@jbrowse/bandage-core 11.5.0 → 11.7.0

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

@@ -2,10 +2,10 @@ import {
   stripGeneGaps,
   walkStripFrame,
   walkStripLabelsTree
-} from "./chunk-A32ZKSHN.js";
+} from "./chunk-HELOUO6K.js";
 import {
   Canvas2DRenderer
-} from "./chunk-EJRJAAN7.js";
+} from "./chunk-4DMSPNYV.js";
 import {
   svgCanvas
 } from "./chunk-V4YML3GR.js";
@@ -13,7 +13,7 @@ import {
   walkRowsKey,
   walkRowsKeyTree,
   walkRowsTree
-} from "./chunk-TRGKMLXT.js";
+} from "./chunk-A7Q7RTWX.js";
 import {
   EXON_COLOR,
   exonOutlineTree,
@@ -21,45 +21,45 @@ import {
 } from "./chunk-JSUCGZ6K.js";
 import {
   geneLabelCandidates
-} from "./chunk-PSCSZSVK.js";
+} from "./chunk-KA4F3N55.js";
 import {
   nodesUnderBox
-} from "./chunk-OMUPUB4J.js";
+} from "./chunk-56L6R6D2.js";
 import {
   escapeAttr,
   serializeEl
 } from "./chunk-H2H4Y3TV.js";
 import {
   genePins
-} from "./chunk-77EGQQJU.js";
+} from "./chunk-BFUS3ENH.js";
 import {
   version
-} from "./chunk-WLR4KJVI.js";
+} from "./chunk-ZHZRAYEM.js";
 import {
   axisScaleOf
-} from "./chunk-XKZ56L5A.js";
+} from "./chunk-5ZQKQ24Z.js";
 import {
   figureScene
-} from "./chunk-3BCVMZUT.js";
+} from "./chunk-WWIUC4N4.js";
 import {
   encodingStops
-} from "./chunk-HN3WHMPJ.js";
+} from "./chunk-2XEAITWM.js";
 import {
   rangeText
-} from "./chunk-D4ZFRBB4.js";
+} from "./chunk-SVPR7IZO.js";
 import {
   walkRowLabels
-} from "./chunk-FWSERUJV.js";
+} from "./chunk-SENPGW4O.js";
 import {
   nodeInk
-} from "./chunk-CRCD3ODN.js";
+} from "./chunk-ZANALBSX.js";
 import {
   FIGURE_DEFAULTS
-} from "./chunk-K5LDBMLX.js";
+} from "./chunk-NTKWT6XL.js";
 import {
   FIT_PADDING,
   fitTransform
-} from "./chunk-WG5D2H7X.js";
+} from "./chunk-YER6TUXV.js";
 import {
   LABEL_CHAR_PX,
   LABEL_PAD,
@@ -72,7 +72,7 @@ import {
   FACET_PAD_PX,
   FACET_TITLE_PX,
   facetGrid
-} from "./chunk-TGUFT6KK.js";
+} from "./chunk-BLUEFYIR.js";
 
 // src/figure.ts
 var FONT = 'font-family="Helvetica, Arial, sans-serif" font-size="11"';

package/dist/chunks/{chunk-3U3C4PRK.js → chunk-HMEAGAGC.js}

@@ -6,13 +6,13 @@ import {
 } from "./chunk-MYDHU2UV.js";
 import {
   readColor
-} from "./chunk-A7H753BA.js";
+} from "./chunk-SDI6BVG7.js";
 import {
   referenceWalkName
-} from "./chunk-64FCX424.js";
+} from "./chunk-G7SG4XMK.js";
 import {
   pathOrigin
-} from "./chunk-B5X2RLJG.js";
+} from "./chunk-3YBP46PB.js";
 import {
   pushTo
 } from "./chunk-BSOZW3FC.js";

package/dist/chunks/{chunk-WC6HX6GJ.js → chunk-IJCSW6MV.js}

@@ -1,9 +1,9 @@
 import {
   pathSteps
-} from "./chunk-RK3HRRCW.js";
+} from "./chunk-SIA75TEG.js";
 import {
   pathOrigin
-} from "./chunk-B5X2RLJG.js";
+} from "./chunk-3YBP46PB.js";
 import {
   PathVisitsBuilder
 } from "./chunk-ZPZ7GNBT.js";

package/dist/chunks/{chunk-JOWKKQAL.js → chunk-JGHZ3N34.js}

@@ -10,17 +10,18 @@ import {
 } from "./chunk-GQZVR5DW.js";
 import {
   baseEdgeCurves
-} from "./chunk-WA5WNP6V.js";
+} from "./chunk-OYCQVJYY.js";
 import {
   PATH_LIGHTNESS,
   PATH_SATURATION,
   nameHue,
   pathHueAt
-} from "./chunk-3GP3KT5L.js";
+} from "./chunk-BW2NMXRV.js";
 import {
   meanDepth,
-  nodeWidthPx
-} from "./chunk-CRCD3ODN.js";
+  nodeWidthPx,
+  walkLaneWidthPx
+} from "./chunk-ZANALBSX.js";
 import {
   referenceMidpoints
 } from "./chunk-VX656OAZ.js";
@@ -31,7 +32,7 @@ import {
   strandSides,
   translateCurves,
   yToXOf
-} from "./chunk-UBQSRCWR.js";
+} from "./chunk-VACK24HF.js";
 import {
   pushTo
 } from "./chunk-BSOZW3FC.js";
@@ -51,7 +52,6 @@ var LIFT_BACKDROP_CSS = abgrToCssRgba(
 );
 var DELETION_DASH_PX = 11;
 var MIN_PATH_STRIPE_PX = 1.2;
-var MIN_WALK_LANE_PX = 4;
 var MIN_SCALE_FOR_OFFSET = 1e-6;
 var ARROW_LENGTH_BASE_PX = 7;
 var ARROW_LENGTH_PER_EDGE_PX = 3;
@@ -518,7 +518,12 @@ function buildGeometry(options) {
     const inView = (curves) => !viewportBounds || isBezierInBounds(curves, viewportBounds);
     const stroke = (curves, thickness, color) => {
       if (isDeletion) {
-        for (const dash of dashCurves(curves, DELETION_DASH_PX / scale)) {
+        for (const dash of dashCurves(
+          curves,
+          DELETION_DASH_PX / scale,
+          yToX,
+          viewportBounds
+        )) {
           edgeCurves.push({ curves: dash, thickness, color });
         }
       } else {
@@ -546,7 +551,7 @@ function buildGeometry(options) {
     if (laneWalks) {
       const fromNode = nodeById.get(edge.from);
       const width = fromNode ? nodeWidthPx(fromNode, contigThickness, nodeWidth, depthNorm) : contigThickness;
-      const laneWidth = Math.max(width / laneWalks.length, MIN_WALK_LANE_PX);
+      const laneWidth = walkLaneWidthPx(width, laneWalks.length);
       const normals = pointNormalsOf(fromSegments, yToX);
       const { nx, ny } = (leavesStart(
         edge,
@@ -638,7 +643,7 @@ function buildGeometry(options) {
     const drawable = segments.length >= 2;
     const lanes = highlight?.walks.length && !faded && !slots?.length ? highlight.walks : void 0;
     if (drawable && lanes) {
-      const laneWidth = Math.max(width / lanes.length, MIN_WALK_LANE_PX);
+      const laneWidth = walkLaneWidthPx(width, lanes.length);
       const normals = pointNormalsOf(segments, yToX);
       lanes.forEach((walk, lane) => {
         const laneColor = walk.colors.get(nodeId);

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

@@ -1,10 +1,10 @@
 import {
   nodesUnderBox
-} from "./chunk-OMUPUB4J.js";
+} from "./chunk-56L6R6D2.js";
 import {
   graphLabels,
   rowLabelBox
-} from "./chunk-PFRQBCGC.js";
+} from "./chunk-T3H5ELLA.js";
 import {
   LABEL_CHAR_PX,
   LABEL_PAD,
@@ -25,7 +25,7 @@ function geneCoverageNote(pin) {
   if (pin.covered >= 0.98) {
     return void 0;
   }
-  const [per, unit] = length >= 1e6 ? [1e6, "Mb"] : length >= 1e3 ? [1e3, "kb"] : [1, "bp"];
+  const [per, unit] = length >= 999500 ? [1e6, "Mb"] : length >= 1e3 ? [1e3, "kb"] : [1, "bp"];
   const amount = (bp) => +(bp / per).toFixed(per === 1 ? 0 : 1);
   return `${amount(pin.covered * length)} of ${amount(length)} ${unit}`;
 }
@@ -114,7 +114,7 @@ function layoutLabels(m) {
     frame,
     take
   );
-  const ticks = m.bubbleHalos.filter((h) => h.tick && !h.whole).map((h) => ({ item: h, ...above(h, 2) })).filter((t) => t.x >= 0 && t.x <= width && t.y >= 0 && t.y <= height);
+  const ticks = m.bubbleHalos.filter((h) => h.tick).map((h) => ({ item: h, ...above(h, 2) })).filter((t) => t.x >= 0 && t.x <= width && t.y >= 0 && t.y <= height);
   const genes = placeLabels(
     geneLabelCandidates(
       m.genePins,

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

@@ -1,6 +1,6 @@
 import {
   ownStrand
-} from "./chunk-UBQSRCWR.js";
+} from "./chunk-VACK24HF.js";
 import {
   groupBy
 } from "./chunk-BSOZW3FC.js";

package/dist/chunks/{chunk-E4ZM4OOJ.js → chunk-KZMSSPS6.js}

@@ -1,10 +1,10 @@
 import {
   bubbleSegmentIds,
   classifyBubble
-} from "./chunk-A4JDEUAI.js";
+} from "./chunk-SNF2MIEF.js";
 import {
   svgPath
-} from "./chunk-UBQSRCWR.js";
+} from "./chunk-VACK24HF.js";
 import {
   isBackbone
 } from "./chunk-RJWPJCIB.js";

package/dist/chunks/{chunk-EIY2SKD3.js → chunk-LG2UK4MB.js}

@@ -5,7 +5,8 @@ var STOP_KINDS = ["elsewhere", "break", "end"];
 var GAP_CAUSE_TEXT = {
   missing: "not in the graph",
   elsewhere: "on nodes filed elsewhere",
-  unknown: "gap, cause unknown"
+  unknown: "gap, cause unknown",
+  abridged: "abridged: steps not loaded"
 };
 var OUTSIDE_TEXT = "outside the extracted subgraph";
 function gapParts(bp, after, before) {

package/dist/chunks/{chunk-PNMJFFNB.js → chunk-MHZTTLBU.js}

@@ -1,6 +1,6 @@
 import {
   trimOrigins
-} from "./chunk-B5X2RLJG.js";
+} from "./chunk-3YBP46PB.js";
 
 // src/bubbles/popBubble.ts
 function bubbleSubgraph(graph, segmentIds) {

package/dist/chunks/{chunk-K5LDBMLX.js → chunk-NTKWT6XL.js}

@@ -1,6 +1,6 @@
 import {
   ENGINE_DEFAULTS
-} from "./chunk-WG5D2H7X.js";
+} from "./chunk-YER6TUXV.js";
 
 // src/figureSettings.ts
 var FIGURE_DEFAULTS = {

package/dist/chunks/{chunk-WA5WNP6V.js → chunk-OYCQVJYY.js}

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

package/dist/chunks/{chunk-JOLLU34X.js → chunk-PQIFYQVI.js}

@@ -1,5 +1,5 @@
 // src/locus.ts
-var LOCUS = /^\s*([^:\s]+):\s*([\d,]+)(?:\s*(?:-|\.\.)\s*([\d,]+))?\s*$/;
+var LOCUS = /^\s*(\S+?):\s*([\d,]+)(?:\s*(?:-|\.\.)\s*([\d,]+))?\s*$/;
 function parseLocus(text) {
   const m = LOCUS.exec(text);
   if (!m) {

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

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

package/dist/chunks/{chunk-A7H753BA.js → chunk-SDI6BVG7.js}

@@ -1,13 +1,13 @@
 import {
   parseCs
-} from "./chunk-C44YRP5F.js";
+} from "./chunk-5OJZV6YT.js";
+import {
+  ownStrand
+} from "./chunk-VACK24HF.js";
 
 // src/tubeMap/reads.ts
-function canonicalStrand(node) {
-  return node.id.endsWith("-") ? "-" : "+";
-}
 function stepName(node, strand) {
-  return strand === canonicalStrand(node) ? node.id : `-${node.id}`;
+  return strand === ownStrand(node.id) ? node.id : `-${node.id}`;
 }
 function stepStarts(lengths, total) {
   const starts = lengths.map(() => void 0);
@@ -137,7 +137,6 @@ function readColor(read) {
 }
 
 export {
-  canonicalStrand,
   stepName,
   tubeMapReads,
   FORWARD_READ_COLORS,

package/dist/chunks/{chunk-FWSERUJV.js → chunk-SENPGW4O.js}

@@ -1,6 +1,6 @@
 import {
   walkRows
-} from "./chunk-IOWLTUEB.js";
+} from "./chunk-BXE3SBBN.js";
 import {
   ROW_HEIGHT_PX
 } from "./chunk-CPMHA4W5.js";

package/dist/chunks/{chunk-RK3HRRCW.js → chunk-SIA75TEG.js}

@@ -1,22 +1,21 @@
 import {
-  canonicalStrand,
   stepName,
   tubeMapReads
-} from "./chunk-A7H753BA.js";
+} from "./chunk-SDI6BVG7.js";
 import {
   referenceWalkName
-} from "./chunk-64FCX424.js";
+} from "./chunk-G7SG4XMK.js";
 import {
   pathCssColor,
   pathGreyCssColor
-} from "./chunk-3GP3KT5L.js";
+} from "./chunk-BW2NMXRV.js";
 import {
   pathOrigin
-} from "./chunk-B5X2RLJG.js";
+} from "./chunk-3YBP46PB.js";
 import {
   ownStrand,
   strandSides
-} from "./chunk-UBQSRCWR.js";
+} from "./chunk-VACK24HF.js";
 import {
   groupBy
 } from "./chunk-BSOZW3FC.js";
@@ -39,7 +38,7 @@ function pathSteps(graph) {
       }
       const at = visits && next ? next(visits.slot(node.name), walk) : -1;
       return [
-        { node, strand: at >= 0 ? visits.strand(at) : canonicalStrand(node) }
+        { node, strand: at >= 0 ? visits.strand(at) : ownStrand(node.id) }
       ];
     });
   });

package/dist/chunks/{chunk-A4JDEUAI.js → chunk-SNF2MIEF.js}

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

package/dist/chunks/{chunk-D4ZFRBB4.js → chunk-SVPR7IZO.js}

@@ -1,17 +1,17 @@
 import {
   GAP_CAUSE_TEXT,
   OUTSIDE_TEXT
-} from "./chunk-EIY2SKD3.js";
+} from "./chunk-LG2UK4MB.js";
 import {
   formatBp,
   groupDigits
-} from "./chunk-PFRQBCGC.js";
+} from "./chunk-T3H5ELLA.js";
 
 // src/walkKey.ts
 function rangeText(contig, start, end) {
   const s = Math.round(start);
   const e = Math.round(end);
-  return `${contig ? `${contig}:` : ""}${groupDigits(s)}-${groupDigits(e)} (${formatBp(e - s)})`;
+  return `${contig ? `${contig}:` : ""}${groupDigits(s + 1)}-${groupDigits(e)} (${formatBp(e - s)})`;
 }
 function walkKey(walk, reference) {
   const { field } = walk.encoding;
@@ -42,7 +42,7 @@ function walkPosition(walk, nodeId, length) {
   const start = Math.round(
     range.start + progress * (range.end - range.start) - length / 2
   );
-  return `${range.contig}:${groupDigits(start)}-${groupDigits(start + length)}`;
+  return `${range.contig}:${groupDigits(start + 1)}-${groupDigits(start + length)}`;
 }
 
 export {

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

@@ -7,15 +7,15 @@ import {
 } from "./chunk-AB35TJST.js";
 import {
   polylineMidpoint
-} from "./chunk-BZFOFC4D.js";
+} from "./chunk-2VMKQKVO.js";
 import {
   edgeCurvesOf
-} from "./chunk-CGMSKIEO.js";
+} from "./chunk-DV5B5UU7.js";
 import {
   curveBounds,
   curveMidpoint,
   polylinePx
-} from "./chunk-UBQSRCWR.js";
+} from "./chunk-VACK24HF.js";
 
 // src/graphLabels.ts
 var MIN_DELETION_LABEL_PX = 26;
@@ -55,7 +55,7 @@ function groupDigits(n) {
   return String(n).replace(/\B(?=(\d{3})+$)/g, ",");
 }
 function formatBp(bp) {
-  const [value, unit] = bp >= 1e6 ? [bp / 1e6, "Mb"] : bp >= 1e3 ? [bp / 1e3, "kb"] : [];
+  const [value, unit] = bp >= 999500 ? [bp / 1e6, "Mb"] : bp >= 1e3 ? [bp / 1e3, "kb"] : [];
   if (value === void 0) {
     return `${bp} bp`;
   }

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

@@ -1,13 +1,13 @@
 import {
   stableCoordinate
-} from "./chunk-5I3K4R2G.js";
+} from "./chunk-CFXXFHRK.js";
+import {
+  walkStopFields
+} from "./chunk-LG2UK4MB.js";
 import {
   pathOrigin,
   surveyPaths
-} from "./chunk-B5X2RLJG.js";
-import {
-  walkStopFields
-} from "./chunk-EIY2SKD3.js";
+} from "./chunk-3YBP46PB.js";
 
 // src/gfa/gfaConverter.ts
 function surveySegments(gfaGraph, pathSteps) {

package/dist/chunks/{chunk-UBQSRCWR.js → chunk-VACK24HF.js}

@@ -71,16 +71,56 @@ function curveTangentAt(c, t) {
     y: a * (c.cy0 - c.y0) + b * (c.cy1 - c.cy0) + d * (c.y1 - c.cy1)
   };
 }
-function dashCurves(curves, dashWorld) {
+var VISIBLE_SAMPLES = 32;
+function visibleStretches(curves, lengths, bounds, yToX) {
+  const stretches = [];
+  let start = 0;
+  curves.forEach((c, k) => {
+    const length = lengths[k];
+    const pad = length / VISIBLE_SAMPLES;
+    let last = curvePointAt(c, 0);
+    for (let i = 1; i <= VISIBLE_SAMPLES; i++) {
+      const next = curvePointAt(c, i / VISIBLE_SAMPLES);
+      if (Math.max(last.x, next.x) + pad >= bounds.minX && Math.min(last.x, next.x) - pad <= bounds.maxX && Math.max(last.y, next.y) + pad / yToX >= bounds.minY && Math.min(last.y, next.y) - pad / yToX <= bounds.maxY) {
+        const from = start + length * (i - 1) / VISIBLE_SAMPLES;
+        const to = start + length * i / VISIBLE_SAMPLES;
+        const prev = stretches.at(-1);
+        if (prev && prev[1] >= from) {
+          prev[1] = to;
+        } else {
+          stretches.push([from, to]);
+        }
+      }
+      last = next;
+    }
+    start += length;
+  });
+  return stretches;
+}
+function dashCurves(curves, dashWorld, yToX = 1, bounds) {
   const lengths = curves.map(
-    (c) => Math.hypot(c.cx0 - c.x0, c.cy0 - c.y0) + Math.hypot(c.cx1 - c.cx0, c.cy1 - c.cy0) + Math.hypot(c.x1 - c.cx1, c.y1 - c.cy1)
+    (c) => Math.hypot(c.cx0 - c.x0, (c.cy0 - c.y0) * yToX) + Math.hypot(c.cx1 - c.cx0, (c.cy1 - c.cy0) * yToX) + Math.hypot(c.x1 - c.cx1, (c.y1 - c.cy1) * yToX)
   );
   const total = lengths.reduce((a, b) => a + b, 0);
-  const spans = Math.max(3, Math.round(total / dashWorld) | 1);
+  const periods = Math.round(total / dashWorld);
+  const spans = Math.max(3, periods % 2 ? periods : periods + 1);
+  const stretches = bounds ? visibleStretches(curves, lengths, bounds, yToX) : void 0;
+  let seen = 0;
   const out = [];
   for (let i = 0; i < spans; i += 2) {
     const from = i / spans * total;
     const to = (i + 1) / spans * total;
+    if (stretches) {
+      while (seen < stretches.length && stretches[seen][1] < from) {
+        seen++;
+      }
+      if (seen === stretches.length) {
+        break;
+      }
+      if (stretches[seen][0] > to) {
+        continue;
+      }
+    }
     const dash = [];
     let start = 0;
     curves.forEach((c, k) => {

package/dist/chunks/{chunk-HSVFCA2J.js → chunk-VO6FKNZE.js}

@@ -1,6 +1,6 @@
 import {
   formatBp
-} from "./chunk-PFRQBCGC.js";
+} from "./chunk-T3H5ELLA.js";
 import {
   pushTo
 } from "./chunk-BSOZW3FC.js";

package/dist/chunks/{chunk-DZR37KXT.js → chunk-VSSIYQYF.js}

@@ -3,7 +3,7 @@ import {
   START_STOP_TAG,
   StopColumns,
   parseStopTag
-} from "./chunk-EIY2SKD3.js";
+} from "./chunk-LG2UK4MB.js";
 import {
   Column
 } from "./chunk-ZPZ7GNBT.js";

package/dist/chunks/{chunk-3BCVMZUT.js → chunk-WWIUC4N4.js}

@@ -4,41 +4,41 @@ import {
 import {
   facetLifts,
   walkLift
-} from "./chunk-VQ7474EH.js";
+} from "./chunk-DUREQSOJ.js";
 import {
   buildGeometry,
   computeReferenceRamp
-} from "./chunk-JOWKKQAL.js";
+} from "./chunk-JGHZ3N34.js";
 import {
   walkKey
-} from "./chunk-D4ZFRBB4.js";
+} from "./chunk-SVPR7IZO.js";
 import {
   walkRowsExtent
-} from "./chunk-FWSERUJV.js";
+} from "./chunk-SENPGW4O.js";
 import {
   pathLegend,
   walkLabelsOf
-} from "./chunk-3GP3KT5L.js";
+} from "./chunk-BW2NMXRV.js";
 import {
   FIGURE_DEFAULTS
-} from "./chunk-K5LDBMLX.js";
+} from "./chunk-NTKWT6XL.js";
 import {
   drawingBounds
-} from "./chunk-WG5D2H7X.js";
+} from "./chunk-YER6TUXV.js";
 import {
   referenceLabel
-} from "./chunk-234NFZS4.js";
+} from "./chunk-5ORP7EFJ.js";
 import {
   resolveColorScheme
 } from "./chunk-JKJWSY4V.js";
 import {
   deletionDrawing,
   deletionEdges
-} from "./chunk-CGMSKIEO.js";
+} from "./chunk-DV5B5UU7.js";
 import {
   facetCells,
   facetSettingOf
-} from "./chunk-TGUFT6KK.js";
+} from "./chunk-BLUEFYIR.js";
 
 // src/figureScene.ts
 function figureScene(graph, layout, o) {

package/dist/chunks/{chunk-GJU6BJJA.js → chunk-XR2HMGAS.js}

@@ -12,7 +12,7 @@ import {
 } from "./chunk-RJWPJCIB.js";
 import {
   panSNSample
-} from "./chunk-4XWZNPQ2.js";
+} from "./chunk-2JL2JVZ2.js";
 
 // src/layout/sampleRowLayout.ts
 function contributingSamples(graph, keep) {

package/dist/chunks/{chunk-WG5D2H7X.js → chunk-YER6TUXV.js}

@@ -14,23 +14,20 @@ import {
 } from "./chunk-VPE4AYP7.js";
 import {
   convertGFAToGraph
-} from "./chunk-FFHJGWDK.js";
+} from "./chunk-TUMJNAOL.js";
 import {
   parseGFA
-} from "./chunk-5I3K4R2G.js";
+} from "./chunk-CFXXFHRK.js";
 import {
   graphFromTables
-} from "./chunk-NJGYLYU7.js";
-import {
-  anchorGraph
-} from "./chunk-B5X2RLJG.js";
+} from "./chunk-7L7MN2OM.js";
 import {
   gfaTables
-} from "./chunk-DZR37KXT.js";
+} from "./chunk-VSSIYQYF.js";
 import {
   mergeRuns,
   splitRuns
-} from "./chunk-BZFOFC4D.js";
+} from "./chunk-2VMKQKVO.js";
 import {
   spreadFor
 } from "./chunk-HKYXWZQS.js";
@@ -42,7 +39,10 @@ import {
 import {
   deletionDrawing,
   deletionEdges
-} from "./chunk-CGMSKIEO.js";
+} from "./chunk-DV5B5UU7.js";
+import {
+  anchorGraph
+} from "./chunk-3YBP46PB.js";
 import {
   isBackbone
 } from "./chunk-RJWPJCIB.js";
@@ -56,7 +56,7 @@ function graphOf(source, name) {
   return tables ? graphFromTables(tables, name) : convertGFAToGraph(parseGFA(source), name);
 }
 function loadGraph(source, name, opts = {}) {
-  const graph = anchorGraph(graphOf(source, name), opts.referencePath);
+  const graph = graphOf(source, name);
   if (graph.nodes.length === 0) {
     throw new Error(`No graph segments in ${name}`);
   }
@@ -65,7 +65,7 @@ function loadGraph(source, name, opts = {}) {
       `Graph too large to draw: ${graph.nodes.length.toLocaleString()} nodes (limit ${opts.maxNodes.toLocaleString()}). Zoom in to a smaller region, or raise maxGraphNodes on this view.`
     );
   }
-  return graph;
+  return anchorGraph(graph, opts.referencePath);
 }
 var ENGINE_DEFAULTS = {
   engine: "fmmm",