@jbrowse/bandage-core 11.6.1 → 11.7.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (63) hide show
  1. package/dist/chunks/{chunk-RLCYVZ4B.js → chunk-5ZQKQ24Z.js} +1 -1
  2. package/dist/chunks/{chunk-WI6SUU5B.js → chunk-65YCFVS4.js} +1 -1
  3. package/dist/chunks/{chunk-W2YAW36J.js → chunk-7L7MN2OM.js} +5 -2
  4. package/dist/chunks/{chunk-MXLYBDOX.js → chunk-A7Q7RTWX.js} +12 -6
  5. package/dist/chunks/{chunk-MEVTV4FI.js → chunk-BXE3SBBN.js} +1 -1
  6. package/dist/chunks/{chunk-QD35GH4C.js → chunk-DD5EZG3T.js} +2 -2
  7. package/dist/chunks/{chunk-F3KQQDKP.js → chunk-DTEXQ65J.js} +1 -1
  8. package/dist/chunks/{chunk-EVXXFMZ7.js → chunk-DUREQSOJ.js} +1 -1
  9. package/dist/chunks/{chunk-XXOBCANT.js → chunk-EH5JZETS.js} +7 -7
  10. package/dist/chunks/{chunk-5WB7O7IT.js → chunk-FNDNSDKW.js} +1 -1
  11. package/dist/chunks/{chunk-D3E7AXBB.js → chunk-G7SG4XMK.js} +23 -6
  12. package/dist/chunks/{chunk-4WXFQOYV.js → chunk-HELOUO6K.js} +2 -2
  13. package/dist/chunks/{chunk-ROLACYCO.js → chunk-HERVZPWA.js} +9 -9
  14. package/dist/chunks/{chunk-HV35LDYH.js → chunk-HMEAGAGC.js} +1 -1
  15. package/dist/chunks/{chunk-OUM54ZSQ.js → chunk-IJCSW6MV.js} +1 -1
  16. package/dist/chunks/{chunk-EIY2SKD3.js → chunk-LG2UK4MB.js} +2 -1
  17. package/dist/chunks/{chunk-3FWNQNF7.js → chunk-NTKWT6XL.js} +1 -1
  18. package/dist/chunks/{chunk-P5PBJONQ.js → chunk-SENPGW4O.js} +1 -1
  19. package/dist/chunks/{chunk-NXBW6KY6.js → chunk-SIA75TEG.js} +1 -1
  20. package/dist/chunks/{chunk-JGQQAUVL.js → chunk-SVPR7IZO.js} +1 -1
  21. package/dist/chunks/{chunk-2C5SATRZ.js → chunk-TUMJNAOL.js} +1 -1
  22. package/dist/chunks/{chunk-DZR37KXT.js → chunk-VSSIYQYF.js} +1 -1
  23. package/dist/chunks/{chunk-BVWMVWLJ.js → chunk-WWIUC4N4.js} +5 -5
  24. package/dist/chunks/{chunk-7OTWJQGA.js → chunk-YER6TUXV.js} +3 -3
  25. package/dist/chunks/{chunk-TXTSE44S.js → chunk-ZHZRAYEM.js} +1 -1
  26. package/dist/chunks/{chunk-SVVFWTG4.js → chunk-ZKSC7QVE.js} +1 -1
  27. package/dist/cli/figure.js +22 -22
  28. package/dist/cli/fold.js +5 -5
  29. package/dist/figure.js +17 -17
  30. package/dist/figureData.js +19 -19
  31. package/dist/figureScene.js +12 -12
  32. package/dist/figureSettings.js +6 -6
  33. package/dist/gbzCut.js +4 -4
  34. package/dist/gbzWindow.js +3 -3
  35. package/dist/gfa/gfaConverter.js +2 -2
  36. package/dist/gfa/gfaTables.js +2 -2
  37. package/dist/gfa/graphTables.js +2 -2
  38. package/dist/gfa/walkStops.js +1 -1
  39. package/dist/index.js +25 -25
  40. package/dist/layout/forceCache.js +6 -6
  41. package/dist/layout/tubeMapLayout.js +5 -5
  42. package/dist/layout/walkRowDraw.js +4 -2
  43. package/dist/layout/walkRowLayout.js +5 -5
  44. package/dist/layout/walkRowRuns.js +3 -3
  45. package/dist/layout/walkRows.js +4 -4
  46. package/dist/layout/walkStrip.js +7 -7
  47. package/dist/layoutModes.js +7 -7
  48. package/dist/pipeline.js +5 -5
  49. package/dist/tubeMap/bundle.js +6 -6
  50. package/dist/tubeMap/coarsen.js +6 -6
  51. package/dist/tubeMap/deviations.js +6 -6
  52. package/dist/tubeMap/draw.js +5 -5
  53. package/dist/types/gfa/graphTables.d.ts +2 -0
  54. package/dist/types/gfa/walkStops.d.ts +1 -1
  55. package/dist/types/layout/walkRowDraw.d.ts +2 -1
  56. package/dist/types/layout/walkRows.d.ts +1 -0
  57. package/dist/types/types.d.ts +4 -0
  58. package/dist/types/version.d.ts +1 -1
  59. package/dist/version.js +1 -1
  60. package/dist/viewport.js +6 -6
  61. package/dist/walkHighlight.js +2 -2
  62. package/dist/walkKey.js +2 -2
  63. package/package.json +1 -1
package/dist/layoutModes.js CHANGED
@@ -4,8 +4,8 @@ import {
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  LAYOUT_MODE_VALUES,
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  layoutModeByValue,
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  modeUsesLayoutEngine
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- } from "./chunks/chunk-QD35GH4C.js";
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- import "./chunks/chunk-NXBW6KY6.js";
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+ } from "./chunks/chunk-DD5EZG3T.js";
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+ import "./chunks/chunk-SIA75TEG.js";
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  import "./chunks/chunk-SDI6BVG7.js";
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  import "./chunks/chunk-XR2HMGAS.js";
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  import "./chunks/chunk-GJLZ2MKE.js";
@@ -13,13 +13,13 @@ import "./chunks/chunk-MYLAJDKB.js";
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  import "./chunks/chunk-5OJZV6YT.js";
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  import "./chunks/chunk-UAFATXYA.js";
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  import "./chunks/chunk-3GLG3ZLE.js";
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- import "./chunks/chunk-P5PBJONQ.js";
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- import "./chunks/chunk-MEVTV4FI.js";
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- import "./chunks/chunk-D3E7AXBB.js";
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+ import "./chunks/chunk-SENPGW4O.js";
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+ import "./chunks/chunk-BXE3SBBN.js";
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+ import "./chunks/chunk-G7SG4XMK.js";
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  import "./chunks/chunk-BW2NMXRV.js";
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- import "./chunks/chunk-W2YAW36J.js";
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+ import "./chunks/chunk-7L7MN2OM.js";
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  import "./chunks/chunk-VX656OAZ.js";
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- import "./chunks/chunk-EIY2SKD3.js";
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+ import "./chunks/chunk-LG2UK4MB.js";
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  import "./chunks/chunk-T3H5ELLA.js";
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  import "./chunks/chunk-HMXCN6PG.js";
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  import "./chunks/chunk-AB35TJST.js";
package/dist/pipeline.js CHANGED
@@ -11,18 +11,18 @@ import {
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  forceLayout,
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  layoutExtent,
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  loadGraph
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- } from "./chunks/chunk-7OTWJQGA.js";
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+ } from "./chunks/chunk-YER6TUXV.js";
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  import "./chunks/chunk-OPPVSPEF.js";
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  import "./chunks/chunk-3PZSBNLI.js";
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  import "./chunks/chunk-CKUVEHSS.js";
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  import "./chunks/chunk-VPE4AYP7.js";
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- import "./chunks/chunk-2C5SATRZ.js";
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+ import "./chunks/chunk-TUMJNAOL.js";
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  import "./chunks/chunk-QYBZZI5H.js";
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  import "./chunks/chunk-CFXXFHRK.js";
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- import "./chunks/chunk-W2YAW36J.js";
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+ import "./chunks/chunk-7L7MN2OM.js";
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  import "./chunks/chunk-VX656OAZ.js";
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- import "./chunks/chunk-DZR37KXT.js";
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- import "./chunks/chunk-EIY2SKD3.js";
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+ import "./chunks/chunk-VSSIYQYF.js";
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+ import "./chunks/chunk-LG2UK4MB.js";
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  import "./chunks/chunk-2VMKQKVO.js";
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  import "./chunks/chunk-HKYXWZQS.js";
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  import "./chunks/chunk-34BOZKIE.js";
package/dist/tubeMap/bundle.js CHANGED
@@ -1,14 +1,14 @@
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  import {
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  bundleRoutes
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- } from "../chunks/chunk-WI6SUU5B.js";
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- import "../chunks/chunk-NXBW6KY6.js";
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+ } from "../chunks/chunk-65YCFVS4.js";
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+ import "../chunks/chunk-SIA75TEG.js";
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  import "../chunks/chunk-SDI6BVG7.js";
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  import "../chunks/chunk-5OJZV6YT.js";
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- import "../chunks/chunk-MEVTV4FI.js";
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- import "../chunks/chunk-D3E7AXBB.js";
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+ import "../chunks/chunk-BXE3SBBN.js";
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+ import "../chunks/chunk-G7SG4XMK.js";
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  import "../chunks/chunk-BW2NMXRV.js";
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- import "../chunks/chunk-W2YAW36J.js";
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- import "../chunks/chunk-EIY2SKD3.js";
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+ import "../chunks/chunk-7L7MN2OM.js";
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+ import "../chunks/chunk-LG2UK4MB.js";
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  import "../chunks/chunk-T3H5ELLA.js";
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  import "../chunks/chunk-HMXCN6PG.js";
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  import "../chunks/chunk-AB35TJST.js";
package/dist/tubeMap/coarsen.js CHANGED
@@ -1,15 +1,15 @@
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  import {
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  coarsenTubeMap,
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  lastAtMost
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- } from "../chunks/chunk-OUM54ZSQ.js";
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- import "../chunks/chunk-NXBW6KY6.js";
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+ } from "../chunks/chunk-IJCSW6MV.js";
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+ import "../chunks/chunk-SIA75TEG.js";
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  import "../chunks/chunk-SDI6BVG7.js";
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  import "../chunks/chunk-5OJZV6YT.js";
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- import "../chunks/chunk-MEVTV4FI.js";
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- import "../chunks/chunk-D3E7AXBB.js";
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+ import "../chunks/chunk-BXE3SBBN.js";
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+ import "../chunks/chunk-G7SG4XMK.js";
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  import "../chunks/chunk-BW2NMXRV.js";
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- import "../chunks/chunk-W2YAW36J.js";
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- import "../chunks/chunk-EIY2SKD3.js";
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+ import "../chunks/chunk-7L7MN2OM.js";
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+ import "../chunks/chunk-LG2UK4MB.js";
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  import "../chunks/chunk-T3H5ELLA.js";
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  import "../chunks/chunk-HMXCN6PG.js";
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  import "../chunks/chunk-AB35TJST.js";
package/dist/tubeMap/deviations.js CHANGED
@@ -1,18 +1,18 @@
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  import {
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  lastAtMost
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- } from "../chunks/chunk-OUM54ZSQ.js";
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+ } from "../chunks/chunk-IJCSW6MV.js";
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  import {
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  boxX,
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  referenceBoxes
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  } from "../chunks/chunk-VO6FKNZE.js";
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- import "../chunks/chunk-NXBW6KY6.js";
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+ import "../chunks/chunk-SIA75TEG.js";
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  import "../chunks/chunk-SDI6BVG7.js";
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  import "../chunks/chunk-5OJZV6YT.js";
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- import "../chunks/chunk-MEVTV4FI.js";
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- import "../chunks/chunk-D3E7AXBB.js";
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+ import "../chunks/chunk-BXE3SBBN.js";
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+ import "../chunks/chunk-G7SG4XMK.js";
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  import "../chunks/chunk-BW2NMXRV.js";
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- import "../chunks/chunk-W2YAW36J.js";
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- import "../chunks/chunk-EIY2SKD3.js";
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+ import "../chunks/chunk-7L7MN2OM.js";
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+ import "../chunks/chunk-LG2UK4MB.js";
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  import "../chunks/chunk-T3H5ELLA.js";
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  import "../chunks/chunk-HMXCN6PG.js";
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  import "../chunks/chunk-AB35TJST.js";
package/dist/tubeMap/draw.js CHANGED
@@ -8,15 +8,15 @@ import {
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  tubeMapMismatchAt,
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  tubeMapPicture,
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  tubeMapTrackAt
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- } from "../chunks/chunk-HV35LDYH.js";
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+ } from "../chunks/chunk-HMEAGAGC.js";
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  import "../chunks/chunk-BX4AUMZE.js";
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  import "../chunks/chunk-MYDHU2UV.js";
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  import "../chunks/chunk-SDI6BVG7.js";
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  import "../chunks/chunk-5OJZV6YT.js";
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- import "../chunks/chunk-MEVTV4FI.js";
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- import "../chunks/chunk-D3E7AXBB.js";
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- import "../chunks/chunk-W2YAW36J.js";
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- import "../chunks/chunk-EIY2SKD3.js";
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+ import "../chunks/chunk-BXE3SBBN.js";
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+ import "../chunks/chunk-G7SG4XMK.js";
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+ import "../chunks/chunk-7L7MN2OM.js";
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+ import "../chunks/chunk-LG2UK4MB.js";
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  import "../chunks/chunk-3YBP46PB.js";
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  import "../chunks/chunk-VACK24HF.js";
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  import "../chunks/chunk-CPMHA4W5.js";
package/dist/types/gfa/graphTables.d.ts CHANGED
@@ -30,6 +30,8 @@ export interface GraphTables {
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  reversed: Uint8Array;
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  before?: WalkStopTable;
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  after?: WalkStopTable;
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+ abridgedSteps?: Float64Array;
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+ abridgedBp?: Float64Array;
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  };
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  }
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  /** The GraphPath `graphFromTables` builds of walk `p`, less its steps */
package/dist/types/gfa/walkStops.d.ts CHANGED
@@ -1,7 +1,7 @@
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  import type { PathStop, StopChunk } from '../types.js';
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  export declare const START_STOP_TAG = "ws";
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  export declare const END_STOP_TAG = "we";
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- export type GapCause = 'missing' | 'elsewhere' | 'unknown';
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+ export type GapCause = 'missing' | 'elsewhere' | 'unknown' | 'abridged';
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  export declare const GAP_CAUSE_TEXT: Record<GapCause, string>;
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  export declare const OUTSIDE_TEXT = "outside the extracted subgraph";
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  export interface GapPart {
package/dist/types/layout/walkRowDraw.d.ts CHANGED
@@ -7,6 +7,7 @@ export declare const OFF_REFERENCE = "#8e3fbf";
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  export declare const OUTSIDE_CUT = "#bdbdbd";
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  export declare const MISSING_INK = "#8a8a8a";
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  export declare const UNKNOWN_GAP = "#e2e2e2";
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+ export declare const ABRIDGED_GAP = "#d9a441";
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  export declare const GENE_INK = "#1c1c22";
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  export declare const BAR_PX = 12;
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  export declare const GAP_PX = 4;
@@ -17,7 +18,7 @@ export interface ReadoutCall {
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  spanningReads?: number;
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  agrees?: boolean;
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  }
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- export declare function walkRowReadout(row: Pick<WalkRow, 'bp' | 'gapBp' | 'complete' | 'stop'> & {
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+ export declare function walkRowReadout(row: Pick<WalkRow, 'bp' | 'gapBp' | 'complete' | 'stop' | 'abridgedSteps'> & {
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  runs?: WalkRun[];
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  }, reference: Pick<WalkRow, 'bp'> | undefined, unit?: number, call?: ReadoutCall): string;
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  export declare function readoutPlacement(text: string, endX: number, width: number): {
package/dist/types/layout/walkRows.d.ts CHANGED
@@ -36,6 +36,7 @@ export interface WalkRow {
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  gapBp: number;
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  complete: boolean;
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  stop?: WalkStop;
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+ abridgedSteps?: number;
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  runs: WalkRun[];
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  visits?: WalkVisit[];
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  axis?: WalkAxis;
package/dist/types/types.d.ts CHANGED
@@ -27,6 +27,10 @@ export interface GraphPath {
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  members?: string[];
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  before?: PathStop;
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  after?: PathStop;
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+ abridged?: {
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+ steps: number;
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+ bp: number;
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+ };
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  }
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  export type PathStop = ({
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  kind: 'elsewhere';
package/dist/types/version.d.ts CHANGED
@@ -1 +1 @@
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- export declare const version = "11.6.1";
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+ export declare const version = "11.7.0";
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-TXTSE44S.js";
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+ } from "./chunks/chunk-ZHZRAYEM.js";
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  export {
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  version
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  };
package/dist/viewport.js CHANGED
@@ -5,19 +5,19 @@ import {
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  screenToLayout,
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  viewportOf,
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  zoomAbout
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- } from "./chunks/chunk-RLCYVZ4B.js";
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- import "./chunks/chunk-7OTWJQGA.js";
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+ } from "./chunks/chunk-5ZQKQ24Z.js";
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+ import "./chunks/chunk-YER6TUXV.js";
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  import "./chunks/chunk-OPPVSPEF.js";
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  import "./chunks/chunk-3PZSBNLI.js";
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  import "./chunks/chunk-CKUVEHSS.js";
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  import "./chunks/chunk-VPE4AYP7.js";
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- import "./chunks/chunk-2C5SATRZ.js";
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+ import "./chunks/chunk-TUMJNAOL.js";
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  import "./chunks/chunk-QYBZZI5H.js";
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  import "./chunks/chunk-CFXXFHRK.js";
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- import "./chunks/chunk-W2YAW36J.js";
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+ import "./chunks/chunk-7L7MN2OM.js";
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  import "./chunks/chunk-VX656OAZ.js";
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- import "./chunks/chunk-DZR37KXT.js";
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- import "./chunks/chunk-EIY2SKD3.js";
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+ import "./chunks/chunk-VSSIYQYF.js";
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+ import "./chunks/chunk-LG2UK4MB.js";
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  import "./chunks/chunk-2VMKQKVO.js";
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package/dist/walkHighlight.js CHANGED
@@ -2,7 +2,7 @@ import {
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- } from "./chunks/chunk-EVXXFMZ7.js";
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+ } from "./chunks/chunk-DUREQSOJ.js";
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  import "./chunks/chunk-2XEAITWM.js";
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  import "./chunks/chunk-JGHZ3N34.js";
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@@ -11,7 +11,7 @@ import "./chunks/chunk-OYCQVJYY.js";
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  import "./chunks/chunk-BW2NMXRV.js";
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  import "./chunks/chunk-ZANALBSX.js";
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  import "./chunks/chunk-VX656OAZ.js";
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- import "./chunks/chunk-EIY2SKD3.js";
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+ import "./chunks/chunk-LG2UK4MB.js";
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  import "./chunks/chunk-T3H5ELLA.js";
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  import "./chunks/chunk-HMXCN6PG.js";
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package/dist/walkKey.js CHANGED
@@ -2,8 +2,8 @@ import {
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  rangeText,
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  walkPosition
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- } from "./chunks/chunk-JGQQAUVL.js";
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- import "./chunks/chunk-EIY2SKD3.js";
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+ } from "./chunks/chunk-SVPR7IZO.js";
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+ import "./chunks/chunk-LG2UK4MB.js";
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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": "11.6.1",
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+ "version": "11.7.0",
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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": {