@jbrowse/bandage-core 9.8.1 → 9.9.1

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 (61) hide show
  1. package/dist/bubbles/popBubble.js +2 -2
  2. package/dist/bubbles/superbubbles.js +3 -3
  3. package/dist/chunks/{chunk-G3SZWUPA.js → chunk-2NROXCK3.js} +1 -1
  4. package/dist/chunks/{chunk-MAUEPAMG.js → chunk-6PYZYBBF.js} +1 -1
  5. package/dist/chunks/{chunk-VHW7FDHU.js → chunk-A6PSWTLX.js} +1 -1
  6. package/dist/chunks/{chunk-JRADQSGK.js → chunk-D4I6GGFX.js} +13 -13
  7. package/dist/chunks/{chunk-YMMZUMYE.js → chunk-EC4UZHWQ.js} +1 -1
  8. package/dist/chunks/{chunk-7GBL7SJY.js → chunk-EDASNMLY.js} +1 -1
  9. package/dist/chunks/{chunk-3FVITQAJ.js → chunk-EE37PVQY.js} +2 -2
  10. package/dist/chunks/{chunk-BOHK5BD3.js → chunk-F4BKWWLS.js} +1 -1
  11. package/dist/chunks/{chunk-AM3P3WWO.js → chunk-F5BYHLIN.js} +1 -1
  12. package/dist/chunks/{chunk-ZGRYFUXE.js → chunk-FPTI3WAV.js} +13 -6
  13. package/dist/chunks/chunk-G45YY72K.js +220 -0
  14. package/dist/chunks/{chunk-6N7H22SS.js → chunk-HOZI3FBG.js} +2 -2
  15. package/dist/chunks/{chunk-ST2IBUAN.js → chunk-IGJCTPFB.js} +30 -5
  16. package/dist/chunks/{chunk-Z7UWHVOM.js → chunk-IJRNMO4D.js} +2 -2
  17. package/dist/chunks/{chunk-OCMBULGN.js → chunk-J7YKQ5YW.js} +1 -1
  18. package/dist/chunks/{chunk-ZBWMTXTM.js → chunk-KJEMKHVB.js} +1 -1
  19. package/dist/chunks/{chunk-QMJXHYVQ.js → chunk-MECWJY2R.js} +2 -2
  20. package/dist/chunks/{chunk-EPREHMKU.js → chunk-P6O4RSOQ.js} +2 -2
  21. package/dist/chunks/{chunk-373Y3KUJ.js → chunk-RK3MF4FD.js} +1 -1
  22. package/dist/chunks/{chunk-C55SC5AJ.js → chunk-ROQGMTFB.js} +1 -1
  23. package/dist/chunks/{chunk-3C5UXR2U.js → chunk-TOVOJNT7.js} +1 -1
  24. package/dist/chunks/{chunk-5QOMIEHX.js → chunk-WVBYR6Y7.js} +2 -2
  25. package/dist/chunks/{chunk-BV64PQ2C.js → chunk-YAN2ZPNV.js} +1 -1
  26. package/dist/chunks/{chunk-BLRJ6IGK.js → chunk-YGN4KL7W.js} +1 -1
  27. package/dist/chunks/{chunk-QG5IVMRS.js → chunk-YS7VA5SI.js} +1 -1
  28. package/dist/chunks/{chunk-XKM5OHQQ.js → chunk-ZBLKAWSD.js} +1 -1
  29. package/dist/cli/figure.js +19 -18
  30. package/dist/cli/fold.js +4 -3
  31. package/dist/figure.js +17 -16
  32. package/dist/figureSettings.js +5 -4
  33. package/dist/gfa/gfaConverter.js +2 -2
  34. package/dist/gfa/gfaTables.js +6 -0
  35. package/dist/index.js +40 -36
  36. package/dist/layout/forceCache.js +5 -4
  37. package/dist/layout/trimToWindow.js +1 -1
  38. package/dist/layout/tubeMapLayout.js +3 -3
  39. package/dist/layout/walkRowDraw.js +5 -5
  40. package/dist/layout/walkRowLayout.js +3 -3
  41. package/dist/layout/walkRows.js +2 -2
  42. package/dist/layout/walkStrip.js +6 -6
  43. package/dist/layoutModes.js +6 -6
  44. package/dist/pathAnchoring.js +1 -1
  45. package/dist/pathColors.js +2 -2
  46. package/dist/pipeline.js +4 -3
  47. package/dist/referenceRampCss.js +4 -4
  48. package/dist/referenceStrip.js +4 -4
  49. package/dist/renderer/GeometryBuilder.js +3 -3
  50. package/dist/tubeMap/bundle.js +4 -4
  51. package/dist/tubeMap/coarsen.js +3 -3
  52. package/dist/tubeMap/draw.js +2 -2
  53. package/dist/tubeMap/nodeColors.js +4 -4
  54. package/dist/types/gfa/gfaTables.d.ts +10 -0
  55. package/dist/types/index.d.ts +1 -0
  56. package/dist/types/version.d.ts +1 -1
  57. package/dist/version.js +1 -1
  58. package/dist/viewport.js +5 -4
  59. package/dist/walkEncoding.js +4 -4
  60. package/dist/walkHighlight.js +5 -5
  61. package/package.json +2 -2
package/dist/referenceStrip.js CHANGED
@@ -7,16 +7,16 @@ import {
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  stripBlockAt,
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  stripOverhang,
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  stripPixels
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- } from "./chunks/chunk-373Y3KUJ.js";
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- import "./chunks/chunk-BOHK5BD3.js";
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+ } from "./chunks/chunk-RK3MF4FD.js";
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+ import "./chunks/chunk-F4BKWWLS.js";
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  import "./chunks/chunk-G2FD7S3C.js";
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- import "./chunks/chunk-7GBL7SJY.js";
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+ import "./chunks/chunk-EDASNMLY.js";
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  import "./chunks/chunk-PBENCR5L.js";
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  import "./chunks/chunk-WFB5TXRA.js";
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  import "./chunks/chunk-3ZZSX5HN.js";
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  import "./chunks/chunk-AB35TJST.js";
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  import "./chunks/chunk-ES2N6V56.js";
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- import "./chunks/chunk-ST2IBUAN.js";
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+ import "./chunks/chunk-IGJCTPFB.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-N6FECAXP.js";
package/dist/renderer/GeometryBuilder.js CHANGED
@@ -11,15 +11,15 @@ import {
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  endTangent,
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  getNodeColor,
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  hslToRgb
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- } from "../chunks/chunk-BOHK5BD3.js";
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+ } from "../chunks/chunk-F4BKWWLS.js";
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  import "../chunks/chunk-G2FD7S3C.js";
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- import "../chunks/chunk-7GBL7SJY.js";
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+ import "../chunks/chunk-EDASNMLY.js";
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  import "../chunks/chunk-PBENCR5L.js";
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  import "../chunks/chunk-WFB5TXRA.js";
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  import "../chunks/chunk-3ZZSX5HN.js";
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  import "../chunks/chunk-AB35TJST.js";
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  import "../chunks/chunk-ES2N6V56.js";
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- import "../chunks/chunk-ST2IBUAN.js";
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+ import "../chunks/chunk-IGJCTPFB.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-N6FECAXP.js";
package/dist/tubeMap/bundle.js CHANGED
@@ -1,13 +1,13 @@
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  import {
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  bundleRoutes
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- } from "../chunks/chunk-5QOMIEHX.js";
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- import "../chunks/chunk-6N7H22SS.js";
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+ } from "../chunks/chunk-WVBYR6Y7.js";
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+ import "../chunks/chunk-HOZI3FBG.js";
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  import "../chunks/chunk-CWFNEKST.js";
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  import "../chunks/chunk-C44YRP5F.js";
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- import "../chunks/chunk-7GBL7SJY.js";
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+ import "../chunks/chunk-EDASNMLY.js";
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  import "../chunks/chunk-3ZZSX5HN.js";
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  import "../chunks/chunk-AB35TJST.js";
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- import "../chunks/chunk-ST2IBUAN.js";
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+ import "../chunks/chunk-IGJCTPFB.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-N6FECAXP.js";
package/dist/tubeMap/coarsen.js CHANGED
@@ -1,14 +1,14 @@
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  import {
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  pathSteps
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- } from "../chunks/chunk-6N7H22SS.js";
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+ } from "../chunks/chunk-HOZI3FBG.js";
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  import "../chunks/chunk-CWFNEKST.js";
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  import "../chunks/chunk-C44YRP5F.js";
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- import "../chunks/chunk-7GBL7SJY.js";
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+ import "../chunks/chunk-EDASNMLY.js";
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  import "../chunks/chunk-3ZZSX5HN.js";
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  import "../chunks/chunk-AB35TJST.js";
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  import {
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  pathOrigin
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- } from "../chunks/chunk-ST2IBUAN.js";
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+ } from "../chunks/chunk-IGJCTPFB.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-N6FECAXP.js";
package/dist/tubeMap/draw.js CHANGED
@@ -8,11 +8,11 @@ import {
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  tubeMapMismatchAt,
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  tubeMapPicture,
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  tubeMapTrackAt
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- } from "../chunks/chunk-G3SZWUPA.js";
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+ } from "../chunks/chunk-2NROXCK3.js";
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  import "../chunks/chunk-XXT2JCAC.js";
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  import "../chunks/chunk-CWFNEKST.js";
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  import "../chunks/chunk-C44YRP5F.js";
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- import "../chunks/chunk-ST2IBUAN.js";
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+ import "../chunks/chunk-IGJCTPFB.js";
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  import "../chunks/chunk-BPLIXMH7.js";
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  import "../chunks/chunk-FYQWPEEY.js";
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  export {
package/dist/tubeMap/nodeColors.js CHANGED
@@ -1,15 +1,15 @@
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  import {
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  tubeMapNodeColors
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- } from "../chunks/chunk-ZBWMTXTM.js";
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- import "../chunks/chunk-BOHK5BD3.js";
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+ } from "../chunks/chunk-KJEMKHVB.js";
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+ import "../chunks/chunk-F4BKWWLS.js";
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  import "../chunks/chunk-G2FD7S3C.js";
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- import "../chunks/chunk-7GBL7SJY.js";
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+ import "../chunks/chunk-EDASNMLY.js";
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  import "../chunks/chunk-PBENCR5L.js";
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  import "../chunks/chunk-WFB5TXRA.js";
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  import "../chunks/chunk-3ZZSX5HN.js";
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  import "../chunks/chunk-AB35TJST.js";
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  import "../chunks/chunk-ES2N6V56.js";
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- import "../chunks/chunk-ST2IBUAN.js";
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+ import "../chunks/chunk-IGJCTPFB.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-N6FECAXP.js";
package/dist/types/gfa/gfaTables.d.ts ADDED
@@ -0,0 +1,10 @@
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+ import type { GraphTables } from './graphTables.js';
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+ /**
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+ * The tables a GFA of S, L and W lines stands for, which `graphFromTables`
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+ * turns into the Graph `convertGFAToGraph` makes of the text. No string or
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+ * object is made per walk step: a gbz-base cut of every haplotype is millions
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+ * of steps, which the text route took seconds over. Undefined for a GFA the
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+ * tables cannot hold (P or GFA2 records, a segment declared twice, an S tag
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+ * other than LN/SN/SO/SR), which converts as text instead.
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+ */
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+ export declare function gfaTables(text: string): GraphTables | undefined;
package/dist/types/index.d.ts CHANGED
@@ -93,6 +93,7 @@ export { LABEL_CHAR_PX, LABEL_PAD, LABEL_PX } from './overlayLabels.js';
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  export type { Graph, GraphEdge, GraphNode, LayoutResult, NodeSegment, } from './types.js';
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  export { cutWindowGFA, haplotypeWanted, referencePathQuery, referenceSamplesOf, resolveReferenceSample, } from './gbzWindow.js';
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  export type { GbzWindowOptions } from './gbzWindow.js';
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+ export { gfaTables } from './gfa/gfaTables.js';
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  export { graphFromTables, graphTablesGFA } from './gfa/graphTables.js';
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  export type { GraphTables } from './gfa/graphTables.js';
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  export { engineKey } from './pipeline.js';
package/dist/types/version.d.ts CHANGED
@@ -1 +1 @@
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- export declare const version = "9.8.1";
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+ export declare const version = "9.9.1";
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-YMMZUMYE.js";
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+ } from "./chunks/chunk-EC4UZHWQ.js";
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  export {
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  version
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  };
package/dist/viewport.js CHANGED
@@ -5,17 +5,18 @@ import {
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  screenToLayout,
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  viewportOf,
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  zoomAbout
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- } from "./chunks/chunk-XKM5OHQQ.js";
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- import "./chunks/chunk-ZGRYFUXE.js";
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+ } from "./chunks/chunk-ZBLKAWSD.js";
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+ import "./chunks/chunk-FPTI3WAV.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-OCMBULGN.js";
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+ import "./chunks/chunk-J7YKQ5YW.js";
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+ import "./chunks/chunk-G45YY72K.js";
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  import "./chunks/chunk-OA7RIMZ2.js";
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  import "./chunks/chunk-QYBZZI5H.js";
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  import "./chunks/chunk-CDLPYR5O.js";
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  import "./chunks/chunk-JVLURPFW.js";
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  import "./chunks/chunk-ES2N6V56.js";
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- import "./chunks/chunk-ST2IBUAN.js";
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+ import "./chunks/chunk-IGJCTPFB.js";
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  import "./chunks/chunk-BPLIXMH7.js";
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  import "./chunks/chunk-TAMCZHLW.js";
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package/dist/walkEncoding.js CHANGED
@@ -9,16 +9,16 @@ import {
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  schemeColor,
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  schemeCss,
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  schemeRgb
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- } from "./chunks/chunk-AM3P3WWO.js";
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- import "./chunks/chunk-BOHK5BD3.js";
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+ } from "./chunks/chunk-F5BYHLIN.js";
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+ import "./chunks/chunk-F4BKWWLS.js";
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  import "./chunks/chunk-G2FD7S3C.js";
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- import "./chunks/chunk-7GBL7SJY.js";
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+ import "./chunks/chunk-EDASNMLY.js";
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  import "./chunks/chunk-PBENCR5L.js";
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  import "./chunks/chunk-WFB5TXRA.js";
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  import "./chunks/chunk-3ZZSX5HN.js";
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  import "./chunks/chunk-AB35TJST.js";
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- import "./chunks/chunk-ST2IBUAN.js";
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+ import "./chunks/chunk-IGJCTPFB.js";
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package/dist/walkHighlight.js CHANGED
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  walkLift
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- } from "./chunks/chunk-3FVITQAJ.js";
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- import "./chunks/chunk-AM3P3WWO.js";
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- import "./chunks/chunk-BOHK5BD3.js";
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+ } from "./chunks/chunk-EE37PVQY.js";
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+ import "./chunks/chunk-F5BYHLIN.js";
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+ import "./chunks/chunk-F4BKWWLS.js";
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  import "./chunks/chunk-G2FD7S3C.js";
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- import "./chunks/chunk-7GBL7SJY.js";
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+ import "./chunks/chunk-EDASNMLY.js";
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  import "./chunks/chunk-PBENCR5L.js";
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- import "./chunks/chunk-ST2IBUAN.js";
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+ import "./chunks/chunk-IGJCTPFB.js";
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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": "9.8.1",
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+ "version": "9.9.1",
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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": {
@@ -37,7 +37,7 @@
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  "dependencies": {
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  "@gmod/gbz-base": "^7.0.0",
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  "@gmod/tabix": "^3.9.1",
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- "@jbrowse/tubemap-core": "^0.2.2"
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+ "@jbrowse/tubemap-core": "^0.2.3"
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  },
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  "devDependencies": {
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  "@eslint/js": "^10.0.1",