@jbrowse/bandage-core 10.2.2 → 10.2.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (137) hide show
  1. package/README.md +6 -7
  2. package/dist/bubbles/bubbleHalos.js +7 -3
  3. package/dist/bubbles/bubblesFromGraph.js +4 -2
  4. package/dist/bubbles/classifyBubble.js +10 -5
  5. package/dist/bubbles/superbubbles.js +10 -6
  6. package/dist/chunks/{chunk-N6FECAXP.js → chunk-24WITXQY.js} +17 -8
  7. package/dist/chunks/{chunk-XTCNEKO5.js → chunk-2QLLQJ72.js} +15 -13
  8. package/dist/chunks/{chunk-ASSNZXCF.js → chunk-3AOGOCCQ.js} +44 -103
  9. package/dist/chunks/{chunk-TWRLC3KK.js → chunk-3XSM4OZU.js} +1 -1
  10. package/dist/chunks/{chunk-WEDZ76AK.js → chunk-4DRQTBBE.js} +1 -1
  11. package/dist/chunks/{chunk-2LQ5BWT7.js → chunk-4ETPXDO6.js} +1 -1
  12. package/dist/chunks/{chunk-FP4H7SFT.js → chunk-4HWM3FNK.js} +2 -2
  13. package/dist/chunks/{chunk-C7MZJSPT.js → chunk-54POIBVC.js} +2 -8
  14. package/dist/chunks/{chunk-PKFMP65V.js → chunk-5GMFEPWR.js} +1 -1
  15. package/dist/chunks/{chunk-CDLPYR5O.js → chunk-5I3K4R2G.js} +7 -6
  16. package/dist/chunks/{chunk-TICYLD5F.js → chunk-7CC7N3XC.js} +35 -78
  17. package/dist/chunks/{chunk-2CVHXFK7.js → chunk-7SRWJLSC.js} +19 -22
  18. package/dist/chunks/{chunk-SBMJNRTV.js → chunk-A4PFFC4Q.js} +37 -27
  19. package/dist/chunks/{chunk-IW6CYVX2.js → chunk-AR4BUBMU.js} +6 -1
  20. package/dist/chunks/{chunk-IUDJKOLB.js → chunk-B6IW3IRE.js} +15 -33
  21. package/dist/chunks/{chunk-JUIJI7RC.js → chunk-BAETMD3J.js} +9 -4
  22. package/dist/chunks/{chunk-L5WF4ZPS.js → chunk-BS4UZ44I.js} +1 -1
  23. package/dist/chunks/{chunk-HNQPEMYE.js → chunk-CM6LO6OC.js} +0 -1
  24. package/dist/chunks/{chunk-CLOP7UVD.js → chunk-CQHUZHET.js} +11 -8
  25. package/dist/chunks/{chunk-R456ME6J.js → chunk-CU6P5RUG.js} +17 -6
  26. package/dist/chunks/chunk-D5D36ZF6.js +107 -0
  27. package/dist/chunks/{chunk-AFP3NWSL.js → chunk-DY3JCAMX.js} +1 -1
  28. package/dist/chunks/{chunk-NRV7R36Q.js → chunk-EFQLEGWM.js} +3 -3
  29. package/dist/chunks/{chunk-BXEPA4KS.js → chunk-G6UIYQZR.js} +5 -2
  30. package/dist/chunks/{chunk-NNODIW4U.js → chunk-H2H4Y3TV.js} +1 -0
  31. package/dist/chunks/{chunk-MVFDSFV2.js → chunk-HNCXR2VS.js} +1 -1
  32. package/dist/chunks/{chunk-EYK7DJZV.js → chunk-J5FWKGOY.js} +1 -1
  33. package/dist/chunks/{chunk-PBENCR5L.js → chunk-JBCZIBFC.js} +0 -2
  34. package/dist/chunks/{chunk-EHUBJDDB.js → chunk-JFY5PWQC.js} +5 -3
  35. package/dist/chunks/{chunk-5BGP5Z64.js → chunk-JLSJMCDJ.js} +1 -1
  36. package/dist/chunks/{chunk-DT2GGH4D.js → chunk-JMABOQWL.js} +2 -6
  37. package/dist/chunks/{chunk-3S3YVOJ7.js → chunk-JSUCGZ6K.js} +1 -1
  38. package/dist/chunks/{chunk-MLSWIMZO.js → chunk-KBEP7VYK.js} +2 -2
  39. package/dist/chunks/{chunk-TAMCZHLW.js → chunk-N73TI3VG.js} +2 -2
  40. package/dist/chunks/chunk-O4EGE27I.js +10 -0
  41. package/dist/chunks/{chunk-3ZZSX5HN.js → chunk-PTABFYQ7.js} +10 -6
  42. package/dist/chunks/{chunk-WBCOREDZ.js → chunk-QLWI2PZ3.js} +16 -7
  43. package/dist/chunks/chunk-RBCE2OQH.js +32 -0
  44. package/dist/chunks/{chunk-BUBZ32IC.js → chunk-RPRHR56C.js} +4 -8
  45. package/dist/chunks/{chunk-47DYCZOK.js → chunk-RUCH6ZFL.js} +4 -0
  46. package/dist/chunks/{chunk-GNTTI6LA.js → chunk-T2PCSAFY.js} +1 -1
  47. package/dist/chunks/{chunk-XKWD2RY3.js → chunk-URZ3CH2R.js} +3 -10
  48. package/dist/chunks/{chunk-ALDGONEI.js → chunk-VQC7KELB.js} +1 -1
  49. package/dist/chunks/{chunk-FLFBYSJO.js → chunk-VQWHMWLF.js} +5 -1
  50. package/dist/chunks/{chunk-4R6QNG23.js → chunk-WL6ZKUVC.js} +3 -3
  51. package/dist/chunks/{chunk-CRTD2SBP.js → chunk-WZNPX7Q6.js} +6 -2
  52. package/dist/chunks/{chunk-FNGIQF43.js → chunk-XA5A27CS.js} +6 -14
  53. package/dist/chunks/{chunk-DK5P2YOL.js → chunk-XI3ZUTWF.js} +2 -2
  54. package/dist/chunks/{chunk-ZIUKZUPJ.js → chunk-XL472HHD.js} +1 -1
  55. package/dist/chunks/{chunk-BPRXQ2SS.js → chunk-XMW266WS.js} +1 -1
  56. package/dist/chunks/{chunk-DRG4236Y.js → chunk-YN6FDIBT.js} +2 -2
  57. package/dist/chunks/{chunk-WFB5TXRA.js → chunk-ZY2AFL4Y.js} +13 -31
  58. package/dist/cli/decodeText.js +6 -0
  59. package/dist/cli/figure.js +59 -60
  60. package/dist/cli/fold.js +13 -13
  61. package/dist/deletionEdges.js +6 -4
  62. package/dist/el.js +3 -1
  63. package/dist/figure.js +33 -31
  64. package/dist/figureData.js +32 -27
  65. package/dist/figureScene.js +43 -0
  66. package/dist/figureSettings.js +8 -8
  67. package/dist/foldVariants.js +2 -2
  68. package/dist/gbzCut.js +1 -1
  69. package/dist/genes/exonOutline.js +2 -2
  70. package/dist/genes/geneFiles.js +1 -1
  71. package/dist/genes/genePins.js +3 -3
  72. package/dist/gfa/gfaConverter.js +2 -2
  73. package/dist/gfa-core/gfaParser.js +1 -1
  74. package/dist/gfa-core/index.js +1 -1
  75. package/dist/graphLabels.js +4 -4
  76. package/dist/index.js +72 -73
  77. package/dist/labelLayout.js +8 -8
  78. package/dist/layout/forceCache.js +8 -8
  79. package/dist/layout/mergeRuns.js +2 -2
  80. package/dist/layout/orderedLayout.js +1 -3
  81. package/dist/layout/tubeMapLayout.js +6 -6
  82. package/dist/layout/walkRowDraw.js +11 -11
  83. package/dist/layout/walkRowLayout.js +3 -1
  84. package/dist/layout/walkStrip.js +14 -12
  85. package/dist/layoutEngines.js +1 -2
  86. package/dist/layoutModes.js +9 -9
  87. package/dist/nodeWidths.js +1 -3
  88. package/dist/pathColors.js +5 -5
  89. package/dist/pipeline.js +7 -7
  90. package/dist/referenceRampCss.js +9 -9
  91. package/dist/referenceStrip.js +9 -9
  92. package/dist/renderer/Canvas2DRenderer.js +2 -2
  93. package/dist/renderer/GeometryBuilder.js +8 -8
  94. package/dist/renderer/canvas.js +1 -1
  95. package/dist/renderer/svgCanvas.js +1 -1
  96. package/dist/tubeMap/axis.js +5 -5
  97. package/dist/tubeMap/bundle.js +7 -7
  98. package/dist/tubeMap/coarsen.js +6 -6
  99. package/dist/tubeMap/deviations.js +5 -5
  100. package/dist/tubeMap/draw.js +1 -1
  101. package/dist/tubeMap/genes.js +6 -6
  102. package/dist/tubeMap/nodeColors.js +9 -9
  103. package/dist/types/bubbles/bubblesFromGraph.d.ts +1 -0
  104. package/dist/types/bubbles/classifyBubble.d.ts +0 -1
  105. package/dist/types/cli/decodeText.d.ts +1 -0
  106. package/dist/types/cli/figure.d.ts +4 -15
  107. package/dist/types/deletionEdges.d.ts +3 -5
  108. package/dist/types/el.d.ts +1 -0
  109. package/dist/types/figureData.d.ts +7 -26
  110. package/dist/types/figureScene.d.ts +31 -0
  111. package/dist/types/genes/geneFiles.d.ts +2 -1
  112. package/dist/types/index.d.ts +1 -1
  113. package/dist/types/layout/deletionRoutes.d.ts +1 -1
  114. package/dist/types/layout/orderedLayout.d.ts +0 -6
  115. package/dist/types/layout/walkRowLayout.d.ts +1 -0
  116. package/dist/types/nodeWidths.d.ts +0 -1
  117. package/dist/types/renderer/Canvas2DRenderer.d.ts +1 -0
  118. package/dist/types/renderer/canvas.d.ts +2 -2
  119. package/dist/types/tubeMap/draw.d.ts +1 -0
  120. package/dist/types/util/geometry.d.ts +3 -3
  121. package/dist/types/version.d.ts +1 -1
  122. package/dist/util/SpatialIndex.js +4 -4
  123. package/dist/util/edgeCurves.js +3 -3
  124. package/dist/util/geometry.js +3 -3
  125. package/dist/util/hitDetection.js +5 -5
  126. package/dist/version.js +1 -1
  127. package/dist/viewport.js +8 -8
  128. package/dist/walkEncoding.js +9 -9
  129. package/dist/walkHighlight.js +10 -10
  130. package/dist/walkKey.js +5 -5
  131. package/package.json +3 -6
  132. package/dist/chunks/bandage-layout-3AR6BCUD.js +0 -4694
  133. package/dist/chunks/chunk-4BYTEJGW.js +0 -44
  134. package/dist/chunks/chunk-7XHHVYG7.js +0 -13
  135. package/dist/loadBandage.js +0 -6
  136. package/dist/types/bandage/bandage-layout.d.ts +0 -14
  137. package/dist/types/loadBandage.d.ts +0 -3
package/dist/types/tubeMap/draw.d.ts CHANGED
@@ -44,6 +44,7 @@ interface Rect extends Filled {
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  }
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  interface Shape extends Filled {
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  commands: Command[];
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+ outline: [number, number][];
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  }
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  interface Layer {
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  rects: Rect[];
package/dist/types/util/geometry.d.ts CHANGED
@@ -41,8 +41,8 @@ export interface AxisScale {
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  pixelRows?: boolean;
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  }
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  export declare function yToXOf({ scaleX, scaleY }: AxisScale): number;
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- export declare const PATH_RIBBON_SPACING = 3;
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- export declare function pathRibbonOffsets(fromSegments: NodeSegment[], toSegments: NodeSegment[], count: number, axis: AxisScale, spacing?: number): {
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+ export declare const PATH_RIBBON_SPACING_PX = 3;
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+ export declare function pathRibbonOffsets(fromSegments: NodeSegment[], toSegments: NodeSegment[], count: number, axis: AxisScale): {
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  x: number;
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  y: number;
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  }[];
@@ -50,6 +50,6 @@ export type SelfLink = boolean | Side;
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  export declare function selfLinkOf(edge: GraphEdge): SelfLink;
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  export type EdgeJoin = SelfLink | EdgeSides;
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  export declare function edgeJoinOf(edge: GraphEdge, stranded?: boolean): EdgeJoin;
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- export declare function computeEdgeCurves(fromSegments: NodeSegment[], toSegments: NodeSegment[], join: EdgeJoin, offsetX: number, offsetY: number, axis: AxisScale, bypassed?: NodeSegment[], maxBowIn?: number): BezierCurve[];
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+ export declare function computeEdgeCurves(fromSegments: NodeSegment[], toSegments: NodeSegment[], join: EdgeJoin, axis: AxisScale, bypassed?: NodeSegment[], maxBowIn?: number): BezierCurve[];
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  export declare function routedEdgeCurves(fromSegments: NodeSegment[], toSegments: NodeSegment[], route: NodeSegment[], sides?: EdgeSides): BezierCurve[];
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  export {};
package/dist/types/version.d.ts CHANGED
@@ -1 +1 @@
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- export declare const version = "10.2.2";
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+ export declare const version = "10.2.3";
package/dist/util/SpatialIndex.js CHANGED
@@ -1,10 +1,10 @@
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  import {
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  EdgeSpatialIndex,
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  SpatialIndex
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- } from "../chunks/chunk-MLSWIMZO.js";
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- import "../chunks/chunk-WFB5TXRA.js";
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- import "../chunks/chunk-N6FECAXP.js";
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- import "../chunks/chunk-2CVHXFK7.js";
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+ } from "../chunks/chunk-KBEP7VYK.js";
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+ import "../chunks/chunk-ZY2AFL4Y.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-CPMHA4W5.js";
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  import "../chunks/chunk-FYQWPEEY.js";
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  export {
package/dist/util/edgeCurves.js CHANGED
@@ -1,8 +1,8 @@
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  import {
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  baseEdgeCurves
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- } from "../chunks/chunk-WFB5TXRA.js";
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- import "../chunks/chunk-N6FECAXP.js";
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- import "../chunks/chunk-2CVHXFK7.js";
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+ } from "../chunks/chunk-ZY2AFL4Y.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-CPMHA4W5.js";
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  import "../chunks/chunk-FYQWPEEY.js";
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  export {
package/dist/util/geometry.js CHANGED
@@ -1,5 +1,5 @@
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  import {
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- PATH_RIBBON_SPACING,
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+ PATH_RIBBON_SPACING_PX,
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  bowAround,
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  computeEdgeCurves,
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  curveBounds,
@@ -16,10 +16,10 @@ import {
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  svgPath,
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  translateCurves,
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  yToXOf
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- } from "../chunks/chunk-2CVHXFK7.js";
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+ } from "../chunks/chunk-7SRWJLSC.js";
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  import "../chunks/chunk-CPMHA4W5.js";
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  export {
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- PATH_RIBBON_SPACING,
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+ PATH_RIBBON_SPACING_PX,
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  bowAround,
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  computeEdgeCurves,
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  curveBounds,
package/dist/util/hitDetection.js CHANGED
@@ -4,11 +4,11 @@ import {
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  findHoveredEdge,
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  findHoveredNode,
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  nodesUnderBox
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- } from "../chunks/chunk-FP4H7SFT.js";
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- import "../chunks/chunk-MLSWIMZO.js";
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- import "../chunks/chunk-WFB5TXRA.js";
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- import "../chunks/chunk-N6FECAXP.js";
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- import "../chunks/chunk-2CVHXFK7.js";
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+ } from "../chunks/chunk-4HWM3FNK.js";
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+ import "../chunks/chunk-KBEP7VYK.js";
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+ import "../chunks/chunk-ZY2AFL4Y.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-CPMHA4W5.js";
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  import "../chunks/chunk-FYQWPEEY.js";
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  export {
package/dist/version.js CHANGED
@@ -1,6 +1,6 @@
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  import {
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  version
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- } from "./chunks/chunk-EYK7DJZV.js";
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+ } from "./chunks/chunk-J5FWKGOY.js";
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  export {
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  version
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  };
package/dist/viewport.js CHANGED
@@ -5,26 +5,26 @@ import {
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  screenToLayout,
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  viewportOf,
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  zoomAbout
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- } from "./chunks/chunk-L5WF4ZPS.js";
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- import "./chunks/chunk-XTCNEKO5.js";
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+ } from "./chunks/chunk-BS4UZ44I.js";
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+ import "./chunks/chunk-2QLLQJ72.js";
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+ import "./chunks/chunk-PUG7LXDF.js";
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  import "./chunks/chunk-IGVV37VI.js";
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  import "./chunks/chunk-OPPVSPEF.js";
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  import "./chunks/chunk-VPE4AYP7.js";
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- import "./chunks/chunk-PUG7LXDF.js";
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- import "./chunks/chunk-IW6CYVX2.js";
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+ import "./chunks/chunk-AR4BUBMU.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-PSMKPSO4.js";
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- import "./chunks/chunk-CDLPYR5O.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-G45YY72K.js";
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  import "./chunks/chunk-BPLIXMH7.js";
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- import "./chunks/chunk-TAMCZHLW.js";
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+ import "./chunks/chunk-N73TI3VG.js";
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  import "./chunks/chunk-UVBGRJQX.js";
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  import "./chunks/chunk-6JEWNXCQ.js";
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- import "./chunks/chunk-N6FECAXP.js";
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- import "./chunks/chunk-2CVHXFK7.js";
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+ import "./chunks/chunk-24WITXQY.js";
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+ import "./chunks/chunk-7SRWJLSC.js";
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  export {
package/dist/walkEncoding.js CHANGED
@@ -9,21 +9,21 @@ import {
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  schemeColor,
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  schemeCss,
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  schemeRgb
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- } from "./chunks/chunk-ALDGONEI.js";
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- import "./chunks/chunk-SBMJNRTV.js";
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+ } from "./chunks/chunk-VQC7KELB.js";
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+ import "./chunks/chunk-A4PFFC4Q.js";
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  import "./chunks/chunk-G2FD7S3C.js";
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- import "./chunks/chunk-WFB5TXRA.js";
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- import "./chunks/chunk-TWRLC3KK.js";
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- import "./chunks/chunk-PBENCR5L.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-3ZZSX5HN.js";
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+ import "./chunks/chunk-PTABFYQ7.js";
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- import "./chunks/chunk-TAMCZHLW.js";
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- import "./chunks/chunk-N6FECAXP.js";
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- import "./chunks/chunk-2CVHXFK7.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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package/dist/walkHighlight.js CHANGED
@@ -2,22 +2,22 @@ import {
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  facetLifts,
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  walkLift
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- } from "./chunks/chunk-R456ME6J.js";
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- import "./chunks/chunk-ALDGONEI.js";
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- import "./chunks/chunk-SBMJNRTV.js";
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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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  import "./chunks/chunk-G2FD7S3C.js";
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- import "./chunks/chunk-WFB5TXRA.js";
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- import "./chunks/chunk-TWRLC3KK.js";
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- import "./chunks/chunk-PBENCR5L.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-3ZZSX5HN.js";
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+ import "./chunks/chunk-PTABFYQ7.js";
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  import "./chunks/chunk-AB35TJST.js";
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- import "./chunks/chunk-TAMCZHLW.js";
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- import "./chunks/chunk-N6FECAXP.js";
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- import "./chunks/chunk-2CVHXFK7.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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  export {
package/dist/walkKey.js CHANGED
@@ -2,12 +2,12 @@ import {
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  rangeText,
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  walkKey,
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  walkPosition
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- } from "./chunks/chunk-2LQ5BWT7.js";
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- import "./chunks/chunk-3ZZSX5HN.js";
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+ } from "./chunks/chunk-4ETPXDO6.js";
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+ import "./chunks/chunk-PTABFYQ7.js";
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  import "./chunks/chunk-AB35TJST.js";
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- import "./chunks/chunk-TAMCZHLW.js";
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- import "./chunks/chunk-N6FECAXP.js";
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- import "./chunks/chunk-2CVHXFK7.js";
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+ import "./chunks/chunk-N73TI3VG.js";
9
+ import "./chunks/chunk-24WITXQY.js";
10
+ import "./chunks/chunk-7SRWJLSC.js";
11
11
  import "./chunks/chunk-CPMHA4W5.js";
12
12
  import "./chunks/chunk-FYQWPEEY.js";
13
13
  export {
package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@jbrowse/bandage-core",
3
- "version": "10.2.2",
3
+ "version": "10.2.3",
4
4
  "description": "Pangenome graph layout and drawing with no host: GFA in, the Bandage force-directed engine and reference-anchored layouts, a Canvas2D renderer, hit testing and labels out",
5
5
  "license": "GPL-3.0-or-later",
6
6
  "repository": {
@@ -37,6 +37,7 @@
37
37
  "dependencies": {
38
38
  "@gmod/gbz-base": "^7.4.0",
39
39
  "@gmod/tabix": "^3.10.1",
40
+ "@jbrowse/graph-fmmm-layout": "^1.0.2",
40
41
  "@jbrowse/graph-stress-layout": "^1.0.0",
41
42
  "@jbrowse/tubemap-core": "^1.1.0"
42
43
  },
@@ -69,11 +70,7 @@
69
70
  "test": "vitest run",
70
71
  "test:watch": "vitest",
71
72
  "bench": "vitest bench --run",
72
- "build:wasm": "./scripts/build-wasm.sh",
73
- "test:wasm": "node scripts/smoke-wasm.mjs",
74
- "bench:layout": "node scripts/bench-layout.mjs",
75
- "layout-digest": "node scripts/layout-digest.mjs",
76
- "preversion": "pnpm lint && pnpm format:check && pnpm typecheck && pnpm test && pnpm build && pnpm test:wasm",
73
+ "preversion": "pnpm lint && pnpm format:check && pnpm typecheck && pnpm test && pnpm build",
77
74
  "version": "node scripts/version.mjs",
78
75
  "postversion": "git push --follow-tags"
79
76
  }