@jbrowse/bandage-core 10.0.1 → 10.2.0

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 (65) hide show
  1. package/README.md +3 -0
  2. package/dist/bubbles/popBubble.js +2 -2
  3. package/dist/bubbles/superbubbles.js +3 -3
  4. package/dist/chunks/{chunk-IFOZFVZK.js → chunk-4R6QNG23.js} +2 -2
  5. package/dist/chunks/{chunk-KJYSOHVN.js → chunk-5BGP5Z64.js} +1 -1
  6. package/dist/chunks/{chunk-B4645SM2.js → chunk-AFP3NWSL.js} +45 -16
  7. package/dist/chunks/{chunk-VOWI544A.js → chunk-ALDGONEI.js} +1 -1
  8. package/dist/chunks/{chunk-3XE3OUEN.js → chunk-C7MZJSPT.js} +1 -1
  9. package/dist/chunks/{chunk-AZJF2PZE.js → chunk-CPVZGVDL.js} +8 -8
  10. package/dist/chunks/{chunk-CFNFT4RA.js → chunk-CRTD2SBP.js} +1 -1
  11. package/dist/chunks/{chunk-IM4SJUPO.js → chunk-DK5P2YOL.js} +2 -2
  12. package/dist/chunks/{chunk-FLUQODT2.js → chunk-DT2GGH4D.js} +1 -1
  13. package/dist/chunks/{chunk-FFFYXMOP.js → chunk-EDR4CGCQ.js} +10 -10
  14. package/dist/chunks/{chunk-BEWLQADP.js → chunk-FNGIQF43.js} +1 -1
  15. package/dist/chunks/{chunk-OEPCRURR.js → chunk-GNTTI6LA.js} +1 -1
  16. package/dist/chunks/{chunk-HQ2AHRMH.js → chunk-IUDJKOLB.js} +1 -1
  17. package/dist/chunks/{chunk-QXAB2FLJ.js → chunk-IW6CYVX2.js} +1 -1
  18. package/dist/chunks/{chunk-QORSYW7J.js → chunk-L5WF4ZPS.js} +1 -1
  19. package/dist/chunks/{chunk-KY4LV2Z6.js → chunk-M3NPTHSE.js} +1 -1
  20. package/dist/chunks/{chunk-EMUUNWRU.js → chunk-M6LK4GII.js} +7 -1
  21. package/dist/chunks/{chunk-ZR7A7DKQ.js → chunk-MVFDSFV2.js} +1 -1
  22. package/dist/chunks/{chunk-FG762CCP.js → chunk-PKFMP65V.js} +2 -2
  23. package/dist/chunks/{chunk-QIVPRZ4H.js → chunk-R456ME6J.js} +2 -2
  24. package/dist/chunks/{chunk-A647OH7N.js → chunk-RIPAA7OK.js} +1 -1
  25. package/dist/chunks/{chunk-WI7ZHJ27.js → chunk-RPDXZLCG.js} +2 -2
  26. package/dist/chunks/{chunk-NP356MC2.js → chunk-SBMJNRTV.js} +1 -1
  27. package/dist/chunks/{chunk-4QTNXTGW.js → chunk-T6V4KI2L.js} +1 -1
  28. package/dist/chunks/{chunk-REE4GUDM.js → chunk-TWRLC3KK.js} +1 -1
  29. package/dist/chunks/{chunk-MSX3BDO4.js → chunk-XTCNEKO5.js} +2 -2
  30. package/dist/chunks/{chunk-VZNKA3K2.js → chunk-XYP6WL2N.js} +7 -3
  31. package/dist/chunks/{chunk-DCJC32QW.js → chunk-ZIUKZUPJ.js} +1 -1
  32. package/dist/cli/figure.js +18 -18
  33. package/dist/cli/fold.js +4 -4
  34. package/dist/figure.js +15 -15
  35. package/dist/figureData.js +15 -15
  36. package/dist/figureSettings.js +4 -4
  37. package/dist/foldVariants.js +1 -1
  38. package/dist/gfa/gfaConverter.js +2 -2
  39. package/dist/index.js +27 -27
  40. package/dist/layout/forceCache.js +4 -4
  41. package/dist/layout/trimToWindow.js +1 -1
  42. package/dist/layout/tubeMapLayout.js +3 -3
  43. package/dist/layout/walkRowDraw.js +5 -5
  44. package/dist/layout/walkRowLayout.js +3 -3
  45. package/dist/layout/walkRows.js +2 -2
  46. package/dist/layout/walkStrip.js +6 -6
  47. package/dist/layoutEngines.js +1 -1
  48. package/dist/layoutModes.js +6 -6
  49. package/dist/pathAnchoring.js +1 -1
  50. package/dist/pathColors.js +2 -2
  51. package/dist/pipeline.js +3 -3
  52. package/dist/referenceRampCss.js +4 -4
  53. package/dist/referenceStrip.js +4 -4
  54. package/dist/renderer/GeometryBuilder.js +3 -3
  55. package/dist/tubeMap/bundle.js +4 -4
  56. package/dist/tubeMap/coarsen.js +3 -3
  57. package/dist/tubeMap/draw.js +2 -2
  58. package/dist/tubeMap/nodeColors.js +4 -4
  59. package/dist/types/layoutEngines.d.ts +1 -1
  60. package/dist/types/version.d.ts +1 -1
  61. package/dist/version.js +1 -1
  62. package/dist/viewport.js +4 -4
  63. package/dist/walkEncoding.js +4 -4
  64. package/dist/walkHighlight.js +5 -5
  65. package/package.json +1 -1
package/dist/pipeline.js CHANGED
@@ -11,16 +11,16 @@ import {
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  forceLayout,
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  layoutExtent,
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  loadGraph
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- } from "./chunks/chunk-MSX3BDO4.js";
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+ } from "./chunks/chunk-XTCNEKO5.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-QXAB2FLJ.js";
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+ import "./chunks/chunk-IW6CYVX2.js";
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  import "./chunks/chunk-QYBZZI5H.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-EMUUNWRU.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";
package/dist/referenceRampCss.js CHANGED
@@ -4,13 +4,13 @@ import {
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  rampHue,
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  rampHueCss,
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  rampStops
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- } from "./chunks/chunk-DCJC32QW.js";
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- import "./chunks/chunk-NP356MC2.js";
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+ } from "./chunks/chunk-ZIUKZUPJ.js";
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+ import "./chunks/chunk-SBMJNRTV.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-REE4GUDM.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-EMUUNWRU.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";
package/dist/referenceStrip.js CHANGED
@@ -7,13 +7,13 @@ import {
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  stripBlockAt,
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  stripOverhang,
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  stripPixels
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- } from "./chunks/chunk-KJYSOHVN.js";
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- import "./chunks/chunk-NP356MC2.js";
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+ } from "./chunks/chunk-5BGP5Z64.js";
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+ import "./chunks/chunk-SBMJNRTV.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-REE4GUDM.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-EMUUNWRU.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";
package/dist/renderer/GeometryBuilder.js CHANGED
@@ -11,12 +11,12 @@ import {
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  endTangent,
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  getNodeColor,
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  hslToRgb
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- } from "../chunks/chunk-NP356MC2.js";
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+ } from "../chunks/chunk-SBMJNRTV.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-REE4GUDM.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-EMUUNWRU.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";
package/dist/tubeMap/bundle.js CHANGED
@@ -1,11 +1,11 @@
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  import {
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  bundleRoutes
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- } from "../chunks/chunk-FG762CCP.js";
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- import "../chunks/chunk-IM4SJUPO.js";
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+ } from "../chunks/chunk-PKFMP65V.js";
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+ import "../chunks/chunk-DK5P2YOL.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-REE4GUDM.js";
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- import "../chunks/chunk-EMUUNWRU.js";
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+ import "../chunks/chunk-TWRLC3KK.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-BPLIXMH7.js";
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  import "../chunks/chunk-3ZZSX5HN.js";
package/dist/tubeMap/coarsen.js CHANGED
@@ -1,12 +1,12 @@
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  import {
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  pathSteps
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- } from "../chunks/chunk-IM4SJUPO.js";
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+ } from "../chunks/chunk-DK5P2YOL.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-REE4GUDM.js";
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+ import "../chunks/chunk-TWRLC3KK.js";
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  import {
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  pathOrigin
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- } from "../chunks/chunk-EMUUNWRU.js";
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+ } from "../chunks/chunk-M6LK4GII.js";
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  import {
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  PathVisitsBuilder
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  } from "../chunks/chunk-RAEABQNW.js";
package/dist/tubeMap/draw.js CHANGED
@@ -8,12 +8,12 @@ import {
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  tubeMapMismatchAt,
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  tubeMapPicture,
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  tubeMapTrackAt
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- } from "../chunks/chunk-HQ2AHRMH.js";
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+ } from "../chunks/chunk-IUDJKOLB.js";
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  import "../chunks/chunk-XXT2JCAC.js";
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  import "../chunks/chunk-HK5Y2YWV.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-EMUUNWRU.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-BPLIXMH7.js";
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  import "../chunks/chunk-FYQWPEEY.js";
package/dist/tubeMap/nodeColors.js CHANGED
@@ -1,12 +1,12 @@
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  import {
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  tubeMapNodeColors
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- } from "../chunks/chunk-OEPCRURR.js";
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- import "../chunks/chunk-NP356MC2.js";
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+ } from "../chunks/chunk-GNTTI6LA.js";
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+ import "../chunks/chunk-SBMJNRTV.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-REE4GUDM.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-EMUUNWRU.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";
package/dist/types/layoutEngines.d.ts CHANGED
@@ -6,7 +6,7 @@ export declare const LAYOUT_ENGINES: readonly [{
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  }, {
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  readonly value: "stress";
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  readonly label: "Stress";
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- readonly description: "Stress layout by stochastic gradient descent in plain JS: distances along the graph become distances on the page, so the reference reads straight and a repeat loop reads as a ring.";
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+ readonly description: "Plain JS: the reference drawn straight and each variant placed against it, an allele as a lens, a repeat loop as a ring, a deletion as an arch; stress by stochastic gradient descent for components with no reference.";
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  }];
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  export type LayoutEngineKind = (typeof LAYOUT_ENGINES)[number]['value'];
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  export declare const LAYOUT_ENGINE_VALUES: ("fmmm" | "stress")[];
package/dist/types/version.d.ts CHANGED
@@ -1 +1 @@
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- export declare const version = "10.0.1";
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+ export declare const version = "10.2.0";
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-KY4LV2Z6.js";
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+ } from "./chunks/chunk-M3NPTHSE.js";
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  export {
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  version
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  };
package/dist/viewport.js CHANGED
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  screenToLayout,
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  viewportOf,
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  zoomAbout
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- } from "./chunks/chunk-QORSYW7J.js";
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- import "./chunks/chunk-MSX3BDO4.js";
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+ } from "./chunks/chunk-L5WF4ZPS.js";
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+ import "./chunks/chunk-XTCNEKO5.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-QXAB2FLJ.js";
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+ import "./chunks/chunk-IW6CYVX2.js";
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  import "./chunks/chunk-QYBZZI5H.js";
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  import "./chunks/chunk-PSMKPSO4.js";
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- import "./chunks/chunk-EMUUNWRU.js";
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+ import "./chunks/chunk-M6LK4GII.js";
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package/dist/walkEncoding.js CHANGED
@@ -9,13 +9,13 @@ import {
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  schemeColor,
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  schemeCss,
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  schemeRgb
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- } from "./chunks/chunk-VOWI544A.js";
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- import "./chunks/chunk-NP356MC2.js";
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+ } from "./chunks/chunk-ALDGONEI.js";
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+ import "./chunks/chunk-SBMJNRTV.js";
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  import "./chunks/chunk-G2FD7S3C.js";
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- import "./chunks/chunk-REE4GUDM.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-EMUUNWRU.js";
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+ import "./chunks/chunk-M6LK4GII.js";
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package/dist/walkHighlight.js CHANGED
@@ -2,14 +2,14 @@ import {
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  walkLift
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- } from "./chunks/chunk-QIVPRZ4H.js";
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- import "./chunks/chunk-VOWI544A.js";
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- import "./chunks/chunk-NP356MC2.js";
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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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- import "./chunks/chunk-REE4GUDM.js";
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+ import "./chunks/chunk-TWRLC3KK.js";
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- import "./chunks/chunk-EMUUNWRU.js";
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+ import "./chunks/chunk-M6LK4GII.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": "10.0.1",
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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": {