@jbrowse/bandage-core 11.8.0 → 11.10.0

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 (90) hide show
  1. package/dist/bubbles/bubbleHalos.js +6 -6
  2. package/dist/bubbles/classifyBubble.js +5 -5
  3. package/dist/bubbles/superbubbles.js +7 -7
  4. package/dist/chunks/{chunk-S4CH434Z.js → chunk-2A6Z2DHF.js} +1 -1
  5. package/dist/chunks/{chunk-6MD4VS2F.js → chunk-2MXFG3W7.js} +1 -1
  6. package/dist/chunks/{chunk-L2RQV23D.js → chunk-2NCZ5YYN.js} +1 -1
  7. package/dist/chunks/{chunk-ZKIH2USC.js → chunk-337LZP7C.js} +1 -1
  8. package/dist/chunks/{chunk-2RCKHCF7.js → chunk-3DHGSHC3.js} +1 -1
  9. package/dist/chunks/{chunk-3CXZUC2Y.js → chunk-3GORESBG.js} +1 -1
  10. package/dist/chunks/{chunk-R4XCTRIU.js → chunk-4BYGFDQB.js} +1 -1
  11. package/dist/chunks/{chunk-NHOXLUIL.js → chunk-4JDO7ZLN.js} +2 -2
  12. package/dist/chunks/{chunk-7GDNDQD7.js → chunk-4KBZ7WPP.js} +176 -101
  13. package/dist/chunks/{chunk-2H3ALI6L.js → chunk-53DZE3SA.js} +184 -161
  14. package/dist/chunks/{chunk-YF6T33PU.js → chunk-54C73ICS.js} +37 -17
  15. package/dist/chunks/{chunk-U6JPSXJ3.js → chunk-55DRWHBF.js} +9 -9
  16. package/dist/chunks/{chunk-4OVIUCSB.js → chunk-77O67GIB.js} +1 -1
  17. package/dist/chunks/{chunk-7PEYA3NA.js → chunk-7YSIP3O2.js} +2 -2
  18. package/dist/chunks/{chunk-LA6JHEVV.js → chunk-ALOF5SOT.js} +1 -1
  19. package/dist/chunks/{chunk-3XYLEK4H.js → chunk-ARXDNQLF.js} +1 -1
  20. package/dist/chunks/{chunk-6CXLLJ2C.js → chunk-AURNOR27.js} +3 -3
  21. package/dist/chunks/{chunk-G4WQBRDS.js → chunk-BDS5VZYZ.js} +3 -3
  22. package/dist/chunks/{chunk-MO4DIRHD.js → chunk-CHGTUO3C.js} +13 -13
  23. package/dist/chunks/{chunk-X5ULFAMM.js → chunk-HEYIAMTC.js} +2 -2
  24. package/dist/chunks/{chunk-S7BCZVRK.js → chunk-HIN56TLA.js} +1 -1
  25. package/dist/chunks/{chunk-YIWN32ZX.js → chunk-HNNP5QUN.js} +1 -1
  26. package/dist/chunks/{chunk-XOIYBEU7.js → chunk-I53QYITQ.js} +1 -1
  27. package/dist/chunks/{chunk-SDDMV2MM.js → chunk-IZKM4NY7.js} +1 -1
  28. package/dist/chunks/{chunk-SIXFXXRI.js → chunk-J7RNXBXA.js} +3 -3
  29. package/dist/chunks/{chunk-735MPLUL.js → chunk-JJV2GT2Z.js} +22 -14
  30. package/dist/chunks/{chunk-S3ICPPXC.js → chunk-JVT3XTKN.js} +3 -3
  31. package/dist/chunks/{chunk-J4PDHWP2.js → chunk-KKHXMJEE.js} +1 -1
  32. package/dist/chunks/{chunk-22ZMVREZ.js → chunk-NAYS472K.js} +1 -1
  33. package/dist/chunks/{chunk-OIOAK7BS.js → chunk-NWEVR2OQ.js} +1 -1
  34. package/dist/chunks/{chunk-VSRRIFRF.js → chunk-P2GJBFNA.js} +1 -1
  35. package/dist/chunks/{chunk-N2GAA7RB.js → chunk-RT4U3DH3.js} +1 -1
  36. package/dist/chunks/{chunk-AXE3RR7J.js → chunk-S6E3PMH7.js} +1 -1
  37. package/dist/chunks/{chunk-NQWEYJDD.js → chunk-SPEB75UH.js} +1 -1
  38. package/dist/chunks/{chunk-4YPCUVMC.js → chunk-SZYFZNCO.js} +2 -2
  39. package/dist/chunks/{chunk-G3GLGDKV.js → chunk-TQ26XEFL.js} +2 -2
  40. package/dist/chunks/{chunk-N4AJV4GH.js → chunk-UVRCXTBY.js} +37 -10
  41. package/dist/chunks/{chunk-YEDZ37PH.js → chunk-VNCHWWLG.js} +1 -1
  42. package/dist/chunks/{chunk-JKIAHYAW.js → chunk-VQ353UDK.js} +1 -1
  43. package/dist/chunks/{chunk-R3NPBUKT.js → chunk-YQAZNH37.js} +7 -7
  44. package/dist/cli/figure.js +28 -28
  45. package/dist/cli/fold.js +6 -6
  46. package/dist/deletionEdges.js +2 -2
  47. package/dist/figure.js +24 -24
  48. package/dist/figureData.js +22 -22
  49. package/dist/figureScene.js +15 -15
  50. package/dist/figureSettings.js +6 -6
  51. package/dist/foldVariants.js +2 -2
  52. package/dist/genes/genePins.js +3 -3
  53. package/dist/graphLabels.js +4 -4
  54. package/dist/index.js +38 -38
  55. package/dist/labelLayout.js +8 -8
  56. package/dist/layout/forceCache.js +6 -6
  57. package/dist/layout/mergeRuns.js +2 -2
  58. package/dist/layout/orientToReference.js +2 -2
  59. package/dist/layout/tubeMapLayout.js +7 -7
  60. package/dist/layout/walkRowDraw.js +9 -9
  61. package/dist/layout/walkStrip.js +10 -10
  62. package/dist/layoutModes.js +8 -8
  63. package/dist/pathColors.js +5 -5
  64. package/dist/pipeline.js +5 -5
  65. package/dist/referenceStrip.js +9 -9
  66. package/dist/renderer/GeometryBuilder.js +8 -8
  67. package/dist/renderer/walkLanes.js +4 -2
  68. package/dist/tubeMap/axis.js +5 -5
  69. package/dist/tubeMap/bundle.js +8 -8
  70. package/dist/tubeMap/coarsen.js +8 -8
  71. package/dist/tubeMap/deviations.js +9 -9
  72. package/dist/tubeMap/draw.js +3 -3
  73. package/dist/tubeMap/genes.js +6 -6
  74. package/dist/tubeMap/nodeColors.js +9 -9
  75. package/dist/tubeMap/reads.js +2 -2
  76. package/dist/types/renderer/walkLanes.d.ts +19 -2
  77. package/dist/types/util/geometry.d.ts +1 -1
  78. package/dist/types/version.d.ts +1 -1
  79. package/dist/types/walkEncoding.d.ts +8 -2
  80. package/dist/types/walkHighlight.d.ts +2 -0
  81. package/dist/util/SpatialIndex.js +4 -4
  82. package/dist/util/edgeCurves.js +3 -3
  83. package/dist/util/geometry.js +1 -1
  84. package/dist/util/hitDetection.js +5 -5
  85. package/dist/version.js +1 -1
  86. package/dist/viewport.js +6 -6
  87. package/dist/walkEncoding.js +13 -11
  88. package/dist/walkHighlight.js +10 -10
  89. package/dist/walkKey.js +5 -5
  90. package/package.json +1 -1
package/dist/layout/mergeRuns.js CHANGED
@@ -3,8 +3,8 @@ import {
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  polylineMidpoint,
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  polylineSlice,
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  splitRuns
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- } from "../chunks/chunk-YIWN32ZX.js";
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- import "../chunks/chunk-735MPLUL.js";
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+ } from "../chunks/chunk-HNNP5QUN.js";
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+ import "../chunks/chunk-JJV2GT2Z.js";
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  import "../chunks/chunk-CPMHA4W5.js";
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  import "../chunks/chunk-BSOZW3FC.js";
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  import "../chunks/chunk-RJWPJCIB.js";
package/dist/layout/orientToReference.js CHANGED
@@ -1,7 +1,7 @@
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  import {
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  orientToReference
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- } from "../chunks/chunk-22ZMVREZ.js";
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- import "../chunks/chunk-735MPLUL.js";
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+ } from "../chunks/chunk-NAYS472K.js";
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+ import "../chunks/chunk-JJV2GT2Z.js";
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  import "../chunks/chunk-CPMHA4W5.js";
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  import "../chunks/chunk-RJWPJCIB.js";
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  import "../chunks/chunk-HOAIOEI7.js";
package/dist/layout/tubeMapLayout.js CHANGED
@@ -5,22 +5,22 @@ import {
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  tubeMapLayout,
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  tubeMapReferenceLayout,
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  tubeMapTracks
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- } from "../chunks/chunk-G4WQBRDS.js";
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- import "../chunks/chunk-J4PDHWP2.js";
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+ } from "../chunks/chunk-BDS5VZYZ.js";
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+ import "../chunks/chunk-KKHXMJEE.js";
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  import "../chunks/chunk-5OJZV6YT.js";
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  import "../chunks/chunk-C3KAPREU.js";
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  import "../chunks/chunk-LODKC7PJ.js";
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- import "../chunks/chunk-JKIAHYAW.js";
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+ import "../chunks/chunk-VQ353UDK.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-6CXLLJ2C.js";
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+ import "../chunks/chunk-AURNOR27.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-YIWN32ZX.js";
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- import "../chunks/chunk-3CXZUC2Y.js";
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+ import "../chunks/chunk-HNNP5QUN.js";
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+ import "../chunks/chunk-3GORESBG.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-735MPLUL.js";
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+ import "../chunks/chunk-JJV2GT2Z.js";
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  import "../chunks/chunk-CPMHA4W5.js";
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  import "../chunks/chunk-ZPZ7GNBT.js";
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package/dist/layout/walkRowDraw.js CHANGED
@@ -30,25 +30,25 @@ import {
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  walkRowsKey,
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  walkRowsKeyTree,
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  walkRowsTree
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- } from "../chunks/chunk-LA6JHEVV.js";
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+ } from "../chunks/chunk-ALOF5SOT.js";
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  import "../chunks/chunk-H2H4Y3TV.js";
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- import "../chunks/chunk-2H3ALI6L.js";
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- import "../chunks/chunk-7GDNDQD7.js";
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+ import "../chunks/chunk-53DZE3SA.js";
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+ import "../chunks/chunk-4KBZ7WPP.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-VSRRIFRF.js";
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- import "../chunks/chunk-JKIAHYAW.js";
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+ import "../chunks/chunk-P2GJBFNA.js";
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+ import "../chunks/chunk-VQ353UDK.js";
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  import "../chunks/chunk-ZANALBSX.js";
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  import "../chunks/chunk-VX656OAZ.js";
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  import "../chunks/chunk-LG2UK4MB.js";
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- import "../chunks/chunk-6CXLLJ2C.js";
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+ import "../chunks/chunk-AURNOR27.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-YIWN32ZX.js";
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- import "../chunks/chunk-3CXZUC2Y.js";
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+ import "../chunks/chunk-HNNP5QUN.js";
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+ import "../chunks/chunk-3GORESBG.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-735MPLUL.js";
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+ import "../chunks/chunk-JJV2GT2Z.js";
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  import "../chunks/chunk-CPMHA4W5.js";
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  import "../chunks/chunk-ZPZ7GNBT.js";
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  import "../chunks/chunk-BSOZW3FC.js";
package/dist/layout/walkStrip.js CHANGED
@@ -9,32 +9,32 @@ import {
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  walkStripApplies,
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  walkStripFrame,
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  walkStripLabelsTree
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- } from "../chunks/chunk-4OVIUCSB.js";
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+ } from "../chunks/chunk-77O67GIB.js";
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  import {
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  LABELLED_ROW_PX
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- } from "../chunks/chunk-LA6JHEVV.js";
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+ } from "../chunks/chunk-ALOF5SOT.js";
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  import "../chunks/chunk-H2H4Y3TV.js";
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- import "../chunks/chunk-2H3ALI6L.js";
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- import "../chunks/chunk-7GDNDQD7.js";
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+ import "../chunks/chunk-53DZE3SA.js";
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+ import "../chunks/chunk-4KBZ7WPP.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-VSRRIFRF.js";
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+ import "../chunks/chunk-P2GJBFNA.js";
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  import "../chunks/chunk-VCUOYVLC.js";
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  import "../chunks/chunk-C3KAPREU.js";
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  import "../chunks/chunk-LODKC7PJ.js";
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- import "../chunks/chunk-JKIAHYAW.js";
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+ import "../chunks/chunk-VQ353UDK.js";
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  import "../chunks/chunk-ZANALBSX.js";
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  import "../chunks/chunk-7L7MN2OM.js";
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  import "../chunks/chunk-VX656OAZ.js";
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  import "../chunks/chunk-LG2UK4MB.js";
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- import "../chunks/chunk-6CXLLJ2C.js";
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+ import "../chunks/chunk-AURNOR27.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-YIWN32ZX.js";
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- import "../chunks/chunk-3CXZUC2Y.js";
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+ import "../chunks/chunk-HNNP5QUN.js";
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+ import "../chunks/chunk-3GORESBG.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-735MPLUL.js";
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+ import "../chunks/chunk-JJV2GT2Z.js";
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package/dist/layoutModes.js CHANGED
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  LAYOUT_MODE_VALUES,
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  layoutModeByValue,
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  modeUsesLayoutEngine
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- } from "./chunks/chunk-3XYLEK4H.js";
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- import "./chunks/chunk-G4WQBRDS.js";
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- import "./chunks/chunk-J4PDHWP2.js";
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+ } from "./chunks/chunk-ARXDNQLF.js";
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+ import "./chunks/chunk-BDS5VZYZ.js";
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+ import "./chunks/chunk-KKHXMJEE.js";
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  import "./chunks/chunk-XR2HMGAS.js";
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  import "./chunks/chunk-GJLZ2MKE.js";
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@@ -16,18 +16,18 @@ import "./chunks/chunk-3GLG3ZLE.js";
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  import "./chunks/chunk-VCUOYVLC.js";
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- import "./chunks/chunk-JKIAHYAW.js";
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+ import "./chunks/chunk-VQ353UDK.js";
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+ import "./chunks/chunk-AURNOR27.js";
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- import "./chunks/chunk-YIWN32ZX.js";
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- import "./chunks/chunk-3CXZUC2Y.js";
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+ import "./chunks/chunk-HNNP5QUN.js";
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+ import "./chunks/chunk-3GORESBG.js";
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- import "./chunks/chunk-735MPLUL.js";
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+ import "./chunks/chunk-JJV2GT2Z.js";
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package/dist/pathColors.js CHANGED
@@ -9,15 +9,15 @@ import {
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  pathLegend,
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  walkLabelsOf
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- } from "./chunks/chunk-JKIAHYAW.js";
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- import "./chunks/chunk-6CXLLJ2C.js";
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+ } from "./chunks/chunk-VQ353UDK.js";
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+ import "./chunks/chunk-AURNOR27.js";
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- import "./chunks/chunk-YIWN32ZX.js";
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- import "./chunks/chunk-3CXZUC2Y.js";
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+ import "./chunks/chunk-HNNP5QUN.js";
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+ import "./chunks/chunk-3GORESBG.js";
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+ import "./chunks/chunk-JJV2GT2Z.js";
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package/dist/pipeline.js CHANGED
@@ -11,9 +11,9 @@ import {
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  loadGraph
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- } from "./chunks/chunk-S3ICPPXC.js";
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+ } from "./chunks/chunk-JVT3XTKN.js";
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  import "./chunks/chunk-OPPVSPEF.js";
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- import "./chunks/chunk-22ZMVREZ.js";
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+ import "./chunks/chunk-NAYS472K.js";
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@@ -23,13 +23,13 @@ import "./chunks/chunk-7L7MN2OM.js";
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- import "./chunks/chunk-YIWN32ZX.js";
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+ import "./chunks/chunk-HNNP5QUN.js";
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package/dist/referenceStrip.js CHANGED
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- } from "./chunks/chunk-NQWEYJDD.js";
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- import "./chunks/chunk-2H3ALI6L.js";
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- import "./chunks/chunk-7GDNDQD7.js";
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+ } from "./chunks/chunk-SPEB75UH.js";
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+ import "./chunks/chunk-53DZE3SA.js";
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+ import "./chunks/chunk-4KBZ7WPP.js";
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- import "./chunks/chunk-JKIAHYAW.js";
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+ import "./chunks/chunk-P2GJBFNA.js";
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+ import "./chunks/chunk-VQ353UDK.js";
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- import "./chunks/chunk-6CXLLJ2C.js";
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+ import "./chunks/chunk-AURNOR27.js";
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+ import "./chunks/chunk-HNNP5QUN.js";
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+ import "./chunks/chunk-3GORESBG.js";
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package/dist/renderer/GeometryBuilder.js CHANGED
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- } from "../chunks/chunk-2H3ALI6L.js";
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- import "../chunks/chunk-7GDNDQD7.js";
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+ } from "../chunks/chunk-53DZE3SA.js";
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+ import "../chunks/chunk-4KBZ7WPP.js";
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  import {
18
18
  REFERENCE_RAMP_MAX_HUE
19
19
  } from "../chunks/chunk-GQZVR5DW.js";
20
- import "../chunks/chunk-VSRRIFRF.js";
21
- import "../chunks/chunk-JKIAHYAW.js";
20
+ import "../chunks/chunk-P2GJBFNA.js";
21
+ import "../chunks/chunk-VQ353UDK.js";
22
22
  import "../chunks/chunk-ZANALBSX.js";
23
23
  import "../chunks/chunk-VX656OAZ.js";
24
- import "../chunks/chunk-6CXLLJ2C.js";
24
+ import "../chunks/chunk-AURNOR27.js";
25
25
  import "../chunks/chunk-HMXCN6PG.js";
26
26
  import "../chunks/chunk-AB35TJST.js";
27
- import "../chunks/chunk-YIWN32ZX.js";
28
- import "../chunks/chunk-3CXZUC2Y.js";
27
+ import "../chunks/chunk-HNNP5QUN.js";
28
+ import "../chunks/chunk-3GORESBG.js";
29
29
  import "../chunks/chunk-TLWXLNLY.js";
30
30
  import "../chunks/chunk-3YBP46PB.js";
31
- import "../chunks/chunk-735MPLUL.js";
31
+ import "../chunks/chunk-JJV2GT2Z.js";
32
32
  import "../chunks/chunk-CPMHA4W5.js";
33
33
  import "../chunks/chunk-ZPZ7GNBT.js";
34
34
  import "../chunks/chunk-BSOZW3FC.js";
package/dist/renderer/walkLanes.js CHANGED
@@ -14,12 +14,13 @@ import {
14
14
  laneLines,
15
15
  laneRuns,
16
16
  laneSlideAt,
17
+ liftLanes,
17
18
  passesKey,
18
19
  slotCentres,
19
20
  threadsPasses,
20
21
  walkThreads
21
- } from "../chunks/chunk-7GDNDQD7.js";
22
- import "../chunks/chunk-735MPLUL.js";
22
+ } from "../chunks/chunk-4KBZ7WPP.js";
23
+ import "../chunks/chunk-JJV2GT2Z.js";
23
24
  import "../chunks/chunk-CPMHA4W5.js";
24
25
  export {
25
26
  LANE_SMOOTHING_PX,
@@ -37,6 +38,7 @@ export {
37
38
  laneLines,
38
39
  laneRuns,
39
40
  laneSlideAt,
41
+ liftLanes,
40
42
  passesKey,
41
43
  slotCentres,
42
44
  threadsPasses,
package/dist/tubeMap/axis.js CHANGED
@@ -7,15 +7,15 @@ import {
7
7
  rulerMarks,
8
8
  tubeSpan,
9
9
  tubeX
10
- } from "../chunks/chunk-XOIYBEU7.js";
11
- import "../chunks/chunk-6CXLLJ2C.js";
10
+ } from "../chunks/chunk-I53QYITQ.js";
11
+ import "../chunks/chunk-AURNOR27.js";
12
12
  import "../chunks/chunk-HMXCN6PG.js";
13
13
  import "../chunks/chunk-AB35TJST.js";
14
- import "../chunks/chunk-YIWN32ZX.js";
15
- import "../chunks/chunk-3CXZUC2Y.js";
14
+ import "../chunks/chunk-HNNP5QUN.js";
15
+ import "../chunks/chunk-3GORESBG.js";
16
16
  import "../chunks/chunk-TLWXLNLY.js";
17
17
  import "../chunks/chunk-3YBP46PB.js";
18
- import "../chunks/chunk-735MPLUL.js";
18
+ import "../chunks/chunk-JJV2GT2Z.js";
19
19
  import "../chunks/chunk-CPMHA4W5.js";
20
20
  import "../chunks/chunk-ZPZ7GNBT.js";
21
21
  import "../chunks/chunk-BSOZW3FC.js";
package/dist/tubeMap/bundle.js CHANGED
@@ -1,22 +1,22 @@
1
1
  import {
2
2
  bundleRoutes
3
- } from "../chunks/chunk-AXE3RR7J.js";
4
- import "../chunks/chunk-G4WQBRDS.js";
5
- import "../chunks/chunk-J4PDHWP2.js";
3
+ } from "../chunks/chunk-S6E3PMH7.js";
4
+ import "../chunks/chunk-BDS5VZYZ.js";
5
+ import "../chunks/chunk-KKHXMJEE.js";
6
6
  import "../chunks/chunk-5OJZV6YT.js";
7
7
  import "../chunks/chunk-C3KAPREU.js";
8
8
  import "../chunks/chunk-LODKC7PJ.js";
9
- import "../chunks/chunk-JKIAHYAW.js";
9
+ import "../chunks/chunk-VQ353UDK.js";
10
10
  import "../chunks/chunk-7L7MN2OM.js";
11
11
  import "../chunks/chunk-LG2UK4MB.js";
12
- import "../chunks/chunk-6CXLLJ2C.js";
12
+ import "../chunks/chunk-AURNOR27.js";
13
13
  import "../chunks/chunk-HMXCN6PG.js";
14
14
  import "../chunks/chunk-AB35TJST.js";
15
- import "../chunks/chunk-YIWN32ZX.js";
16
- import "../chunks/chunk-3CXZUC2Y.js";
15
+ import "../chunks/chunk-HNNP5QUN.js";
16
+ import "../chunks/chunk-3GORESBG.js";
17
17
  import "../chunks/chunk-TLWXLNLY.js";
18
18
  import "../chunks/chunk-3YBP46PB.js";
19
- import "../chunks/chunk-735MPLUL.js";
19
+ import "../chunks/chunk-JJV2GT2Z.js";
20
20
  import "../chunks/chunk-CPMHA4W5.js";
21
21
  import "../chunks/chunk-ZPZ7GNBT.js";
22
22
  import "../chunks/chunk-BSOZW3FC.js";
package/dist/tubeMap/coarsen.js CHANGED
@@ -1,23 +1,23 @@
1
1
  import {
2
2
  coarsenTubeMap,
3
3
  lastAtMost
4
- } from "../chunks/chunk-YEDZ37PH.js";
5
- import "../chunks/chunk-G4WQBRDS.js";
6
- import "../chunks/chunk-J4PDHWP2.js";
4
+ } from "../chunks/chunk-VNCHWWLG.js";
5
+ import "../chunks/chunk-BDS5VZYZ.js";
6
+ import "../chunks/chunk-KKHXMJEE.js";
7
7
  import "../chunks/chunk-5OJZV6YT.js";
8
8
  import "../chunks/chunk-C3KAPREU.js";
9
9
  import "../chunks/chunk-LODKC7PJ.js";
10
- import "../chunks/chunk-JKIAHYAW.js";
10
+ import "../chunks/chunk-VQ353UDK.js";
11
11
  import "../chunks/chunk-7L7MN2OM.js";
12
12
  import "../chunks/chunk-LG2UK4MB.js";
13
- import "../chunks/chunk-6CXLLJ2C.js";
13
+ import "../chunks/chunk-AURNOR27.js";
14
14
  import "../chunks/chunk-HMXCN6PG.js";
15
15
  import "../chunks/chunk-AB35TJST.js";
16
- import "../chunks/chunk-YIWN32ZX.js";
17
- import "../chunks/chunk-3CXZUC2Y.js";
16
+ import "../chunks/chunk-HNNP5QUN.js";
17
+ import "../chunks/chunk-3GORESBG.js";
18
18
  import "../chunks/chunk-TLWXLNLY.js";
19
19
  import "../chunks/chunk-3YBP46PB.js";
20
- import "../chunks/chunk-735MPLUL.js";
20
+ import "../chunks/chunk-JJV2GT2Z.js";
21
21
  import "../chunks/chunk-CPMHA4W5.js";
22
22
  import "../chunks/chunk-ZPZ7GNBT.js";
23
23
  import "../chunks/chunk-BSOZW3FC.js";
package/dist/tubeMap/deviations.js CHANGED
@@ -1,28 +1,28 @@
1
1
  import {
2
2
  lastAtMost
3
- } from "../chunks/chunk-YEDZ37PH.js";
3
+ } from "../chunks/chunk-VNCHWWLG.js";
4
4
  import {
5
5
  boxX,
6
6
  referenceBoxes
7
- } from "../chunks/chunk-XOIYBEU7.js";
8
- import "../chunks/chunk-G4WQBRDS.js";
9
- import "../chunks/chunk-J4PDHWP2.js";
7
+ } from "../chunks/chunk-I53QYITQ.js";
8
+ import "../chunks/chunk-BDS5VZYZ.js";
9
+ import "../chunks/chunk-KKHXMJEE.js";
10
10
  import "../chunks/chunk-5OJZV6YT.js";
11
11
  import "../chunks/chunk-C3KAPREU.js";
12
12
  import "../chunks/chunk-LODKC7PJ.js";
13
- import "../chunks/chunk-JKIAHYAW.js";
13
+ import "../chunks/chunk-VQ353UDK.js";
14
14
  import "../chunks/chunk-7L7MN2OM.js";
15
15
  import "../chunks/chunk-LG2UK4MB.js";
16
- import "../chunks/chunk-6CXLLJ2C.js";
16
+ import "../chunks/chunk-AURNOR27.js";
17
17
  import "../chunks/chunk-HMXCN6PG.js";
18
18
  import "../chunks/chunk-AB35TJST.js";
19
- import "../chunks/chunk-YIWN32ZX.js";
20
- import "../chunks/chunk-3CXZUC2Y.js";
19
+ import "../chunks/chunk-HNNP5QUN.js";
20
+ import "../chunks/chunk-3GORESBG.js";
21
21
  import "../chunks/chunk-TLWXLNLY.js";
22
22
  import {
23
23
  pathOrigin
24
24
  } from "../chunks/chunk-3YBP46PB.js";
25
- import "../chunks/chunk-735MPLUL.js";
25
+ import "../chunks/chunk-JJV2GT2Z.js";
26
26
  import "../chunks/chunk-CPMHA4W5.js";
27
27
  import "../chunks/chunk-ZPZ7GNBT.js";
28
28
  import {
package/dist/tubeMap/draw.js CHANGED
@@ -8,17 +8,17 @@ import {
8
8
  tubeMapMismatchAt,
9
9
  tubeMapPicture,
10
10
  tubeMapTrackAt
11
- } from "../chunks/chunk-S7BCZVRK.js";
11
+ } from "../chunks/chunk-HIN56TLA.js";
12
12
  import "../chunks/chunk-BX4AUMZE.js";
13
13
  import "../chunks/chunk-MYDHU2UV.js";
14
- import "../chunks/chunk-J4PDHWP2.js";
14
+ import "../chunks/chunk-KKHXMJEE.js";
15
15
  import "../chunks/chunk-5OJZV6YT.js";
16
16
  import "../chunks/chunk-C3KAPREU.js";
17
17
  import "../chunks/chunk-LODKC7PJ.js";
18
18
  import "../chunks/chunk-7L7MN2OM.js";
19
19
  import "../chunks/chunk-LG2UK4MB.js";
20
20
  import "../chunks/chunk-3YBP46PB.js";
21
- import "../chunks/chunk-735MPLUL.js";
21
+ import "../chunks/chunk-JJV2GT2Z.js";
22
22
  import "../chunks/chunk-CPMHA4W5.js";
23
23
  import "../chunks/chunk-ZPZ7GNBT.js";
24
24
  import "../chunks/chunk-BSOZW3FC.js";
package/dist/tubeMap/genes.js CHANGED
@@ -3,16 +3,16 @@ import {
3
3
  drawTubeMapGenes,
4
4
  tubeMapGeneRows,
5
5
  tubeMapGenes
6
- } from "../chunks/chunk-N2GAA7RB.js";
7
- import "../chunks/chunk-XOIYBEU7.js";
8
- import "../chunks/chunk-6CXLLJ2C.js";
6
+ } from "../chunks/chunk-RT4U3DH3.js";
7
+ import "../chunks/chunk-I53QYITQ.js";
8
+ import "../chunks/chunk-AURNOR27.js";
9
9
  import "../chunks/chunk-HMXCN6PG.js";
10
10
  import "../chunks/chunk-AB35TJST.js";
11
- import "../chunks/chunk-YIWN32ZX.js";
12
- import "../chunks/chunk-3CXZUC2Y.js";
11
+ import "../chunks/chunk-HNNP5QUN.js";
12
+ import "../chunks/chunk-3GORESBG.js";
13
13
  import "../chunks/chunk-TLWXLNLY.js";
14
14
  import "../chunks/chunk-3YBP46PB.js";
15
- import "../chunks/chunk-735MPLUL.js";
15
+ import "../chunks/chunk-JJV2GT2Z.js";
16
16
  import "../chunks/chunk-CPMHA4W5.js";
17
17
  import "../chunks/chunk-ZPZ7GNBT.js";
18
18
  import "../chunks/chunk-BSOZW3FC.js";
package/dist/tubeMap/nodeColors.js CHANGED
@@ -1,22 +1,22 @@
1
1
  import {
2
2
  tubeMapNodeColors
3
- } from "../chunks/chunk-ZKIH2USC.js";
4
- import "../chunks/chunk-2H3ALI6L.js";
5
- import "../chunks/chunk-7GDNDQD7.js";
3
+ } from "../chunks/chunk-337LZP7C.js";
4
+ import "../chunks/chunk-53DZE3SA.js";
5
+ import "../chunks/chunk-4KBZ7WPP.js";
6
6
  import "../chunks/chunk-G2FD7S3C.js";
7
7
  import "../chunks/chunk-GQZVR5DW.js";
8
- import "../chunks/chunk-VSRRIFRF.js";
9
- import "../chunks/chunk-JKIAHYAW.js";
8
+ import "../chunks/chunk-P2GJBFNA.js";
9
+ import "../chunks/chunk-VQ353UDK.js";
10
10
  import "../chunks/chunk-ZANALBSX.js";
11
11
  import "../chunks/chunk-VX656OAZ.js";
12
- import "../chunks/chunk-6CXLLJ2C.js";
12
+ import "../chunks/chunk-AURNOR27.js";
13
13
  import "../chunks/chunk-HMXCN6PG.js";
14
14
  import "../chunks/chunk-AB35TJST.js";
15
- import "../chunks/chunk-YIWN32ZX.js";
16
- import "../chunks/chunk-3CXZUC2Y.js";
15
+ import "../chunks/chunk-HNNP5QUN.js";
16
+ import "../chunks/chunk-3GORESBG.js";
17
17
  import "../chunks/chunk-TLWXLNLY.js";
18
18
  import "../chunks/chunk-3YBP46PB.js";
19
- import "../chunks/chunk-735MPLUL.js";
19
+ import "../chunks/chunk-JJV2GT2Z.js";
20
20
  import "../chunks/chunk-CPMHA4W5.js";
21
21
  import "../chunks/chunk-ZPZ7GNBT.js";
22
22
  import "../chunks/chunk-BSOZW3FC.js";
package/dist/tubeMap/reads.js CHANGED
@@ -4,9 +4,9 @@ import {
4
4
  readColor,
5
5
  stepName,
6
6
  tubeMapReads
7
- } from "../chunks/chunk-J4PDHWP2.js";
7
+ } from "../chunks/chunk-KKHXMJEE.js";
8
8
  import "../chunks/chunk-5OJZV6YT.js";
9
- import "../chunks/chunk-735MPLUL.js";
9
+ import "../chunks/chunk-JJV2GT2Z.js";
10
10
  import "../chunks/chunk-CPMHA4W5.js";
11
11
  export {
12
12
  FORWARD_READ_COLORS,
package/dist/types/renderer/walkLanes.d.ts CHANGED
@@ -1,5 +1,6 @@
1
1
  import type { LaneSlide } from './types.js';
2
2
  import type { NodeSegment } from '../types.js';
3
+ import type { LiftedWalk } from '../walkHighlight.js';
3
4
  export declare const THREAD_PX = 2;
4
5
  export declare const THREAD_GAP_PX = 1.5;
5
6
  export declare const SLOT_GAP_PX = 4;
@@ -46,8 +47,9 @@ export declare function laneLines(lanes: LaneRuns, nodePositions: Record<string,
46
47
  };
47
48
  export interface WalkThreads {
48
49
  span: ReadonlyMap<string, number>;
49
- nodeThreads: Map<string, number[]>;
50
- linkThreads: Map<string, [number, number][]>;
50
+ nodeThreads: Map<string, readonly number[]>;
51
+ threadPasses: Map<string, readonly number[]>;
52
+ linkThreads: Map<string, Map<string, [number, number][]>>;
51
53
  }
52
54
  export declare function walkThreads(route: readonly (readonly string[])[], passes: ReadonlyMap<string, number>, nodePositions: Record<string, NodeSegment[]>, yToX: number, reach: number): WalkThreads;
53
55
  export declare function bandSpans(lanes: LaneRuns, spans: readonly ReadonlyMap<string, number>[], { reach, taper }: {
@@ -57,4 +59,19 @@ export declare function bandSpans(lanes: LaneRuns, spans: readonly ReadonlyMap<s
57
59
  slot: number[];
58
60
  held: number[];
59
61
  }>;
62
+ export declare function liftLanes(walks: readonly LiftedWalk[], nodePositions: Record<string, NodeSegment[]>, yToX: number, worldPerScreenPx: number): {
63
+ lines: {
64
+ normals: Map<string, (Normal | undefined)[]>;
65
+ shifts: Map<string, (Shift | undefined)[]>;
66
+ };
67
+ threads: WalkThreads[] | undefined;
68
+ spans: Map<string, {
69
+ slot: number[];
70
+ held: number[];
71
+ }> | undefined;
72
+ furthestShift: {
73
+ dx: number;
74
+ dy: number;
75
+ };
76
+ };
60
77
  export {};
package/dist/types/util/geometry.d.ts CHANGED
@@ -43,7 +43,7 @@ export interface Slide {
43
43
  dy: number;
44
44
  }
45
45
  export declare const slideAt: (from: Slide, to: Slide, along: number) => Slide;
46
- export declare function slideCurves(curves: BezierCurve[], from: Slide, to: Slide): BezierCurve[];
46
+ export declare function slideCurves(curves: BezierCurve[], fromDx: number, fromDy: number, toDx: number, toDy: number): BezierCurve[];
47
47
  export declare function translateCurves(curves: BezierCurve[], dx: number, dy: number): BezierCurve[];
48
48
  type Side = 'start' | 'end';
49
49
  export interface EdgeSides {
package/dist/types/version.d.ts CHANGED
@@ -1 +1 @@
1
- export declare const version = "11.8.0";
1
+ export declare const version = "11.10.0";
package/dist/types/walkEncoding.d.ts CHANGED
@@ -29,6 +29,10 @@ export declare const WALK_SCHEMES: readonly [{
29
29
  readonly value: "green";
30
30
  readonly label: "Lime to forest";
31
31
  readonly ends: readonly ["#b6e36c", "#0b5d3b"];
32
+ }, {
33
+ readonly value: "orange";
34
+ readonly label: "Peach to rust";
35
+ readonly ends: readonly ["#ffc285", "#8f3a00"];
32
36
  }, {
33
37
  readonly value: "rainbow";
34
38
  readonly label: "Rainbow";
@@ -39,18 +43,20 @@ export interface WalkEncoding {
39
43
  scheme: WalkScheme;
40
44
  darkest?: number;
41
45
  shade?: number;
46
+ stretch?: readonly [number, number];
42
47
  }
43
48
  export interface WalkLayer {
44
49
  walk: string;
45
50
  color?: Partial<WalkEncoding>;
46
51
  }
47
52
  export declare function resolveEncoding(layer: WalkLayer, reference: boolean, picked: number, alone?: boolean): WalkEncoding;
53
+ export declare function splitFamilies(encodings: readonly WalkEncoding[]): WalkEncoding[];
48
54
  export declare function schemeRgb(scheme: WalkScheme, t: number, darkest?: number): number[];
49
55
  export declare function schemeCss(scheme: WalkScheme, t: number, darkest?: number): string;
50
56
  export declare function schemeColor(scheme: WalkScheme, t: number, darkest?: number): number;
51
- export declare function encodedColor({ field, scheme, darkest, shade }: WalkEncoding, t?: number): number;
57
+ export declare function encodedColor(encoding: WalkEncoding, t?: number): number;
52
58
  export declare const NO_VALUE_COLOR: number;
53
- export declare function encodingStops({ field, scheme, darkest, shade, }: WalkEncoding): {
59
+ export declare function encodingStops(encoding: WalkEncoding): {
54
60
  offset: number;
55
61
  color: string;
56
62
  abgr: number;
package/dist/types/walkHighlight.d.ts CHANGED
@@ -7,6 +7,7 @@ export interface WalkHighlight {
7
7
  nodeIds: Set<string>;
8
8
  edgeIndexes: Set<number>;
9
9
  progress: Map<string, number>;
10
+ passProgress: Map<string, number[]>;
10
11
  passes: Map<string, number>;
11
12
  mostPasses: number;
12
13
  route: readonly (readonly string[])[];
@@ -24,6 +25,7 @@ export interface WalkHighlight {
24
25
  export interface LiftedWalk extends WalkHighlight {
25
26
  encoding: WalkEncoding;
26
27
  colors: Map<string, number>;
28
+ passColors: Map<string, number[]>;
27
29
  reversed: Set<string>;
28
30
  reversedBp: number;
29
31
  }