@jbrowse/bandage-core 11.5.0 → 11.7.0

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 (147) hide show
  1. package/dist/alleleProjection/projectAlleles.js +1 -1
  2. package/dist/bubbles/bubbleHalos.js +9 -6
  3. package/dist/bubbles/classifyBubble.js +8 -5
  4. package/dist/bubbles/popBubble.js +3 -3
  5. package/dist/bubbles/superbubbles.js +11 -11
  6. package/dist/chunks/{chunk-4XWZNPQ2.js → chunk-2JL2JVZ2.js} +1 -1
  7. package/dist/chunks/{chunk-BZFOFC4D.js → chunk-2VMKQKVO.js} +17 -7
  8. package/dist/chunks/{chunk-HN3WHMPJ.js → chunk-2XEAITWM.js} +15 -5
  9. package/dist/chunks/{chunk-7BTO7MZS.js → chunk-376YFQOY.js} +2 -2
  10. package/dist/chunks/{chunk-B5X2RLJG.js → chunk-3YBP46PB.js} +27 -2
  11. package/dist/chunks/{chunk-EJRJAAN7.js → chunk-4DMSPNYV.js} +47 -27
  12. package/dist/chunks/{chunk-OMUPUB4J.js → chunk-56L6R6D2.js} +2 -2
  13. package/dist/chunks/{chunk-C44YRP5F.js → chunk-5OJZV6YT.js} +3 -2
  14. package/dist/chunks/{chunk-234NFZS4.js → chunk-5ORP7EFJ.js} +1 -1
  15. package/dist/chunks/{chunk-XKZ56L5A.js → chunk-5ZQKQ24Z.js} +1 -1
  16. package/dist/chunks/{chunk-VD4MLYEK.js → chunk-65YCFVS4.js} +2 -2
  17. package/dist/chunks/{chunk-3VCKBSML.js → chunk-6YRSOL4K.js} +2 -2
  18. package/dist/chunks/{chunk-NJGYLYU7.js → chunk-7L7MN2OM.js} +6 -3
  19. package/dist/chunks/{chunk-TRGKMLXT.js → chunk-A7Q7RTWX.js} +26 -19
  20. package/dist/chunks/{chunk-77EGQQJU.js → chunk-BFUS3ENH.js} +2 -2
  21. package/dist/chunks/{chunk-TGUFT6KK.js → chunk-BLUEFYIR.js} +4 -1
  22. package/dist/chunks/{chunk-3GP3KT5L.js → chunk-BW2NMXRV.js} +5 -5
  23. package/dist/chunks/{chunk-IOWLTUEB.js → chunk-BXE3SBBN.js} +1 -1
  24. package/dist/chunks/{chunk-2E25TX4G.js → chunk-C6E6HXP5.js} +4 -4
  25. package/dist/chunks/{chunk-5I3K4R2G.js → chunk-CFXXFHRK.js} +2 -1
  26. package/dist/chunks/{chunk-JMABOQWL.js → chunk-CO6RGQAD.js} +1 -6
  27. package/dist/chunks/{chunk-5F4D35U5.js → chunk-DD5EZG3T.js} +3 -3
  28. package/dist/chunks/{chunk-AKLSY4GD.js → chunk-DTEXQ65J.js} +1 -1
  29. package/dist/chunks/{chunk-VQ7474EH.js → chunk-DUREQSOJ.js} +9 -8
  30. package/dist/chunks/{chunk-CGMSKIEO.js → chunk-DV5B5UU7.js} +55 -8
  31. package/dist/chunks/{chunk-KOJKFNCW.js → chunk-EH5JZETS.js} +26 -12
  32. package/dist/chunks/{chunk-G6UIYQZR.js → chunk-EQDQ7P4Y.js} +3 -2
  33. package/dist/chunks/{chunk-J3JODFDF.js → chunk-FNDNSDKW.js} +3 -3
  34. package/dist/chunks/{chunk-64FCX424.js → chunk-G7SG4XMK.js} +62 -14
  35. package/dist/chunks/{chunk-6EOB6ANX.js → chunk-GZ36HNPJ.js} +1 -1
  36. package/dist/chunks/{chunk-A32ZKSHN.js → chunk-HELOUO6K.js} +5 -5
  37. package/dist/chunks/{chunk-PQBALYSO.js → chunk-HERVZPWA.js} +16 -16
  38. package/dist/chunks/{chunk-3U3C4PRK.js → chunk-HMEAGAGC.js} +3 -3
  39. package/dist/chunks/{chunk-WC6HX6GJ.js → chunk-IJCSW6MV.js} +2 -2
  40. package/dist/chunks/{chunk-JOWKKQAL.js → chunk-JGHZ3N34.js} +14 -9
  41. package/dist/chunks/{chunk-PSCSZSVK.js → chunk-KA4F3N55.js} +4 -4
  42. package/dist/chunks/{chunk-SOMZGDVS.js → chunk-KJDERUQF.js} +1 -1
  43. package/dist/chunks/{chunk-E4ZM4OOJ.js → chunk-KZMSSPS6.js} +2 -2
  44. package/dist/chunks/{chunk-EIY2SKD3.js → chunk-LG2UK4MB.js} +2 -1
  45. package/dist/chunks/{chunk-PNMJFFNB.js → chunk-MHZTTLBU.js} +1 -1
  46. package/dist/chunks/{chunk-K5LDBMLX.js → chunk-NTKWT6XL.js} +1 -1
  47. package/dist/chunks/{chunk-WA5WNP6V.js → chunk-OYCQVJYY.js} +1 -1
  48. package/dist/chunks/{chunk-JOLLU34X.js → chunk-PQIFYQVI.js} +1 -1
  49. package/dist/chunks/{chunk-EGBBIXTG.js → chunk-QCOVHLJO.js} +1 -1
  50. package/dist/chunks/{chunk-A7H753BA.js → chunk-SDI6BVG7.js} +5 -6
  51. package/dist/chunks/{chunk-FWSERUJV.js → chunk-SENPGW4O.js} +1 -1
  52. package/dist/chunks/{chunk-RK3HRRCW.js → chunk-SIA75TEG.js} +6 -7
  53. package/dist/chunks/{chunk-A4JDEUAI.js → chunk-SNF2MIEF.js} +1 -1
  54. package/dist/chunks/{chunk-D4ZFRBB4.js → chunk-SVPR7IZO.js} +4 -4
  55. package/dist/chunks/{chunk-PFRQBCGC.js → chunk-T3H5ELLA.js} +4 -4
  56. package/dist/chunks/{chunk-FFHJGWDK.js → chunk-TUMJNAOL.js} +5 -5
  57. package/dist/chunks/{chunk-UBQSRCWR.js → chunk-VACK24HF.js} +43 -3
  58. package/dist/chunks/{chunk-HSVFCA2J.js → chunk-VO6FKNZE.js} +1 -1
  59. package/dist/chunks/{chunk-DZR37KXT.js → chunk-VSSIYQYF.js} +1 -1
  60. package/dist/chunks/{chunk-3BCVMZUT.js → chunk-WWIUC4N4.js} +10 -10
  61. package/dist/chunks/{chunk-GJU6BJJA.js → chunk-XR2HMGAS.js} +1 -1
  62. package/dist/chunks/{chunk-WG5D2H7X.js → chunk-YER6TUXV.js} +11 -11
  63. package/dist/chunks/{chunk-7EDGWT67.js → chunk-YEYQFNFQ.js} +1 -1
  64. package/dist/chunks/{chunk-UFUSPK2A.js → chunk-YYIU7P73.js} +4 -1
  65. package/dist/chunks/{chunk-CRCD3ODN.js → chunk-ZANALBSX.js} +11 -3
  66. package/dist/chunks/{chunk-WLR4KJVI.js → chunk-ZHZRAYEM.js} +1 -1
  67. package/dist/chunks/{chunk-NMWQUFPF.js → chunk-ZKSC7QVE.js} +3 -3
  68. package/dist/cli/figure.js +53 -48
  69. package/dist/cli/fold.js +13 -13
  70. package/dist/deletionEdges.js +5 -2
  71. package/dist/facetGrid.js +2 -2
  72. package/dist/figure.js +37 -37
  73. package/dist/figureData.js +39 -39
  74. package/dist/figureScene.js +27 -27
  75. package/dist/figureSettings.js +13 -13
  76. package/dist/foldVariants.js +2 -2
  77. package/dist/gaf/parseGaf.js +1 -1
  78. package/dist/gbzCut.js +6 -6
  79. package/dist/gbzWindow.js +5 -5
  80. package/dist/genes/backboneGenes.js +4 -4
  81. package/dist/genes/geneFiles.js +1 -1
  82. package/dist/genes/genePins.js +3 -3
  83. package/dist/gfa/gfaConverter.js +5 -5
  84. package/dist/gfa/gfaTables.js +2 -2
  85. package/dist/gfa/graphTables.js +3 -3
  86. package/dist/gfa/walkStops.js +1 -1
  87. package/dist/gfa-core/gfaParser.js +1 -1
  88. package/dist/gfa-core/index.js +1 -1
  89. package/dist/graphLabels.js +7 -4
  90. package/dist/index.js +64 -64
  91. package/dist/labelLayout.js +11 -8
  92. package/dist/layout/anchoredLayout.js +1 -1
  93. package/dist/layout/forceCache.js +13 -13
  94. package/dist/layout/mergeRuns.js +2 -2
  95. package/dist/layout/placeOffReference.js +1 -1
  96. package/dist/layout/sampleRowLayout.js +2 -2
  97. package/dist/layout/trimToWindow.js +2 -2
  98. package/dist/layout/tubeMapLayout.js +15 -15
  99. package/dist/layout/walkRowDraw.js +15 -13
  100. package/dist/layout/walkRowLayout.js +8 -8
  101. package/dist/layout/walkRowLinks.js +1 -1
  102. package/dist/layout/walkRowRuns.js +5 -5
  103. package/dist/layout/walkRows.js +6 -6
  104. package/dist/layout/walkStrip.js +18 -18
  105. package/dist/layoutEngines.js +1 -1
  106. package/dist/layoutModes.js +18 -18
  107. package/dist/locus.js +1 -1
  108. package/dist/nodeWidths.js +5 -3
  109. package/dist/pansn.js +1 -1
  110. package/dist/pathAnchoring.js +4 -2
  111. package/dist/pathColors.js +8 -8
  112. package/dist/pipeline.js +12 -12
  113. package/dist/reference.js +2 -2
  114. package/dist/referenceStrip.js +12 -12
  115. package/dist/renderer/Canvas2DRenderer.js +1 -1
  116. package/dist/renderer/GeometryBuilder.js +11 -11
  117. package/dist/tubeMap/axis.js +8 -5
  118. package/dist/tubeMap/bundle.js +16 -16
  119. package/dist/tubeMap/coarsen.js +16 -16
  120. package/dist/tubeMap/deviations.js +19 -19
  121. package/dist/tubeMap/draw.js +11 -9
  122. package/dist/tubeMap/genes.js +9 -6
  123. package/dist/tubeMap/nodeColors.js +12 -12
  124. package/dist/tubeMap/reads.js +4 -4
  125. package/dist/types/figureData.d.ts +12 -0
  126. package/dist/types/gaf/parseGaf.d.ts +1 -1
  127. package/dist/types/gfa/graphTables.d.ts +2 -0
  128. package/dist/types/gfa/walkStops.d.ts +1 -1
  129. package/dist/types/layout/walkRowDraw.d.ts +2 -1
  130. package/dist/types/layout/walkRows.d.ts +1 -0
  131. package/dist/types/nodeWidths.d.ts +2 -1
  132. package/dist/types/pathAnchoring.d.ts +2 -0
  133. package/dist/types/renderer/Canvas2DRenderer.d.ts +2 -0
  134. package/dist/types/tubeMap/reads.d.ts +0 -1
  135. package/dist/types/types.d.ts +4 -0
  136. package/dist/types/util/geometry.d.ts +7 -1
  137. package/dist/types/version.d.ts +1 -1
  138. package/dist/util/SpatialIndex.js +7 -4
  139. package/dist/util/edgeCurves.js +6 -3
  140. package/dist/util/geometry.js +1 -1
  141. package/dist/util/hitDetection.js +8 -5
  142. package/dist/version.js +1 -1
  143. package/dist/viewport.js +13 -13
  144. package/dist/walkEncoding.js +12 -12
  145. package/dist/walkHighlight.js +14 -14
  146. package/dist/walkKey.js +9 -6
  147. package/package.json +1 -1
package/dist/viewport.js CHANGED
@@ -5,31 +5,31 @@ import {
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  screenToLayout,
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  viewportOf,
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  zoomAbout
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- } from "./chunks/chunk-XKZ56L5A.js";
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- import "./chunks/chunk-WG5D2H7X.js";
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+ } from "./chunks/chunk-5ZQKQ24Z.js";
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+ import "./chunks/chunk-YER6TUXV.js";
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  import "./chunks/chunk-OPPVSPEF.js";
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  import "./chunks/chunk-3PZSBNLI.js";
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  import "./chunks/chunk-CKUVEHSS.js";
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  import "./chunks/chunk-VPE4AYP7.js";
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- import "./chunks/chunk-FFHJGWDK.js";
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+ import "./chunks/chunk-TUMJNAOL.js";
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  import "./chunks/chunk-QYBZZI5H.js";
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- import "./chunks/chunk-5I3K4R2G.js";
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- import "./chunks/chunk-NJGYLYU7.js";
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- import "./chunks/chunk-B5X2RLJG.js";
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+ import "./chunks/chunk-CFXXFHRK.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-DZR37KXT.js";
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- import "./chunks/chunk-EIY2SKD3.js";
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- import "./chunks/chunk-ZPZ7GNBT.js";
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- import "./chunks/chunk-BZFOFC4D.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-2VMKQKVO.js";
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  import "./chunks/chunk-HKYXWZQS.js";
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  import "./chunks/chunk-34BOZKIE.js";
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- import "./chunks/chunk-CGMSKIEO.js";
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- import "./chunks/chunk-UBQSRCWR.js";
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+ import "./chunks/chunk-DV5B5UU7.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";
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+ import "./chunks/chunk-ZPZ7GNBT.js";
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  import "./chunks/chunk-BSOZW3FC.js";
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  import "./chunks/chunk-RJWPJCIB.js";
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  import "./chunks/chunk-HOAIOEI7.js";
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- import "./chunks/chunk-4XWZNPQ2.js";
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+ import "./chunks/chunk-2JL2JVZ2.js";
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  export {
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  axisScaleOf,
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  contains,
package/dist/walkEncoding.js CHANGED
@@ -9,27 +9,27 @@ import {
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  schemeColor,
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  schemeCss,
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  schemeRgb
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- } from "./chunks/chunk-HN3WHMPJ.js";
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- import "./chunks/chunk-JOWKKQAL.js";
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+ } from "./chunks/chunk-2XEAITWM.js";
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+ import "./chunks/chunk-JGHZ3N34.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-WA5WNP6V.js";
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- import "./chunks/chunk-3GP3KT5L.js";
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- import "./chunks/chunk-CRCD3ODN.js";
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- import "./chunks/chunk-B5X2RLJG.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-ZANALBSX.js";
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  import "./chunks/chunk-VX656OAZ.js";
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- import "./chunks/chunk-ZPZ7GNBT.js";
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- import "./chunks/chunk-PFRQBCGC.js";
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+ import "./chunks/chunk-T3H5ELLA.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-BZFOFC4D.js";
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- import "./chunks/chunk-CGMSKIEO.js";
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- import "./chunks/chunk-UBQSRCWR.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-3YBP46PB.js";
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+ import "./chunks/chunk-VACK24HF.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-RJWPJCIB.js";
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- import "./chunks/chunk-4XWZNPQ2.js";
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+ import "./chunks/chunk-2JL2JVZ2.js";
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  export {
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package/dist/walkHighlight.js CHANGED
@@ -2,29 +2,29 @@ import {
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  facetLifts,
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  walkHighlight,
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  walkLift
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- } from "./chunks/chunk-VQ7474EH.js";
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- import "./chunks/chunk-HN3WHMPJ.js";
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- import "./chunks/chunk-JOWKKQAL.js";
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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";
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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-WA5WNP6V.js";
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- import "./chunks/chunk-3GP3KT5L.js";
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- import "./chunks/chunk-CRCD3ODN.js";
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- import "./chunks/chunk-B5X2RLJG.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-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-ZPZ7GNBT.js";
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- import "./chunks/chunk-PFRQBCGC.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-HMXCN6PG.js";
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  import "./chunks/chunk-AB35TJST.js";
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- import "./chunks/chunk-BZFOFC4D.js";
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- import "./chunks/chunk-CGMSKIEO.js";
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- import "./chunks/chunk-UBQSRCWR.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-3YBP46PB.js";
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+ import "./chunks/chunk-VACK24HF.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-4XWZNPQ2.js";
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+ import "./chunks/chunk-2JL2JVZ2.js";
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  export {
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package/dist/walkKey.js CHANGED
@@ -2,18 +2,21 @@ import {
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- } from "./chunks/chunk-D4ZFRBB4.js";
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- import "./chunks/chunk-EIY2SKD3.js";
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- import "./chunks/chunk-PFRQBCGC.js";
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+ } from "./chunks/chunk-SVPR7IZO.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-HMXCN6PG.js";
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  import "./chunks/chunk-AB35TJST.js";
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- import "./chunks/chunk-BZFOFC4D.js";
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- import "./chunks/chunk-CGMSKIEO.js";
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- import "./chunks/chunk-UBQSRCWR.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-3YBP46PB.js";
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+ import "./chunks/chunk-VACK24HF.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-2JL2JVZ2.js";
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  export {
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package/package.json CHANGED
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  {
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  "name": "@jbrowse/bandage-core",
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- "version": "11.5.0",
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  "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",
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  "license": "GPL-3.0-or-later",
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  "repository": {