@jbrowse/bandage-core 9.9.2 → 10.0.0

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 (79) hide show
  1. package/README.md +3 -0
  2. package/dist/bubbles/popBubble.js +3 -2
  3. package/dist/bubbles/superbubbles.js +5 -4
  4. package/dist/chunks/{chunk-YAN2ZPNV.js → chunk-33T67FPZ.js} +1 -1
  5. package/dist/chunks/{chunk-TOVOJNT7.js → chunk-3APK25GI.js} +1 -1
  6. package/dist/chunks/{chunk-A6PSWTLX.js → chunk-4QTNXTGW.js} +1 -1
  7. package/dist/chunks/{chunk-ROQGMTFB.js → chunk-BEWLQADP.js} +6 -6
  8. package/dist/chunks/{chunk-BQ33OOLC.js → chunk-CDPYXHVR.js} +1 -1
  9. package/dist/chunks/{chunk-YS7VA5SI.js → chunk-DCJC32QW.js} +1 -1
  10. package/dist/chunks/{chunk-YGN4KL7W.js → chunk-E5UEYZWK.js} +1 -1
  11. package/dist/chunks/{chunk-IGJCTPFB.js → chunk-EMUUNWRU.js} +52 -43
  12. package/dist/chunks/{chunk-PIN7ZMTZ.js → chunk-EU6FBTQF.js} +4 -4
  13. package/dist/chunks/{chunk-WVBYR6Y7.js → chunk-FG762CCP.js} +3 -8
  14. package/dist/chunks/{chunk-73RSLGZT.js → chunk-FLFBYSJO.js} +1 -1
  15. package/dist/chunks/{chunk-IJRNMO4D.js → chunk-ICXMWYOA.js} +5 -5
  16. package/dist/chunks/{chunk-HOZI3FBG.js → chunk-IM4SJUPO.js} +12 -22
  17. package/dist/chunks/{chunk-6PYZYBBF.js → chunk-KAN2WTG5.js} +1 -1
  18. package/dist/chunks/{chunk-RK3MF4FD.js → chunk-KJYSOHVN.js} +1 -1
  19. package/dist/chunks/{chunk-F4BKWWLS.js → chunk-NP356MC2.js} +4 -4
  20. package/dist/chunks/{chunk-KJEMKHVB.js → chunk-OEPCRURR.js} +1 -1
  21. package/dist/chunks/{chunk-ZBLKAWSD.js → chunk-OOLNLCIO.js} +1 -1
  22. package/dist/chunks/chunk-OPPVSPEF.js +57 -0
  23. package/dist/chunks/{chunk-OA7RIMZ2.js → chunk-PSMKPSO4.js} +89 -22
  24. package/dist/chunks/chunk-Q6IOQP4J.js +292 -0
  25. package/dist/chunks/{chunk-LTUWJKHD.js → chunk-Q7LYHGGQ.js} +114 -6
  26. package/dist/chunks/{chunk-EE37PVQY.js → chunk-QIVPRZ4H.js} +12 -7
  27. package/dist/chunks/{chunk-J7YKQ5YW.js → chunk-QXAB2FLJ.js} +1 -1
  28. package/dist/chunks/chunk-RAEABQNW.js +227 -0
  29. package/dist/chunks/{chunk-EDASNMLY.js → chunk-REE4GUDM.js} +4 -4
  30. package/dist/chunks/{chunk-IZ3W5IU2.js → chunk-RJXPPYA7.js} +36 -36
  31. package/dist/chunks/{chunk-F5BYHLIN.js → chunk-VOWI544A.js} +1 -1
  32. package/dist/chunks/{chunk-P6O4RSOQ.js → chunk-VZNKA3K2.js} +5 -5
  33. package/dist/chunks/{chunk-FPTI3WAV.js → chunk-W4GZCVUK.js} +18 -13
  34. package/dist/chunks/{chunk-MECWJY2R.js → chunk-WI7ZHJ27.js} +5 -5
  35. package/dist/cli/figure.js +50 -48
  36. package/dist/cli/fold.js +8 -6
  37. package/dist/figure.js +31 -29
  38. package/dist/figureData.js +63 -0
  39. package/dist/figureSettings.js +9 -7
  40. package/dist/gbzCut.js +3 -2
  41. package/dist/gbzWindow.js +6 -1
  42. package/dist/gfa/gfaConverter.js +3 -2
  43. package/dist/gfa/graphTables.js +2 -1
  44. package/dist/index.js +173 -156
  45. package/dist/layout/forceCache.js +9 -7
  46. package/dist/layout/smoothChains.js +6 -0
  47. package/dist/layout/trimToWindow.js +17 -23
  48. package/dist/layout/tubeMapLayout.js +5 -4
  49. package/dist/layout/walkRowDraw.js +10 -9
  50. package/dist/layout/walkRowLayout.js +4 -3
  51. package/dist/layout/walkRows.js +3 -2
  52. package/dist/layout/walkStrip.js +11 -10
  53. package/dist/layoutModes.js +11 -10
  54. package/dist/pathAnchoring.js +2 -1
  55. package/dist/pathColors.js +4 -3
  56. package/dist/pathVisits.js +8 -0
  57. package/dist/pipeline.js +8 -6
  58. package/dist/referenceRampCss.js +8 -7
  59. package/dist/referenceStrip.js +8 -7
  60. package/dist/renderer/GeometryBuilder.js +7 -6
  61. package/dist/tubeMap/bundle.js +6 -5
  62. package/dist/tubeMap/coarsen.js +17 -15
  63. package/dist/tubeMap/draw.js +4 -3
  64. package/dist/tubeMap/nodeColors.js +8 -7
  65. package/dist/types/figureData.d.ts +146 -0
  66. package/dist/types/gbzWindow.d.ts +15 -1
  67. package/dist/types/gfa/gfaConverter.d.ts +1 -1
  68. package/dist/types/index.d.ts +4 -1
  69. package/dist/types/layout/deletionRoutes.d.ts +1 -1
  70. package/dist/types/layout/smoothChains.d.ts +2 -0
  71. package/dist/types/pathAnchoring.d.ts +3 -2
  72. package/dist/types/pathVisits.d.ts +64 -0
  73. package/dist/types/types.d.ts +2 -1
  74. package/dist/types/version.d.ts +1 -1
  75. package/dist/version.js +1 -1
  76. package/dist/viewport.js +9 -7
  77. package/dist/walkEncoding.js +8 -7
  78. package/dist/walkHighlight.js +9 -8
  79. package/package.json +1 -1
package/dist/index.js CHANGED
@@ -1,26 +1,35 @@
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  import {
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  wheelZoomFactor
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  } from "./chunks/chunk-TDQLINVI.js";
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+ import {
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+ connectorAt,
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+ drawLitConnector,
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+ drawTubeMapConnectors,
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+ tubeMapConnectors
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+ } from "./chunks/chunk-2ZT7ZF7A.js";
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+ import {
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+ drawTubeMap,
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+ drawTubeMapHighlight,
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+ tubeMapMismatchAt,
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+ tubeMapPicture,
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+ tubeMapTrackAt
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+ } from "./chunks/chunk-EU6FBTQF.js";
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  import {
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  tubeMapFrame,
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  tubeMapNodeAt
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  } from "./chunks/chunk-2CMYNW3E.js";
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+ import {
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+ referenceKnots,
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+ warpX
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+ } from "./chunks/chunk-HK5Y2YWV.js";
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  import {
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  drawTubeMapGenes,
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  tubeMapGenes
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  } from "./chunks/chunk-WEDZ76AK.js";
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+ import "./chunks/chunk-XXT2JCAC.js";
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  import {
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  tubeMapNodeColors
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- } from "./chunks/chunk-KJEMKHVB.js";
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- import {
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- bundleRoutes
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- } from "./chunks/chunk-WVBYR6Y7.js";
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- import {
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- connectorAt,
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- drawLitConnector,
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- drawTubeMapConnectors,
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- tubeMapConnectors
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- } from "./chunks/chunk-2ZT7ZF7A.js";
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+ } from "./chunks/chunk-OEPCRURR.js";
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  import {
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  drawTubeMapRuler,
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  referenceBoxes,
@@ -28,27 +37,21 @@ import {
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  tubeX
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  } from "./chunks/chunk-BPRXQ2SS.js";
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  import {
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- drawTubeMap,
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- drawTubeMapHighlight,
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- tubeMapMismatchAt,
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- tubeMapPicture,
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- tubeMapTrackAt
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- } from "./chunks/chunk-PIN7ZMTZ.js";
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- import "./chunks/chunk-XXT2JCAC.js";
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- import {
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- referenceKnots,
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- warpX
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- } from "./chunks/chunk-HK5Y2YWV.js";
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+ bundleRoutes
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+ } from "./chunks/chunk-FG762CCP.js";
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  import {
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  createForceLayoutCache
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- } from "./chunks/chunk-YAN2ZPNV.js";
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+ } from "./chunks/chunk-33T67FPZ.js";
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  import {
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  graphBubbles,
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  superbubblesFromGraph
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- } from "./chunks/chunk-ROQGMTFB.js";
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+ } from "./chunks/chunk-BEWLQADP.js";
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+ import {
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+ bubblesFromGraph
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+ } from "./chunks/chunk-CLOP7UVD.js";
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  import {
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  bubbleSubgraph
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- } from "./chunks/chunk-A6PSWTLX.js";
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+ } from "./chunks/chunk-4QTNXTGW.js";
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  import {
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  genesFromBed,
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  genesFromGff3Lines,
@@ -64,65 +67,27 @@ import {
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  bubbleSegmentIds,
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  classifyBubble
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  } from "./chunks/chunk-XKWD2RY3.js";
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- import {
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- bubblesFromGraph
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- } from "./chunks/chunk-CLOP7UVD.js";
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  import "./chunks/chunk-FX4RDMDN.js";
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  import {
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  REFERENCE_STRIP_ZONE_PX,
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  drawReferenceStrip,
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  referenceStripBlocks,
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  stripBlockAt
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- } from "./chunks/chunk-RK3MF4FD.js";
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- import {
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- LAYOUT_ENGINES,
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- layoutEngine
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- } from "./chunks/chunk-VK6XMP6B.js";
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- import {
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- stressLayout
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- } from "./chunks/chunk-Q6FRNVDU.js";
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- import "./chunks/chunk-LYJ4US66.js";
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- import {
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- FORCE_LAYOUT_LABEL,
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- LAYOUT_MODES,
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- layoutModeByValue,
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- modeUsesLayoutEngine
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- } from "./chunks/chunk-IJRNMO4D.js";
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- import "./chunks/chunk-LOEA5IHZ.js";
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- import "./chunks/chunk-HOZI3FBG.js";
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- import "./chunks/chunk-CWFNEKST.js";
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- import "./chunks/chunk-L3O7AWLI.js";
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- import "./chunks/chunk-TZFWUT2C.js";
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- import "./chunks/chunk-C44YRP5F.js";
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- import "./chunks/chunk-RVS2QCOX.js";
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- import "./chunks/chunk-HNQPEMYE.js";
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+ } from "./chunks/chunk-KJYSOHVN.js";
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  import {
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  LAYOUT_QUALITIES
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  } from "./chunks/chunk-K5SIJGAE.js";
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  import {
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- loadBandage
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- } from "./chunks/chunk-7XHHVYG7.js";
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- import {
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- HPRC_GBZ,
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- cutGbzRegion,
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- openGbz,
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- parseRegion
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- } from "./chunks/chunk-73RSLGZT.js";
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- import {
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- cutWindowGFA,
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- haplotypeWanted,
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- referencePathQuery,
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- referenceSamplesOf,
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- resolveReferenceSample
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- } from "./chunks/chunk-LTUWJKHD.js";
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- import "./chunks/chunk-WSIFAZU7.js";
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+ FIGURE_DEFAULTS,
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+ figureSpecSettings
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+ } from "./chunks/chunk-E5UEYZWK.js";
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  import {
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  edgeHoverText,
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  regionLabel
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  } from "./chunks/chunk-AZFVORTC.js";
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  import {
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  figureSvg
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- } from "./chunks/chunk-IZ3W5IU2.js";
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+ } from "./chunks/chunk-RJXPPYA7.js";
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  import {
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  svgCanvas
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  } from "./chunks/chunk-47DYCZOK.js";
@@ -137,16 +102,7 @@ import {
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  walkStripApplies,
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  walkStripFrame,
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  walkStripLabelsTree
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- } from "./chunks/chunk-MECWJY2R.js";
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- import {
142
- Canvas2DRenderer
143
- } from "./chunks/chunk-WBCOREDZ.js";
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- import {
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- getDpr
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- } from "./chunks/chunk-4BYTEJGW.js";
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- import {
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- layoutGeometryInputs
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- } from "./chunks/chunk-LOCJN3BZ.js";
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+ } from "./chunks/chunk-WI7ZHJ27.js";
150
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  import {
151
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  BAR_PX,
152
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  CALL_TICK,
@@ -173,15 +129,93 @@ import {
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  walkRowsKey,
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  walkRowsKeyTree,
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  walkRowsTree
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- } from "./chunks/chunk-P6O4RSOQ.js";
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+ } from "./chunks/chunk-VZNKA3K2.js";
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  import {
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- genePins
179
- } from "./chunks/chunk-BUBZ32IC.js";
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+ Canvas2DRenderer
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+ } from "./chunks/chunk-WBCOREDZ.js";
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+ import {
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+ getDpr
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+ } from "./chunks/chunk-4BYTEJGW.js";
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  import {
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  EXON_COLOR,
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  exonOutlineTree,
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  exonStretches
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  } from "./chunks/chunk-3S3YVOJ7.js";
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+ import {
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+ genePins
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+ } from "./chunks/chunk-BUBZ32IC.js";
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+ import {
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+ RAMP_GRADIENT_CSS,
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+ rampHue,
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+ rampHueCss,
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+ rampStops
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+ } from "./chunks/chunk-DCJC32QW.js";
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+ import {
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+ HALO_FACTOR,
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+ LEGEND_INSET_PX,
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+ geneCoverageNote,
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+ layoutLabels
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+ } from "./chunks/chunk-DRG4236Y.js";
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+ import {
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+ findHoveredEdge,
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+ findHoveredNode
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+ } from "./chunks/chunk-FP4H7SFT.js";
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+ import "./chunks/chunk-MLSWIMZO.js";
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+ import {
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+ el,
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+ serializeEl
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+ } from "./chunks/chunk-NNODIW4U.js";
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+ import {
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+ figureData,
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+ gfaFigureData
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+ } from "./chunks/chunk-Q6IOQP4J.js";
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+ import {
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+ LAYOUT_ENGINES,
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+ layoutEngine
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+ } from "./chunks/chunk-VK6XMP6B.js";
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+ import {
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+ stressLayout
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+ } from "./chunks/chunk-Q6FRNVDU.js";
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+ import "./chunks/chunk-LYJ4US66.js";
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+ import {
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+ FORCE_LAYOUT_LABEL,
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+ LAYOUT_MODES,
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+ layoutModeByValue,
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+ modeUsesLayoutEngine
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+ } from "./chunks/chunk-ICXMWYOA.js";
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+ import "./chunks/chunk-IM4SJUPO.js";
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+ import "./chunks/chunk-CWFNEKST.js";
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+ import "./chunks/chunk-LOEA5IHZ.js";
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+ import "./chunks/chunk-L3O7AWLI.js";
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+ import "./chunks/chunk-TZFWUT2C.js";
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+ import "./chunks/chunk-HNQPEMYE.js";
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+ import "./chunks/chunk-C44YRP5F.js";
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+ import "./chunks/chunk-RVS2QCOX.js";
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+ import {
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+ loadBandage
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+ } from "./chunks/chunk-7XHHVYG7.js";
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+ import {
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+ HPRC_GBZ,
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+ cutGbzRegion,
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+ openGbz,
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+ parseRegion
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+ } from "./chunks/chunk-FLFBYSJO.js";
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+ import {
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+ compactTables,
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+ cutWindowGFA,
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+ cutWindowTables,
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+ haplotypeWanted,
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+ referencePathQuery,
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+ referenceSamplesOf,
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+ resolveReferenceSample
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+ } from "./chunks/chunk-Q7LYHGGQ.js";
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+ import "./chunks/chunk-WSIFAZU7.js";
213
+ import {
214
+ layoutGeometryInputs
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+ } from "./chunks/chunk-LOCJN3BZ.js";
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+ import {
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+ version
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+ } from "./chunks/chunk-CDPYXHVR.js";
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  import {
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  axisScaleOf,
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  contains,
@@ -189,12 +223,12 @@ import {
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  screenToLayout,
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  viewportOf,
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  zoomAbout
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- } from "./chunks/chunk-ZBLKAWSD.js";
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+ } from "./chunks/chunk-OOLNLCIO.js";
193
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  import {
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  facetLifts,
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  walkHighlight,
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  walkLift
197
- } from "./chunks/chunk-EE37PVQY.js";
231
+ } from "./chunks/chunk-QIVPRZ4H.js";
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  import {
199
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  WALK_FIELDS,
200
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  WALK_SCHEMES,
@@ -202,40 +236,32 @@ import {
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  encodingSwatchCss,
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  resolveEncoding,
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  schemeCss
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- } from "./chunks/chunk-F5BYHLIN.js";
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+ } from "./chunks/chunk-VOWI544A.js";
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  import {
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  rangeText,
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  walkKey,
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  walkPosition
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  } from "./chunks/chunk-2LQ5BWT7.js";
211
- import {
212
- RAMP_GRADIENT_CSS,
213
- rampHue,
214
- rampHueCss,
215
- rampStops
216
- } from "./chunks/chunk-YS7VA5SI.js";
217
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  import {
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  REFERENCE_RAMP_MAX_HUE,
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  buildGeometry,
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  computeReferenceRamp
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- } from "./chunks/chunk-F4BKWWLS.js";
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+ } from "./chunks/chunk-NP356MC2.js";
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  import "./chunks/chunk-G2FD7S3C.js";
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- import {
224
- version
225
- } from "./chunks/chunk-BQ33OOLC.js";
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+ import "./chunks/chunk-WFB5TXRA.js";
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  import {
227
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  walkRowLabels,
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  walkRowsExtent
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- } from "./chunks/chunk-TOVOJNT7.js";
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+ } from "./chunks/chunk-3APK25GI.js";
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  import {
231
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  filterSamples,
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  walkRows
233
- } from "./chunks/chunk-6PYZYBBF.js";
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+ } from "./chunks/chunk-KAN2WTG5.js";
234
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  import {
235
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  pathColorsLegible,
236
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  pathLegend,
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  walkLabelsOf
238
- } from "./chunks/chunk-EDASNMLY.js";
264
+ } from "./chunks/chunk-REE4GUDM.js";
239
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  import {
240
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  NODE_WIDTHS,
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  maxNodeWidthPx,
@@ -243,57 +269,6 @@ import {
243
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  nodeInk,
244
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  nodeWidthPx
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  } from "./chunks/chunk-PBENCR5L.js";
246
- import {
247
- WELL_KNOWN_SAMPLES,
248
- assemblyWalk,
249
- backboneAssembly,
250
- featuresOnBackbone,
251
- graphBackbone,
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- refNameBinding,
253
- referenceLabel,
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- wellKnownSample
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- } from "./chunks/chunk-RAKOB6IV.js";
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- import {
257
- HALO_FACTOR,
258
- LEGEND_INSET_PX,
259
- geneCoverageNote,
260
- layoutLabels
261
- } from "./chunks/chunk-DRG4236Y.js";
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- import {
263
- findHoveredEdge,
264
- findHoveredNode
265
- } from "./chunks/chunk-FP4H7SFT.js";
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- import "./chunks/chunk-MLSWIMZO.js";
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- import "./chunks/chunk-WFB5TXRA.js";
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- import {
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- formatBp
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- } from "./chunks/chunk-3ZZSX5HN.js";
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- import {
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- LABEL_CHAR_PX,
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- LABEL_PAD,
274
- LABEL_PX
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- } from "./chunks/chunk-AB35TJST.js";
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- import {
277
- COLOR_SCHEMES,
278
- resolveColorScheme
279
- } from "./chunks/chunk-JKJWSY4V.js";
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- import {
281
- el,
282
- serializeEl
283
- } from "./chunks/chunk-NNODIW4U.js";
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- import {
285
- FACET_FIELDS,
286
- FACET_GAP_PX,
287
- FACET_PAD_PX,
288
- FACET_TITLE_PX,
289
- facetCells,
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- facetGrid,
291
- facetSettingOf
292
- } from "./chunks/chunk-XV4P5KEQ.js";
293
- import {
294
- FIGURE_DEFAULTS,
295
- figureSpecSettings
296
- } from "./chunks/chunk-YGN4KL7W.js";
297
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  import {
298
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  ENGINE_DEFAULTS,
299
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  FIT_PADDING,
@@ -306,32 +281,59 @@ import {
306
281
  forceLayout,
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  layoutExtent,
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  loadGraph
309
- } from "./chunks/chunk-FPTI3WAV.js";
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- import "./chunks/chunk-PUG7LXDF.js";
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+ } from "./chunks/chunk-W4GZCVUK.js";
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  import "./chunks/chunk-IGVV37VI.js";
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- import "./chunks/chunk-J7YKQ5YW.js";
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- import {
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- gfaTables
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- } from "./chunks/chunk-G45YY72K.js";
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+ import "./chunks/chunk-OPPVSPEF.js";
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+ import "./chunks/chunk-PUG7LXDF.js";
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+ import "./chunks/chunk-QXAB2FLJ.js";
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+ import "./chunks/chunk-QYBZZI5H.js";
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  import {
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  graphFromTables,
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  graphTablesGFA
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- } from "./chunks/chunk-OA7RIMZ2.js";
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- import "./chunks/chunk-QYBZZI5H.js";
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+ } from "./chunks/chunk-PSMKPSO4.js";
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  import "./chunks/chunk-CDLPYR5O.js";
322
295
  import "./chunks/chunk-JVLURPFW.js";
296
+ import "./chunks/chunk-EMUUNWRU.js";
297
+ import {
298
+ PathVisits,
299
+ PathVisitsBuilder
300
+ } from "./chunks/chunk-RAEABQNW.js";
323
301
  import "./chunks/chunk-ES2N6V56.js";
324
- import "./chunks/chunk-IGJCTPFB.js";
302
+ import {
303
+ WELL_KNOWN_SAMPLES,
304
+ assemblyWalk,
305
+ backboneAssembly,
306
+ featuresOnBackbone,
307
+ graphBackbone,
308
+ refNameBinding,
309
+ referenceLabel,
310
+ wellKnownSample
311
+ } from "./chunks/chunk-RAKOB6IV.js";
312
+ import {
313
+ gfaTables
314
+ } from "./chunks/chunk-G45YY72K.js";
325
315
  import {
326
316
  panSNContig,
327
317
  panSNHaplotype,
328
318
  panSNSample
329
319
  } from "./chunks/chunk-BPLIXMH7.js";
320
+ import {
321
+ formatBp
322
+ } from "./chunks/chunk-3ZZSX5HN.js";
323
+ import {
324
+ LABEL_CHAR_PX,
325
+ LABEL_PAD,
326
+ LABEL_PX
327
+ } from "./chunks/chunk-AB35TJST.js";
330
328
  import "./chunks/chunk-TAMCZHLW.js";
331
329
  import {
332
330
  BUBBLE_SPREADS
333
331
  } from "./chunks/chunk-UVBGRJQX.js";
334
332
  import "./chunks/chunk-6JEWNXCQ.js";
333
+ import {
334
+ COLOR_SCHEMES,
335
+ resolveColorScheme
336
+ } from "./chunks/chunk-JKJWSY4V.js";
335
337
  import {
336
338
  deletionDrawing,
337
339
  deletionEdges
@@ -341,6 +343,15 @@ import {
341
343
  ROW_HEIGHT_PX
342
344
  } from "./chunks/chunk-CPMHA4W5.js";
343
345
  import "./chunks/chunk-FYQWPEEY.js";
346
+ import {
347
+ FACET_FIELDS,
348
+ FACET_GAP_PX,
349
+ FACET_PAD_PX,
350
+ FACET_TITLE_PX,
351
+ facetCells,
352
+ facetGrid,
353
+ facetSettingOf
354
+ } from "./chunks/chunk-XV4P5KEQ.js";
344
355
  export {
345
356
  BUBBLE_KIND_COLORS,
346
357
  BUBBLE_KIND_NAMES,
@@ -367,6 +378,8 @@ export {
367
378
  LAYOUT_QUALITIES,
368
379
  LEGEND_INSET_PX,
369
380
  NODE_WIDTHS,
381
+ PathVisits,
382
+ PathVisitsBuilder,
370
383
  RAMP_GRADIENT_CSS,
371
384
  REFERENCE_RAMP_MAX_HUE,
372
385
  REFERENCE_STRIP_ZONE_PX,
@@ -398,12 +411,14 @@ export {
398
411
  clampZoom,
399
412
  classifyBubble,
400
413
  coalesceRuns,
414
+ compactTables,
401
415
  computeReferenceRamp,
402
416
  connectorAt,
403
417
  contains,
404
418
  createForceLayoutCache,
405
419
  cutGbzRegion,
406
420
  cutWindowGFA,
421
+ cutWindowTables,
407
422
  cutsWholeWalks,
408
423
  deletionDrawing,
409
424
  deletionEdges,
@@ -429,6 +444,7 @@ export {
429
444
  facetLifts,
430
445
  facetSettingOf,
431
446
  featuresOnBackbone,
447
+ figureData,
432
448
  figureSpecSettings,
433
449
  figureSvg,
434
450
  filterSamples,
@@ -444,6 +460,7 @@ export {
444
460
  genesFromText,
445
461
  genesOnRow,
446
462
  getDpr,
463
+ gfaFigureData,
447
464
  gfaTables,
448
465
  graphBackbone,
449
466
  graphBubbles,
@@ -1,17 +1,19 @@
1
1
  import {
2
2
  createForceLayoutCache
3
- } from "../chunks/chunk-YAN2ZPNV.js";
4
- import "../chunks/chunk-FPTI3WAV.js";
5
- import "../chunks/chunk-PUG7LXDF.js";
3
+ } from "../chunks/chunk-33T67FPZ.js";
4
+ import "../chunks/chunk-W4GZCVUK.js";
6
5
  import "../chunks/chunk-IGVV37VI.js";
7
- import "../chunks/chunk-J7YKQ5YW.js";
8
- import "../chunks/chunk-G45YY72K.js";
9
- import "../chunks/chunk-OA7RIMZ2.js";
6
+ import "../chunks/chunk-OPPVSPEF.js";
7
+ import "../chunks/chunk-PUG7LXDF.js";
8
+ import "../chunks/chunk-QXAB2FLJ.js";
10
9
  import "../chunks/chunk-QYBZZI5H.js";
10
+ import "../chunks/chunk-PSMKPSO4.js";
11
11
  import "../chunks/chunk-CDLPYR5O.js";
12
12
  import "../chunks/chunk-JVLURPFW.js";
13
+ import "../chunks/chunk-EMUUNWRU.js";
14
+ import "../chunks/chunk-RAEABQNW.js";
13
15
  import "../chunks/chunk-ES2N6V56.js";
14
- import "../chunks/chunk-IGJCTPFB.js";
16
+ import "../chunks/chunk-G45YY72K.js";
15
17
  import "../chunks/chunk-BPLIXMH7.js";
16
18
  import "../chunks/chunk-TAMCZHLW.js";
17
19
  import "../chunks/chunk-UVBGRJQX.js";
@@ -0,0 +1,6 @@
1
+ import {
2
+ smoothChain
3
+ } from "../chunks/chunk-OPPVSPEF.js";
4
+ export {
5
+ smoothChain
6
+ };
@@ -1,7 +1,10 @@
1
1
  import {
2
2
  pathOrigin,
3
3
  trimOrigins
4
- } from "../chunks/chunk-IGJCTPFB.js";
4
+ } from "../chunks/chunk-EMUUNWRU.js";
5
+ import {
6
+ PathVisitsBuilder
7
+ } from "../chunks/chunk-RAEABQNW.js";
5
8
  import "../chunks/chunk-BPLIXMH7.js";
6
9
  import {
7
10
  isBackbone,
@@ -64,35 +67,26 @@ function trimToWindow(graph, window) {
64
67
  };
65
68
  }
66
69
  function trimVisits(visits, paths, spans, nameOf) {
67
- const cursor = /* @__PURE__ */ new Map();
68
- const out = /* @__PURE__ */ new Map();
70
+ const next = visits.replay();
71
+ const out = new PathVisitsBuilder();
69
72
  paths.forEach((path, p) => {
70
- const origin = pathOrigin(path.name).name;
73
+ const origin = visits.pathIndex(pathOrigin(path.name).name);
71
74
  const span = spans[p];
72
75
  path.nodeIds.forEach((id, i) => {
73
76
  const segment = nameOf.get(id) ?? id;
74
- const list = visits.get(segment);
75
- if (!list) {
76
- return;
77
- }
78
- const key = `${origin} ${segment}`;
79
- let at = cursor.get(key) ?? 0;
80
- while (at < list.length && list[at].path !== origin) {
81
- at++;
82
- }
83
- const visit = list[at];
84
- cursor.set(key, at + 1);
85
- if (visit && span && i >= span.first && i <= span.last) {
86
- const keptVisits = out.get(segment);
87
- if (keptVisits) {
88
- keptVisits.push(visit);
89
- } else {
90
- out.set(segment, [visit]);
91
- }
77
+ const at = next(visits.slot(segment), origin);
78
+ if (at >= 0 && span && i >= span.first && i <= span.last) {
79
+ out.add(
80
+ segment,
81
+ visits.paths[origin],
82
+ visits.samples[origin],
83
+ visits.start[at],
84
+ visits.reversed[at] === 1
85
+ );
92
86
  }
93
87
  });
94
88
  });
95
- return out;
89
+ return out.build();
96
90
  }
97
91
  function clipToWindow(graph, window, reachBp) {
98
92
  const nodes = graph.nodes.map((node) => {
@@ -8,14 +8,15 @@ import {
8
8
  tubeMapReferenceLayout,
9
9
  tubeMapTracks,
10
10
  tubeWidth
11
- } from "../chunks/chunk-HOZI3FBG.js";
11
+ } from "../chunks/chunk-IM4SJUPO.js";
12
12
  import "../chunks/chunk-CWFNEKST.js";
13
13
  import "../chunks/chunk-C44YRP5F.js";
14
- import "../chunks/chunk-EDASNMLY.js";
14
+ import "../chunks/chunk-REE4GUDM.js";
15
+ import "../chunks/chunk-EMUUNWRU.js";
16
+ import "../chunks/chunk-RAEABQNW.js";
17
+ import "../chunks/chunk-BPLIXMH7.js";
15
18
  import "../chunks/chunk-3ZZSX5HN.js";
16
19
  import "../chunks/chunk-AB35TJST.js";
17
- import "../chunks/chunk-IGJCTPFB.js";
18
- import "../chunks/chunk-BPLIXMH7.js";
19
20
  import "../chunks/chunk-TAMCZHLW.js";
20
21
  import "../chunks/chunk-N6FECAXP.js";
21
22
  import "../chunks/chunk-2CVHXFK7.js";
@@ -26,19 +26,20 @@ import {
26
26
  walkRowsKey,
27
27
  walkRowsKeyTree,
28
28
  walkRowsTree
29
- } from "../chunks/chunk-P6O4RSOQ.js";
30
- import "../chunks/chunk-YS7VA5SI.js";
31
- import "../chunks/chunk-F4BKWWLS.js";
29
+ } from "../chunks/chunk-VZNKA3K2.js";
30
+ import "../chunks/chunk-DCJC32QW.js";
31
+ import "../chunks/chunk-NNODIW4U.js";
32
+ import "../chunks/chunk-NP356MC2.js";
32
33
  import "../chunks/chunk-G2FD7S3C.js";
33
- import "../chunks/chunk-EDASNMLY.js";
34
- import "../chunks/chunk-PBENCR5L.js";
35
34
  import "../chunks/chunk-WFB5TXRA.js";
36
- import "../chunks/chunk-3ZZSX5HN.js";
37
- import "../chunks/chunk-AB35TJST.js";
38
- import "../chunks/chunk-NNODIW4U.js";
35
+ import "../chunks/chunk-REE4GUDM.js";
36
+ import "../chunks/chunk-PBENCR5L.js";
37
+ import "../chunks/chunk-EMUUNWRU.js";
38
+ import "../chunks/chunk-RAEABQNW.js";
39
39
  import "../chunks/chunk-ES2N6V56.js";
40
- import "../chunks/chunk-IGJCTPFB.js";
41
40
  import "../chunks/chunk-BPLIXMH7.js";
41
+ import "../chunks/chunk-3ZZSX5HN.js";
42
+ import "../chunks/chunk-AB35TJST.js";
42
43
  import "../chunks/chunk-TAMCZHLW.js";
43
44
  import "../chunks/chunk-N6FECAXP.js";
44
45
  import "../chunks/chunk-2CVHXFK7.js";
@@ -2,9 +2,10 @@ import {
2
2
  walkRowLabels,
3
3
  walkRowLayout,
4
4
  walkRowsExtent
5
- } from "../chunks/chunk-TOVOJNT7.js";
6
- import "../chunks/chunk-6PYZYBBF.js";
7
- import "../chunks/chunk-IGJCTPFB.js";
5
+ } from "../chunks/chunk-3APK25GI.js";
6
+ import "../chunks/chunk-KAN2WTG5.js";
7
+ import "../chunks/chunk-EMUUNWRU.js";
8
+ import "../chunks/chunk-RAEABQNW.js";
8
9
  import "../chunks/chunk-BPLIXMH7.js";
9
10
  import "../chunks/chunk-CPMHA4W5.js";
10
11
  import "../chunks/chunk-FYQWPEEY.js";
@@ -1,8 +1,9 @@
1
1
  import {
2
2
  filterSamples,
3
3
  walkRows
4
- } from "../chunks/chunk-6PYZYBBF.js";
5
- import "../chunks/chunk-IGJCTPFB.js";
4
+ } from "../chunks/chunk-KAN2WTG5.js";
5
+ import "../chunks/chunk-EMUUNWRU.js";
6
+ import "../chunks/chunk-RAEABQNW.js";
6
7
  import "../chunks/chunk-BPLIXMH7.js";
7
8
  import "../chunks/chunk-FYQWPEEY.js";
8
9
  export {