@jbrowse/bandage-core 7.2.1 → 7.4.0

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 (57) hide show
  1. package/dist/chunks/{chunk-MH5IA57M.js → chunk-3LXG54PN.js} +1 -1
  2. package/dist/chunks/{chunk-Y7UR3MDE.js → chunk-4UBWXZVX.js} +1 -1
  3. package/dist/chunks/{chunk-MQSOTYVF.js → chunk-5XHORHYK.js} +43 -49
  4. package/dist/chunks/{chunk-2T3SRIFH.js → chunk-7G7TFATC.js} +5 -5
  5. package/dist/chunks/{chunk-E7FWQQHP.js → chunk-7GBL7SJY.js} +15 -4
  6. package/dist/chunks/{chunk-VECR253P.js → chunk-AVJK272H.js} +1 -1
  7. package/dist/chunks/{chunk-4FQTTG5F.js → chunk-AYOSNXLQ.js} +1 -1
  8. package/dist/chunks/chunk-AZFVORTC.js +19 -0
  9. package/dist/chunks/{chunk-JKXE6CIP.js → chunk-FRR2RGBT.js} +5 -5
  10. package/dist/chunks/chunk-H5S2ONCJ.js +27 -0
  11. package/dist/chunks/chunk-K5SIJGAE.js +12 -0
  12. package/dist/chunks/{chunk-CNQSHEBS.js → chunk-KEVQ46GG.js} +1 -1
  13. package/dist/chunks/{chunk-BZKEMAWC.js → chunk-LNSAKOXP.js} +1 -1
  14. package/dist/chunks/chunk-LOCJN3BZ.js +14 -0
  15. package/dist/chunks/{chunk-3JANT2SW.js → chunk-MP7LXLWV.js} +13 -0
  16. package/dist/chunks/{chunk-OY3CDWFN.js → chunk-PY7EZFL3.js} +4 -4
  17. package/dist/chunks/{chunk-VST5SR4C.js → chunk-RCWYY6XA.js} +4 -4
  18. package/dist/chunks/{chunk-EXSXBIMH.js → chunk-UJ6GYL6T.js} +1 -1
  19. package/dist/chunks/{chunk-EPWYRSHH.js → chunk-WZATPZNH.js} +30 -8
  20. package/dist/chunks/chunk-XVSBZ4ZW.js +54 -0
  21. package/dist/chunks/{chunk-TQ7VCGJR.js → chunk-ZNMHIPUZ.js} +1 -1
  22. package/dist/cli/figure.js +60 -70
  23. package/dist/figure.js +28 -27
  24. package/dist/figureSettings.js +25 -0
  25. package/dist/hoverText.js +8 -0
  26. package/dist/index.js +153 -121
  27. package/dist/layout/forceCache.js +23 -0
  28. package/dist/layout/tubeMapLayout.js +4 -4
  29. package/dist/layout/walkRowDraw.js +8 -8
  30. package/dist/layout/walkRowLayout.js +4 -2
  31. package/dist/layout/walkStrip.js +9 -9
  32. package/dist/layoutModes.js +9 -9
  33. package/dist/layoutQualities.js +6 -0
  34. package/dist/pathColors.js +7 -5
  35. package/dist/pipeline.js +8 -4
  36. package/dist/referenceRampCss.js +6 -6
  37. package/dist/referenceStrip.js +6 -6
  38. package/dist/renderer/GeometryBuilder.js +5 -5
  39. package/dist/renderer/geometryInputs.js +6 -0
  40. package/dist/tubeMap/coarsen.js +5 -5
  41. package/dist/tubeMap/nodeColors.js +6 -6
  42. package/dist/types/figure.d.ts +1 -0
  43. package/dist/types/figureSettings.d.ts +15 -0
  44. package/dist/types/hoverText.d.ts +17 -0
  45. package/dist/types/index.d.ts +11 -2
  46. package/dist/types/layout/forceCache.d.ts +11 -0
  47. package/dist/types/layout/walkRowLayout.d.ts +2 -1
  48. package/dist/types/layoutQualities.d.ts +17 -0
  49. package/dist/types/pathColors.d.ts +4 -0
  50. package/dist/types/pipeline.d.ts +2 -0
  51. package/dist/types/renderer/geometryInputs.d.ts +11 -0
  52. package/dist/types/version.d.ts +1 -1
  53. package/dist/version.js +1 -1
  54. package/dist/viewport.js +5 -5
  55. package/dist/walkEncoding.js +6 -6
  56. package/dist/walkHighlight.js +7 -7
  57. package/package.json +1 -1
package/dist/cli/figure.js CHANGED
@@ -4,96 +4,98 @@ import {
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  genesFromGff3Lines,
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  genesFromText
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  } from "../chunks/chunk-BXEPA4KS.js";
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- import {
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- LAYOUT_ENGINE_VALUES,
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- isLayoutEngineKind,
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- layoutEngine
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- } from "../chunks/chunk-6EJIU6IA.js";
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- import "../chunks/chunk-UNOE2NDN.js";
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- import "../chunks/chunk-LYJ4US66.js";
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  import {
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  LAYOUT_MODES,
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  layoutModeByValue
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- } from "../chunks/chunk-JKXE6CIP.js";
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- import "../chunks/chunk-4FQTTG5F.js";
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- import "../chunks/chunk-TEDQJPMI.js";
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+ } from "../chunks/chunk-FRR2RGBT.js";
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  import "../chunks/chunk-LOEA5IHZ.js";
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+ import "../chunks/chunk-AYOSNXLQ.js";
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+ import "../chunks/chunk-TEDQJPMI.js";
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  import "../chunks/chunk-L3O7AWLI.js";
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  import "../chunks/chunk-TZFWUT2C.js";
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+ import "../chunks/chunk-C44YRP5F.js";
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  import "../chunks/chunk-RVS2QCOX.js";
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  import "../chunks/chunk-HNQPEMYE.js";
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- import "../chunks/chunk-C44YRP5F.js";
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+ import {
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+ HPRC_GBZ,
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+ cutGbzRegion,
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+ haplotypeIndexBeside,
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+ openGbz,
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+ parseRegion
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+ } from "../chunks/chunk-73RSLGZT.js";
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+ import "../chunks/chunk-LTUWJKHD.js";
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+ import "../chunks/chunk-WSIFAZU7.js";
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+ import {
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+ LAYOUT_ENGINE_VALUES,
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+ isLayoutEngineKind,
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+ layoutEngine
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+ } from "../chunks/chunk-6EJIU6IA.js";
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+ import "../chunks/chunk-UNOE2NDN.js";
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+ import "../chunks/chunk-LYJ4US66.js";
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  import "../chunks/chunk-7XHHVYG7.js";
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  import {
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  figureSvg
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- } from "../chunks/chunk-MQSOTYVF.js";
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- import "../chunks/chunk-CH3DLBUT.js";
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- import "../chunks/chunk-4BYTEJGW.js";
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+ } from "../chunks/chunk-5XHORHYK.js";
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+ import "../chunks/chunk-LOCJN3BZ.js";
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  import "../chunks/chunk-47DYCZOK.js";
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- import "../chunks/chunk-OY3CDWFN.js";
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+ import "../chunks/chunk-PY7EZFL3.js";
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  import {
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  genesOnRow,
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  placeRowGenes
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- } from "../chunks/chunk-2T3SRIFH.js";
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+ } from "../chunks/chunk-7G7TFATC.js";
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+ import "../chunks/chunk-CH3DLBUT.js";
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+ import "../chunks/chunk-4BYTEJGW.js";
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  import "../chunks/chunk-3S3YVOJ7.js";
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  import "../chunks/chunk-BUBZ32IC.js";
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- import "../chunks/chunk-BZKEMAWC.js";
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- import "../chunks/chunk-Y7UR3MDE.js";
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- import "../chunks/chunk-MH5IA57M.js";
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- import "../chunks/chunk-TQ7VCGJR.js";
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+ import "../chunks/chunk-3LXG54PN.js";
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+ import "../chunks/chunk-ZNMHIPUZ.js";
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  import "../chunks/chunk-2LQ5BWT7.js";
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- import {
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- forceLayout,
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- loadGraph
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- } from "../chunks/chunk-EPWYRSHH.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-72N5DJHZ.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-VECR253P.js";
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- import "../chunks/chunk-VST5SR4C.js";
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+ import "../chunks/chunk-AVJK272H.js";
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+ import "../chunks/chunk-RCWYY6XA.js";
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  import "../chunks/chunk-UMNCCYBN.js";
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+ import "../chunks/chunk-LNSAKOXP.js";
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+ import "../chunks/chunk-4UBWXZVX.js";
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+ import "../chunks/chunk-MP7LXLWV.js";
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+ import {
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+ filterSamples,
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+ walkRows
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+ } from "../chunks/chunk-SZNZ2T6D.js";
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  import "../chunks/chunk-PBENCR5L.js";
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+ import "../chunks/chunk-7GBL7SJY.js";
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+ import {
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+ featuresOnBackbone,
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+ graphBackbone,
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+ refNameBinding
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+ } from "../chunks/chunk-RAKOB6IV.js";
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  import "../chunks/chunk-GJMC3PGM.js";
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  import "../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-JVLURPFW.js";
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- import "../chunks/chunk-3JANT2SW.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-JKJWSY4V.js";
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+ import "../chunks/chunk-NNODIW4U.js";
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+ import "../chunks/chunk-6SBUFFTB.js";
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  import {
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- filterSamples,
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- walkRows
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- } from "../chunks/chunk-SZNZ2T6D.js";
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- import "../chunks/chunk-E7FWQQHP.js";
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+ engineSettingsOf,
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+ forceLayout,
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+ loadGraph
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+ } from "../chunks/chunk-WZATPZNH.js";
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+ import "../chunks/chunk-IGVV37VI.js";
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+ import "../chunks/chunk-PUG7LXDF.js";
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+ import "../chunks/chunk-72N5DJHZ.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-ES2N6V56.js";
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  import "../chunks/chunk-ST2IBUAN.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-BPLIXMH7.js";
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  import "../chunks/chunk-TAMCZHLW.js";
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+ import "../chunks/chunk-JVLURPFW.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-JKJWSY4V.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-CPMHA4W5.js";
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- import "../chunks/chunk-NNODIW4U.js";
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- import "../chunks/chunk-6SBUFFTB.js";
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- import {
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- HPRC_GBZ,
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- cutGbzRegion,
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- haplotypeIndexBeside,
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- openGbz,
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- parseRegion
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- } from "../chunks/chunk-73RSLGZT.js";
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- import "../chunks/chunk-LTUWJKHD.js";
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- import "../chunks/chunk-WSIFAZU7.js";
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- import {
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- featuresOnBackbone,
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- graphBackbone,
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- refNameBinding
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- } from "../chunks/chunk-RAKOB6IV.js";
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- import "../chunks/chunk-BPLIXMH7.js";
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  import "../chunks/chunk-FYQWPEEY.js";
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  // src/cli/figure.ts
@@ -241,19 +243,7 @@ async function renderSpec(spec, base) {
241
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  const graph = loadGraph(source.text, source.name, {
242
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  referencePath: spec.referencePath
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  });
244
- const layout = layoutModeByValue(spec.layout ?? "force").run(graph, source.region) ?? (await forceLayout(
245
- graph,
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- {
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- quality: spec.quality ?? 2,
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- linearLayout: false,
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- bubbleSpread: spec.bubbleSpread ?? "auto",
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- engine: spec.engine,
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- spacing: spec.spacing,
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- componentSeparation: spec.componentSeparation,
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- showDeletionEdges: spec.showDeletionEdges
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- },
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- layoutEngine
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- )).result;
246
+ const layout = layoutModeByValue(spec.layout ?? "force").run(graph, source.region) ?? (await forceLayout(graph, engineSettingsOf(spec), layoutEngine)).result;
257
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  const bars = spec.walkStrip ? walkRows(graph, source.region) : void 0;
258
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  const stripRows = bars && {
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  ...bars,
package/dist/figure.js CHANGED
@@ -1,51 +1,52 @@
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  import {
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  figureSvg
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- } from "./chunks/chunk-MQSOTYVF.js";
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+ } from "./chunks/chunk-5XHORHYK.js";
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+ import "./chunks/chunk-LOCJN3BZ.js";
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+ import "./chunks/chunk-47DYCZOK.js";
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+ import "./chunks/chunk-PY7EZFL3.js";
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+ import "./chunks/chunk-7G7TFATC.js";
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  import "./chunks/chunk-CH3DLBUT.js";
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  import "./chunks/chunk-4BYTEJGW.js";
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- import "./chunks/chunk-47DYCZOK.js";
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- import "./chunks/chunk-OY3CDWFN.js";
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- import "./chunks/chunk-2T3SRIFH.js";
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  import "./chunks/chunk-3S3YVOJ7.js";
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  import "./chunks/chunk-BUBZ32IC.js";
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- import "./chunks/chunk-BZKEMAWC.js";
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- import "./chunks/chunk-Y7UR3MDE.js";
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- import "./chunks/chunk-MH5IA57M.js";
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- import "./chunks/chunk-TQ7VCGJR.js";
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+ import "./chunks/chunk-3LXG54PN.js";
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+ import "./chunks/chunk-ZNMHIPUZ.js";
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  import "./chunks/chunk-2LQ5BWT7.js";
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- import "./chunks/chunk-EPWYRSHH.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-72N5DJHZ.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-VECR253P.js";
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- import "./chunks/chunk-VST5SR4C.js";
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+ import "./chunks/chunk-AVJK272H.js";
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+ import "./chunks/chunk-RCWYY6XA.js";
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  import "./chunks/chunk-UMNCCYBN.js";
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+ import "./chunks/chunk-LNSAKOXP.js";
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+ import "./chunks/chunk-4UBWXZVX.js";
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+ import "./chunks/chunk-MP7LXLWV.js";
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+ import "./chunks/chunk-SZNZ2T6D.js";
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  import "./chunks/chunk-PBENCR5L.js";
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+ import "./chunks/chunk-7GBL7SJY.js";
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+ import "./chunks/chunk-RAKOB6IV.js";
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  import "./chunks/chunk-GJMC3PGM.js";
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  import "./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-JVLURPFW.js";
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- import "./chunks/chunk-3JANT2SW.js";
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- import "./chunks/chunk-SZNZ2T6D.js";
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- import "./chunks/chunk-E7FWQQHP.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-3ZZSX5HN.js";
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  import "./chunks/chunk-AB35TJST.js";
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+ import "./chunks/chunk-JKJWSY4V.js";
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+ import "./chunks/chunk-NNODIW4U.js";
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+ import "./chunks/chunk-6SBUFFTB.js";
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+ import "./chunks/chunk-WZATPZNH.js";
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+ import "./chunks/chunk-IGVV37VI.js";
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+ import "./chunks/chunk-PUG7LXDF.js";
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+ import "./chunks/chunk-72N5DJHZ.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-ES2N6V56.js";
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+ import "./chunks/chunk-ST2IBUAN.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-JVLURPFW.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-JKJWSY4V.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-CPMHA4W5.js";
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- import "./chunks/chunk-NNODIW4U.js";
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- import "./chunks/chunk-6SBUFFTB.js";
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- import "./chunks/chunk-RAKOB6IV.js";
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- import "./chunks/chunk-BPLIXMH7.js";
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  import "./chunks/chunk-FYQWPEEY.js";
50
51
  export {
51
52
  figureSvg
package/dist/figureSettings.js ADDED
@@ -0,0 +1,25 @@
1
+ import {
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+ FIGURE_DEFAULTS,
3
+ figureSpecSettings
4
+ } from "./chunks/chunk-H5S2ONCJ.js";
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+ import "./chunks/chunk-WZATPZNH.js";
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+ import "./chunks/chunk-IGVV37VI.js";
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+ import "./chunks/chunk-PUG7LXDF.js";
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+ import "./chunks/chunk-72N5DJHZ.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-ES2N6V56.js";
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+ import "./chunks/chunk-ST2IBUAN.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-JVLURPFW.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-CPMHA4W5.js";
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+ import "./chunks/chunk-FYQWPEEY.js";
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+ export {
23
+ FIGURE_DEFAULTS,
24
+ figureSpecSettings
25
+ };
package/dist/hoverText.js ADDED
@@ -0,0 +1,8 @@
1
+ import {
2
+ edgeHoverText,
3
+ regionLabel
4
+ } from "./chunks/chunk-AZFVORTC.js";
5
+ export {
6
+ edgeHoverText,
7
+ regionLabel
8
+ };