@jbrowse/bandage-core 11.6.1 → 11.7.1

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 (99) hide show
  1. package/dist/bubbles/bubbleHalos.js +5 -4
  2. package/dist/bubbles/classifyBubble.js +4 -3
  3. package/dist/bubbles/superbubbles.js +6 -5
  4. package/dist/chunks/{chunk-BW2NMXRV.js → chunk-3UGWYQNY.js} +1 -1
  5. package/dist/chunks/{chunk-YEYQFNFQ.js → chunk-3WSA4NNP.js} +1 -1
  6. package/dist/chunks/{chunk-SNF2MIEF.js → chunk-3Y2EFDID.js} +1 -1
  7. package/dist/chunks/{chunk-DV5B5UU7.js → chunk-5NZRT7GL.js} +5 -1
  8. package/dist/chunks/{chunk-MXLYBDOX.js → chunk-6XDTAKO7.js} +13 -7
  9. package/dist/chunks/{chunk-W2YAW36J.js → chunk-7L7MN2OM.js} +5 -2
  10. package/dist/chunks/{chunk-EVXXFMZ7.js → chunk-APLWFV4I.js} +3 -3
  11. package/dist/chunks/{chunk-KA4F3N55.js → chunk-ATDVS2CW.js} +2 -2
  12. package/dist/chunks/{chunk-MEVTV4FI.js → chunk-BXE3SBBN.js} +1 -1
  13. package/dist/chunks/{chunk-WI6SUU5B.js → chunk-CWCVQJYY.js} +1 -1
  14. package/dist/chunks/{chunk-BVWMVWLJ.js → chunk-EZGNBDHD.js} +8 -8
  15. package/dist/chunks/{chunk-4WXFQOYV.js → chunk-F7O56DVR.js} +2 -2
  16. package/dist/chunks/{chunk-RLCYVZ4B.js → chunk-FBPAX5K6.js} +1 -1
  17. package/dist/chunks/{chunk-5WB7O7IT.js → chunk-FNDNSDKW.js} +1 -1
  18. package/dist/chunks/{chunk-T3H5ELLA.js → chunk-FU57ZNRQ.js} +1 -1
  19. package/dist/chunks/{chunk-D3E7AXBB.js → chunk-G7SG4XMK.js} +23 -6
  20. package/dist/chunks/{chunk-HV35LDYH.js → chunk-HMEAGAGC.js} +1 -1
  21. package/dist/chunks/{chunk-7OTWJQGA.js → chunk-HTF32WSW.js} +4 -4
  22. package/dist/chunks/{chunk-2XEAITWM.js → chunk-I5SGYTRM.js} +1 -1
  23. package/dist/chunks/{chunk-6YRSOL4K.js → chunk-IN4IYSA2.js} +1 -1
  24. package/dist/chunks/{chunk-C6E6HXP5.js → chunk-J6XHW4KI.js} +2 -2
  25. package/dist/chunks/{chunk-KZMSSPS6.js → chunk-JGH2V54E.js} +1 -1
  26. package/dist/chunks/{chunk-OUM54ZSQ.js → chunk-JLIVX2SF.js} +1 -1
  27. package/dist/chunks/{chunk-EIY2SKD3.js → chunk-LG2UK4MB.js} +2 -1
  28. package/dist/chunks/{chunk-XXOBCANT.js → chunk-LKQOIPGE.js} +8 -8
  29. package/dist/chunks/{chunk-F3KQQDKP.js → chunk-OXW5OHYQ.js} +1 -1
  30. package/dist/chunks/{chunk-GZ36HNPJ.js → chunk-PCHEUVHB.js} +1 -1
  31. package/dist/chunks/{chunk-VO6FKNZE.js → chunk-PJWLYGRL.js} +1 -1
  32. package/dist/chunks/{chunk-56L6R6D2.js → chunk-Q7I563MH.js} +1 -1
  33. package/dist/chunks/{chunk-NXBW6KY6.js → chunk-RB2MDFQU.js} +2 -2
  34. package/dist/chunks/{chunk-ROLACYCO.js → chunk-RK7ZOFPR.js} +12 -12
  35. package/dist/chunks/{chunk-QCOVHLJO.js → chunk-RT4K2JMZ.js} +1 -1
  36. package/dist/chunks/{chunk-3FWNQNF7.js → chunk-SACSQ45G.js} +1 -1
  37. package/dist/chunks/{chunk-P5PBJONQ.js → chunk-SENPGW4O.js} +1 -1
  38. package/dist/chunks/{chunk-TXTSE44S.js → chunk-TCSV3II7.js} +1 -1
  39. package/dist/chunks/chunk-TLWXLNLY.js +124 -0
  40. package/dist/chunks/{chunk-2C5SATRZ.js → chunk-TUMJNAOL.js} +1 -1
  41. package/dist/chunks/{chunk-JGQQAUVL.js → chunk-UV2IJMIG.js} +2 -2
  42. package/dist/chunks/{chunk-JGHZ3N34.js → chunk-VB4IXIPM.js} +2 -2
  43. package/dist/chunks/{chunk-DZR37KXT.js → chunk-VSSIYQYF.js} +1 -1
  44. package/dist/chunks/{chunk-QD35GH4C.js → chunk-WUZH2OJ6.js} +2 -2
  45. package/dist/chunks/{chunk-OYCQVJYY.js → chunk-XTF2VWJN.js} +1 -1
  46. package/dist/chunks/{chunk-SVVFWTG4.js → chunk-ZKSC7QVE.js} +1 -1
  47. package/dist/cli/figure.js +32 -31
  48. package/dist/cli/fold.js +7 -6
  49. package/dist/deletionEdges.js +2 -1
  50. package/dist/figure.js +27 -26
  51. package/dist/figureData.js +26 -25
  52. package/dist/figureScene.js +19 -18
  53. package/dist/figureSettings.js +8 -7
  54. package/dist/gbzCut.js +4 -4
  55. package/dist/gbzWindow.js +3 -3
  56. package/dist/gfa/gfaConverter.js +2 -2
  57. package/dist/gfa/gfaTables.js +2 -2
  58. package/dist/gfa/graphTables.js +2 -2
  59. package/dist/gfa/walkStops.js +1 -1
  60. package/dist/graphLabels.js +3 -2
  61. package/dist/index.js +42 -41
  62. package/dist/labelLayout.js +7 -6
  63. package/dist/layout/forceCache.js +8 -7
  64. package/dist/layout/trimToWindow.js +9 -101
  65. package/dist/layout/tubeMapLayout.js +9 -8
  66. package/dist/layout/walkRowDraw.js +10 -7
  67. package/dist/layout/walkRowLayout.js +5 -5
  68. package/dist/layout/walkRowRuns.js +3 -3
  69. package/dist/layout/walkRows.js +4 -4
  70. package/dist/layout/walkStrip.js +13 -12
  71. package/dist/layoutModes.js +11 -10
  72. package/dist/pathColors.js +4 -3
  73. package/dist/pipeline.js +7 -6
  74. package/dist/referenceStrip.js +7 -6
  75. package/dist/renderer/GeometryBuilder.js +6 -5
  76. package/dist/tubeMap/axis.js +4 -3
  77. package/dist/tubeMap/bundle.js +10 -9
  78. package/dist/tubeMap/coarsen.js +10 -9
  79. package/dist/tubeMap/deviations.js +11 -10
  80. package/dist/tubeMap/draw.js +5 -5
  81. package/dist/tubeMap/genes.js +5 -4
  82. package/dist/tubeMap/nodeColors.js +7 -6
  83. package/dist/types/deletionEdges.d.ts +1 -1
  84. package/dist/types/gfa/graphTables.d.ts +2 -0
  85. package/dist/types/gfa/walkStops.d.ts +1 -1
  86. package/dist/types/layout/trimToWindow.d.ts +1 -0
  87. package/dist/types/layout/walkRowDraw.d.ts +2 -1
  88. package/dist/types/layout/walkRows.d.ts +1 -0
  89. package/dist/types/types.d.ts +8 -0
  90. package/dist/types/version.d.ts +1 -1
  91. package/dist/util/SpatialIndex.js +4 -3
  92. package/dist/util/edgeCurves.js +3 -2
  93. package/dist/util/hitDetection.js +5 -4
  94. package/dist/version.js +1 -1
  95. package/dist/viewport.js +8 -7
  96. package/dist/walkEncoding.js +7 -6
  97. package/dist/walkHighlight.js +9 -8
  98. package/dist/walkKey.js +5 -4
  99. package/package.json +1 -1
package/dist/layout/tubeMapLayout.js CHANGED
@@ -5,19 +5,20 @@ import {
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  tubeMapLayout,
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  tubeMapReferenceLayout,
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  tubeMapTracks
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- } from "../chunks/chunk-NXBW6KY6.js";
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+ } from "../chunks/chunk-RB2MDFQU.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-MEVTV4FI.js";
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- import "../chunks/chunk-D3E7AXBB.js";
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- import "../chunks/chunk-BW2NMXRV.js";
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- import "../chunks/chunk-W2YAW36J.js";
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- import "../chunks/chunk-EIY2SKD3.js";
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- import "../chunks/chunk-T3H5ELLA.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-3UGWYQNY.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-FU57ZNRQ.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-5NZRT7GL.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/layout/walkRowDraw.js CHANGED
@@ -1,4 +1,5 @@
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  import {
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+ ABRIDGED_GAP,
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  BAR_PX,
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  CALL_TICK,
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  DISAGREES,
@@ -29,21 +30,22 @@ import {
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  walkRowsKey,
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  walkRowsKeyTree,
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  walkRowsTree
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- } from "../chunks/chunk-MXLYBDOX.js";
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+ } from "../chunks/chunk-6XDTAKO7.js";
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  import "../chunks/chunk-H2H4Y3TV.js";
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- import "../chunks/chunk-JGHZ3N34.js";
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+ import "../chunks/chunk-VB4IXIPM.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-XTF2VWJN.js";
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+ import "../chunks/chunk-3UGWYQNY.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-EIY2SKD3.js";
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- import "../chunks/chunk-T3H5ELLA.js";
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+ import "../chunks/chunk-LG2UK4MB.js";
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+ import "../chunks/chunk-FU57ZNRQ.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-5NZRT7GL.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";
@@ -53,6 +55,7 @@ import "../chunks/chunk-RJWPJCIB.js";
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  import "../chunks/chunk-HOAIOEI7.js";
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  import "../chunks/chunk-2JL2JVZ2.js";
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  export {
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+ ABRIDGED_GAP,
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  BAR_PX,
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  CALL_TICK,
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  DISAGREES,
package/dist/layout/walkRowLayout.js CHANGED
@@ -5,11 +5,11 @@ import {
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  walkRowLayout,
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  walkRowLayoutOf,
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  walkRowsExtent
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- } from "../chunks/chunk-P5PBJONQ.js";
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- import "../chunks/chunk-MEVTV4FI.js";
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- import "../chunks/chunk-D3E7AXBB.js";
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- import "../chunks/chunk-W2YAW36J.js";
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- import "../chunks/chunk-EIY2SKD3.js";
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+ } from "../chunks/chunk-SENPGW4O.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-7L7MN2OM.js";
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+ import "../chunks/chunk-LG2UK4MB.js";
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  import "../chunks/chunk-3YBP46PB.js";
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  import "../chunks/chunk-CPMHA4W5.js";
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  import "../chunks/chunk-ZPZ7GNBT.js";
package/dist/layout/walkRowRuns.js CHANGED
@@ -3,9 +3,9 @@ import {
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  runAt,
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  walkRowRuns,
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  walkRowsOf
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- } from "../chunks/chunk-D3E7AXBB.js";
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- import "../chunks/chunk-W2YAW36J.js";
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- import "../chunks/chunk-EIY2SKD3.js";
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+ } from "../chunks/chunk-G7SG4XMK.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-3YBP46PB.js";
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  import "../chunks/chunk-ZPZ7GNBT.js";
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package/dist/layout/walkRows.js CHANGED
@@ -1,12 +1,12 @@
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  import {
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  filterSamples,
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  walkRows
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- } from "../chunks/chunk-MEVTV4FI.js";
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+ } from "../chunks/chunk-BXE3SBBN.js";
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  import {
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  referenceWalkName
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- } from "../chunks/chunk-D3E7AXBB.js";
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- import "../chunks/chunk-W2YAW36J.js";
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- import "../chunks/chunk-EIY2SKD3.js";
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+ } from "../chunks/chunk-G7SG4XMK.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-3YBP46PB.js";
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  import "../chunks/chunk-ZPZ7GNBT.js";
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package/dist/layout/walkStrip.js CHANGED
@@ -9,28 +9,29 @@ import {
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  walkStripApplies,
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  walkStripFrame,
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  walkStripLabelsTree
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- } from "../chunks/chunk-4WXFQOYV.js";
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+ } from "../chunks/chunk-F7O56DVR.js";
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  import {
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  LABELLED_ROW_PX
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- } from "../chunks/chunk-MXLYBDOX.js";
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+ } from "../chunks/chunk-6XDTAKO7.js";
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  import "../chunks/chunk-H2H4Y3TV.js";
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- import "../chunks/chunk-JGHZ3N34.js";
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+ import "../chunks/chunk-VB4IXIPM.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-P5PBJONQ.js";
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- import "../chunks/chunk-MEVTV4FI.js";
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- import "../chunks/chunk-D3E7AXBB.js";
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- import "../chunks/chunk-BW2NMXRV.js";
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+ import "../chunks/chunk-XTF2VWJN.js";
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+ import "../chunks/chunk-SENPGW4O.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-3UGWYQNY.js";
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- import "../chunks/chunk-W2YAW36J.js";
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+ import "../chunks/chunk-7L7MN2OM.js";
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- import "../chunks/chunk-EIY2SKD3.js";
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- import "../chunks/chunk-T3H5ELLA.js";
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+ import "../chunks/chunk-LG2UK4MB.js";
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+ import "../chunks/chunk-FU57ZNRQ.js";
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- import "../chunks/chunk-DV5B5UU7.js";
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+ import "../chunks/chunk-5NZRT7GL.js";
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+ import "../chunks/chunk-TLWXLNLY.js";
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package/dist/layoutModes.js CHANGED
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  modeUsesLayoutEngine
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- } from "./chunks/chunk-QD35GH4C.js";
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- import "./chunks/chunk-NXBW6KY6.js";
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+ } from "./chunks/chunk-WUZH2OJ6.js";
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+ import "./chunks/chunk-RB2MDFQU.js";
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@@ -13,18 +13,19 @@ import "./chunks/chunk-MYLAJDKB.js";
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  import "./chunks/chunk-5OJZV6YT.js";
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  import "./chunks/chunk-UAFATXYA.js";
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- import "./chunks/chunk-P5PBJONQ.js";
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- import "./chunks/chunk-MEVTV4FI.js";
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- import "./chunks/chunk-D3E7AXBB.js";
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- import "./chunks/chunk-BW2NMXRV.js";
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- import "./chunks/chunk-W2YAW36J.js";
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+ import "./chunks/chunk-SENPGW4O.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-3UGWYQNY.js";
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+ import "./chunks/chunk-7L7MN2OM.js";
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- import "./chunks/chunk-EIY2SKD3.js";
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- import "./chunks/chunk-T3H5ELLA.js";
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+ import "./chunks/chunk-LG2UK4MB.js";
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+ import "./chunks/chunk-FU57ZNRQ.js";
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+ import "./chunks/chunk-5NZRT7GL.js";
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+ import "./chunks/chunk-TLWXLNLY.js";
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package/dist/pathColors.js CHANGED
@@ -9,12 +9,13 @@ import {
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- } from "./chunks/chunk-BW2NMXRV.js";
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- import "./chunks/chunk-T3H5ELLA.js";
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+ } from "./chunks/chunk-3UGWYQNY.js";
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+ import "./chunks/chunk-FU57ZNRQ.js";
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- import "./chunks/chunk-DV5B5UU7.js";
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+ import "./chunks/chunk-5NZRT7GL.js";
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+ import "./chunks/chunk-TLWXLNLY.js";
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package/dist/pipeline.js CHANGED
@@ -11,22 +11,23 @@ import {
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- } from "./chunks/chunk-7OTWJQGA.js";
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+ } from "./chunks/chunk-HTF32WSW.js";
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+ import "./chunks/chunk-TUMJNAOL.js";
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+ import "./chunks/chunk-7L7MN2OM.js";
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- import "./chunks/chunk-DZR37KXT.js";
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- import "./chunks/chunk-EIY2SKD3.js";
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+ import "./chunks/chunk-VSSIYQYF.js";
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+ import "./chunks/chunk-LG2UK4MB.js";
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+ import "./chunks/chunk-5NZRT7GL.js";
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+ import "./chunks/chunk-TLWXLNLY.js";
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package/dist/referenceStrip.js CHANGED
@@ -7,19 +7,20 @@ import {
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  stripPixels
10
- } from "./chunks/chunk-QCOVHLJO.js";
11
- import "./chunks/chunk-JGHZ3N34.js";
10
+ } from "./chunks/chunk-RT4K2JMZ.js";
11
+ import "./chunks/chunk-VB4IXIPM.js";
12
12
  import "./chunks/chunk-G2FD7S3C.js";
13
13
  import "./chunks/chunk-GQZVR5DW.js";
14
- import "./chunks/chunk-OYCQVJYY.js";
15
- import "./chunks/chunk-BW2NMXRV.js";
14
+ import "./chunks/chunk-XTF2VWJN.js";
15
+ import "./chunks/chunk-3UGWYQNY.js";
16
16
  import "./chunks/chunk-ZANALBSX.js";
17
17
  import "./chunks/chunk-VX656OAZ.js";
18
- import "./chunks/chunk-T3H5ELLA.js";
18
+ import "./chunks/chunk-FU57ZNRQ.js";
19
19
  import "./chunks/chunk-HMXCN6PG.js";
20
20
  import "./chunks/chunk-AB35TJST.js";
21
21
  import "./chunks/chunk-2VMKQKVO.js";
22
- import "./chunks/chunk-DV5B5UU7.js";
22
+ import "./chunks/chunk-5NZRT7GL.js";
23
+ import "./chunks/chunk-TLWXLNLY.js";
23
24
  import "./chunks/chunk-3YBP46PB.js";
24
25
  import "./chunks/chunk-VACK24HF.js";
25
26
  import "./chunks/chunk-CPMHA4W5.js";
package/dist/renderer/GeometryBuilder.js CHANGED
@@ -11,20 +11,21 @@ import {
11
11
  getNodeColor,
12
12
  hslToRgb,
13
13
  rampFraction
14
- } from "../chunks/chunk-JGHZ3N34.js";
14
+ } from "../chunks/chunk-VB4IXIPM.js";
15
15
  import "../chunks/chunk-G2FD7S3C.js";
16
16
  import {
17
17
  REFERENCE_RAMP_MAX_HUE
18
18
  } from "../chunks/chunk-GQZVR5DW.js";
19
- import "../chunks/chunk-OYCQVJYY.js";
20
- import "../chunks/chunk-BW2NMXRV.js";
19
+ import "../chunks/chunk-XTF2VWJN.js";
20
+ import "../chunks/chunk-3UGWYQNY.js";
21
21
  import "../chunks/chunk-ZANALBSX.js";
22
22
  import "../chunks/chunk-VX656OAZ.js";
23
- import "../chunks/chunk-T3H5ELLA.js";
23
+ import "../chunks/chunk-FU57ZNRQ.js";
24
24
  import "../chunks/chunk-HMXCN6PG.js";
25
25
  import "../chunks/chunk-AB35TJST.js";
26
26
  import "../chunks/chunk-2VMKQKVO.js";
27
- import "../chunks/chunk-DV5B5UU7.js";
27
+ import "../chunks/chunk-5NZRT7GL.js";
28
+ import "../chunks/chunk-TLWXLNLY.js";
28
29
  import "../chunks/chunk-3YBP46PB.js";
29
30
  import "../chunks/chunk-VACK24HF.js";
30
31
  import "../chunks/chunk-CPMHA4W5.js";
package/dist/tubeMap/axis.js CHANGED
@@ -7,12 +7,13 @@ import {
7
7
  rulerMarks,
8
8
  tubeSpan,
9
9
  tubeX
10
- } from "../chunks/chunk-VO6FKNZE.js";
11
- import "../chunks/chunk-T3H5ELLA.js";
10
+ } from "../chunks/chunk-PJWLYGRL.js";
11
+ import "../chunks/chunk-FU57ZNRQ.js";
12
12
  import "../chunks/chunk-HMXCN6PG.js";
13
13
  import "../chunks/chunk-AB35TJST.js";
14
14
  import "../chunks/chunk-2VMKQKVO.js";
15
- import "../chunks/chunk-DV5B5UU7.js";
15
+ import "../chunks/chunk-5NZRT7GL.js";
16
+ import "../chunks/chunk-TLWXLNLY.js";
16
17
  import "../chunks/chunk-3YBP46PB.js";
17
18
  import "../chunks/chunk-VACK24HF.js";
18
19
  import "../chunks/chunk-CPMHA4W5.js";
package/dist/tubeMap/bundle.js CHANGED
@@ -1,19 +1,20 @@
1
1
  import {
2
2
  bundleRoutes
3
- } from "../chunks/chunk-WI6SUU5B.js";
4
- import "../chunks/chunk-NXBW6KY6.js";
3
+ } from "../chunks/chunk-CWCVQJYY.js";
4
+ import "../chunks/chunk-RB2MDFQU.js";
5
5
  import "../chunks/chunk-SDI6BVG7.js";
6
6
  import "../chunks/chunk-5OJZV6YT.js";
7
- import "../chunks/chunk-MEVTV4FI.js";
8
- import "../chunks/chunk-D3E7AXBB.js";
9
- import "../chunks/chunk-BW2NMXRV.js";
10
- import "../chunks/chunk-W2YAW36J.js";
11
- import "../chunks/chunk-EIY2SKD3.js";
12
- import "../chunks/chunk-T3H5ELLA.js";
7
+ import "../chunks/chunk-BXE3SBBN.js";
8
+ import "../chunks/chunk-G7SG4XMK.js";
9
+ import "../chunks/chunk-3UGWYQNY.js";
10
+ import "../chunks/chunk-7L7MN2OM.js";
11
+ import "../chunks/chunk-LG2UK4MB.js";
12
+ import "../chunks/chunk-FU57ZNRQ.js";
13
13
  import "../chunks/chunk-HMXCN6PG.js";
14
14
  import "../chunks/chunk-AB35TJST.js";
15
15
  import "../chunks/chunk-2VMKQKVO.js";
16
- import "../chunks/chunk-DV5B5UU7.js";
16
+ import "../chunks/chunk-5NZRT7GL.js";
17
+ import "../chunks/chunk-TLWXLNLY.js";
17
18
  import "../chunks/chunk-3YBP46PB.js";
18
19
  import "../chunks/chunk-VACK24HF.js";
19
20
  import "../chunks/chunk-CPMHA4W5.js";
package/dist/tubeMap/coarsen.js CHANGED
@@ -1,20 +1,21 @@
1
1
  import {
2
2
  coarsenTubeMap,
3
3
  lastAtMost
4
- } from "../chunks/chunk-OUM54ZSQ.js";
5
- import "../chunks/chunk-NXBW6KY6.js";
4
+ } from "../chunks/chunk-JLIVX2SF.js";
5
+ import "../chunks/chunk-RB2MDFQU.js";
6
6
  import "../chunks/chunk-SDI6BVG7.js";
7
7
  import "../chunks/chunk-5OJZV6YT.js";
8
- import "../chunks/chunk-MEVTV4FI.js";
9
- import "../chunks/chunk-D3E7AXBB.js";
10
- import "../chunks/chunk-BW2NMXRV.js";
11
- import "../chunks/chunk-W2YAW36J.js";
12
- import "../chunks/chunk-EIY2SKD3.js";
13
- import "../chunks/chunk-T3H5ELLA.js";
8
+ import "../chunks/chunk-BXE3SBBN.js";
9
+ import "../chunks/chunk-G7SG4XMK.js";
10
+ import "../chunks/chunk-3UGWYQNY.js";
11
+ import "../chunks/chunk-7L7MN2OM.js";
12
+ import "../chunks/chunk-LG2UK4MB.js";
13
+ import "../chunks/chunk-FU57ZNRQ.js";
14
14
  import "../chunks/chunk-HMXCN6PG.js";
15
15
  import "../chunks/chunk-AB35TJST.js";
16
16
  import "../chunks/chunk-2VMKQKVO.js";
17
- import "../chunks/chunk-DV5B5UU7.js";
17
+ import "../chunks/chunk-5NZRT7GL.js";
18
+ import "../chunks/chunk-TLWXLNLY.js";
18
19
  import "../chunks/chunk-3YBP46PB.js";
19
20
  import "../chunks/chunk-VACK24HF.js";
20
21
  import "../chunks/chunk-CPMHA4W5.js";
package/dist/tubeMap/deviations.js CHANGED
@@ -1,23 +1,24 @@
1
1
  import {
2
2
  lastAtMost
3
- } from "../chunks/chunk-OUM54ZSQ.js";
3
+ } from "../chunks/chunk-JLIVX2SF.js";
4
4
  import {
5
5
  boxX,
6
6
  referenceBoxes
7
- } from "../chunks/chunk-VO6FKNZE.js";
8
- import "../chunks/chunk-NXBW6KY6.js";
7
+ } from "../chunks/chunk-PJWLYGRL.js";
8
+ import "../chunks/chunk-RB2MDFQU.js";
9
9
  import "../chunks/chunk-SDI6BVG7.js";
10
10
  import "../chunks/chunk-5OJZV6YT.js";
11
- import "../chunks/chunk-MEVTV4FI.js";
12
- import "../chunks/chunk-D3E7AXBB.js";
13
- import "../chunks/chunk-BW2NMXRV.js";
14
- import "../chunks/chunk-W2YAW36J.js";
15
- import "../chunks/chunk-EIY2SKD3.js";
16
- import "../chunks/chunk-T3H5ELLA.js";
11
+ import "../chunks/chunk-BXE3SBBN.js";
12
+ import "../chunks/chunk-G7SG4XMK.js";
13
+ import "../chunks/chunk-3UGWYQNY.js";
14
+ import "../chunks/chunk-7L7MN2OM.js";
15
+ import "../chunks/chunk-LG2UK4MB.js";
16
+ import "../chunks/chunk-FU57ZNRQ.js";
17
17
  import "../chunks/chunk-HMXCN6PG.js";
18
18
  import "../chunks/chunk-AB35TJST.js";
19
19
  import "../chunks/chunk-2VMKQKVO.js";
20
- import "../chunks/chunk-DV5B5UU7.js";
20
+ import "../chunks/chunk-5NZRT7GL.js";
21
+ import "../chunks/chunk-TLWXLNLY.js";
21
22
  import {
22
23
  pathOrigin
23
24
  } from "../chunks/chunk-3YBP46PB.js";
package/dist/tubeMap/draw.js CHANGED
@@ -8,15 +8,15 @@ import {
8
8
  tubeMapMismatchAt,
9
9
  tubeMapPicture,
10
10
  tubeMapTrackAt
11
- } from "../chunks/chunk-HV35LDYH.js";
11
+ } from "../chunks/chunk-HMEAGAGC.js";
12
12
  import "../chunks/chunk-BX4AUMZE.js";
13
13
  import "../chunks/chunk-MYDHU2UV.js";
14
14
  import "../chunks/chunk-SDI6BVG7.js";
15
15
  import "../chunks/chunk-5OJZV6YT.js";
16
- import "../chunks/chunk-MEVTV4FI.js";
17
- import "../chunks/chunk-D3E7AXBB.js";
18
- import "../chunks/chunk-W2YAW36J.js";
19
- import "../chunks/chunk-EIY2SKD3.js";
16
+ import "../chunks/chunk-BXE3SBBN.js";
17
+ import "../chunks/chunk-G7SG4XMK.js";
18
+ import "../chunks/chunk-7L7MN2OM.js";
19
+ import "../chunks/chunk-LG2UK4MB.js";
20
20
  import "../chunks/chunk-3YBP46PB.js";
21
21
  import "../chunks/chunk-VACK24HF.js";
22
22
  import "../chunks/chunk-CPMHA4W5.js";
package/dist/tubeMap/genes.js CHANGED
@@ -3,13 +3,14 @@ import {
3
3
  drawTubeMapGenes,
4
4
  tubeMapGeneRows,
5
5
  tubeMapGenes
6
- } from "../chunks/chunk-GZ36HNPJ.js";
7
- import "../chunks/chunk-VO6FKNZE.js";
8
- import "../chunks/chunk-T3H5ELLA.js";
6
+ } from "../chunks/chunk-PCHEUVHB.js";
7
+ import "../chunks/chunk-PJWLYGRL.js";
8
+ import "../chunks/chunk-FU57ZNRQ.js";
9
9
  import "../chunks/chunk-HMXCN6PG.js";
10
10
  import "../chunks/chunk-AB35TJST.js";
11
11
  import "../chunks/chunk-2VMKQKVO.js";
12
- import "../chunks/chunk-DV5B5UU7.js";
12
+ import "../chunks/chunk-5NZRT7GL.js";
13
+ import "../chunks/chunk-TLWXLNLY.js";
13
14
  import "../chunks/chunk-3YBP46PB.js";
14
15
  import "../chunks/chunk-VACK24HF.js";
15
16
  import "../chunks/chunk-CPMHA4W5.js";
package/dist/tubeMap/nodeColors.js CHANGED
@@ -1,18 +1,19 @@
1
1
  import {
2
2
  tubeMapNodeColors
3
- } from "../chunks/chunk-YEYQFNFQ.js";
4
- import "../chunks/chunk-JGHZ3N34.js";
3
+ } from "../chunks/chunk-3WSA4NNP.js";
4
+ import "../chunks/chunk-VB4IXIPM.js";
5
5
  import "../chunks/chunk-G2FD7S3C.js";
6
6
  import "../chunks/chunk-GQZVR5DW.js";
7
- import "../chunks/chunk-OYCQVJYY.js";
8
- import "../chunks/chunk-BW2NMXRV.js";
7
+ import "../chunks/chunk-XTF2VWJN.js";
8
+ import "../chunks/chunk-3UGWYQNY.js";
9
9
  import "../chunks/chunk-ZANALBSX.js";
10
10
  import "../chunks/chunk-VX656OAZ.js";
11
- import "../chunks/chunk-T3H5ELLA.js";
11
+ import "../chunks/chunk-FU57ZNRQ.js";
12
12
  import "../chunks/chunk-HMXCN6PG.js";
13
13
  import "../chunks/chunk-AB35TJST.js";
14
14
  import "../chunks/chunk-2VMKQKVO.js";
15
- import "../chunks/chunk-DV5B5UU7.js";
15
+ import "../chunks/chunk-5NZRT7GL.js";
16
+ import "../chunks/chunk-TLWXLNLY.js";
16
17
  import "../chunks/chunk-3YBP46PB.js";
17
18
  import "../chunks/chunk-VACK24HF.js";
18
19
  import "../chunks/chunk-CPMHA4W5.js";
package/dist/types/deletionEdges.d.ts CHANGED
@@ -13,7 +13,7 @@ export interface DeletionEdge {
13
13
  bypassed: string[];
14
14
  }
15
15
  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;
16
- export declare function deletionEdges(graph: Graph): DeletionEdge[];
16
+ export declare function deletionEdges(cut: Graph): DeletionEdge[];
17
17
  export declare function closableDeletions(graph: Graph, deletions: DeletionEdge[]): Set<number>;
18
18
  export interface DeletionDrawing {
19
19
  shown: DeletionEdge[];
package/dist/types/gfa/graphTables.d.ts CHANGED
@@ -30,6 +30,8 @@ export interface GraphTables {
30
30
  reversed: Uint8Array;
31
31
  before?: WalkStopTable;
32
32
  after?: WalkStopTable;
33
+ abridgedSteps?: Float64Array;
34
+ abridgedBp?: Float64Array;
33
35
  };
34
36
  }
35
37
  /** The GraphPath `graphFromTables` builds of walk `p`, less its steps */
package/dist/types/gfa/walkStops.d.ts CHANGED
@@ -1,7 +1,7 @@
1
1
  import type { PathStop, StopChunk } from '../types.js';
2
2
  export declare const START_STOP_TAG = "ws";
3
3
  export declare const END_STOP_TAG = "we";
4
- export type GapCause = 'missing' | 'elsewhere' | 'unknown';
4
+ export type GapCause = 'missing' | 'elsewhere' | 'unknown' | 'abridged';
5
5
  export declare const GAP_CAUSE_TEXT: Record<GapCause, string>;
6
6
  export declare const OUTSIDE_TEXT = "outside the extracted subgraph";
7
7
  export interface GapPart {
package/dist/types/layout/trimToWindow.d.ts CHANGED
@@ -7,3 +7,4 @@ export declare function clipToWindow(graph: Graph, window: {
7
7
  start: number;
8
8
  end: number;
9
9
  }, reachBp: number): Graph;
10
+ export declare function unclipped(graph: Graph): Graph;
package/dist/types/layout/walkRowDraw.d.ts CHANGED
@@ -7,6 +7,7 @@ export declare const OFF_REFERENCE = "#8e3fbf";
7
7
  export declare const OUTSIDE_CUT = "#bdbdbd";
8
8
  export declare const MISSING_INK = "#8a8a8a";
9
9
  export declare const UNKNOWN_GAP = "#e2e2e2";
10
+ export declare const ABRIDGED_GAP = "#d9a441";
10
11
  export declare const GENE_INK = "#1c1c22";
11
12
  export declare const BAR_PX = 12;
12
13
  export declare const GAP_PX = 4;
@@ -17,7 +18,7 @@ export interface ReadoutCall {
17
18
  spanningReads?: number;
18
19
  agrees?: boolean;
19
20
  }
20
- export declare function walkRowReadout(row: Pick<WalkRow, 'bp' | 'gapBp' | 'complete' | 'stop'> & {
21
+ export declare function walkRowReadout(row: Pick<WalkRow, 'bp' | 'gapBp' | 'complete' | 'stop' | 'abridgedSteps'> & {
21
22
  runs?: WalkRun[];
22
23
  }, reference: Pick<WalkRow, 'bp'> | undefined, unit?: number, call?: ReadoutCall): string;
23
24
  export declare function readoutPlacement(text: string, endX: number, width: number): {
package/dist/types/layout/walkRows.d.ts CHANGED
@@ -36,6 +36,7 @@ export interface WalkRow {
36
36
  gapBp: number;
37
37
  complete: boolean;
38
38
  stop?: WalkStop;
39
+ abridgedSteps?: number;
39
40
  runs: WalkRun[];
40
41
  visits?: WalkVisit[];
41
42
  axis?: WalkAxis;
package/dist/types/types.d.ts CHANGED
@@ -9,6 +9,10 @@ export interface GraphNode {
9
9
  depth: number;
10
10
  stable?: StableCoordinate;
11
11
  samples?: string[];
12
+ unclipped?: {
13
+ start: number;
14
+ length: number;
15
+ };
12
16
  }
13
17
  export interface GraphEdge {
14
18
  from: string;
@@ -27,6 +31,10 @@ export interface GraphPath {
27
31
  members?: string[];
28
32
  before?: PathStop;
29
33
  after?: PathStop;
34
+ abridged?: {
35
+ steps: number;
36
+ bp: number;
37
+ };
30
38
  }
31
39
  export type PathStop = ({
32
40
  kind: 'elsewhere';
package/dist/types/version.d.ts CHANGED
@@ -1 +1 @@
1
- export declare const version = "11.6.1";
1
+ export declare const version = "11.7.1";
package/dist/util/SpatialIndex.js CHANGED
@@ -1,10 +1,11 @@
1
1
  import {
2
2
  EdgeSpatialIndex,
3
3
  SpatialIndex
4
- } from "../chunks/chunk-6YRSOL4K.js";
5
- import "../chunks/chunk-OYCQVJYY.js";
4
+ } from "../chunks/chunk-IN4IYSA2.js";
5
+ import "../chunks/chunk-XTF2VWJN.js";
6
6
  import "../chunks/chunk-HMXCN6PG.js";
7
- import "../chunks/chunk-DV5B5UU7.js";
7
+ import "../chunks/chunk-5NZRT7GL.js";
8
+ import "../chunks/chunk-TLWXLNLY.js";
8
9
  import "../chunks/chunk-3YBP46PB.js";
9
10
  import "../chunks/chunk-VACK24HF.js";
10
11
  import "../chunks/chunk-CPMHA4W5.js";
package/dist/util/edgeCurves.js CHANGED
@@ -1,8 +1,9 @@
1
1
  import {
2
2
  baseEdgeCurves
3
- } from "../chunks/chunk-OYCQVJYY.js";
3
+ } from "../chunks/chunk-XTF2VWJN.js";
4
4
  import "../chunks/chunk-HMXCN6PG.js";
5
- import "../chunks/chunk-DV5B5UU7.js";
5
+ import "../chunks/chunk-5NZRT7GL.js";
6
+ import "../chunks/chunk-TLWXLNLY.js";
6
7
  import "../chunks/chunk-3YBP46PB.js";
7
8
  import "../chunks/chunk-VACK24HF.js";
8
9
  import "../chunks/chunk-CPMHA4W5.js";
package/dist/util/hitDetection.js CHANGED
@@ -4,11 +4,12 @@ import {
4
4
  findHoveredEdge,
5
5
  findHoveredNode,
6
6
  nodesUnderBox
7
- } from "../chunks/chunk-56L6R6D2.js";
8
- import "../chunks/chunk-6YRSOL4K.js";
9
- import "../chunks/chunk-OYCQVJYY.js";
7
+ } from "../chunks/chunk-Q7I563MH.js";
8
+ import "../chunks/chunk-IN4IYSA2.js";
9
+ import "../chunks/chunk-XTF2VWJN.js";
10
10
  import "../chunks/chunk-HMXCN6PG.js";
11
- import "../chunks/chunk-DV5B5UU7.js";
11
+ import "../chunks/chunk-5NZRT7GL.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";