@jbrowse/bandage-core 11.7.0 → 11.7.3

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 (81) hide show
  1. package/README.md +58 -40
  2. package/dist/bubbles/bubbleHalos.js +5 -4
  3. package/dist/bubbles/classifyBubble.js +4 -3
  4. package/dist/bubbles/superbubbles.js +6 -5
  5. package/dist/chunks/{chunk-YEYQFNFQ.js → chunk-2T3V6Z3M.js} +1 -1
  6. package/dist/chunks/{chunk-6YRSOL4K.js → chunk-2US43KNG.js} +1 -1
  7. package/dist/chunks/{chunk-OYCQVJYY.js → chunk-33KUO34R.js} +1 -1
  8. package/dist/chunks/{chunk-KJDERUQF.js → chunk-4KOYS5WR.js} +44 -9
  9. package/dist/chunks/{chunk-NTKWT6XL.js → chunk-4SN7R4UF.js} +1 -1
  10. package/dist/chunks/{chunk-SIA75TEG.js → chunk-63XWYNID.js} +1 -1
  11. package/dist/chunks/{chunk-2XEAITWM.js → chunk-6RB5ZQ34.js} +1 -1
  12. package/dist/chunks/{chunk-ZHZRAYEM.js → chunk-AJQRKN3X.js} +1 -1
  13. package/dist/chunks/{chunk-SNF2MIEF.js → chunk-AWJJSA7D.js} +1 -1
  14. package/dist/chunks/{chunk-KZMSSPS6.js → chunk-BLDUBB7X.js} +1 -1
  15. package/dist/chunks/{chunk-IJCSW6MV.js → chunk-CL6ELLVF.js} +1 -1
  16. package/dist/chunks/{chunk-A7Q7RTWX.js → chunk-EPOPGV5G.js} +1 -1
  17. package/dist/chunks/{chunk-5ZQKQ24Z.js → chunk-F4CDC72I.js} +1 -1
  18. package/dist/chunks/{chunk-BW2NMXRV.js → chunk-GD6RUZU5.js} +1 -1
  19. package/dist/chunks/{chunk-GZ36HNPJ.js → chunk-IHM43Y7B.js} +1 -1
  20. package/dist/chunks/{chunk-DTEXQ65J.js → chunk-K4KVAMEF.js} +1 -1
  21. package/dist/chunks/{chunk-C6E6HXP5.js → chunk-KMLATBNT.js} +2 -2
  22. package/dist/chunks/{chunk-56L6R6D2.js → chunk-LH436HS2.js} +1 -1
  23. package/dist/chunks/{chunk-T3H5ELLA.js → chunk-N73RA4DR.js} +1 -1
  24. package/dist/chunks/{chunk-DV5B5UU7.js → chunk-P276TWPM.js} +6 -2
  25. package/dist/chunks/{chunk-HELOUO6K.js → chunk-PKGPSTRW.js} +1 -1
  26. package/dist/chunks/{chunk-KA4F3N55.js → chunk-QJC63NFR.js} +2 -2
  27. package/dist/chunks/{chunk-QCOVHLJO.js → chunk-QLLKALSH.js} +1 -1
  28. package/dist/chunks/{chunk-HERVZPWA.js → chunk-QXBQDHKL.js} +11 -11
  29. package/dist/chunks/{chunk-SVPR7IZO.js → chunk-SG7VQB4F.js} +1 -1
  30. package/dist/chunks/{chunk-EH5JZETS.js → chunk-T3MEG5D3.js} +7 -7
  31. package/dist/chunks/chunk-TLWXLNLY.js +124 -0
  32. package/dist/chunks/{chunk-WWIUC4N4.js → chunk-UTDMFVC7.js} +7 -7
  33. package/dist/chunks/{chunk-DD5EZG3T.js → chunk-VNF236GG.js} +1 -1
  34. package/dist/chunks/{chunk-JGHZ3N34.js → chunk-VXKL2ZLR.js} +2 -2
  35. package/dist/chunks/{chunk-VO6FKNZE.js → chunk-W5YRBEWQ.js} +1 -1
  36. package/dist/chunks/{chunk-YER6TUXV.js → chunk-XKPXOIWD.js} +2 -2
  37. package/dist/chunks/{chunk-65YCFVS4.js → chunk-XTCIKBWM.js} +1 -1
  38. package/dist/chunks/{chunk-DUREQSOJ.js → chunk-Z4HXW6ZH.js} +2 -2
  39. package/dist/chunks/{chunk-3PZSBNLI.js → chunk-ZZZ6NVLW.js} +19 -14
  40. package/dist/cli/figure.js +24 -23
  41. package/dist/cli/fold.js +5 -4
  42. package/dist/deletionEdges.js +2 -1
  43. package/dist/figure.js +21 -20
  44. package/dist/figureData.js +18 -17
  45. package/dist/figureScene.js +13 -12
  46. package/dist/figureSettings.js +5 -4
  47. package/dist/foldVariants.js +1 -1
  48. package/dist/graphLabels.js +3 -2
  49. package/dist/index.js +33 -32
  50. package/dist/labelLayout.js +7 -6
  51. package/dist/layout/forceCache.js +5 -4
  52. package/dist/layout/orientToReference.js +3 -1
  53. package/dist/layout/trimToWindow.js +9 -101
  54. package/dist/layout/tubeMapLayout.js +5 -4
  55. package/dist/layout/walkRowDraw.js +7 -6
  56. package/dist/layout/walkStrip.js +8 -7
  57. package/dist/layoutModes.js +6 -5
  58. package/dist/pathColors.js +4 -3
  59. package/dist/pipeline.js +4 -3
  60. package/dist/referenceStrip.js +7 -6
  61. package/dist/renderer/GeometryBuilder.js +6 -5
  62. package/dist/tubeMap/axis.js +4 -3
  63. package/dist/tubeMap/bundle.js +6 -5
  64. package/dist/tubeMap/coarsen.js +6 -5
  65. package/dist/tubeMap/deviations.js +7 -6
  66. package/dist/tubeMap/genes.js +5 -4
  67. package/dist/tubeMap/nodeColors.js +7 -6
  68. package/dist/types/deletionEdges.d.ts +1 -1
  69. package/dist/types/foldVariants.d.ts +3 -1
  70. package/dist/types/layout/trimToWindow.d.ts +1 -0
  71. package/dist/types/types.d.ts +5 -0
  72. package/dist/types/version.d.ts +1 -1
  73. package/dist/util/SpatialIndex.js +4 -3
  74. package/dist/util/edgeCurves.js +3 -2
  75. package/dist/util/hitDetection.js +5 -4
  76. package/dist/version.js +1 -1
  77. package/dist/viewport.js +5 -4
  78. package/dist/walkEncoding.js +7 -6
  79. package/dist/walkHighlight.js +8 -7
  80. package/dist/walkKey.js +4 -3
  81. package/package.json +1 -1
package/dist/tubeMap/bundle.js CHANGED
@@ -1,19 +1,20 @@
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  import {
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  bundleRoutes
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- } from "../chunks/chunk-65YCFVS4.js";
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- import "../chunks/chunk-SIA75TEG.js";
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+ } from "../chunks/chunk-XTCIKBWM.js";
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+ import "../chunks/chunk-63XWYNID.js";
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  import "../chunks/chunk-SDI6BVG7.js";
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  import "../chunks/chunk-5OJZV6YT.js";
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  import "../chunks/chunk-BXE3SBBN.js";
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  import "../chunks/chunk-G7SG4XMK.js";
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- import "../chunks/chunk-BW2NMXRV.js";
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+ import "../chunks/chunk-GD6RUZU5.js";
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  import "../chunks/chunk-7L7MN2OM.js";
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  import "../chunks/chunk-LG2UK4MB.js";
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- import "../chunks/chunk-T3H5ELLA.js";
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+ import "../chunks/chunk-N73RA4DR.js";
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  import "../chunks/chunk-HMXCN6PG.js";
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  import "../chunks/chunk-AB35TJST.js";
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  import "../chunks/chunk-2VMKQKVO.js";
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- import "../chunks/chunk-DV5B5UU7.js";
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+ import "../chunks/chunk-P276TWPM.js";
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+ import "../chunks/chunk-TLWXLNLY.js";
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  import "../chunks/chunk-3YBP46PB.js";
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  import "../chunks/chunk-VACK24HF.js";
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  import "../chunks/chunk-CPMHA4W5.js";
package/dist/tubeMap/coarsen.js CHANGED
@@ -1,20 +1,21 @@
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  import {
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  coarsenTubeMap,
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  lastAtMost
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- } from "../chunks/chunk-IJCSW6MV.js";
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- import "../chunks/chunk-SIA75TEG.js";
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+ } from "../chunks/chunk-CL6ELLVF.js";
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+ import "../chunks/chunk-63XWYNID.js";
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  import "../chunks/chunk-SDI6BVG7.js";
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  import "../chunks/chunk-5OJZV6YT.js";
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  import "../chunks/chunk-BXE3SBBN.js";
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  import "../chunks/chunk-G7SG4XMK.js";
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- import "../chunks/chunk-BW2NMXRV.js";
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+ import "../chunks/chunk-GD6RUZU5.js";
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  import "../chunks/chunk-7L7MN2OM.js";
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  import "../chunks/chunk-LG2UK4MB.js";
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- import "../chunks/chunk-T3H5ELLA.js";
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+ import "../chunks/chunk-N73RA4DR.js";
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  import "../chunks/chunk-HMXCN6PG.js";
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  import "../chunks/chunk-AB35TJST.js";
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  import "../chunks/chunk-2VMKQKVO.js";
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- import "../chunks/chunk-DV5B5UU7.js";
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+ import "../chunks/chunk-P276TWPM.js";
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+ import "../chunks/chunk-TLWXLNLY.js";
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  import "../chunks/chunk-3YBP46PB.js";
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  import "../chunks/chunk-VACK24HF.js";
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  import "../chunks/chunk-CPMHA4W5.js";
package/dist/tubeMap/deviations.js CHANGED
@@ -1,23 +1,24 @@
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  import {
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  lastAtMost
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- } from "../chunks/chunk-IJCSW6MV.js";
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+ } from "../chunks/chunk-CL6ELLVF.js";
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  import {
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  boxX,
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  referenceBoxes
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- } from "../chunks/chunk-VO6FKNZE.js";
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- import "../chunks/chunk-SIA75TEG.js";
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+ } from "../chunks/chunk-W5YRBEWQ.js";
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+ import "../chunks/chunk-63XWYNID.js";
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  import "../chunks/chunk-SDI6BVG7.js";
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  import "../chunks/chunk-5OJZV6YT.js";
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  import "../chunks/chunk-BXE3SBBN.js";
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  import "../chunks/chunk-G7SG4XMK.js";
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- import "../chunks/chunk-BW2NMXRV.js";
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+ import "../chunks/chunk-GD6RUZU5.js";
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  import "../chunks/chunk-7L7MN2OM.js";
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  import "../chunks/chunk-LG2UK4MB.js";
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- import "../chunks/chunk-T3H5ELLA.js";
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+ import "../chunks/chunk-N73RA4DR.js";
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  import "../chunks/chunk-HMXCN6PG.js";
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  import "../chunks/chunk-AB35TJST.js";
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  import "../chunks/chunk-2VMKQKVO.js";
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- import "../chunks/chunk-DV5B5UU7.js";
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+ import "../chunks/chunk-P276TWPM.js";
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+ import "../chunks/chunk-TLWXLNLY.js";
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  import {
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  pathOrigin
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  } from "../chunks/chunk-3YBP46PB.js";
package/dist/tubeMap/genes.js CHANGED
@@ -3,13 +3,14 @@ import {
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  drawTubeMapGenes,
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  tubeMapGeneRows,
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  tubeMapGenes
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- } from "../chunks/chunk-GZ36HNPJ.js";
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- import "../chunks/chunk-VO6FKNZE.js";
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- import "../chunks/chunk-T3H5ELLA.js";
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+ } from "../chunks/chunk-IHM43Y7B.js";
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+ import "../chunks/chunk-W5YRBEWQ.js";
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+ import "../chunks/chunk-N73RA4DR.js";
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  import "../chunks/chunk-HMXCN6PG.js";
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  import "../chunks/chunk-AB35TJST.js";
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  import "../chunks/chunk-2VMKQKVO.js";
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- import "../chunks/chunk-DV5B5UU7.js";
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+ import "../chunks/chunk-P276TWPM.js";
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+ import "../chunks/chunk-TLWXLNLY.js";
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  import "../chunks/chunk-3YBP46PB.js";
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  import "../chunks/chunk-VACK24HF.js";
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  import "../chunks/chunk-CPMHA4W5.js";
package/dist/tubeMap/nodeColors.js CHANGED
@@ -1,18 +1,19 @@
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  import {
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  tubeMapNodeColors
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- } from "../chunks/chunk-YEYQFNFQ.js";
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- import "../chunks/chunk-JGHZ3N34.js";
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+ } from "../chunks/chunk-2T3V6Z3M.js";
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+ import "../chunks/chunk-VXKL2ZLR.js";
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  import "../chunks/chunk-G2FD7S3C.js";
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  import "../chunks/chunk-GQZVR5DW.js";
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- import "../chunks/chunk-OYCQVJYY.js";
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- import "../chunks/chunk-BW2NMXRV.js";
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+ import "../chunks/chunk-33KUO34R.js";
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+ import "../chunks/chunk-GD6RUZU5.js";
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  import "../chunks/chunk-ZANALBSX.js";
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  import "../chunks/chunk-VX656OAZ.js";
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- import "../chunks/chunk-T3H5ELLA.js";
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+ import "../chunks/chunk-N73RA4DR.js";
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  import "../chunks/chunk-HMXCN6PG.js";
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  import "../chunks/chunk-AB35TJST.js";
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  import "../chunks/chunk-2VMKQKVO.js";
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- import "../chunks/chunk-DV5B5UU7.js";
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+ import "../chunks/chunk-P276TWPM.js";
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+ import "../chunks/chunk-TLWXLNLY.js";
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  import "../chunks/chunk-3YBP46PB.js";
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  import "../chunks/chunk-VACK24HF.js";
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  import "../chunks/chunk-CPMHA4W5.js";
package/dist/types/deletionEdges.d.ts CHANGED
@@ -13,7 +13,7 @@ export interface DeletionEdge {
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  bypassed: string[];
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  }
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  export declare function edgeCurvesOf(nodePositions: Record<string, NodeSegment[]>, edge: GraphEdge, axis: AxisScale, bypassed: string[] | undefined, route: NodeSegment[] | undefined, stranded: boolean): import("./util/geometry.js").BezierCurve[] | undefined;
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- export declare function deletionEdges(graph: Graph): DeletionEdge[];
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+ export declare function deletionEdges(cut: Graph): DeletionEdge[];
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  export declare function closableDeletions(graph: Graph, deletions: DeletionEdge[]): Set<number>;
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  export interface DeletionDrawing {
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  shown: DeletionEdge[];
package/dist/types/foldVariants.d.ts CHANGED
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  import type { Graph } from './types.js';
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- export declare function foldVariants(graph: Graph, belowBp: number): Graph;
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+ export declare function foldVariants(graph: Graph, belowBp: number, { cut }?: {
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+ cut?: boolean;
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+ }): Graph;
package/dist/types/layout/trimToWindow.d.ts CHANGED
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  start: number;
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  end: number;
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  }, reachBp: number): Graph;
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+ export declare function unclipped(graph: Graph): Graph;
package/dist/types/types.d.ts CHANGED
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  depth: number;
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  stable?: StableCoordinate;
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+ unclipped?: {
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+ start: number;
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+ length: number;
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+ };
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+ foldBridge?: boolean;
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  export interface GraphPath {
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package/dist/types/version.d.ts CHANGED
@@ -1 +1 @@
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- export declare const version = "11.7.0";
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+ export declare const version = "11.7.3";
package/dist/util/SpatialIndex.js CHANGED
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- } from "../chunks/chunk-6YRSOL4K.js";
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- import "../chunks/chunk-OYCQVJYY.js";
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+ } from "../chunks/chunk-2US43KNG.js";
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+ import "../chunks/chunk-33KUO34R.js";
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  import "../chunks/chunk-HMXCN6PG.js";
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- import "../chunks/chunk-DV5B5UU7.js";
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+ import "../chunks/chunk-P276TWPM.js";
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+ import "../chunks/chunk-TLWXLNLY.js";
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  import "../chunks/chunk-3YBP46PB.js";
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package/dist/util/edgeCurves.js CHANGED
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- } from "../chunks/chunk-OYCQVJYY.js";
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+ } from "../chunks/chunk-33KUO34R.js";
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- import "../chunks/chunk-DV5B5UU7.js";
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+ import "../chunks/chunk-P276TWPM.js";
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+ import "../chunks/chunk-TLWXLNLY.js";
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package/dist/util/hitDetection.js CHANGED
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- } from "../chunks/chunk-56L6R6D2.js";
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- import "../chunks/chunk-6YRSOL4K.js";
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- import "../chunks/chunk-OYCQVJYY.js";
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+ } from "../chunks/chunk-LH436HS2.js";
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+ import "../chunks/chunk-2US43KNG.js";
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+ import "../chunks/chunk-33KUO34R.js";
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- import "../chunks/chunk-DV5B5UU7.js";
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+ import "../chunks/chunk-P276TWPM.js";
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+ import "../chunks/chunk-TLWXLNLY.js";
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package/dist/version.js CHANGED
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- } from "./chunks/chunk-ZHZRAYEM.js";
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+ } from "./chunks/chunk-AJQRKN3X.js";
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package/dist/viewport.js CHANGED
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- } from "./chunks/chunk-5ZQKQ24Z.js";
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- import "./chunks/chunk-YER6TUXV.js";
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+ } from "./chunks/chunk-F4CDC72I.js";
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+ import "./chunks/chunk-XKPXOIWD.js";
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- import "./chunks/chunk-3PZSBNLI.js";
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+ import "./chunks/chunk-ZZZ6NVLW.js";
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@@ -21,7 +21,8 @@ import "./chunks/chunk-LG2UK4MB.js";
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+ import "./chunks/chunk-TLWXLNLY.js";
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package/dist/walkEncoding.js CHANGED
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- } from "./chunks/chunk-2XEAITWM.js";
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- import "./chunks/chunk-JGHZ3N34.js";
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+ } from "./chunks/chunk-6RB5ZQ34.js";
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+ import "./chunks/chunk-VXKL2ZLR.js";
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  import "./chunks/chunk-G2FD7S3C.js";
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- import "./chunks/chunk-OYCQVJYY.js";
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- import "./chunks/chunk-BW2NMXRV.js";
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+ import "./chunks/chunk-33KUO34R.js";
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+ import "./chunks/chunk-GD6RUZU5.js";
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- import "./chunks/chunk-T3H5ELLA.js";
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+ import "./chunks/chunk-N73RA4DR.js";
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+ import "./chunks/chunk-P276TWPM.js";
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+ import "./chunks/chunk-TLWXLNLY.js";
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package/dist/walkHighlight.js CHANGED
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- } from "./chunks/chunk-DUREQSOJ.js";
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- import "./chunks/chunk-2XEAITWM.js";
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- import "./chunks/chunk-JGHZ3N34.js";
5
+ } from "./chunks/chunk-Z4HXW6ZH.js";
6
+ import "./chunks/chunk-6RB5ZQ34.js";
7
+ import "./chunks/chunk-VXKL2ZLR.js";
8
8
  import "./chunks/chunk-G2FD7S3C.js";
9
9
  import "./chunks/chunk-GQZVR5DW.js";
10
- import "./chunks/chunk-OYCQVJYY.js";
11
- import "./chunks/chunk-BW2NMXRV.js";
10
+ import "./chunks/chunk-33KUO34R.js";
11
+ import "./chunks/chunk-GD6RUZU5.js";
12
12
  import "./chunks/chunk-ZANALBSX.js";
13
13
  import "./chunks/chunk-VX656OAZ.js";
14
14
  import "./chunks/chunk-LG2UK4MB.js";
15
- import "./chunks/chunk-T3H5ELLA.js";
15
+ import "./chunks/chunk-N73RA4DR.js";
16
16
  import "./chunks/chunk-HMXCN6PG.js";
17
17
  import "./chunks/chunk-AB35TJST.js";
18
18
  import "./chunks/chunk-2VMKQKVO.js";
19
- import "./chunks/chunk-DV5B5UU7.js";
19
+ import "./chunks/chunk-P276TWPM.js";
20
+ import "./chunks/chunk-TLWXLNLY.js";
20
21
  import "./chunks/chunk-3YBP46PB.js";
21
22
  import "./chunks/chunk-VACK24HF.js";
22
23
  import "./chunks/chunk-CPMHA4W5.js";
package/dist/walkKey.js CHANGED
@@ -2,13 +2,14 @@ import {
2
2
  rangeText,
3
3
  walkKey,
4
4
  walkPosition
5
- } from "./chunks/chunk-SVPR7IZO.js";
5
+ } from "./chunks/chunk-SG7VQB4F.js";
6
6
  import "./chunks/chunk-LG2UK4MB.js";
7
- import "./chunks/chunk-T3H5ELLA.js";
7
+ import "./chunks/chunk-N73RA4DR.js";
8
8
  import "./chunks/chunk-HMXCN6PG.js";
9
9
  import "./chunks/chunk-AB35TJST.js";
10
10
  import "./chunks/chunk-2VMKQKVO.js";
11
- import "./chunks/chunk-DV5B5UU7.js";
11
+ import "./chunks/chunk-P276TWPM.js";
12
+ import "./chunks/chunk-TLWXLNLY.js";
12
13
  import "./chunks/chunk-3YBP46PB.js";
13
14
  import "./chunks/chunk-VACK24HF.js";
14
15
  import "./chunks/chunk-CPMHA4W5.js";
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/bandage-core",
3
- "version": "11.7.0",
3
+ "version": "11.7.3",
4
4
  "description": "Pangenome graph layout and drawing with no host: GFA in, the Bandage force-directed engine and reference-anchored layouts, a Canvas2D renderer, hit testing and labels out",
5
5
  "license": "GPL-3.0-or-later",
6
6
  "repository": {