LINE_PX,
+    markup: `<g transform="translate(${x} ${y})" ${FONT}><line y1="9" y2="9" x2="${SWATCH_PX}" stroke="${color}" stroke-width="2" stroke-dasharray="4 3"/><text x="${SWATCH_PX + 5}" y="13">${note}</text></g>`
+  };
+}
 function passesKeySvg(x, y, note) {
   const lines = [6, 9, 12].map(
     (ly) => `<line y1="${ly}" y2="${ly}" x2="${SWATCH_PX}" stroke="#444" stroke-width="${THREAD_PX}"/>`
@@ -176,6 +187,7 @@ function figureSvg(graph, layout, o = {}) {
     labelOf,
     referenceName,
     keyText,
+    drawnDeletions,
     contigThickness,
     nodeWidth,
     geometry
@@ -363,6 +375,16 @@ function figureSvg(graph, layout, o = {}) {
         )
       );
     }
+    if (drawnDeletions.shown.length > 0) {
+      keys.push(
+        (x, y) => deletionKeySvg(
+          x,
+          y,
+          deletionKey(referenceName),
+          lift ? FADED : DELETION_INK
+        )
+      );
+    }
     if (pins.some((pin) => pin.exonsByNode.length > 0)) {
       keys.push((x, y) => exonKeySvg(x, y));
     }

package/dist/chunks/{chunk-TUMJNAOL.js → chunk-MSVYSCAH.js}

@@ -75,11 +75,13 @@ function statedDepth({ tags, length }) {
   return positive(tags.dp) ?? positive(tags.DP) ?? (count !== void 0 && length > 0 ? count / length : void 0);
 }
 function makeNode(gfaNode, strand, depth) {
+  const frequency = gfaNode.tags.AF;
   return {
     id: `${gfaNode.id}${strand}`,
     name: gfaNode.id,
     length: gfaNode.length,
     depth,
+    ...typeof frequency === "number" && frequency >= 0 ? { frequency } : {},
     stable: stableCoordinate(gfaNode),
     samples: carriedSamples(gfaNode)
   };

package/dist/chunks/{chunk-IZKM4NY7.js → chunk-OKH32P3Z.js}

@@ -5,7 +5,7 @@ import {
 import {
   formatBp,
   groupDigits
-} from "./chunk-AURNOR27.js";
+} from "./chunk-ENBFQH7Y.js";
 
 // src/walkKey.ts
 function rangeText(contig, start, end) {

package/dist/chunks/{chunk-3GORESBG.js → chunk-OMQWCVOJ.js}

@@ -23,6 +23,7 @@ import {
 
 // src/deletionEdges.ts
 var MIN_DELETION_BP = 1;
+var deletionKey = (reference) => `skips ${reference ?? "the reference"} sequence (a deletion)`;
 function bypassedPoints(nodePositions, bypassed) {
   return bypassed.flatMap((id) => nodePositions[id] ?? []);
 }
@@ -204,6 +205,7 @@ function deletionDrawing(graph, deletions, show = true) {
 }
 
 export {
+  deletionKey,
   edgeCurvesOf,
   deletionEdges,
   closableDeletions,

package/dist/chunks/{chunk-K4RGSISK.js → chunk-OND5MXTK.js}

@@ -2,7 +2,7 @@ import {
   LIFT_BACKDROP_CSS,
   computeColorSchemeRange,
   getNodeColor
-} from "./chunk-JUYPCLF4.js";
+} from "./chunk-DTBQNR7P.js";
 import {
   abgrToCssRgba
 } from "./chunk-G2FD7S3C.js";

package/dist/chunks/{chunk-OYBYCF2O.js → chunk-PIPNW3VY.js}

@@ -1,6 +1,6 @@
 import {
   REFERENCE_RAMP_ALT_CSS
-} from "./chunk-JUYPCLF4.js";
+} from "./chunk-DTBQNR7P.js";
 import {
   RAMP_GRADIENT_CSS,
   RAMP_GRADIENT_STOPS,

package/dist/chunks/{chunk-MB4UWYDG.js → chunk-PL6X2IJC.js}

@@ -2,10 +2,10 @@ import {
   encodedColor,
   resolveEncoding,
   splitFamilies
-} from "./chunk-EOB4Y3EM.js";
+} from "./chunk-BDMISSNR.js";
 import {
   rampFraction
-} from "./chunk-JUYPCLF4.js";
+} from "./chunk-DTBQNR7P.js";
 import {
   gapParts
 } from "./chunk-LG2UK4MB.js";

package/dist/chunks/{chunk-4JDO7ZLN.js → chunk-QWLCHMNS.js}

@@ -1,7 +1,7 @@
 import {
   EdgeSpatialIndex,
   SpatialIndex
-} from "./chunk-7YSIP3O2.js";
+} from "./chunk-WTWO2IPM.js";
 import {
   weakMemo
 } from "./chunk-HMXCN6PG.js";

package/dist/chunks/{chunk-SZYFZNCO.js → chunk-RATN62M3.js}

@@ -1,7 +1,7 @@
 import {
   bubbleSegmentIds,
   classifyBubble
-} from "./chunk-NWEVR2OQ.js";
+} from "./chunk-HYVIQS4D.js";
 import {
   svgPath
 } from "./chunk-JJV2GT2Z.js";

package/dist/chunks/{chunk-QL673EK5.js → chunk-STUG7I25.js}

@@ -3,7 +3,7 @@ import {
   boxesGenes,
   rowPitch,
   rowSpan
-} from "./chunk-OYBYCF2O.js";
+} from "./chunk-PIPNW3VY.js";
 import {
   READOUT_ROOM,
   longestBar

package/dist/chunks/{chunk-RT4U3DH3.js → chunk-TICU3HMJ.js}

@@ -1,6 +1,6 @@
 import {
   tubeSpan
-} from "./chunk-I53QYITQ.js";
+} from "./chunk-TK2ANC2S.js";
 
 // src/tubeMap/genes.ts
 function tubeMapGenes(byRefName, genes) {