@jbrowse/bandage-core 10.2.6 → 10.3.0

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 (191) hide show
  1. package/dist/alleleProjection/projectAlleles.js +8 -4
  2. package/dist/anchoredNodes.js +2 -1
  3. package/dist/bubbleSpreads.js +2 -2
  4. package/dist/bubbles/bubbleHalos.js +10 -11
  5. package/dist/bubbles/bubblesFromGraph.js +8 -3
  6. package/dist/bubbles/classifyBubble.js +9 -6
  7. package/dist/bubbles/popBubble.js +7 -5
  8. package/dist/bubbles/superbubbles.js +18 -14
  9. package/dist/chunks/{chunk-RAKOB6IV.js → chunk-234NFZS4.js} +8 -6
  10. package/dist/chunks/{chunk-A4PFFC4Q.js → chunk-2XEQR54X.js} +60 -102
  11. package/dist/chunks/{chunk-6JEWNXCQ.js → chunk-34BOZKIE.js} +0 -2
  12. package/dist/chunks/{chunk-RVS2QCOX.js → chunk-3GLG3ZLE.js} +2 -11
  13. package/dist/chunks/{chunk-PUG7LXDF.js → chunk-3PZSBNLI.js} +4 -1
  14. package/dist/chunks/{chunk-KBEP7VYK.js → chunk-3VCKBSML.js} +4 -4
  15. package/dist/chunks/{chunk-BPLIXMH7.js → chunk-4XWZNPQ2.js} +14 -0
  16. package/dist/chunks/{chunk-LKW2TP4N.js → chunk-5YILQTHE.js} +18 -16
  17. package/dist/chunks/{chunk-B6IW3IRE.js → chunk-65ILXEIN.js} +14 -15
  18. package/dist/chunks/{chunk-4DRQTBBE.js → chunk-6EOB6ANX.js} +1 -1
  19. package/dist/chunks/{chunk-XBHMXTOR.js → chunk-7JGLJK44.js} +41 -36
  20. package/dist/chunks/{chunk-T2PCSAFY.js → chunk-7XR26JST.js} +2 -2
  21. package/dist/chunks/{chunk-URZ3CH2R.js → chunk-A4JDEUAI.js} +1 -1
  22. package/dist/chunks/{chunk-JLSJMCDJ.js → chunk-A54O52XZ.js} +3 -3
  23. package/dist/chunks/chunk-A55OZVYX.js +327 -0
  24. package/dist/chunks/{chunk-CWFNEKST.js → chunk-A7H753BA.js} +3 -3
  25. package/dist/chunks/{chunk-FB5RKZQY.js → chunk-AMX4OQAW.js} +18 -27
  26. package/dist/chunks/{chunk-RPRHR56C.js → chunk-BS6HPYCZ.js} +3 -3
  27. package/dist/chunks/chunk-BSOZW3FC.js +30 -0
  28. package/dist/chunks/{chunk-CU6P5RUG.js → chunk-BVYR7IFN.js} +22 -16
  29. package/dist/chunks/{chunk-XXT2JCAC.js → chunk-BX4AUMZE.js} +11 -13
  30. package/dist/chunks/{chunk-N73TI3VG.js → chunk-BZFOFC4D.js} +6 -9
  31. package/dist/chunks/{chunk-4ETPXDO6.js → chunk-CGFPFBT2.js} +1 -1
  32. package/dist/chunks/{chunk-24WITXQY.js → chunk-CGMSKIEO.js} +9 -25
  33. package/dist/chunks/{chunk-IGVV37VI.js → chunk-CKUVEHSS.js} +3 -3
  34. package/dist/chunks/{chunk-JBCZIBFC.js → chunk-CRCD3ODN.js} +0 -1
  35. package/dist/chunks/{chunk-PSMKPSO4.js → chunk-DBLV7PGG.js} +33 -27
  36. package/dist/chunks/{chunk-JA2HJIYS.js → chunk-E4ZM4OOJ.js} +3 -5
  37. package/dist/chunks/{chunk-ABUIN5AK.js → chunk-EHXBZ5JZ.js} +29 -24
  38. package/dist/chunks/{chunk-QLWI2PZ3.js → chunk-EJRJAAN7.js} +24 -21
  39. package/dist/chunks/{chunk-Q7LYHGGQ.js → chunk-GIHTHYXY.js} +5 -4
  40. package/dist/chunks/{chunk-L3O7AWLI.js → chunk-GJLZ2MKE.js} +2 -2
  41. package/dist/chunks/{chunk-LOEA5IHZ.js → chunk-GJU6BJJA.js} +8 -8
  42. package/dist/chunks/{chunk-XL472HHD.js → chunk-GQZVR5DW.js} +12 -7
  43. package/dist/chunks/{chunk-UVBGRJQX.js → chunk-HKYXWZQS.js} +1 -1
  44. package/dist/chunks/chunk-HMXCN6PG.js +17 -0
  45. package/dist/chunks/{chunk-WSIFAZU7.js → chunk-HNWJ4B7S.js} +12 -13
  46. package/dist/chunks/chunk-HOAIOEI7.js +18 -0
  47. package/dist/chunks/{chunk-XMW266WS.js → chunk-HSVFCA2J.js} +18 -20
  48. package/dist/chunks/{chunk-3XSM4OZU.js → chunk-IYALCKNB.js} +5 -5
  49. package/dist/chunks/{chunk-2QLLQJ72.js → chunk-KWHWNOTY.js} +22 -17
  50. package/dist/chunks/{chunk-M6LK4GII.js → chunk-LGJBB5BP.js} +8 -9
  51. package/dist/chunks/{chunk-VQWHMWLF.js → chunk-M5NPD55W.js} +18 -14
  52. package/dist/chunks/{chunk-TKIJ5535.js → chunk-MD5VPXXT.js} +6 -6
  53. package/dist/chunks/{chunk-HK5Y2YWV.js → chunk-MYDHU2UV.js} +6 -11
  54. package/dist/chunks/{chunk-TZFWUT2C.js → chunk-MYLAJDKB.js} +2 -2
  55. package/dist/chunks/{chunk-4HWM3FNK.js → chunk-OMUPUB4J.js} +39 -56
  56. package/dist/chunks/{chunk-PTABFYQ7.js → chunk-PFRQBCGC.js} +49 -60
  57. package/dist/chunks/{chunk-T6V4KI2L.js → chunk-PPDE4IVT.js} +1 -1
  58. package/dist/chunks/{chunk-KC7T5RWG.js → chunk-PSCSZSVK.js} +9 -16
  59. package/dist/chunks/{chunk-YYMW5XOF.js → chunk-PTQPTDZH.js} +1 -1
  60. package/dist/chunks/{chunk-L2HDM2R3.js → chunk-QQCOVMMT.js} +7 -7
  61. package/dist/chunks/{chunk-CQHUZHET.js → chunk-RFG42VIO.js} +46 -30
  62. package/dist/chunks/{chunk-FYQWPEEY.js → chunk-RJWPJCIB.js} +5 -11
  63. package/dist/chunks/{chunk-AR4BUBMU.js → chunk-RWKP7UO4.js} +34 -35
  64. package/dist/chunks/{chunk-WBSWROE6.js → chunk-SHKGYGM4.js} +14 -18
  65. package/dist/chunks/{chunk-2CMYNW3E.js → chunk-SI3BB4DO.js} +1 -1
  66. package/dist/chunks/{chunk-DY3JCAMX.js → chunk-SOMZGDVS.js} +7 -16
  67. package/dist/chunks/{chunk-EFQLEGWM.js → chunk-SZHQK6GL.js} +7 -8
  68. package/dist/chunks/{chunk-5GMFEPWR.js → chunk-TCOLHD7N.js} +16 -28
  69. package/dist/chunks/{chunk-XV4P5KEQ.js → chunk-TGUFT6KK.js} +6 -3
  70. package/dist/chunks/{chunk-CM6LO6OC.js → chunk-UAFATXYA.js} +10 -14
  71. package/dist/chunks/{chunk-7SRWJLSC.js → chunk-UBQSRCWR.js} +11 -8
  72. package/dist/chunks/{chunk-RUCH6ZFL.js → chunk-V4YML3GR.js} +2 -1
  73. package/dist/chunks/{chunk-VQC7KELB.js → chunk-V7J6U4XC.js} +11 -3
  74. package/dist/chunks/{chunk-ES2N6V56.js → chunk-VX656OAZ.js} +6 -11
  75. package/dist/chunks/chunk-WA5WNP6V.js +37 -0
  76. package/dist/chunks/{chunk-WZNPX7Q6.js → chunk-WJ4TIAVA.js} +1 -1
  77. package/dist/chunks/{chunk-BS4UZ44I.js → chunk-WONB6LMC.js} +1 -1
  78. package/dist/chunks/{chunk-HFVGGB3U.js → chunk-XUT4HXVE.js} +29 -13
  79. package/dist/chunks/{chunk-G45YY72K.js → chunk-Z6XZWPXK.js} +17 -25
  80. package/dist/chunks/{chunk-XI3ZUTWF.js → chunk-ZNJ4JAPT.js} +14 -20
  81. package/dist/chunks/{chunk-HNCXR2VS.js → chunk-ZPBEUOBM.js} +3 -1
  82. package/dist/chunks/{chunk-RAEABQNW.js → chunk-ZPZ7GNBT.js} +1 -0
  83. package/dist/cli/figure.js +59 -56
  84. package/dist/cli/fold.js +19 -17
  85. package/dist/deletionEdges.js +5 -7
  86. package/dist/facetGrid.js +2 -1
  87. package/dist/figure.js +45 -42
  88. package/dist/figureData.js +48 -44
  89. package/dist/figureScene.js +34 -29
  90. package/dist/figureSettings.js +19 -17
  91. package/dist/foldVariants.js +5 -3
  92. package/dist/gbzCut.js +12 -7
  93. package/dist/gbzJoin.js +2 -1
  94. package/dist/gbzWindow.js +11 -6
  95. package/dist/genes/genePins.js +6 -4
  96. package/dist/gfa/gfaConverter.js +7 -5
  97. package/dist/gfa/gfaTables.js +2 -1
  98. package/dist/gfa/graphTables.js +3 -3
  99. package/dist/graphLabels.js +8 -5
  100. package/dist/index.js +88 -85
  101. package/dist/labelLayout.js +12 -9
  102. package/dist/layout/anchoredLayout.js +8 -5
  103. package/dist/layout/drawnScale.js +1 -5
  104. package/dist/layout/forceCache.js +19 -17
  105. package/dist/layout/mergeRuns.js +5 -3
  106. package/dist/layout/orderedLayout.js +5 -2
  107. package/dist/layout/orientToReference.js +3 -2
  108. package/dist/layout/placeOffReference.js +7 -4
  109. package/dist/layout/referenceSeeds.js +6 -4
  110. package/dist/layout/sampleRowLayout.js +8 -5
  111. package/dist/layout/trimToWindow.js +6 -4
  112. package/dist/layout/tubeMapLayout.js +17 -19
  113. package/dist/layout/walkRowDraw.js +18 -17
  114. package/dist/layout/walkRowLayout.js +10 -6
  115. package/dist/layout/walkRows.js +9 -5
  116. package/dist/layout/walkStrip.js +21 -18
  117. package/dist/layoutModes.js +23 -20
  118. package/dist/nodeWidths.js +1 -3
  119. package/dist/pansn.js +5 -1
  120. package/dist/pathAnchoring.js +6 -4
  121. package/dist/pathColors.js +12 -9
  122. package/dist/pathVisits.js +3 -1
  123. package/dist/pipeline.js +18 -16
  124. package/dist/reference.js +5 -3
  125. package/dist/referenceRampCss.js +9 -17
  126. package/dist/referenceSpan.js +4 -2
  127. package/dist/referenceStrip.js +18 -14
  128. package/dist/renderer/Canvas2DRenderer.js +1 -1
  129. package/dist/renderer/GeometryBuilder.js +19 -14
  130. package/dist/renderer/svgCanvas.js +1 -1
  131. package/dist/tubeMap/axis.js +11 -6
  132. package/dist/tubeMap/bundle.js +16 -12
  133. package/dist/tubeMap/coarsen.js +20 -345
  134. package/dist/tubeMap/deviations.js +53 -23
  135. package/dist/tubeMap/draw.js +11 -8
  136. package/dist/tubeMap/frame.js +3 -2
  137. package/dist/tubeMap/genes.js +10 -7
  138. package/dist/tubeMap/mismatches.js +1 -1
  139. package/dist/tubeMap/nodeColors.js +18 -14
  140. package/dist/tubeMap/reads.js +1 -1
  141. package/dist/tubeMap/warp.js +2 -1
  142. package/dist/types/alleleProjection/projectAlleles.d.ts +1 -4
  143. package/dist/types/bubbles/bubbleHalos.d.ts +0 -2
  144. package/dist/types/bubbles/bubblesFromGraph.d.ts +6 -4
  145. package/dist/types/bubbles/classifyBubble.d.ts +2 -1
  146. package/dist/types/deletionEdges.d.ts +0 -8
  147. package/dist/types/figureScene.d.ts +17 -7
  148. package/dist/types/figureSettings.d.ts +2 -0
  149. package/dist/types/gbzCut.d.ts +4 -0
  150. package/dist/types/gbzWindow.d.ts +1 -0
  151. package/dist/types/gfa/graphTables.d.ts +3 -1
  152. package/dist/types/gfa-core/gfaParser.d.ts +1 -1
  153. package/dist/types/graphLabels.d.ts +2 -1
  154. package/dist/types/layout/drawnScale.d.ts +0 -2
  155. package/dist/types/layout/referenceSeeds.d.ts +2 -1
  156. package/dist/types/layout/tubeMapLayout.d.ts +0 -7
  157. package/dist/types/layout/walkRowDraw.d.ts +0 -1
  158. package/dist/types/layout/walkRowLayout.d.ts +1 -0
  159. package/dist/types/layout/walkRows.d.ts +1 -0
  160. package/dist/types/nodeWidths.d.ts +0 -1
  161. package/dist/types/pansn.d.ts +9 -0
  162. package/dist/types/pathVisits.d.ts +6 -0
  163. package/dist/types/referenceRampCss.d.ts +4 -0
  164. package/dist/types/renderer/Canvas2DRenderer.d.ts +1 -0
  165. package/dist/types/renderer/GeometryBuilder.d.ts +3 -2
  166. package/dist/types/tubeMap/axis.d.ts +3 -1
  167. package/dist/types/tubeMap/coarsen.d.ts +3 -1
  168. package/dist/types/tubeMap/deviations.d.ts +2 -1
  169. package/dist/types/tubeMap/mismatches.d.ts +0 -1
  170. package/dist/types/tubeMap/warp.d.ts +2 -1
  171. package/dist/types/util/SpatialIndex.d.ts +1 -1
  172. package/dist/types/util/geometry.d.ts +4 -0
  173. package/dist/types/util/groups.d.ts +3 -0
  174. package/dist/types/util/hitDetection.d.ts +2 -2
  175. package/dist/types/util/partitionPoint.d.ts +1 -0
  176. package/dist/types/util/weakMemo.d.ts +1 -0
  177. package/dist/types/version.d.ts +1 -1
  178. package/dist/util/SpatialIndex.js +8 -5
  179. package/dist/util/edgeCurves.js +7 -4
  180. package/dist/util/geometry.js +3 -1
  181. package/dist/util/groups.js +10 -0
  182. package/dist/util/hitDetection.js +9 -6
  183. package/dist/util/partitionPoint.js +6 -0
  184. package/dist/util/weakMemo.js +6 -0
  185. package/dist/version.js +1 -1
  186. package/dist/viewport.js +19 -17
  187. package/dist/walkEncoding.js +18 -14
  188. package/dist/walkHighlight.js +19 -15
  189. package/dist/walkKey.js +9 -6
  190. package/package.json +2 -2
  191. package/dist/chunks/chunk-ZY2AFL4Y.js +0 -43
@@ -9,23 +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-VQC7KELB.js";
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- import "./chunks/chunk-A4PFFC4Q.js";
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+ } from "./chunks/chunk-V7J6U4XC.js";
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+ import "./chunks/chunk-2XEQR54X.js";
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  import "./chunks/chunk-G2FD7S3C.js";
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- import "./chunks/chunk-ZY2AFL4Y.js";
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- import "./chunks/chunk-3XSM4OZU.js";
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- import "./chunks/chunk-JBCZIBFC.js";
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- import "./chunks/chunk-M6LK4GII.js";
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- import "./chunks/chunk-RAEABQNW.js";
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- import "./chunks/chunk-ES2N6V56.js";
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- import "./chunks/chunk-BPLIXMH7.js";
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- import "./chunks/chunk-PTABFYQ7.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-IYALCKNB.js";
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+ import "./chunks/chunk-CRCD3ODN.js";
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+ import "./chunks/chunk-LGJBB5BP.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-HMXCN6PG.js";
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  import "./chunks/chunk-AB35TJST.js";
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- import "./chunks/chunk-N73TI3VG.js";
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- import "./chunks/chunk-24WITXQY.js";
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- import "./chunks/chunk-7SRWJLSC.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-CPMHA4W5.js";
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- import "./chunks/chunk-FYQWPEEY.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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  export {
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  NO_VALUE_COLOR,
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  WALK_FIELDS,
@@ -2,24 +2,28 @@ import {
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  facetLifts,
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  walkHighlight,
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  walkLift
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- } from "./chunks/chunk-CU6P5RUG.js";
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- import "./chunks/chunk-VQC7KELB.js";
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- import "./chunks/chunk-A4PFFC4Q.js";
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+ } from "./chunks/chunk-BVYR7IFN.js";
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+ import "./chunks/chunk-V7J6U4XC.js";
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+ import "./chunks/chunk-2XEQR54X.js";
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  import "./chunks/chunk-G2FD7S3C.js";
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- import "./chunks/chunk-ZY2AFL4Y.js";
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- import "./chunks/chunk-3XSM4OZU.js";
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- import "./chunks/chunk-JBCZIBFC.js";
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- import "./chunks/chunk-M6LK4GII.js";
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- import "./chunks/chunk-RAEABQNW.js";
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- import "./chunks/chunk-ES2N6V56.js";
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- import "./chunks/chunk-BPLIXMH7.js";
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- import "./chunks/chunk-PTABFYQ7.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-IYALCKNB.js";
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+ import "./chunks/chunk-CRCD3ODN.js";
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+ import "./chunks/chunk-LGJBB5BP.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-HMXCN6PG.js";
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  import "./chunks/chunk-AB35TJST.js";
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- import "./chunks/chunk-N73TI3VG.js";
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- import "./chunks/chunk-24WITXQY.js";
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- import "./chunks/chunk-7SRWJLSC.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-CPMHA4W5.js";
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- import "./chunks/chunk-FYQWPEEY.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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  export {
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  facetLifts,
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  walkHighlight,
package/dist/walkKey.js CHANGED
@@ -2,14 +2,17 @@ import {
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  rangeText,
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  walkKey,
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  walkPosition
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- } from "./chunks/chunk-4ETPXDO6.js";
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- import "./chunks/chunk-PTABFYQ7.js";
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+ } from "./chunks/chunk-CGFPFBT2.js";
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+ import "./chunks/chunk-PFRQBCGC.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-N73TI3VG.js";
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- import "./chunks/chunk-24WITXQY.js";
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- import "./chunks/chunk-7SRWJLSC.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-CPMHA4W5.js";
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- import "./chunks/chunk-FYQWPEEY.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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  export {
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  walkKey,
package/package.json CHANGED
@@ -1,6 +1,6 @@
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  {
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  "name": "@jbrowse/bandage-core",
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- "version": "10.2.6",
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+ "version": "10.3.0",
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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": {
@@ -39,7 +39,7 @@
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  "@gmod/tabix": "^3.10.1",
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  "@jbrowse/graph-fmmm-layout": "^1.0.2",
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  "@jbrowse/graph-stress-layout": "^1.0.0",
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- "@jbrowse/tubemap-core": "^1.1.0"
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+ "@jbrowse/tubemap-core": "^2.0.0"
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  },
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  "devDependencies": {
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  "@eslint/js": "^10.0.1",
@@ -1,43 +0,0 @@
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- import {
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- edgeCurvesOf
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- } from "./chunk-24WITXQY.js";
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-
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- // src/util/edgeCurves.ts
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- var cache = /* @__PURE__ */ new WeakMap();
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- function baseEdgeCurves(nodePositions, graph, axis, deletions, version, routes, stranded = false) {
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- const { scaleX, scaleY } = axis;
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- const cached = cache.get(nodePositions);
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- if (cached?.graph === graph && cached.scaleX === scaleX && cached.scaleY === scaleY && cached.deletions === deletions && cached.routes === routes && cached.stranded === stranded && cached.version === version) {
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- return cached.curves;
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- }
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- const curves = /* @__PURE__ */ new Map();
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- for (let ei = 0; ei < graph.edges.length; ei++) {
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- const bypassed = deletions?.get(ei);
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- const edgeCurves = edgeCurvesOf(
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- nodePositions,
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- graph.edges[ei],
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- axis,
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- bypassed,
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- bypassed && routes?.[ei],
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- stranded
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- );
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- if (edgeCurves) {
25
- curves.set(ei, edgeCurves);
26
- }
27
- }
28
- cache.set(nodePositions, {
29
- graph,
30
- scaleX,
31
- scaleY,
32
- deletions,
33
- routes,
34
- stranded,
35
- version,
36
- curves
37
- });
38
- return curves;
39
- }
40
-
41
- export {
42
- baseEdgeCurves
43
- };