@jbrowse/bandage-core 11.7.0 → 11.7.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (75) hide show
  1. package/dist/bubbles/bubbleHalos.js +5 -4
  2. package/dist/bubbles/classifyBubble.js +4 -3
  3. package/dist/bubbles/superbubbles.js +6 -5
  4. package/dist/chunks/{chunk-BW2NMXRV.js → chunk-3UGWYQNY.js} +1 -1
  5. package/dist/chunks/{chunk-YEYQFNFQ.js → chunk-3WSA4NNP.js} +1 -1
  6. package/dist/chunks/{chunk-SNF2MIEF.js → chunk-3Y2EFDID.js} +1 -1
  7. package/dist/chunks/{chunk-DV5B5UU7.js → chunk-5NZRT7GL.js} +5 -1
  8. package/dist/chunks/{chunk-A7Q7RTWX.js → chunk-6XDTAKO7.js} +1 -1
  9. package/dist/chunks/{chunk-DUREQSOJ.js → chunk-APLWFV4I.js} +2 -2
  10. package/dist/chunks/{chunk-KA4F3N55.js → chunk-ATDVS2CW.js} +2 -2
  11. package/dist/chunks/{chunk-65YCFVS4.js → chunk-CWCVQJYY.js} +1 -1
  12. package/dist/chunks/{chunk-WWIUC4N4.js → chunk-EZGNBDHD.js} +7 -7
  13. package/dist/chunks/{chunk-HELOUO6K.js → chunk-F7O56DVR.js} +1 -1
  14. package/dist/chunks/{chunk-5ZQKQ24Z.js → chunk-FBPAX5K6.js} +1 -1
  15. package/dist/chunks/{chunk-T3H5ELLA.js → chunk-FU57ZNRQ.js} +1 -1
  16. package/dist/chunks/{chunk-YER6TUXV.js → chunk-HTF32WSW.js} +1 -1
  17. package/dist/chunks/{chunk-2XEAITWM.js → chunk-I5SGYTRM.js} +1 -1
  18. package/dist/chunks/{chunk-6YRSOL4K.js → chunk-IN4IYSA2.js} +1 -1
  19. package/dist/chunks/{chunk-C6E6HXP5.js → chunk-J6XHW4KI.js} +2 -2
  20. package/dist/chunks/{chunk-KZMSSPS6.js → chunk-JGH2V54E.js} +1 -1
  21. package/dist/chunks/{chunk-IJCSW6MV.js → chunk-JLIVX2SF.js} +1 -1
  22. package/dist/chunks/{chunk-EH5JZETS.js → chunk-LKQOIPGE.js} +7 -7
  23. package/dist/chunks/{chunk-DTEXQ65J.js → chunk-OXW5OHYQ.js} +1 -1
  24. package/dist/chunks/{chunk-GZ36HNPJ.js → chunk-PCHEUVHB.js} +1 -1
  25. package/dist/chunks/{chunk-VO6FKNZE.js → chunk-PJWLYGRL.js} +1 -1
  26. package/dist/chunks/{chunk-56L6R6D2.js → chunk-Q7I563MH.js} +1 -1
  27. package/dist/chunks/{chunk-SIA75TEG.js → chunk-RB2MDFQU.js} +1 -1
  28. package/dist/chunks/{chunk-HERVZPWA.js → chunk-RK7ZOFPR.js} +11 -11
  29. package/dist/chunks/{chunk-QCOVHLJO.js → chunk-RT4K2JMZ.js} +1 -1
  30. package/dist/chunks/{chunk-NTKWT6XL.js → chunk-SACSQ45G.js} +1 -1
  31. package/dist/chunks/{chunk-ZHZRAYEM.js → chunk-TCSV3II7.js} +1 -1
  32. package/dist/chunks/chunk-TLWXLNLY.js +124 -0
  33. package/dist/chunks/{chunk-SVPR7IZO.js → chunk-UV2IJMIG.js} +1 -1
  34. package/dist/chunks/{chunk-JGHZ3N34.js → chunk-VB4IXIPM.js} +2 -2
  35. package/dist/chunks/{chunk-DD5EZG3T.js → chunk-WUZH2OJ6.js} +1 -1
  36. package/dist/chunks/{chunk-OYCQVJYY.js → chunk-XTF2VWJN.js} +1 -1
  37. package/dist/cli/figure.js +23 -22
  38. package/dist/cli/fold.js +3 -2
  39. package/dist/deletionEdges.js +2 -1
  40. package/dist/figure.js +20 -19
  41. package/dist/figureData.js +17 -16
  42. package/dist/figureScene.js +12 -11
  43. package/dist/figureSettings.js +4 -3
  44. package/dist/graphLabels.js +3 -2
  45. package/dist/index.js +32 -31
  46. package/dist/labelLayout.js +7 -6
  47. package/dist/layout/forceCache.js +4 -3
  48. package/dist/layout/trimToWindow.js +9 -101
  49. package/dist/layout/tubeMapLayout.js +5 -4
  50. package/dist/layout/walkRowDraw.js +7 -6
  51. package/dist/layout/walkStrip.js +8 -7
  52. package/dist/layoutModes.js +6 -5
  53. package/dist/pathColors.js +4 -3
  54. package/dist/pipeline.js +3 -2
  55. package/dist/referenceStrip.js +7 -6
  56. package/dist/renderer/GeometryBuilder.js +6 -5
  57. package/dist/tubeMap/axis.js +4 -3
  58. package/dist/tubeMap/bundle.js +6 -5
  59. package/dist/tubeMap/coarsen.js +6 -5
  60. package/dist/tubeMap/deviations.js +7 -6
  61. package/dist/tubeMap/genes.js +5 -4
  62. package/dist/tubeMap/nodeColors.js +7 -6
  63. package/dist/types/deletionEdges.d.ts +1 -1
  64. package/dist/types/layout/trimToWindow.d.ts +1 -0
  65. package/dist/types/types.d.ts +4 -0
  66. package/dist/types/version.d.ts +1 -1
  67. package/dist/util/SpatialIndex.js +4 -3
  68. package/dist/util/edgeCurves.js +3 -2
  69. package/dist/util/hitDetection.js +5 -4
  70. package/dist/version.js +1 -1
  71. package/dist/viewport.js +4 -3
  72. package/dist/walkEncoding.js +7 -6
  73. package/dist/walkHighlight.js +8 -7
  74. package/dist/walkKey.js +4 -3
  75. package/package.json +1 -1
@@ -1,108 +1,16 @@
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  import {
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- pathOrigin,
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- trimOrigins
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- } from "../chunks/chunk-3YBP46PB.js";
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- import {
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- PathVisitsBuilder
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- } from "../chunks/chunk-ZPZ7GNBT.js";
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+ clipToWindow,
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+ trimToWindow,
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+ unclipped
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+ } from "../chunks/chunk-TLWXLNLY.js";
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+ import "../chunks/chunk-3YBP46PB.js";
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+ import "../chunks/chunk-ZPZ7GNBT.js";
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  import "../chunks/chunk-BSOZW3FC.js";
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- import {
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- isBackbone,
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- overlapsWindow
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- } from "../chunks/chunk-RJWPJCIB.js";
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+ import "../chunks/chunk-RJWPJCIB.js";
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  import "../chunks/chunk-HOAIOEI7.js";
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  import "../chunks/chunk-2JL2JVZ2.js";
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-
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- // src/layout/trimToWindow.ts
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- function trimToWindow(graph, window) {
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- const inWindow = new Set(
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- graph.nodes.filter((n) => isBackbone(n) && overlapsWindow(n, window)).map((n) => n.id)
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- );
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- const paths = graph.paths ?? [];
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- if (inWindow.size === 0 || paths.length === 0) {
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- return graph;
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- }
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- const spans = paths.map((path) => {
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- let first = -1;
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- let last = -1;
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- path.nodeIds.forEach((id, i) => {
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- if (inWindow.has(id)) {
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- if (first < 0) {
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- first = i;
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- }
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- last = i;
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- }
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- });
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- return first < 0 ? void 0 : { first, last };
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- });
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- if (spans.every(
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- (span, i) => span?.first === 0 && span.last === paths[i].nodeIds.length - 1
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- )) {
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- return graph;
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- }
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- const kept = /* @__PURE__ */ new Set();
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- const trimmed = [];
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- const stretches = /* @__PURE__ */ new Map();
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- paths.forEach((path, i) => {
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- const span = spans[i];
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- if (span) {
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- const nodeIds = path.nodeIds.slice(span.first, span.last + 1);
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- for (const id of nodeIds) {
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- kept.add(id);
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- }
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- trimmed.push({ ...path, nodeIds });
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- stretches.set(path.name, { first: span.first, nodeIds });
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- }
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- });
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- return {
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- ...graph,
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- nodes: graph.nodes.filter((n) => kept.has(n.id)),
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- edges: graph.edges.filter((e) => kept.has(e.from) && kept.has(e.to)),
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- paths: trimmed,
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- pathVisits: graph.pathVisits && trimVisits(
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- graph.pathVisits,
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- paths,
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- spans,
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- new Map(graph.nodes.map((n) => [n.id, n.name]))
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- ),
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- anchorPaths: trimOrigins(graph, stretches)
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- };
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- }
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- function trimVisits(visits, paths, spans, nameOf) {
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- const next = visits.replay();
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- const out = new PathVisitsBuilder();
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- paths.forEach((path, p) => {
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- const origin = visits.pathIndex(pathOrigin(path.name).name);
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- const span = spans[p];
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- path.nodeIds.forEach((id, i) => {
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- const segment = nameOf.get(id) ?? id;
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- const at = next(visits.slot(segment), origin);
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- if (at >= 0 && span && i >= span.first && i <= span.last) {
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- out.add(
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- segment,
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- visits.paths[origin],
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- visits.samples[origin],
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- visits.start[at],
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- visits.reversed[at] === 1
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- );
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- }
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- });
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- });
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- return out.build();
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- }
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- function clipToWindow(graph, window, reachBp) {
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- const nodes = graph.nodes.map((node) => {
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- if (!isBackbone(node)) {
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- return node;
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- }
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- const from = node.stable.start;
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- const to = from + node.length;
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- const [start, end] = overlapsWindow(node, window) ? [Math.max(from, window.start), Math.min(to, window.end)] : to <= window.start ? [Math.max(from, to - reachBp), to] : [from, Math.min(to, from + reachBp)];
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- return start === from && end === to ? node : { ...node, length: end - start, stable: { ...node.stable, start } };
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- });
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- return nodes.some((node, i) => node !== graph.nodes[i]) ? { ...graph, nodes } : graph;
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- }
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  export {
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  clipToWindow,
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- trimToWindow
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+ trimToWindow,
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+ unclipped
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  };
@@ -5,19 +5,20 @@ import {
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  tubeMapLayout,
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  tubeMapReferenceLayout,
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  tubeMapTracks
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- } from "../chunks/chunk-SIA75TEG.js";
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+ } from "../chunks/chunk-RB2MDFQU.js";
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  import "../chunks/chunk-SDI6BVG7.js";
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  import "../chunks/chunk-5OJZV6YT.js";
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  import "../chunks/chunk-BXE3SBBN.js";
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  import "../chunks/chunk-G7SG4XMK.js";
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- import "../chunks/chunk-BW2NMXRV.js";
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+ import "../chunks/chunk-3UGWYQNY.js";
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  import "../chunks/chunk-7L7MN2OM.js";
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  import "../chunks/chunk-LG2UK4MB.js";
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- import "../chunks/chunk-T3H5ELLA.js";
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+ import "../chunks/chunk-FU57ZNRQ.js";
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  import "../chunks/chunk-HMXCN6PG.js";
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  import "../chunks/chunk-AB35TJST.js";
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  import "../chunks/chunk-2VMKQKVO.js";
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- import "../chunks/chunk-DV5B5UU7.js";
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+ import "../chunks/chunk-5NZRT7GL.js";
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+ import "../chunks/chunk-TLWXLNLY.js";
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  import "../chunks/chunk-3YBP46PB.js";
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  import "../chunks/chunk-VACK24HF.js";
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  import "../chunks/chunk-CPMHA4W5.js";
@@ -30,21 +30,22 @@ import {
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  walkRowsKey,
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  walkRowsKeyTree,
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  walkRowsTree
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- } from "../chunks/chunk-A7Q7RTWX.js";
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+ } from "../chunks/chunk-6XDTAKO7.js";
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  import "../chunks/chunk-H2H4Y3TV.js";
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- import "../chunks/chunk-JGHZ3N34.js";
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+ import "../chunks/chunk-VB4IXIPM.js";
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  import "../chunks/chunk-G2FD7S3C.js";
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  import "../chunks/chunk-GQZVR5DW.js";
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- import "../chunks/chunk-OYCQVJYY.js";
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- import "../chunks/chunk-BW2NMXRV.js";
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+ import "../chunks/chunk-XTF2VWJN.js";
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+ import "../chunks/chunk-3UGWYQNY.js";
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  import "../chunks/chunk-ZANALBSX.js";
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  import "../chunks/chunk-VX656OAZ.js";
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  import "../chunks/chunk-LG2UK4MB.js";
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- import "../chunks/chunk-T3H5ELLA.js";
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+ import "../chunks/chunk-FU57ZNRQ.js";
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  import "../chunks/chunk-HMXCN6PG.js";
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  import "../chunks/chunk-AB35TJST.js";
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  import "../chunks/chunk-2VMKQKVO.js";
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- import "../chunks/chunk-DV5B5UU7.js";
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+ import "../chunks/chunk-5NZRT7GL.js";
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+ import "../chunks/chunk-TLWXLNLY.js";
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  import "../chunks/chunk-3YBP46PB.js";
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  import "../chunks/chunk-VACK24HF.js";
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  import "../chunks/chunk-CPMHA4W5.js";
@@ -9,28 +9,29 @@ import {
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  walkStripApplies,
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  walkStripFrame,
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  walkStripLabelsTree
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- } from "../chunks/chunk-HELOUO6K.js";
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+ } from "../chunks/chunk-F7O56DVR.js";
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  import {
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  LABELLED_ROW_PX
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- } from "../chunks/chunk-A7Q7RTWX.js";
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+ } from "../chunks/chunk-6XDTAKO7.js";
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  import "../chunks/chunk-H2H4Y3TV.js";
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- import "../chunks/chunk-JGHZ3N34.js";
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+ import "../chunks/chunk-VB4IXIPM.js";
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  import "../chunks/chunk-G2FD7S3C.js";
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  import "../chunks/chunk-GQZVR5DW.js";
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- import "../chunks/chunk-OYCQVJYY.js";
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+ import "../chunks/chunk-XTF2VWJN.js";
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  import "../chunks/chunk-SENPGW4O.js";
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  import "../chunks/chunk-BXE3SBBN.js";
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  import "../chunks/chunk-G7SG4XMK.js";
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- import "../chunks/chunk-BW2NMXRV.js";
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+ import "../chunks/chunk-3UGWYQNY.js";
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  import "../chunks/chunk-ZANALBSX.js";
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  import "../chunks/chunk-7L7MN2OM.js";
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  import "../chunks/chunk-VX656OAZ.js";
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  import "../chunks/chunk-LG2UK4MB.js";
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- import "../chunks/chunk-T3H5ELLA.js";
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+ import "../chunks/chunk-FU57ZNRQ.js";
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- import "../chunks/chunk-DV5B5UU7.js";
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+ import "../chunks/chunk-5NZRT7GL.js";
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+ import "../chunks/chunk-TLWXLNLY.js";
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  import "../chunks/chunk-3YBP46PB.js";
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  import "../chunks/chunk-VACK24HF.js";
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  import "../chunks/chunk-CPMHA4W5.js";
@@ -4,8 +4,8 @@ import {
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  LAYOUT_MODE_VALUES,
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  layoutModeByValue,
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  modeUsesLayoutEngine
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- } from "./chunks/chunk-DD5EZG3T.js";
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- import "./chunks/chunk-SIA75TEG.js";
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+ } from "./chunks/chunk-WUZH2OJ6.js";
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+ import "./chunks/chunk-RB2MDFQU.js";
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  import "./chunks/chunk-SDI6BVG7.js";
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  import "./chunks/chunk-XR2HMGAS.js";
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  import "./chunks/chunk-GJLZ2MKE.js";
@@ -16,15 +16,16 @@ import "./chunks/chunk-3GLG3ZLE.js";
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  import "./chunks/chunk-SENPGW4O.js";
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  import "./chunks/chunk-BXE3SBBN.js";
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  import "./chunks/chunk-G7SG4XMK.js";
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- import "./chunks/chunk-BW2NMXRV.js";
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+ import "./chunks/chunk-3UGWYQNY.js";
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  import "./chunks/chunk-7L7MN2OM.js";
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- import "./chunks/chunk-T3H5ELLA.js";
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+ import "./chunks/chunk-FU57ZNRQ.js";
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  import "./chunks/chunk-HMXCN6PG.js";
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  import "./chunks/chunk-AB35TJST.js";
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- import "./chunks/chunk-DV5B5UU7.js";
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+ import "./chunks/chunk-5NZRT7GL.js";
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+ import "./chunks/chunk-TLWXLNLY.js";
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  import "./chunks/chunk-3YBP46PB.js";
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@@ -9,12 +9,13 @@ import {
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  pathHueAt,
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  pathLegend,
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  walkLabelsOf
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- } from "./chunks/chunk-BW2NMXRV.js";
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- import "./chunks/chunk-T3H5ELLA.js";
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+ } from "./chunks/chunk-3UGWYQNY.js";
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+ import "./chunks/chunk-FU57ZNRQ.js";
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  import "./chunks/chunk-HMXCN6PG.js";
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  import "./chunks/chunk-AB35TJST.js";
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- import "./chunks/chunk-DV5B5UU7.js";
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+ import "./chunks/chunk-5NZRT7GL.js";
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+ import "./chunks/chunk-TLWXLNLY.js";
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  import "./chunks/chunk-3YBP46PB.js";
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package/dist/pipeline.js CHANGED
@@ -11,7 +11,7 @@ import {
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  forceLayout,
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  layoutExtent,
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  loadGraph
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- } from "./chunks/chunk-YER6TUXV.js";
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+ } from "./chunks/chunk-HTF32WSW.js";
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  import "./chunks/chunk-OPPVSPEF.js";
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  import "./chunks/chunk-3PZSBNLI.js";
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@@ -26,7 +26,8 @@ import "./chunks/chunk-LG2UK4MB.js";
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  import "./chunks/chunk-2VMKQKVO.js";
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  import "./chunks/chunk-HKYXWZQS.js";
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- import "./chunks/chunk-DV5B5UU7.js";
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+ import "./chunks/chunk-5NZRT7GL.js";
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+ import "./chunks/chunk-TLWXLNLY.js";
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@@ -7,19 +7,20 @@ import {
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- } from "./chunks/chunk-QCOVHLJO.js";
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- import "./chunks/chunk-JGHZ3N34.js";
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+ } from "./chunks/chunk-RT4K2JMZ.js";
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+ import "./chunks/chunk-VB4IXIPM.js";
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  import "./chunks/chunk-G2FD7S3C.js";
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- import "./chunks/chunk-OYCQVJYY.js";
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- import "./chunks/chunk-BW2NMXRV.js";
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+ import "./chunks/chunk-XTF2VWJN.js";
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+ import "./chunks/chunk-3UGWYQNY.js";
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  import "./chunks/chunk-ZANALBSX.js";
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  import "./chunks/chunk-VX656OAZ.js";
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- import "./chunks/chunk-T3H5ELLA.js";
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+ import "./chunks/chunk-FU57ZNRQ.js";
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- import "./chunks/chunk-DV5B5UU7.js";
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+ import "./chunks/chunk-5NZRT7GL.js";
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+ import "./chunks/chunk-TLWXLNLY.js";
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@@ -11,20 +11,21 @@ import {
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- } from "../chunks/chunk-JGHZ3N34.js";
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+ } from "../chunks/chunk-VB4IXIPM.js";
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- import "../chunks/chunk-OYCQVJYY.js";
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- import "../chunks/chunk-BW2NMXRV.js";
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+ import "../chunks/chunk-XTF2VWJN.js";
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+ import "../chunks/chunk-3UGWYQNY.js";
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  import "../chunks/chunk-VX656OAZ.js";
23
- import "../chunks/chunk-T3H5ELLA.js";
23
+ import "../chunks/chunk-FU57ZNRQ.js";
24
24
  import "../chunks/chunk-HMXCN6PG.js";
25
25
  import "../chunks/chunk-AB35TJST.js";
26
26
  import "../chunks/chunk-2VMKQKVO.js";
27
- import "../chunks/chunk-DV5B5UU7.js";
27
+ import "../chunks/chunk-5NZRT7GL.js";
28
+ import "../chunks/chunk-TLWXLNLY.js";
28
29
  import "../chunks/chunk-3YBP46PB.js";
29
30
  import "../chunks/chunk-VACK24HF.js";
30
31
  import "../chunks/chunk-CPMHA4W5.js";
@@ -7,12 +7,13 @@ import {
7
7
  rulerMarks,
8
8
  tubeSpan,
9
9
  tubeX
10
- } from "../chunks/chunk-VO6FKNZE.js";
11
- import "../chunks/chunk-T3H5ELLA.js";
10
+ } from "../chunks/chunk-PJWLYGRL.js";
11
+ import "../chunks/chunk-FU57ZNRQ.js";
12
12
  import "../chunks/chunk-HMXCN6PG.js";
13
13
  import "../chunks/chunk-AB35TJST.js";
14
14
  import "../chunks/chunk-2VMKQKVO.js";
15
- import "../chunks/chunk-DV5B5UU7.js";
15
+ import "../chunks/chunk-5NZRT7GL.js";
16
+ import "../chunks/chunk-TLWXLNLY.js";
16
17
  import "../chunks/chunk-3YBP46PB.js";
17
18
  import "../chunks/chunk-VACK24HF.js";
18
19
  import "../chunks/chunk-CPMHA4W5.js";
@@ -1,19 +1,20 @@
1
1
  import {
2
2
  bundleRoutes
3
- } from "../chunks/chunk-65YCFVS4.js";
4
- import "../chunks/chunk-SIA75TEG.js";
3
+ } from "../chunks/chunk-CWCVQJYY.js";
4
+ import "../chunks/chunk-RB2MDFQU.js";
5
5
  import "../chunks/chunk-SDI6BVG7.js";
6
6
  import "../chunks/chunk-5OJZV6YT.js";
7
7
  import "../chunks/chunk-BXE3SBBN.js";
8
8
  import "../chunks/chunk-G7SG4XMK.js";
9
- import "../chunks/chunk-BW2NMXRV.js";
9
+ import "../chunks/chunk-3UGWYQNY.js";
10
10
  import "../chunks/chunk-7L7MN2OM.js";
11
11
  import "../chunks/chunk-LG2UK4MB.js";
12
- import "../chunks/chunk-T3H5ELLA.js";
12
+ import "../chunks/chunk-FU57ZNRQ.js";
13
13
  import "../chunks/chunk-HMXCN6PG.js";
14
14
  import "../chunks/chunk-AB35TJST.js";
15
15
  import "../chunks/chunk-2VMKQKVO.js";
16
- import "../chunks/chunk-DV5B5UU7.js";
16
+ import "../chunks/chunk-5NZRT7GL.js";
17
+ import "../chunks/chunk-TLWXLNLY.js";
17
18
  import "../chunks/chunk-3YBP46PB.js";
18
19
  import "../chunks/chunk-VACK24HF.js";
19
20
  import "../chunks/chunk-CPMHA4W5.js";
@@ -1,20 +1,21 @@
1
1
  import {
2
2
  coarsenTubeMap,
3
3
  lastAtMost
4
- } from "../chunks/chunk-IJCSW6MV.js";
5
- import "../chunks/chunk-SIA75TEG.js";
4
+ } from "../chunks/chunk-JLIVX2SF.js";
5
+ import "../chunks/chunk-RB2MDFQU.js";
6
6
  import "../chunks/chunk-SDI6BVG7.js";
7
7
  import "../chunks/chunk-5OJZV6YT.js";
8
8
  import "../chunks/chunk-BXE3SBBN.js";
9
9
  import "../chunks/chunk-G7SG4XMK.js";
10
- import "../chunks/chunk-BW2NMXRV.js";
10
+ import "../chunks/chunk-3UGWYQNY.js";
11
11
  import "../chunks/chunk-7L7MN2OM.js";
12
12
  import "../chunks/chunk-LG2UK4MB.js";
13
- import "../chunks/chunk-T3H5ELLA.js";
13
+ import "../chunks/chunk-FU57ZNRQ.js";
14
14
  import "../chunks/chunk-HMXCN6PG.js";
15
15
  import "../chunks/chunk-AB35TJST.js";
16
16
  import "../chunks/chunk-2VMKQKVO.js";
17
- import "../chunks/chunk-DV5B5UU7.js";
17
+ import "../chunks/chunk-5NZRT7GL.js";
18
+ import "../chunks/chunk-TLWXLNLY.js";
18
19
  import "../chunks/chunk-3YBP46PB.js";
19
20
  import "../chunks/chunk-VACK24HF.js";
20
21
  import "../chunks/chunk-CPMHA4W5.js";
@@ -1,23 +1,24 @@
1
1
  import {
2
2
  lastAtMost
3
- } from "../chunks/chunk-IJCSW6MV.js";
3
+ } from "../chunks/chunk-JLIVX2SF.js";
4
4
  import {
5
5
  boxX,
6
6
  referenceBoxes
7
- } from "../chunks/chunk-VO6FKNZE.js";
8
- import "../chunks/chunk-SIA75TEG.js";
7
+ } from "../chunks/chunk-PJWLYGRL.js";
8
+ import "../chunks/chunk-RB2MDFQU.js";
9
9
  import "../chunks/chunk-SDI6BVG7.js";
10
10
  import "../chunks/chunk-5OJZV6YT.js";
11
11
  import "../chunks/chunk-BXE3SBBN.js";
12
12
  import "../chunks/chunk-G7SG4XMK.js";
13
- import "../chunks/chunk-BW2NMXRV.js";
13
+ import "../chunks/chunk-3UGWYQNY.js";
14
14
  import "../chunks/chunk-7L7MN2OM.js";
15
15
  import "../chunks/chunk-LG2UK4MB.js";
16
- import "../chunks/chunk-T3H5ELLA.js";
16
+ import "../chunks/chunk-FU57ZNRQ.js";
17
17
  import "../chunks/chunk-HMXCN6PG.js";
18
18
  import "../chunks/chunk-AB35TJST.js";
19
19
  import "../chunks/chunk-2VMKQKVO.js";
20
- import "../chunks/chunk-DV5B5UU7.js";
20
+ import "../chunks/chunk-5NZRT7GL.js";
21
+ import "../chunks/chunk-TLWXLNLY.js";
21
22
  import {
22
23
  pathOrigin
23
24
  } from "../chunks/chunk-3YBP46PB.js";
@@ -3,13 +3,14 @@ import {
3
3
  drawTubeMapGenes,
4
4
  tubeMapGeneRows,
5
5
  tubeMapGenes
6
- } from "../chunks/chunk-GZ36HNPJ.js";
7
- import "../chunks/chunk-VO6FKNZE.js";
8
- import "../chunks/chunk-T3H5ELLA.js";
6
+ } from "../chunks/chunk-PCHEUVHB.js";
7
+ import "../chunks/chunk-PJWLYGRL.js";
8
+ import "../chunks/chunk-FU57ZNRQ.js";
9
9
  import "../chunks/chunk-HMXCN6PG.js";
10
10
  import "../chunks/chunk-AB35TJST.js";
11
11
  import "../chunks/chunk-2VMKQKVO.js";
12
- import "../chunks/chunk-DV5B5UU7.js";
12
+ import "../chunks/chunk-5NZRT7GL.js";
13
+ import "../chunks/chunk-TLWXLNLY.js";
13
14
  import "../chunks/chunk-3YBP46PB.js";
14
15
  import "../chunks/chunk-VACK24HF.js";
15
16
  import "../chunks/chunk-CPMHA4W5.js";
@@ -1,18 +1,19 @@
1
1
  import {
2
2
  tubeMapNodeColors
3
- } from "../chunks/chunk-YEYQFNFQ.js";
4
- import "../chunks/chunk-JGHZ3N34.js";
3
+ } from "../chunks/chunk-3WSA4NNP.js";
4
+ import "../chunks/chunk-VB4IXIPM.js";
5
5
  import "../chunks/chunk-G2FD7S3C.js";
6
6
  import "../chunks/chunk-GQZVR5DW.js";
7
- import "../chunks/chunk-OYCQVJYY.js";
8
- import "../chunks/chunk-BW2NMXRV.js";
7
+ import "../chunks/chunk-XTF2VWJN.js";
8
+ import "../chunks/chunk-3UGWYQNY.js";
9
9
  import "../chunks/chunk-ZANALBSX.js";
10
10
  import "../chunks/chunk-VX656OAZ.js";
11
- import "../chunks/chunk-T3H5ELLA.js";
11
+ import "../chunks/chunk-FU57ZNRQ.js";
12
12
  import "../chunks/chunk-HMXCN6PG.js";
13
13
  import "../chunks/chunk-AB35TJST.js";
14
14
  import "../chunks/chunk-2VMKQKVO.js";
15
- import "../chunks/chunk-DV5B5UU7.js";
15
+ import "../chunks/chunk-5NZRT7GL.js";
16
+ import "../chunks/chunk-TLWXLNLY.js";
16
17
  import "../chunks/chunk-3YBP46PB.js";
17
18
  import "../chunks/chunk-VACK24HF.js";
18
19
  import "../chunks/chunk-CPMHA4W5.js";
@@ -13,7 +13,7 @@ export interface DeletionEdge {
13
13
  bypassed: string[];
14
14
  }
15
15
  export declare function edgeCurvesOf(nodePositions: Record<string, NodeSegment[]>, edge: GraphEdge, axis: AxisScale, bypassed: string[] | undefined, route: NodeSegment[] | undefined, stranded: boolean): import("./util/geometry.js").BezierCurve[] | undefined;
16
- export declare function deletionEdges(graph: Graph): DeletionEdge[];
16
+ export declare function deletionEdges(cut: Graph): DeletionEdge[];
17
17
  export declare function closableDeletions(graph: Graph, deletions: DeletionEdge[]): Set<number>;
18
18
  export interface DeletionDrawing {
19
19
  shown: DeletionEdge[];
@@ -7,3 +7,4 @@ export declare function clipToWindow(graph: Graph, window: {
7
7
  start: number;
8
8
  end: number;
9
9
  }, reachBp: number): Graph;
10
+ export declare function unclipped(graph: Graph): Graph;
@@ -9,6 +9,10 @@ export interface GraphNode {
9
9
  depth: number;
10
10
  stable?: StableCoordinate;
11
11
  samples?: string[];
12
+ unclipped?: {
13
+ start: number;
14
+ length: number;
15
+ };
12
16
  }
13
17
  export interface GraphEdge {
14
18
  from: string;
@@ -1 +1 @@
1
- export declare const version = "11.7.0";
1
+ export declare const version = "11.7.1";
@@ -1,10 +1,11 @@
1
1
  import {
2
2
  EdgeSpatialIndex,
3
3
  SpatialIndex
4
- } from "../chunks/chunk-6YRSOL4K.js";
5
- import "../chunks/chunk-OYCQVJYY.js";
4
+ } from "../chunks/chunk-IN4IYSA2.js";
5
+ import "../chunks/chunk-XTF2VWJN.js";
6
6
  import "../chunks/chunk-HMXCN6PG.js";
7
- import "../chunks/chunk-DV5B5UU7.js";
7
+ import "../chunks/chunk-5NZRT7GL.js";
8
+ import "../chunks/chunk-TLWXLNLY.js";
8
9
  import "../chunks/chunk-3YBP46PB.js";
9
10
  import "../chunks/chunk-VACK24HF.js";
10
11
  import "../chunks/chunk-CPMHA4W5.js";
@@ -1,8 +1,9 @@
1
1
  import {
2
2
  baseEdgeCurves
3
- } from "../chunks/chunk-OYCQVJYY.js";
3
+ } from "../chunks/chunk-XTF2VWJN.js";
4
4
  import "../chunks/chunk-HMXCN6PG.js";
5
- import "../chunks/chunk-DV5B5UU7.js";
5
+ import "../chunks/chunk-5NZRT7GL.js";
6
+ import "../chunks/chunk-TLWXLNLY.js";
6
7
  import "../chunks/chunk-3YBP46PB.js";
7
8
  import "../chunks/chunk-VACK24HF.js";
8
9
  import "../chunks/chunk-CPMHA4W5.js";
@@ -4,11 +4,12 @@ import {
4
4
  findHoveredEdge,
5
5
  findHoveredNode,
6
6
  nodesUnderBox
7
- } from "../chunks/chunk-56L6R6D2.js";
8
- import "../chunks/chunk-6YRSOL4K.js";
9
- import "../chunks/chunk-OYCQVJYY.js";
7
+ } from "../chunks/chunk-Q7I563MH.js";
8
+ import "../chunks/chunk-IN4IYSA2.js";
9
+ import "../chunks/chunk-XTF2VWJN.js";
10
10
  import "../chunks/chunk-HMXCN6PG.js";
11
- import "../chunks/chunk-DV5B5UU7.js";
11
+ import "../chunks/chunk-5NZRT7GL.js";
12
+ import "../chunks/chunk-TLWXLNLY.js";
12
13
  import "../chunks/chunk-3YBP46PB.js";
13
14
  import "../chunks/chunk-VACK24HF.js";
14
15
  import "../chunks/chunk-CPMHA4W5.js";
package/dist/version.js CHANGED
@@ -1,6 +1,6 @@
1
1
  import {
2
2
  version
3
- } from "./chunks/chunk-ZHZRAYEM.js";
3
+ } from "./chunks/chunk-TCSV3II7.js";
4
4
  export {
5
5
  version
6
6
  };
package/dist/viewport.js CHANGED
@@ -5,8 +5,8 @@ import {
5
5
  screenToLayout,
6
6
  viewportOf,
7
7
  zoomAbout
8
- } from "./chunks/chunk-5ZQKQ24Z.js";
9
- import "./chunks/chunk-YER6TUXV.js";
8
+ } from "./chunks/chunk-FBPAX5K6.js";
9
+ import "./chunks/chunk-HTF32WSW.js";
10
10
  import "./chunks/chunk-OPPVSPEF.js";
11
11
  import "./chunks/chunk-3PZSBNLI.js";
12
12
  import "./chunks/chunk-CKUVEHSS.js";
@@ -21,7 +21,8 @@ import "./chunks/chunk-LG2UK4MB.js";
21
21
  import "./chunks/chunk-2VMKQKVO.js";
22
22
  import "./chunks/chunk-HKYXWZQS.js";
23
23
  import "./chunks/chunk-34BOZKIE.js";
24
- import "./chunks/chunk-DV5B5UU7.js";
24
+ import "./chunks/chunk-5NZRT7GL.js";
25
+ import "./chunks/chunk-TLWXLNLY.js";
25
26
  import "./chunks/chunk-3YBP46PB.js";
26
27
  import "./chunks/chunk-VACK24HF.js";
27
28
  import "./chunks/chunk-CPMHA4W5.js";
@@ -9,19 +9,20 @@ import {
9
9
  schemeColor,
10
10
  schemeCss,
11
11
  schemeRgb
12
- } from "./chunks/chunk-2XEAITWM.js";
13
- import "./chunks/chunk-JGHZ3N34.js";
12
+ } from "./chunks/chunk-I5SGYTRM.js";
13
+ import "./chunks/chunk-VB4IXIPM.js";
14
14
  import "./chunks/chunk-G2FD7S3C.js";
15
15
  import "./chunks/chunk-GQZVR5DW.js";
16
- import "./chunks/chunk-OYCQVJYY.js";
17
- import "./chunks/chunk-BW2NMXRV.js";
16
+ import "./chunks/chunk-XTF2VWJN.js";
17
+ import "./chunks/chunk-3UGWYQNY.js";
18
18
  import "./chunks/chunk-ZANALBSX.js";
19
19
  import "./chunks/chunk-VX656OAZ.js";
20
- import "./chunks/chunk-T3H5ELLA.js";
20
+ import "./chunks/chunk-FU57ZNRQ.js";
21
21
  import "./chunks/chunk-HMXCN6PG.js";
22
22
  import "./chunks/chunk-AB35TJST.js";
23
23
  import "./chunks/chunk-2VMKQKVO.js";
24
- import "./chunks/chunk-DV5B5UU7.js";
24
+ import "./chunks/chunk-5NZRT7GL.js";
25
+ import "./chunks/chunk-TLWXLNLY.js";
25
26
  import "./chunks/chunk-3YBP46PB.js";
26
27
  import "./chunks/chunk-VACK24HF.js";
27
28
  import "./chunks/chunk-CPMHA4W5.js";