@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/figure.js CHANGED
@@ -1,55 +1,57 @@
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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 "./chunks/chunk-47DYCZOK.js";
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- import "./chunks/chunk-MECWJY2R.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-LOCJN3BZ.js";
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- import "./chunks/chunk-P6O4RSOQ.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-ZBLKAWSD.js";
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- import "./chunks/chunk-EE37PVQY.js";
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- import "./chunks/chunk-F5BYHLIN.js";
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- import "./chunks/chunk-2LQ5BWT7.js";
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- import "./chunks/chunk-YS7VA5SI.js";
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- import "./chunks/chunk-F4BKWWLS.js";
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- import "./chunks/chunk-G2FD7S3C.js";
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- import "./chunks/chunk-BQ33OOLC.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-EDASNMLY.js";
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- import "./chunks/chunk-PBENCR5L.js";
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- import "./chunks/chunk-RAKOB6IV.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-WFB5TXRA.js";
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- import "./chunks/chunk-3ZZSX5HN.js";
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- import "./chunks/chunk-AB35TJST.js";
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- import "./chunks/chunk-JKJWSY4V.js";
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  import "./chunks/chunk-NNODIW4U.js";
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- import "./chunks/chunk-XV4P5KEQ.js";
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- import "./chunks/chunk-FPTI3WAV.js";
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- import "./chunks/chunk-PUG7LXDF.js";
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+ import "./chunks/chunk-LOCJN3BZ.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-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-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-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 "./chunks/chunk-G45YY72K.js";
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- import "./chunks/chunk-OA7RIMZ2.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 "./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-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-IGJCTPFB.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";
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  import "./chunks/chunk-TAMCZHLW.js";
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  import "./chunks/chunk-UVBGRJQX.js";
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  import "./chunks/chunk-6JEWNXCQ.js";
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+ import "./chunks/chunk-JKJWSY4V.js";
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  import "./chunks/chunk-N6FECAXP.js";
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  import "./chunks/chunk-2CVHXFK7.js";
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  import "./chunks/chunk-CPMHA4W5.js";
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  import "./chunks/chunk-FYQWPEEY.js";
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+ import "./chunks/chunk-XV4P5KEQ.js";
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  export {
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  figureSvg
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  };
package/dist/figureData.js ADDED
@@ -0,0 +1,63 @@
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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 "./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-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-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-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-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-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-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-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-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";
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+ import "./chunks/chunk-TAMCZHLW.js";
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+ import "./chunks/chunk-UVBGRJQX.js";
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+ import "./chunks/chunk-6JEWNXCQ.js";
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+ import "./chunks/chunk-JKJWSY4V.js";
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+ import "./chunks/chunk-N6FECAXP.js";
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+ import "./chunks/chunk-2CVHXFK7.js";
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+ import "./chunks/chunk-CPMHA4W5.js";
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+ import "./chunks/chunk-FYQWPEEY.js";
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+ import "./chunks/chunk-XV4P5KEQ.js";
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+ export {
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+ figureData,
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+ gfaFigureData
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+ };
package/dist/figureSettings.js CHANGED
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  import {
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  FIGURE_DEFAULTS,
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  figureSpecSettings
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- } from "./chunks/chunk-YGN4KL7W.js";
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- import "./chunks/chunk-FPTI3WAV.js";
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- import "./chunks/chunk-PUG7LXDF.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-IGVV37VI.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-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 "./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-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-IGJCTPFB.js";
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+ import "./chunks/chunk-G45YY72K.js";
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  import "./chunks/chunk-BPLIXMH7.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-RAKOB6IV.js";
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+ import "./chunks/chunk-G45YY72K.js";
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  export {
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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  import "./chunks/chunk-WSIFAZU7.js";
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  import "./chunks/chunk-RAKOB6IV.js";
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+ import "./chunks/chunk-G45YY72K.js";
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  export {
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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,
package/dist/gfa/gfaConverter.js CHANGED
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  import {
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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-CDLPYR5O.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-BPLIXMH7.js";
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package/dist/gfa/graphTables.js CHANGED
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  import {
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  graphTablesGFA
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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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  import "../chunks/chunk-BPLIXMH7.js";
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  export {
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