@jbrowse/bandage-core 9.10.0 → 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 (74) hide show
  1. package/dist/bubbles/popBubble.js +3 -2
  2. package/dist/bubbles/superbubbles.js +4 -3
  3. package/dist/chunks/{chunk-Q6UIUY6X.js → chunk-33T67FPZ.js} +1 -1
  4. package/dist/chunks/{chunk-TOVOJNT7.js → chunk-3APK25GI.js} +1 -1
  5. package/dist/chunks/{chunk-A6PSWTLX.js → chunk-4QTNXTGW.js} +1 -1
  6. package/dist/chunks/{chunk-5GZEPPEW.js → chunk-BEWLQADP.js} +1 -1
  7. package/dist/chunks/{chunk-2VTM3DHG.js → chunk-CDPYXHVR.js} +1 -1
  8. package/dist/chunks/{chunk-K5NYTPLC.js → chunk-DCJC32QW.js} +1 -1
  9. package/dist/chunks/{chunk-IZI7KIVX.js → chunk-E5UEYZWK.js} +1 -1
  10. package/dist/chunks/{chunk-IGJCTPFB.js → chunk-EMUUNWRU.js} +52 -43
  11. package/dist/chunks/{chunk-PIN7ZMTZ.js → chunk-EU6FBTQF.js} +4 -4
  12. package/dist/chunks/{chunk-LZWSZRUY.js → chunk-FG762CCP.js} +3 -8
  13. package/dist/chunks/{chunk-73RSLGZT.js → chunk-FLFBYSJO.js} +1 -1
  14. package/dist/chunks/{chunk-FUUJ76KD.js → chunk-ICXMWYOA.js} +5 -5
  15. package/dist/chunks/{chunk-CXKZYLYS.js → chunk-IM4SJUPO.js} +12 -22
  16. package/dist/chunks/{chunk-6PYZYBBF.js → chunk-KAN2WTG5.js} +1 -1
  17. package/dist/chunks/{chunk-BDWQQK33.js → chunk-KJYSOHVN.js} +1 -1
  18. package/dist/chunks/{chunk-4IYP43W6.js → chunk-NP356MC2.js} +1 -1
  19. package/dist/chunks/{chunk-TFAFIRZB.js → chunk-OEPCRURR.js} +1 -1
  20. package/dist/chunks/{chunk-PT37VS5B.js → chunk-OOLNLCIO.js} +1 -1
  21. package/dist/chunks/{chunk-OA7RIMZ2.js → chunk-PSMKPSO4.js} +89 -22
  22. package/dist/chunks/{chunk-NGODVSCA.js → chunk-Q6IOQP4J.js} +8 -8
  23. package/dist/chunks/{chunk-LTUWJKHD.js → chunk-Q7LYHGGQ.js} +114 -6
  24. package/dist/chunks/{chunk-MVMP6AGI.js → chunk-QIVPRZ4H.js} +12 -7
  25. package/dist/chunks/{chunk-J7YKQ5YW.js → chunk-QXAB2FLJ.js} +1 -1
  26. package/dist/chunks/chunk-RAEABQNW.js +227 -0
  27. package/dist/chunks/{chunk-XZ2BLAA6.js → chunk-REE4GUDM.js} +1 -1
  28. package/dist/chunks/{chunk-2FLBFVMO.js → chunk-RJXPPYA7.js} +13 -13
  29. package/dist/chunks/{chunk-KYY5363X.js → chunk-VOWI544A.js} +1 -1
  30. package/dist/chunks/{chunk-FJZ2TB46.js → chunk-VZNKA3K2.js} +2 -2
  31. package/dist/chunks/{chunk-HRAU4VTB.js → chunk-W4GZCVUK.js} +6 -6
  32. package/dist/chunks/{chunk-DMH4NL2M.js → chunk-WI7ZHJ27.js} +2 -2
  33. package/dist/cli/figure.js +24 -23
  34. package/dist/cli/fold.js +6 -5
  35. package/dist/figure.js +19 -18
  36. package/dist/figureData.js +20 -19
  37. package/dist/figureSettings.js +7 -6
  38. package/dist/gbzCut.js +3 -2
  39. package/dist/gbzWindow.js +6 -1
  40. package/dist/gfa/gfaConverter.js +3 -2
  41. package/dist/gfa/graphTables.js +2 -1
  42. package/dist/index.js +57 -47
  43. package/dist/layout/forceCache.js +7 -6
  44. package/dist/layout/trimToWindow.js +17 -23
  45. package/dist/layout/tubeMapLayout.js +4 -3
  46. package/dist/layout/walkRowDraw.js +6 -5
  47. package/dist/layout/walkRowLayout.js +4 -3
  48. package/dist/layout/walkRows.js +3 -2
  49. package/dist/layout/walkStrip.js +7 -6
  50. package/dist/layoutModes.js +8 -7
  51. package/dist/pathAnchoring.js +2 -1
  52. package/dist/pathColors.js +3 -2
  53. package/dist/pathVisits.js +8 -0
  54. package/dist/pipeline.js +6 -5
  55. package/dist/referenceRampCss.js +5 -4
  56. package/dist/referenceStrip.js +5 -4
  57. package/dist/renderer/GeometryBuilder.js +4 -3
  58. package/dist/tubeMap/bundle.js +5 -4
  59. package/dist/tubeMap/coarsen.js +15 -13
  60. package/dist/tubeMap/draw.js +4 -3
  61. package/dist/tubeMap/nodeColors.js +5 -4
  62. package/dist/types/gbzWindow.d.ts +15 -1
  63. package/dist/types/gfa/gfaConverter.d.ts +1 -1
  64. package/dist/types/index.d.ts +2 -1
  65. package/dist/types/layout/deletionRoutes.d.ts +1 -1
  66. package/dist/types/pathAnchoring.d.ts +3 -2
  67. package/dist/types/pathVisits.d.ts +64 -0
  68. package/dist/types/types.d.ts +2 -1
  69. package/dist/types/version.d.ts +1 -1
  70. package/dist/version.js +1 -1
  71. package/dist/viewport.js +7 -6
  72. package/dist/walkEncoding.js +5 -4
  73. package/dist/walkHighlight.js +6 -5
  74. package/package.json +1 -1
package/dist/cli/fold.js CHANGED
@@ -7,18 +7,19 @@ import {
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  } from "../chunks/chunk-B4645SM2.js";
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  import {
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  loadGraph
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- } from "../chunks/chunk-HRAU4VTB.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-OPPVSPEF.js";
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  import "../chunks/chunk-PUG7LXDF.js";
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- import "../chunks/chunk-J7YKQ5YW.js";
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- import "../chunks/chunk-G45YY72K.js";
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- import "../chunks/chunk-OA7RIMZ2.js";
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+ import "../chunks/chunk-QXAB2FLJ.js";
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  import "../chunks/chunk-QYBZZI5H.js";
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+ import "../chunks/chunk-PSMKPSO4.js";
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  import "../chunks/chunk-CDLPYR5O.js";
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  import "../chunks/chunk-JVLURPFW.js";
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- import "../chunks/chunk-IGJCTPFB.js";
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+ import "../chunks/chunk-EMUUNWRU.js";
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+ import "../chunks/chunk-RAEABQNW.js";
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  import "../chunks/chunk-ES2N6V56.js";
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+ import "../chunks/chunk-G45YY72K.js";
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  import "../chunks/chunk-BPLIXMH7.js";
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  import "../chunks/chunk-TAMCZHLW.js";
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  import "../chunks/chunk-UVBGRJQX.js";
package/dist/figure.js CHANGED
@@ -1,44 +1,45 @@
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  import {
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  figureSvg
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- } from "./chunks/chunk-2FLBFVMO.js";
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+ } from "./chunks/chunk-RJXPPYA7.js";
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  import "./chunks/chunk-47DYCZOK.js";
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- import "./chunks/chunk-DMH4NL2M.js";
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- import "./chunks/chunk-FJZ2TB46.js";
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+ import "./chunks/chunk-WI7ZHJ27.js";
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+ import "./chunks/chunk-VZNKA3K2.js";
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  import "./chunks/chunk-WBCOREDZ.js";
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  import "./chunks/chunk-4BYTEJGW.js";
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- import "./chunks/chunk-BUBZ32IC.js";
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  import "./chunks/chunk-3S3YVOJ7.js";
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- import "./chunks/chunk-K5NYTPLC.js";
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+ import "./chunks/chunk-BUBZ32IC.js";
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+ import "./chunks/chunk-DCJC32QW.js";
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  import "./chunks/chunk-DRG4236Y.js";
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  import "./chunks/chunk-FP4H7SFT.js";
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  import "./chunks/chunk-MLSWIMZO.js";
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  import "./chunks/chunk-NNODIW4U.js";
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  import "./chunks/chunk-LOCJN3BZ.js";
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- import "./chunks/chunk-2VTM3DHG.js";
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- import "./chunks/chunk-PT37VS5B.js";
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- import "./chunks/chunk-MVMP6AGI.js";
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- import "./chunks/chunk-KYY5363X.js";
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+ import "./chunks/chunk-CDPYXHVR.js";
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+ import "./chunks/chunk-OOLNLCIO.js";
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+ import "./chunks/chunk-QIVPRZ4H.js";
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+ import "./chunks/chunk-VOWI544A.js";
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  import "./chunks/chunk-2LQ5BWT7.js";
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- import "./chunks/chunk-4IYP43W6.js";
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+ import "./chunks/chunk-NP356MC2.js";
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  import "./chunks/chunk-G2FD7S3C.js";
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  import "./chunks/chunk-WFB5TXRA.js";
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- import "./chunks/chunk-TOVOJNT7.js";
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- import "./chunks/chunk-6PYZYBBF.js";
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- import "./chunks/chunk-XZ2BLAA6.js";
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+ import "./chunks/chunk-3APK25GI.js";
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+ import "./chunks/chunk-KAN2WTG5.js";
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+ import "./chunks/chunk-REE4GUDM.js";
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  import "./chunks/chunk-PBENCR5L.js";
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- import "./chunks/chunk-HRAU4VTB.js";
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+ import "./chunks/chunk-W4GZCVUK.js";
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  import "./chunks/chunk-IGVV37VI.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-J7YKQ5YW.js";
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- import "./chunks/chunk-G45YY72K.js";
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- import "./chunks/chunk-OA7RIMZ2.js";
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+ import "./chunks/chunk-QXAB2FLJ.js";
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  import "./chunks/chunk-QYBZZI5H.js";
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+ import "./chunks/chunk-PSMKPSO4.js";
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  import "./chunks/chunk-CDLPYR5O.js";
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  import "./chunks/chunk-JVLURPFW.js";
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- import "./chunks/chunk-IGJCTPFB.js";
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+ import "./chunks/chunk-EMUUNWRU.js";
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+ import "./chunks/chunk-RAEABQNW.js";
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  import "./chunks/chunk-ES2N6V56.js";
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  import "./chunks/chunk-RAKOB6IV.js";
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+ import "./chunks/chunk-G45YY72K.js";
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  import "./chunks/chunk-BPLIXMH7.js";
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  import "./chunks/chunk-3ZZSX5HN.js";
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  import "./chunks/chunk-AB35TJST.js";
@@ -1,49 +1,50 @@
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  import {
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  figureData,
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  gfaFigureData
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- } from "./chunks/chunk-NGODVSCA.js";
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+ } from "./chunks/chunk-Q6IOQP4J.js";
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  import "./chunks/chunk-VK6XMP6B.js";
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  import "./chunks/chunk-Q6FRNVDU.js";
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  import "./chunks/chunk-LYJ4US66.js";
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- import "./chunks/chunk-FUUJ76KD.js";
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- import "./chunks/chunk-LOEA5IHZ.js";
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- import "./chunks/chunk-CXKZYLYS.js";
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+ import "./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 "./chunks/chunk-7XHHVYG7.js";
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- import "./chunks/chunk-73RSLGZT.js";
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- import "./chunks/chunk-LTUWJKHD.js";
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+ import "./chunks/chunk-FLFBYSJO.js";
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+ import "./chunks/chunk-Q7LYHGGQ.js";
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  import "./chunks/chunk-WSIFAZU7.js";
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  import "./chunks/chunk-LOCJN3BZ.js";
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- import "./chunks/chunk-2VTM3DHG.js";
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- import "./chunks/chunk-PT37VS5B.js";
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- import "./chunks/chunk-MVMP6AGI.js";
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- import "./chunks/chunk-KYY5363X.js";
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+ import "./chunks/chunk-CDPYXHVR.js";
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+ import "./chunks/chunk-OOLNLCIO.js";
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+ import "./chunks/chunk-QIVPRZ4H.js";
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+ import "./chunks/chunk-VOWI544A.js";
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  import "./chunks/chunk-2LQ5BWT7.js";
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- import "./chunks/chunk-4IYP43W6.js";
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+ import "./chunks/chunk-NP356MC2.js";
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  import "./chunks/chunk-G2FD7S3C.js";
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  import "./chunks/chunk-WFB5TXRA.js";
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- import "./chunks/chunk-TOVOJNT7.js";
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- import "./chunks/chunk-6PYZYBBF.js";
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- import "./chunks/chunk-XZ2BLAA6.js";
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+ import "./chunks/chunk-3APK25GI.js";
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+ import "./chunks/chunk-KAN2WTG5.js";
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+ import "./chunks/chunk-REE4GUDM.js";
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  import "./chunks/chunk-PBENCR5L.js";
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- import "./chunks/chunk-HRAU4VTB.js";
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+ import "./chunks/chunk-W4GZCVUK.js";
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  import "./chunks/chunk-IGVV37VI.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-J7YKQ5YW.js";
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- import "./chunks/chunk-G45YY72K.js";
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- import "./chunks/chunk-OA7RIMZ2.js";
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+ import "./chunks/chunk-QXAB2FLJ.js";
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  import "./chunks/chunk-QYBZZI5H.js";
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+ import "./chunks/chunk-PSMKPSO4.js";
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  import "./chunks/chunk-CDLPYR5O.js";
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  import "./chunks/chunk-JVLURPFW.js";
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- import "./chunks/chunk-IGJCTPFB.js";
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+ import "./chunks/chunk-EMUUNWRU.js";
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+ import "./chunks/chunk-RAEABQNW.js";
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  import "./chunks/chunk-ES2N6V56.js";
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  import "./chunks/chunk-RAKOB6IV.js";
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+ import "./chunks/chunk-G45YY72K.js";
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@@ -1,19 +1,20 @@
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  import {
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  FIGURE_DEFAULTS,
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  figureSpecSettings
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- } from "./chunks/chunk-IZI7KIVX.js";
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- import "./chunks/chunk-HRAU4VTB.js";
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+ } from "./chunks/chunk-E5UEYZWK.js";
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+ import "./chunks/chunk-W4GZCVUK.js";
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- import "./chunks/chunk-J7YKQ5YW.js";
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- import "./chunks/chunk-G45YY72K.js";
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- import "./chunks/chunk-OA7RIMZ2.js";
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+ import "./chunks/chunk-QXAB2FLJ.js";
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+ import "./chunks/chunk-PSMKPSO4.js";
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- import "./chunks/chunk-IGJCTPFB.js";
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+ import "./chunks/chunk-EMUUNWRU.js";
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+ import "./chunks/chunk-RAEABQNW.js";
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+ import "./chunks/chunk-G45YY72K.js";
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package/dist/gbzCut.js CHANGED
@@ -4,10 +4,11 @@ import {
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  haplotypeIndexBeside,
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  openGbz,
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  parseRegion
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- } from "./chunks/chunk-73RSLGZT.js";
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- import "./chunks/chunk-LTUWJKHD.js";
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+ } from "./chunks/chunk-FLFBYSJO.js";
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+ import "./chunks/chunk-Q7LYHGGQ.js";
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  import "./chunks/chunk-WSIFAZU7.js";
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+ import "./chunks/chunk-G45YY72K.js";
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package/dist/gbzWindow.js CHANGED
@@ -2,23 +2,28 @@ import {
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  GBZ_CUT_DEFAULTS,
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  NoReferenceSampleError,
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  NodeLimitError,
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+ compactTables,
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  cutWindowGFA,
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+ cutWindowTables,
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  haplotypePrefix,
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  haplotypeWanted,
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  nodeLimitError,
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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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+ } from "./chunks/chunk-Q7LYHGGQ.js";
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  NoReferenceSampleError,
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+ compactTables,
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  cutWindowGFA,
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+ cutWindowTables,
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  haplotypePrefix,
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  haplotypeWanted,
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- } from "../chunks/chunk-J7YKQ5YW.js";
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+ } from "../chunks/chunk-QXAB2FLJ.js";
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+ import "../chunks/chunk-EMUUNWRU.js";
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+ import "../chunks/chunk-RAEABQNW.js";
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- } from "../chunks/chunk-OA7RIMZ2.js";
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+ } from "../chunks/chunk-PSMKPSO4.js";
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+ import "../chunks/chunk-RAEABQNW.js";
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package/dist/index.js CHANGED
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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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- } from "./chunks/chunk-PIN7ZMTZ.js";
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+ } from "./chunks/chunk-EU6FBTQF.js";
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+ import {
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+ warpX
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+ } from "./chunks/chunk-HK5Y2YWV.js";
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- } from "./chunks/chunk-HK5Y2YWV.js";
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- import {
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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-FG762CCP.js";
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+ } from "./chunks/chunk-33T67FPZ.js";
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  import {
46
46
  graphBubbles,
47
47
  superbubblesFromGraph
48
- } from "./chunks/chunk-5GZEPPEW.js";
48
+ } from "./chunks/chunk-BEWLQADP.js";
49
49
  import {
50
50
  bubblesFromGraph
51
51
  } from "./chunks/chunk-CLOP7UVD.js";
52
52
  import {
53
53
  bubbleSubgraph
54
- } from "./chunks/chunk-A6PSWTLX.js";
54
+ } from "./chunks/chunk-4QTNXTGW.js";
55
55
  import {
56
56
  genesFromBed,
57
57
  genesFromGff3Lines,
@@ -73,21 +73,21 @@ import {
73
73
  drawReferenceStrip,
74
74
  referenceStripBlocks,
75
75
  stripBlockAt
76
- } from "./chunks/chunk-BDWQQK33.js";
76
+ } from "./chunks/chunk-KJYSOHVN.js";
77
77
  import {
78
78
  LAYOUT_QUALITIES
79
79
  } from "./chunks/chunk-K5SIJGAE.js";
80
80
  import {
81
81
  FIGURE_DEFAULTS,
82
82
  figureSpecSettings
83
- } from "./chunks/chunk-IZI7KIVX.js";
83
+ } from "./chunks/chunk-E5UEYZWK.js";
84
84
  import {
85
85
  edgeHoverText,
86
86
  regionLabel
87
87
  } from "./chunks/chunk-AZFVORTC.js";
88
88
  import {
89
89
  figureSvg
90
- } from "./chunks/chunk-2FLBFVMO.js";
90
+ } from "./chunks/chunk-RJXPPYA7.js";
91
91
  import {
92
92
  svgCanvas
93
93
  } from "./chunks/chunk-47DYCZOK.js";
@@ -102,7 +102,7 @@ import {
102
102
  walkStripApplies,
103
103
  walkStripFrame,
104
104
  walkStripLabelsTree
105
- } from "./chunks/chunk-DMH4NL2M.js";
105
+ } from "./chunks/chunk-WI7ZHJ27.js";
106
106
  import {
107
107
  BAR_PX,
108
108
  CALL_TICK,
@@ -129,27 +129,27 @@ import {
129
129
  walkRowsKey,
130
130
  walkRowsKeyTree,
131
131
  walkRowsTree
132
- } from "./chunks/chunk-FJZ2TB46.js";
132
+ } from "./chunks/chunk-VZNKA3K2.js";
133
133
  import {
134
134
  Canvas2DRenderer
135
135
  } from "./chunks/chunk-WBCOREDZ.js";
136
136
  import {
137
137
  getDpr
138
138
  } from "./chunks/chunk-4BYTEJGW.js";
139
- import {
140
- genePins
141
- } from "./chunks/chunk-BUBZ32IC.js";
142
139
  import {
143
140
  EXON_COLOR,
144
141
  exonOutlineTree,
145
142
  exonStretches
146
143
  } from "./chunks/chunk-3S3YVOJ7.js";
144
+ import {
145
+ genePins
146
+ } from "./chunks/chunk-BUBZ32IC.js";
147
147
  import {
148
148
  RAMP_GRADIENT_CSS,
149
149
  rampHue,
150
150
  rampHueCss,
151
151
  rampStops
152
- } from "./chunks/chunk-K5NYTPLC.js";
152
+ } from "./chunks/chunk-DCJC32QW.js";
153
153
  import {
154
154
  HALO_FACTOR,
155
155
  LEGEND_INSET_PX,
@@ -168,7 +168,7 @@ import {
168
168
  import {
169
169
  figureData,
170
170
  gfaFigureData
171
- } from "./chunks/chunk-NGODVSCA.js";
171
+ } from "./chunks/chunk-Q6IOQP4J.js";
172
172
  import {
173
173
  LAYOUT_ENGINES,
174
174
  layoutEngine
@@ -182,10 +182,10 @@ import {
182
182
  LAYOUT_MODES,
183
183
  layoutModeByValue,
184
184
  modeUsesLayoutEngine
185
- } from "./chunks/chunk-FUUJ76KD.js";
186
- import "./chunks/chunk-LOEA5IHZ.js";
187
- import "./chunks/chunk-CXKZYLYS.js";
185
+ } from "./chunks/chunk-ICXMWYOA.js";
186
+ import "./chunks/chunk-IM4SJUPO.js";
188
187
  import "./chunks/chunk-CWFNEKST.js";
188
+ import "./chunks/chunk-LOEA5IHZ.js";
189
189
  import "./chunks/chunk-L3O7AWLI.js";
190
190
  import "./chunks/chunk-TZFWUT2C.js";
191
191
  import "./chunks/chunk-HNQPEMYE.js";
@@ -199,21 +199,23 @@ import {
199
199
  cutGbzRegion,
200
200
  openGbz,
201
201
  parseRegion
202
- } from "./chunks/chunk-73RSLGZT.js";
202
+ } from "./chunks/chunk-FLFBYSJO.js";
203
203
  import {
204
+ compactTables,
204
205
  cutWindowGFA,
206
+ cutWindowTables,
205
207
  haplotypeWanted,
206
208
  referencePathQuery,
207
209
  referenceSamplesOf,
208
210
  resolveReferenceSample
209
- } from "./chunks/chunk-LTUWJKHD.js";
211
+ } from "./chunks/chunk-Q7LYHGGQ.js";
210
212
  import "./chunks/chunk-WSIFAZU7.js";
211
213
  import {
212
214
  layoutGeometryInputs
213
215
  } from "./chunks/chunk-LOCJN3BZ.js";
214
216
  import {
215
217
  version
216
- } from "./chunks/chunk-2VTM3DHG.js";
218
+ } from "./chunks/chunk-CDPYXHVR.js";
217
219
  import {
218
220
  axisScaleOf,
219
221
  contains,
@@ -221,12 +223,12 @@ import {
221
223
  screenToLayout,
222
224
  viewportOf,
223
225
  zoomAbout
224
- } from "./chunks/chunk-PT37VS5B.js";
226
+ } from "./chunks/chunk-OOLNLCIO.js";
225
227
  import {
226
228
  facetLifts,
227
229
  walkHighlight,
228
230
  walkLift
229
- } from "./chunks/chunk-MVMP6AGI.js";
231
+ } from "./chunks/chunk-QIVPRZ4H.js";
230
232
  import {
231
233
  WALK_FIELDS,
232
234
  WALK_SCHEMES,
@@ -234,7 +236,7 @@ import {
234
236
  encodingSwatchCss,
235
237
  resolveEncoding,
236
238
  schemeCss
237
- } from "./chunks/chunk-KYY5363X.js";
239
+ } from "./chunks/chunk-VOWI544A.js";
238
240
  import {
239
241
  rangeText,
240
242
  walkKey,
@@ -244,22 +246,22 @@ import {
244
246
  REFERENCE_RAMP_MAX_HUE,
245
247
  buildGeometry,
246
248
  computeReferenceRamp
247
- } from "./chunks/chunk-4IYP43W6.js";
249
+ } from "./chunks/chunk-NP356MC2.js";
248
250
  import "./chunks/chunk-G2FD7S3C.js";
249
251
  import "./chunks/chunk-WFB5TXRA.js";
250
252
  import {
251
253
  walkRowLabels,
252
254
  walkRowsExtent
253
- } from "./chunks/chunk-TOVOJNT7.js";
255
+ } from "./chunks/chunk-3APK25GI.js";
254
256
  import {
255
257
  filterSamples,
256
258
  walkRows
257
- } from "./chunks/chunk-6PYZYBBF.js";
259
+ } from "./chunks/chunk-KAN2WTG5.js";
258
260
  import {
259
261
  pathColorsLegible,
260
262
  pathLegend,
261
263
  walkLabelsOf
262
- } from "./chunks/chunk-XZ2BLAA6.js";
264
+ } from "./chunks/chunk-REE4GUDM.js";
263
265
  import {
264
266
  NODE_WIDTHS,
265
267
  maxNodeWidthPx,
@@ -279,22 +281,23 @@ import {
279
281
  forceLayout,
280
282
  layoutExtent,
281
283
  loadGraph
282
- } from "./chunks/chunk-HRAU4VTB.js";
284
+ } from "./chunks/chunk-W4GZCVUK.js";
283
285
  import "./chunks/chunk-IGVV37VI.js";
284
286
  import "./chunks/chunk-OPPVSPEF.js";
285
287
  import "./chunks/chunk-PUG7LXDF.js";
286
- import "./chunks/chunk-J7YKQ5YW.js";
287
- import {
288
- gfaTables
289
- } from "./chunks/chunk-G45YY72K.js";
288
+ import "./chunks/chunk-QXAB2FLJ.js";
289
+ import "./chunks/chunk-QYBZZI5H.js";
290
290
  import {
291
291
  graphFromTables,
292
292
  graphTablesGFA
293
- } from "./chunks/chunk-OA7RIMZ2.js";
294
- import "./chunks/chunk-QYBZZI5H.js";
293
+ } from "./chunks/chunk-PSMKPSO4.js";
295
294
  import "./chunks/chunk-CDLPYR5O.js";
296
295
  import "./chunks/chunk-JVLURPFW.js";
297
- import "./chunks/chunk-IGJCTPFB.js";
296
+ import "./chunks/chunk-EMUUNWRU.js";
297
+ import {
298
+ PathVisits,
299
+ PathVisitsBuilder
300
+ } from "./chunks/chunk-RAEABQNW.js";
298
301
  import "./chunks/chunk-ES2N6V56.js";
299
302
  import {
300
303
  WELL_KNOWN_SAMPLES,
@@ -306,6 +309,9 @@ import {
306
309
  referenceLabel,
307
310
  wellKnownSample
308
311
  } from "./chunks/chunk-RAKOB6IV.js";
312
+ import {
313
+ gfaTables
314
+ } from "./chunks/chunk-G45YY72K.js";
309
315
  import {
310
316
  panSNContig,
311
317
  panSNHaplotype,
@@ -372,6 +378,8 @@ export {
372
378
  LAYOUT_QUALITIES,
373
379
  LEGEND_INSET_PX,
374
380
  NODE_WIDTHS,
381
+ PathVisits,
382
+ PathVisitsBuilder,
375
383
  RAMP_GRADIENT_CSS,
376
384
  REFERENCE_RAMP_MAX_HUE,
377
385
  REFERENCE_STRIP_ZONE_PX,
@@ -403,12 +411,14 @@ export {
403
411
  clampZoom,
404
412
  classifyBubble,
405
413
  coalesceRuns,
414
+ compactTables,
406
415
  computeReferenceRamp,
407
416
  connectorAt,
408
417
  contains,
409
418
  createForceLayoutCache,
410
419
  cutGbzRegion,
411
420
  cutWindowGFA,
421
+ cutWindowTables,
412
422
  cutsWholeWalks,
413
423
  deletionDrawing,
414
424
  deletionEdges,
@@ -1,18 +1,19 @@
1
1
  import {
2
2
  createForceLayoutCache
3
- } from "../chunks/chunk-Q6UIUY6X.js";
4
- import "../chunks/chunk-HRAU4VTB.js";
3
+ } from "../chunks/chunk-33T67FPZ.js";
4
+ import "../chunks/chunk-W4GZCVUK.js";
5
5
  import "../chunks/chunk-IGVV37VI.js";
6
6
  import "../chunks/chunk-OPPVSPEF.js";
7
7
  import "../chunks/chunk-PUG7LXDF.js";
8
- import "../chunks/chunk-J7YKQ5YW.js";
9
- import "../chunks/chunk-G45YY72K.js";
10
- import "../chunks/chunk-OA7RIMZ2.js";
8
+ import "../chunks/chunk-QXAB2FLJ.js";
11
9
  import "../chunks/chunk-QYBZZI5H.js";
10
+ import "../chunks/chunk-PSMKPSO4.js";
12
11
  import "../chunks/chunk-CDLPYR5O.js";
13
12
  import "../chunks/chunk-JVLURPFW.js";
14
- import "../chunks/chunk-IGJCTPFB.js";
13
+ import "../chunks/chunk-EMUUNWRU.js";
14
+ import "../chunks/chunk-RAEABQNW.js";
15
15
  import "../chunks/chunk-ES2N6V56.js";
16
+ import "../chunks/chunk-G45YY72K.js";
16
17
  import "../chunks/chunk-BPLIXMH7.js";
17
18
  import "../chunks/chunk-TAMCZHLW.js";
18
19
  import "../chunks/chunk-UVBGRJQX.js";
@@ -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) => {
@@ -8,11 +8,12 @@ import {
8
8
  tubeMapReferenceLayout,
9
9
  tubeMapTracks,
10
10
  tubeWidth
11
- } from "../chunks/chunk-CXKZYLYS.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-XZ2BLAA6.js";
15
- import "../chunks/chunk-IGJCTPFB.js";
14
+ import "../chunks/chunk-REE4GUDM.js";
15
+ import "../chunks/chunk-EMUUNWRU.js";
16
+ import "../chunks/chunk-RAEABQNW.js";
16
17
  import "../chunks/chunk-BPLIXMH7.js";
17
18
  import "../chunks/chunk-3ZZSX5HN.js";
18
19
  import "../chunks/chunk-AB35TJST.js";