@jbrowse/bandage-core 0.1.1

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Files changed (64) hide show
  1. package/LICENSE +674 -0
  2. package/README.md +29 -0
  3. package/dist/chunks/bandage-layout-3AR6BCUD.js +4694 -0
  4. package/dist/index.js +5409 -0
  5. package/dist/types/alleleProjection/projectAlleles.d.ts +13 -0
  6. package/dist/types/anchoredNodes.d.ts +17 -0
  7. package/dist/types/bandage/bandage-layout.d.ts +14 -0
  8. package/dist/types/bubbleSpreads.d.ts +32 -0
  9. package/dist/types/bubbles/bubbleHalos.d.ts +20 -0
  10. package/dist/types/bubbles/bubbleLine.d.ts +24 -0
  11. package/dist/types/bubbles/bubblesFromGraph.d.ts +3 -0
  12. package/dist/types/bubbles/classifyBubble.d.ts +16 -0
  13. package/dist/types/bubbles/popBubble.d.ts +2 -0
  14. package/dist/types/colorSchemes.d.ts +33 -0
  15. package/dist/types/deletionEdges.d.ts +24 -0
  16. package/dist/types/gaf/parseGaf.d.ts +37 -0
  17. package/dist/types/gbzWindow.d.ts +27 -0
  18. package/dist/types/genes/genePins.d.ts +19 -0
  19. package/dist/types/gfa/gfaConverter.d.ts +11 -0
  20. package/dist/types/gfa-core/gfaParser.d.ts +48 -0
  21. package/dist/types/gfa-core/index.d.ts +2 -0
  22. package/dist/types/graphLabels.d.ts +46 -0
  23. package/dist/types/index.d.ts +50 -0
  24. package/dist/types/labelLayout.d.ts +59 -0
  25. package/dist/types/layout/anchoredLayout.d.ts +5 -0
  26. package/dist/types/layout/drawnScale.d.ts +28 -0
  27. package/dist/types/layout/mergeRuns.d.ts +9 -0
  28. package/dist/types/layout/orderedLayout.d.ts +9 -0
  29. package/dist/types/layout/orientToReference.d.ts +4 -0
  30. package/dist/types/layout/placeOffReference.d.ts +9 -0
  31. package/dist/types/layout/referenceSeeds.d.ts +12 -0
  32. package/dist/types/layout/rowSpacing.d.ts +1 -0
  33. package/dist/types/layout/sampleRowLayout.d.ts +5 -0
  34. package/dist/types/layout/tubeMapLayout.d.ts +19 -0
  35. package/dist/types/layout/variantMapLayout.d.ts +2 -0
  36. package/dist/types/layout/walkRowLayout.d.ts +10 -0
  37. package/dist/types/layout/walkRows.d.ts +25 -0
  38. package/dist/types/layoutModes.d.ts +153 -0
  39. package/dist/types/loadBandage.d.ts +3 -0
  40. package/dist/types/nodeWidths.d.ts +18 -0
  41. package/dist/types/overlayLabels.d.ts +29 -0
  42. package/dist/types/pansn.d.ts +8 -0
  43. package/dist/types/pathAnchoring.d.ts +20 -0
  44. package/dist/types/pathColors.d.ts +14 -0
  45. package/dist/types/pipeline.d.ts +79 -0
  46. package/dist/types/referenceSpan.d.ts +12 -0
  47. package/dist/types/renderer/Canvas2DRenderer.d.ts +32 -0
  48. package/dist/types/renderer/GeometryBuilder.d.ts +63 -0
  49. package/dist/types/renderer/colorBits.d.ts +2 -0
  50. package/dist/types/renderer/types.d.ts +50 -0
  51. package/dist/types/tubeMap/draw.d.ts +66 -0
  52. package/dist/types/tubeMap/frame.d.ts +15 -0
  53. package/dist/types/tubeMap/mismatches.d.ts +24 -0
  54. package/dist/types/tubeMap/reads.d.ts +10 -0
  55. package/dist/types/tubeMap/warp.d.ts +7 -0
  56. package/dist/types/types.d.ts +75 -0
  57. package/dist/types/util/SpatialIndex.d.ts +25 -0
  58. package/dist/types/util/edgeCurves.d.ts +4 -0
  59. package/dist/types/util/geometry.d.ts +46 -0
  60. package/dist/types/util/hitDetection.d.ts +10 -0
  61. package/dist/types/util/wheelZoom.d.ts +5 -0
  62. package/dist/types/viewport.d.ts +22 -0
  63. package/dist/types/walkHighlight.d.ts +10 -0
  64. package/package.json +43 -0
package/README.md ADDED
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+ # @jbrowse/bandage-core
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+
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+ Pangenome graph layout and drawing with no host, the engine behind
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+ [jbrowse-plugin-graphgenomeviewer](https://github.com/GMOD/jbrowse-plugin-graphgenomeviewer)
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+ and [BandageJS](https://github.com/cmdcolin/BandageJS).
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+
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+ ```
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+ npm install @jbrowse/bandage-core
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+ ```
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+
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+ - GFA and rGFA text in (`loadGraph`)
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+ - Layouts: Bandage's FMMM engine as WASM (`loadBandage`, `forceLayout`), variant
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+ map, ordered, anchored, sample rows, walk rows, tube map
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+ - A Canvas2D renderer (`buildGeometry`, `Canvas2DRenderer`), hit testing and
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+ label placement
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+ - Bubbles, deletion edges, path colors, gbz-base windows cut to GFA
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+
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+ Nothing here imports React, MobX or a JBrowse host. BandageJS's
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+ [`src/main.ts`](https://github.com/cmdcolin/BandageJS/blob/main/src/main.ts) is
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+ the worked example.
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+
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+ ## Developing
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+
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+ Lives in the plugin repo as a pnpm workspace package. The plugin imports its
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+ source directly, so a change here needs no publish to reach the plugin.
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+
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+ ```
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+ pnpm release:core # from the repo root: checks, bumps, tags core-v*, pushes
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+ ```