@jbrowse/bandage-core 10.0.1 → 10.1.0

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 (62) 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-VOWI544A.js → chunk-ALDGONEI.js} +1 -1
  7. package/dist/chunks/{chunk-3XE3OUEN.js → chunk-C7MZJSPT.js} +1 -1
  8. package/dist/chunks/{chunk-FFFYXMOP.js → chunk-CFPER2S2.js} +10 -10
  9. package/dist/chunks/{chunk-CFNFT4RA.js → chunk-CRTD2SBP.js} +1 -1
  10. package/dist/chunks/{chunk-IM4SJUPO.js → chunk-DK5P2YOL.js} +2 -2
  11. package/dist/chunks/{chunk-BEWLQADP.js → chunk-FNGIQF43.js} +1 -1
  12. package/dist/chunks/{chunk-OEPCRURR.js → chunk-GNTTI6LA.js} +1 -1
  13. package/dist/chunks/{chunk-HQ2AHRMH.js → chunk-IUDJKOLB.js} +1 -1
  14. package/dist/chunks/{chunk-QXAB2FLJ.js → chunk-IW6CYVX2.js} +1 -1
  15. package/dist/chunks/{chunk-QORSYW7J.js → chunk-L5WF4ZPS.js} +1 -1
  16. package/dist/chunks/{chunk-EMUUNWRU.js → chunk-M6LK4GII.js} +7 -1
  17. package/dist/chunks/{chunk-ZR7A7DKQ.js → chunk-MVFDSFV2.js} +1 -1
  18. package/dist/chunks/{chunk-KY4LV2Z6.js → chunk-MZIOBJZB.js} +1 -1
  19. package/dist/chunks/{chunk-FG762CCP.js → chunk-PKFMP65V.js} +2 -2
  20. package/dist/chunks/{chunk-QIVPRZ4H.js → chunk-R456ME6J.js} +2 -2
  21. package/dist/chunks/{chunk-A647OH7N.js → chunk-RIPAA7OK.js} +1 -1
  22. package/dist/chunks/{chunk-WI7ZHJ27.js → chunk-RPDXZLCG.js} +2 -2
  23. package/dist/chunks/{chunk-NP356MC2.js → chunk-SBMJNRTV.js} +1 -1
  24. package/dist/chunks/{chunk-4QTNXTGW.js → chunk-T6V4KI2L.js} +1 -1
  25. package/dist/chunks/{chunk-REE4GUDM.js → chunk-TWRLC3KK.js} +1 -1
  26. package/dist/chunks/{chunk-AZJF2PZE.js → chunk-VIERZJO2.js} +7 -7
  27. package/dist/chunks/{chunk-MSX3BDO4.js → chunk-XTCNEKO5.js} +2 -2
  28. package/dist/chunks/{chunk-VZNKA3K2.js → chunk-XYP6WL2N.js} +7 -3
  29. package/dist/chunks/{chunk-B4645SM2.js → chunk-YPYWYPHX.js} +3 -3
  30. package/dist/chunks/{chunk-DCJC32QW.js → chunk-ZIUKZUPJ.js} +1 -1
  31. package/dist/cli/figure.js +17 -17
  32. package/dist/cli/fold.js +4 -4
  33. package/dist/figure.js +15 -15
  34. package/dist/figureData.js +14 -14
  35. package/dist/figureSettings.js +4 -4
  36. package/dist/foldVariants.js +1 -1
  37. package/dist/gfa/gfaConverter.js +2 -2
  38. package/dist/index.js +26 -26
  39. package/dist/layout/forceCache.js +4 -4
  40. package/dist/layout/trimToWindow.js +1 -1
  41. package/dist/layout/tubeMapLayout.js +3 -3
  42. package/dist/layout/walkRowDraw.js +5 -5
  43. package/dist/layout/walkRowLayout.js +3 -3
  44. package/dist/layout/walkRows.js +2 -2
  45. package/dist/layout/walkStrip.js +6 -6
  46. package/dist/layoutModes.js +6 -6
  47. package/dist/pathAnchoring.js +1 -1
  48. package/dist/pathColors.js +2 -2
  49. package/dist/pipeline.js +3 -3
  50. package/dist/referenceRampCss.js +4 -4
  51. package/dist/referenceStrip.js +4 -4
  52. package/dist/renderer/GeometryBuilder.js +3 -3
  53. package/dist/tubeMap/bundle.js +4 -4
  54. package/dist/tubeMap/coarsen.js +3 -3
  55. package/dist/tubeMap/draw.js +2 -2
  56. package/dist/tubeMap/nodeColors.js +4 -4
  57. package/dist/types/version.d.ts +1 -1
  58. package/dist/version.js +1 -1
  59. package/dist/viewport.js +4 -4
  60. package/dist/walkEncoding.js +4 -4
  61. package/dist/walkHighlight.js +5 -5
  62. package/package.json +1 -1
package/README.md CHANGED
@@ -25,6 +25,9 @@ npm install @jbrowse/bandage-core
25
25
  and the `bandage-figure` CLI makes one from a JSON spec with no browser:
26
26
  `npx -p @jbrowse/bandage-core bandage-figure spec.json -o figure.svg`. See
27
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  [docs/figures.md](docs/figures.md)
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+ - Coarse tier: the `bandage-fold` CLI folds every variant under a size into the
29
+ reference, so a graph track draws a whole chromosome. See
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+ [docs/coarse-tier.md](docs/coarse-tier.md)
28
31
  - Figure data: `figureData` returns what `figureSvg` would paint as columnar
29
32
  tables, for another graphics system to draw;
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33
  [ggbandage](https://github.com/GMOD/ggbandage) draws them in ggplot2
@@ -1,7 +1,7 @@
1
1
  import {
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  bubbleSubgraph
3
- } from "../chunks/chunk-4QTNXTGW.js";
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- import "../chunks/chunk-EMUUNWRU.js";
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+ } from "../chunks/chunk-T6V4KI2L.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";
@@ -1,14 +1,14 @@
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  import {
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  graphBubbles,
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  superbubblesFromGraph
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- } from "../chunks/chunk-BEWLQADP.js";
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+ } from "../chunks/chunk-FNGIQF43.js";
5
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  import "../chunks/chunk-CLOP7UVD.js";
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- import "../chunks/chunk-4QTNXTGW.js";
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+ import "../chunks/chunk-T6V4KI2L.js";
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  import "../chunks/chunk-EHUBJDDB.js";
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  import "../chunks/chunk-XKWD2RY3.js";
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  import "../chunks/chunk-FX4RDMDN.js";
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  import "../chunks/chunk-HNQPEMYE.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-2CVHXFK7.js";
@@ -6,7 +6,7 @@ import {
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  hasTubeMapPaths,
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  tubeMapLayout,
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  tubeMapReferenceLayout
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- } from "./chunk-IM4SJUPO.js";
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+ } from "./chunk-DK5P2YOL.js";
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  import {
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  anchoredLayout
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  } from "./chunk-L3O7AWLI.js";
@@ -15,7 +15,7 @@ import {
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  } from "./chunk-HNQPEMYE.js";
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  import {
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17
  walkRowLayout
18
- } from "./chunk-3XE3OUEN.js";
18
+ } from "./chunk-C7MZJSPT.js";
19
19
  import {
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20
  isBackbone,
21
21
  isOffReference
@@ -2,7 +2,7 @@ import {
2
2
  LIFT_BACKDROP_CSS,
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3
  computeColorSchemeRange,
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  getNodeColor
5
- } from "./chunk-NP356MC2.js";
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+ } from "./chunk-SBMJNRTV.js";
6
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  import {
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  abgrToCssRgba
8
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  } from "./chunk-G2FD7S3C.js";
@@ -2,7 +2,7 @@ import {
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  REFERENCE_RAMP_ALT_COLOR,
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  REFERENCE_RAMP_MAX_HUE,
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  hslToRgb
5
- } from "./chunk-NP356MC2.js";
5
+ } from "./chunk-SBMJNRTV.js";
6
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  import {
7
7
  packAbgr
8
8
  } from "./chunk-G2FD7S3C.js";
@@ -1,6 +1,6 @@
1
1
  import {
2
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  walkRows
3
- } from "./chunk-A647OH7N.js";
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+ } from "./chunk-RIPAA7OK.js";
4
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  import {
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  ROW_HEIGHT_PX
6
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  } from "./chunk-CPMHA4W5.js";
@@ -5,7 +5,7 @@ import {
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5
  stripGeneGaps,
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  walkStripFrame,
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  walkStripLabelsTree
8
- } from "./chunk-WI7ZHJ27.js";
8
+ } from "./chunk-RPDXZLCG.js";
9
9
  import {
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  Canvas2DRenderer
11
11
  } from "./chunk-WBCOREDZ.js";
@@ -13,7 +13,7 @@ import {
13
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  walkRowsKey,
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  walkRowsKeyTree,
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  walkRowsTree
16
- } from "./chunk-VZNKA3K2.js";
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+ } from "./chunk-XYP6WL2N.js";
17
17
  import {
18
18
  EXON_COLOR,
19
19
  exonOutlineTree,
@@ -36,17 +36,17 @@ import {
36
36
  } from "./chunk-LOCJN3BZ.js";
37
37
  import {
38
38
  version
39
- } from "./chunk-KY4LV2Z6.js";
39
+ } from "./chunk-MZIOBJZB.js";
40
40
  import {
41
41
  axisScaleOf
42
- } from "./chunk-QORSYW7J.js";
42
+ } from "./chunk-L5WF4ZPS.js";
43
43
  import {
44
44
  facetLifts,
45
45
  walkLift
46
- } from "./chunk-QIVPRZ4H.js";
46
+ } from "./chunk-R456ME6J.js";
47
47
  import {
48
48
  encodingStops
49
- } from "./chunk-VOWI544A.js";
49
+ } from "./chunk-ALDGONEI.js";
50
50
  import {
51
51
  rangeText,
52
52
  walkKey
@@ -54,15 +54,15 @@ import {
54
54
  import {
55
55
  buildGeometry,
56
56
  computeReferenceRamp
57
- } from "./chunk-NP356MC2.js";
57
+ } from "./chunk-SBMJNRTV.js";
58
58
  import {
59
59
  walkRowLabels,
60
60
  walkRowsExtent
61
- } from "./chunk-3XE3OUEN.js";
61
+ } from "./chunk-C7MZJSPT.js";
62
62
  import {
63
63
  pathLegend,
64
64
  walkLabelsOf
65
- } from "./chunk-REE4GUDM.js";
65
+ } from "./chunk-TWRLC3KK.js";
66
66
  import {
67
67
  nodeInk
68
68
  } from "./chunk-PBENCR5L.js";
@@ -70,7 +70,7 @@ import {
70
70
  FIT_PADDING,
71
71
  drawingBounds,
72
72
  fitTransform
73
- } from "./chunk-MSX3BDO4.js";
73
+ } from "./chunk-XTCNEKO5.js";
74
74
  import {
75
75
  referenceLabel
76
76
  } from "./chunk-RAKOB6IV.js";
@@ -1,7 +1,7 @@
1
1
  import {
2
2
  engineKey,
3
3
  forceLayout
4
- } from "./chunk-MSX3BDO4.js";
4
+ } from "./chunk-XTCNEKO5.js";
5
5
 
6
6
  // src/layout/forceCache.ts
7
7
  var DEFAULT_SIZE = 4;
@@ -6,10 +6,10 @@ import {
6
6
  import {
7
7
  pathCssColor,
8
8
  pathGreyCssColor
9
- } from "./chunk-REE4GUDM.js";
9
+ } from "./chunk-TWRLC3KK.js";
10
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  import {
11
11
  pathOrigin
12
- } from "./chunk-EMUUNWRU.js";
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+ } from "./chunk-M6LK4GII.js";
13
13
  import {
14
14
  ownStrand,
15
15
  strandSides
@@ -5,7 +5,7 @@ import {
5
5
  } from "./chunk-CLOP7UVD.js";
6
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  import {
7
7
  bubbleSubgraph
8
- } from "./chunk-4QTNXTGW.js";
8
+ } from "./chunk-T6V4KI2L.js";
9
9
  import {
10
10
  coversGraph
11
11
  } from "./chunk-EHUBJDDB.js";
@@ -1,7 +1,7 @@
1
1
  import {
2
2
  computeColorSchemeRange,
3
3
  getNodeColor
4
- } from "./chunk-NP356MC2.js";
4
+ } from "./chunk-SBMJNRTV.js";
5
5
  import {
6
6
  abgrToCssRgba
7
7
  } from "./chunk-G2FD7S3C.js";
@@ -9,7 +9,7 @@ import {
9
9
  } from "./chunk-CWFNEKST.js";
10
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  import {
11
11
  pathOrigin
12
- } from "./chunk-EMUUNWRU.js";
12
+ } from "./chunk-M6LK4GII.js";
13
13
 
14
14
  // src/tubeMap/draw.ts
15
15
  import { curvePaths, nodeOutlinePath } from "@jbrowse/tubemap-core";
@@ -4,7 +4,7 @@ import {
4
4
  import {
5
5
  pathOrigin,
6
6
  surveyPaths
7
- } from "./chunk-EMUUNWRU.js";
7
+ } from "./chunk-M6LK4GII.js";
8
8
 
9
9
  // src/gfa/gfaConverter.ts
10
10
  function surveySegments(gfaGraph) {
@@ -1,6 +1,6 @@
1
1
  import {
2
2
  clampZoom
3
- } from "./chunk-MSX3BDO4.js";
3
+ } from "./chunk-XTCNEKO5.js";
4
4
 
5
5
  // src/viewport.ts
6
6
  function axisScaleOf(scale, pixelRows) {
@@ -10,8 +10,14 @@ import {
10
10
 
11
11
  // src/pathAnchoring.ts
12
12
  var RANGE_SUFFIX = /:(\d+)-\d+$/;
13
+ var VG_FRAGMENT = /^([^#]*#[^#]*#[^#[]*)#(\d+)(?:\[(\d+)-\d+\])?$/;
14
+ var VG_SUBRANGE = /\[(\d+)-\d+\]$/;
13
15
  function pathOrigin(pathName) {
14
- const match = RANGE_SUFFIX.exec(pathName);
16
+ const fragment = VG_FRAGMENT.exec(pathName);
17
+ if (fragment) {
18
+ return { name: fragment[1], start: +fragment[2] + +(fragment[3] ?? 0) };
19
+ }
20
+ const match = RANGE_SUFFIX.exec(pathName) ?? VG_SUBRANGE.exec(pathName);
15
21
  return match ? { name: pathName.slice(0, match.index), start: +match[1] } : { name: pathName, start: 0 };
16
22
  }
17
23
  function surveyPaths(paths, lengthOf) {
@@ -1,6 +1,6 @@
1
1
  import {
2
2
  ENGINE_DEFAULTS
3
- } from "./chunk-MSX3BDO4.js";
3
+ } from "./chunk-XTCNEKO5.js";
4
4
 
5
5
  // src/figureSettings.ts
6
6
  var FIGURE_DEFAULTS = {
@@ -1,5 +1,5 @@
1
1
  // src/version.ts
2
- var version = "10.0.1";
2
+ var version = "10.1.0";
3
3
 
4
4
  export {
5
5
  version
@@ -1,9 +1,9 @@
1
1
  import {
2
2
  pathSteps
3
- } from "./chunk-IM4SJUPO.js";
3
+ } from "./chunk-DK5P2YOL.js";
4
4
  import {
5
5
  pathOrigin
6
- } from "./chunk-EMUUNWRU.js";
6
+ } from "./chunk-M6LK4GII.js";
7
7
 
8
8
  // src/tubeMap/bundle.ts
9
9
  function bundleRoutes(graph, groupOf = () => "", merge = true) {
@@ -1,10 +1,10 @@
1
1
  import {
2
2
  encodedColor,
3
3
  resolveEncoding
4
- } from "./chunk-VOWI544A.js";
4
+ } from "./chunk-ALDGONEI.js";
5
5
  import {
6
6
  pathOrigin
7
- } from "./chunk-EMUUNWRU.js";
7
+ } from "./chunk-M6LK4GII.js";
8
8
  import {
9
9
  panSNContig
10
10
  } from "./chunk-BPLIXMH7.js";
@@ -1,6 +1,6 @@
1
1
  import {
2
2
  pathOrigin
3
- } from "./chunk-EMUUNWRU.js";
3
+ } from "./chunk-M6LK4GII.js";
4
4
  import {
5
5
  panSNContig,
6
6
  panSNSample
@@ -2,13 +2,13 @@ import {
2
2
  alongRow,
3
3
  boxesGenes,
4
4
  rowPitch
5
- } from "./chunk-VZNKA3K2.js";
5
+ } from "./chunk-XYP6WL2N.js";
6
6
  import {
7
7
  el
8
8
  } from "./chunk-NNODIW4U.js";
9
9
  import {
10
10
  pathOrigin
11
- } from "./chunk-EMUUNWRU.js";
11
+ } from "./chunk-M6LK4GII.js";
12
12
  import {
13
13
  LABEL_CHAR_PX
14
14
  } from "./chunk-AB35TJST.js";
@@ -11,7 +11,7 @@ import {
11
11
  PATH_SATURATION,
12
12
  nameHue,
13
13
  pathHueAt
14
- } from "./chunk-REE4GUDM.js";
14
+ } from "./chunk-TWRLC3KK.js";
15
15
  import {
16
16
  meanDepth,
17
17
  nodeWidthPx
@@ -1,6 +1,6 @@
1
1
  import {
2
2
  trimOrigins
3
- } from "./chunk-EMUUNWRU.js";
3
+ } from "./chunk-M6LK4GII.js";
4
4
 
5
5
  // src/bubbles/popBubble.ts
6
6
  function bubbleSubgraph(graph, segmentIds) {
@@ -1,6 +1,6 @@
1
1
  import {
2
2
  pathOrigin
3
- } from "./chunk-EMUUNWRU.js";
3
+ } from "./chunk-M6LK4GII.js";
4
4
  import {
5
5
  isGenericSample
6
6
  } from "./chunk-BPLIXMH7.js";
@@ -3,7 +3,7 @@ import {
3
3
  } from "./chunk-FLUQODT2.js";
4
4
  import {
5
5
  layoutModeByValue
6
- } from "./chunk-IFOZFVZK.js";
6
+ } from "./chunk-4R6QNG23.js";
7
7
  import {
8
8
  parseRegion
9
9
  } from "./chunk-FLFBYSJO.js";
@@ -12,21 +12,21 @@ import {
12
12
  } from "./chunk-LOCJN3BZ.js";
13
13
  import {
14
14
  version
15
- } from "./chunk-KY4LV2Z6.js";
15
+ } from "./chunk-MZIOBJZB.js";
16
16
  import {
17
17
  axisScaleOf
18
- } from "./chunk-QORSYW7J.js";
18
+ } from "./chunk-L5WF4ZPS.js";
19
19
  import {
20
20
  facetLifts,
21
21
  walkLift
22
- } from "./chunk-QIVPRZ4H.js";
22
+ } from "./chunk-R456ME6J.js";
23
23
  import {
24
24
  walkKey
25
25
  } from "./chunk-2LQ5BWT7.js";
26
26
  import {
27
27
  buildGeometry,
28
28
  computeReferenceRamp
29
- } from "./chunk-NP356MC2.js";
29
+ } from "./chunk-SBMJNRTV.js";
30
30
  import {
31
31
  abgrAlpha,
32
32
  abgrBlue,
@@ -36,14 +36,14 @@ import {
36
36
  import {
37
37
  pathLegend,
38
38
  walkLabelsOf
39
- } from "./chunk-REE4GUDM.js";
39
+ } from "./chunk-TWRLC3KK.js";
40
40
  import {
41
41
  drawingBounds,
42
42
  engineSettingsOf,
43
43
  fitTransform,
44
44
  forceLayout,
45
45
  loadGraph
46
- } from "./chunk-MSX3BDO4.js";
46
+ } from "./chunk-XTCNEKO5.js";
47
47
  import {
48
48
  referenceLabel
49
49
  } from "./chunk-RAKOB6IV.js";
@@ -14,7 +14,7 @@ import {
14
14
  } from "./chunk-PUG7LXDF.js";
15
15
  import {
16
16
  convertGFAToGraph
17
- } from "./chunk-QXAB2FLJ.js";
17
+ } from "./chunk-IW6CYVX2.js";
18
18
  import {
19
19
  graphFromTables
20
20
  } from "./chunk-PSMKPSO4.js";
@@ -23,7 +23,7 @@ import {
23
23
  } from "./chunk-CDLPYR5O.js";
24
24
  import {
25
25
  anchorGraph
26
- } from "./chunk-EMUUNWRU.js";
26
+ } from "./chunk-M6LK4GII.js";
27
27
  import {
28
28
  gfaTables
29
29
  } from "./chunk-G45YY72K.js";
@@ -3,13 +3,13 @@ import {
3
3
  RAMP_GRADIENT_STOPS,
4
4
  rampHueCss,
5
5
  rampStops
6
- } from "./chunk-DCJC32QW.js";
6
+ } from "./chunk-ZIUKZUPJ.js";
7
7
  import {
8
8
  el
9
9
  } from "./chunk-NNODIW4U.js";
10
10
  import {
11
11
  REFERENCE_RAMP_ALT_CSS
12
- } from "./chunk-NP356MC2.js";
12
+ } from "./chunk-SBMJNRTV.js";
13
13
  import {
14
14
  LABEL_CHAR_PX
15
15
  } from "./chunk-AB35TJST.js";
@@ -30,6 +30,10 @@ var MIN_TILE_PX = 3;
30
30
  function kb(bp) {
31
31
  return `${(bp / 1e3).toFixed(bp < 1e4 ? 1 : 0)} kb`;
32
32
  }
33
+ function signedLength(delta) {
34
+ const size = Math.abs(delta);
35
+ return `${delta > 0 ? "+" : "\u2212"}${size < 1e3 ? `${size} bp` : kb(size)}`;
36
+ }
33
37
  function units(bp, unit) {
34
38
  return unit ? ` \u2248 ${Math.round(bp / unit)} units` : "";
35
39
  }
@@ -42,7 +46,7 @@ function walkRowReadout(row, reference, unit, call) {
42
46
  const called = call ? ` \xB7 called ${kb(call.bp)}${call.spanningReads === 0 ? " \xB7 no spanning read" : ""}` : "";
43
47
  if (complete) {
44
48
  const delta = bp - reference.bp;
45
- const against = delta === 0 ? "" : ` (${delta > 0 ? "+" : "\u2212"}${kb(Math.abs(delta))})`;
49
+ const against = delta === 0 ? "" : ` (${signedLength(delta)})`;
46
50
  return `${kb(bp)}${units(bp, unit)}${against}${outside}${called}`;
47
51
  }
48
52
  const region = unit ? "repeat" : "window";
@@ -173,7 +173,7 @@ function nearestOutside(i, side, links, allele, dist, nodes) {
173
173
  let best;
174
174
  for (const link of links[i]) {
175
175
  const j = link.other;
176
- if (link.side === side && allele[j] !== allele[i] && Number.isFinite(dist[j]) && (best === void 0 || dist[j] < dist[best] || dist[j] === dist[best] && nodes[j].id < nodes[best].id)) {
176
+ if (link.side === side && allele[j] !== allele[i] && Number.isFinite(dist[j]) && (best === void 0 || dist[j] < dist[best] || dist[j] === dist[best] && nodes[j].name < nodes[best].name)) {
177
177
  best = j;
178
178
  }
179
179
  }
@@ -183,7 +183,7 @@ function distancesFromBackbone(nodes, links) {
183
183
  const dist = new Float64Array(nodes.length).fill(Infinity);
184
184
  const pred = new Int32Array(nodes.length).fill(-1);
185
185
  const heap = new MinHeap(
186
- ([da, a], [db, b]) => da - db || cmp(nodes[a].id, nodes[b].id)
186
+ ([da, a], [db, b]) => da - db || cmp(nodes[a].name, nodes[b].name)
187
187
  );
188
188
  nodes.forEach((node, i) => {
189
189
  if (isBackbone(node)) {
@@ -205,7 +205,7 @@ function distancesFromBackbone(nodes, links) {
205
205
  dist[other] = d;
206
206
  pred[other] = i;
207
207
  heap.push([d, other]);
208
- } else if (d === dist[other] && cmp(nodes[i].id, nodes[pred[other]].id) < 0) {
208
+ } else if (d === dist[other] && cmp(nodes[i].name, nodes[pred[other]].name) < 0) {
209
209
  pred[other] = i;
210
210
  }
211
211
  }
@@ -1,6 +1,6 @@
1
1
  import {
2
2
  REFERENCE_RAMP_MAX_HUE
3
- } from "./chunk-NP356MC2.js";
3
+ } from "./chunk-SBMJNRTV.js";
4
4
 
5
5
  // src/referenceRampCss.ts
6
6
  function rampHueCss(hue) {
@@ -6,18 +6,18 @@ import {
6
6
  } from "../chunks/chunk-BXEPA4KS.js";
7
7
  import {
8
8
  figureSvg
9
- } from "../chunks/chunk-FFFYXMOP.js";
9
+ } from "../chunks/chunk-CFPER2S2.js";
10
10
  import "../chunks/chunk-47DYCZOK.js";
11
- import "../chunks/chunk-WI7ZHJ27.js";
11
+ import "../chunks/chunk-RPDXZLCG.js";
12
12
  import "../chunks/chunk-WBCOREDZ.js";
13
13
  import "../chunks/chunk-4BYTEJGW.js";
14
14
  import {
15
15
  genesOnRow,
16
16
  placeRowGenes
17
- } from "../chunks/chunk-VZNKA3K2.js";
17
+ } from "../chunks/chunk-XYP6WL2N.js";
18
18
  import "../chunks/chunk-3S3YVOJ7.js";
19
19
  import "../chunks/chunk-BUBZ32IC.js";
20
- import "../chunks/chunk-DCJC32QW.js";
20
+ import "../chunks/chunk-ZIUKZUPJ.js";
21
21
  import "../chunks/chunk-DRG4236Y.js";
22
22
  import "../chunks/chunk-FP4H7SFT.js";
23
23
  import "../chunks/chunk-MLSWIMZO.js";
@@ -30,9 +30,9 @@ import {
30
30
  import {
31
31
  LAYOUT_MODES,
32
32
  layoutModeByValue
33
- } from "../chunks/chunk-IFOZFVZK.js";
33
+ } from "../chunks/chunk-4R6QNG23.js";
34
34
  import "../chunks/chunk-LOEA5IHZ.js";
35
- import "../chunks/chunk-IM4SJUPO.js";
35
+ import "../chunks/chunk-DK5P2YOL.js";
36
36
  import "../chunks/chunk-CWFNEKST.js";
37
37
  import "../chunks/chunk-L3O7AWLI.js";
38
38
  import "../chunks/chunk-TZFWUT2C.js";
@@ -50,35 +50,35 @@ import {
50
50
  import "../chunks/chunk-Q7LYHGGQ.js";
51
51
  import "../chunks/chunk-WSIFAZU7.js";
52
52
  import "../chunks/chunk-LOCJN3BZ.js";
53
- import "../chunks/chunk-KY4LV2Z6.js";
54
- import "../chunks/chunk-QORSYW7J.js";
55
- import "../chunks/chunk-QIVPRZ4H.js";
56
- import "../chunks/chunk-VOWI544A.js";
53
+ import "../chunks/chunk-MZIOBJZB.js";
54
+ import "../chunks/chunk-L5WF4ZPS.js";
55
+ import "../chunks/chunk-R456ME6J.js";
56
+ import "../chunks/chunk-ALDGONEI.js";
57
57
  import "../chunks/chunk-2LQ5BWT7.js";
58
- import "../chunks/chunk-NP356MC2.js";
58
+ import "../chunks/chunk-SBMJNRTV.js";
59
59
  import "../chunks/chunk-G2FD7S3C.js";
60
60
  import "../chunks/chunk-WFB5TXRA.js";
61
- import "../chunks/chunk-3XE3OUEN.js";
61
+ import "../chunks/chunk-C7MZJSPT.js";
62
62
  import {
63
63
  filterSamples,
64
64
  walkRows
65
- } from "../chunks/chunk-A647OH7N.js";
66
- import "../chunks/chunk-REE4GUDM.js";
65
+ } from "../chunks/chunk-RIPAA7OK.js";
66
+ import "../chunks/chunk-TWRLC3KK.js";
67
67
  import "../chunks/chunk-PBENCR5L.js";
68
68
  import {
69
69
  engineSettingsOf,
70
70
  forceLayout,
71
71
  loadGraph
72
- } from "../chunks/chunk-MSX3BDO4.js";
72
+ } from "../chunks/chunk-XTCNEKO5.js";
73
73
  import "../chunks/chunk-IGVV37VI.js";
74
74
  import "../chunks/chunk-OPPVSPEF.js";
75
75
  import "../chunks/chunk-VPE4AYP7.js";
76
76
  import "../chunks/chunk-PUG7LXDF.js";
77
- import "../chunks/chunk-QXAB2FLJ.js";
77
+ import "../chunks/chunk-IW6CYVX2.js";
78
78
  import "../chunks/chunk-QYBZZI5H.js";
79
79
  import "../chunks/chunk-PSMKPSO4.js";
80
80
  import "../chunks/chunk-CDLPYR5O.js";
81
- import "../chunks/chunk-EMUUNWRU.js";
81
+ import "../chunks/chunk-M6LK4GII.js";
82
82
  import "../chunks/chunk-RAEABQNW.js";
83
83
  import "../chunks/chunk-ES2N6V56.js";
84
84
  import {
package/dist/cli/fold.js CHANGED
@@ -4,19 +4,19 @@ import {
4
4
  } from "../chunks/chunk-B4YH42OP.js";
5
5
  import {
6
6
  foldVariants
7
- } from "../chunks/chunk-B4645SM2.js";
7
+ } from "../chunks/chunk-YPYWYPHX.js";
8
8
  import {
9
9
  loadGraph
10
- } from "../chunks/chunk-MSX3BDO4.js";
10
+ } from "../chunks/chunk-XTCNEKO5.js";
11
11
  import "../chunks/chunk-IGVV37VI.js";
12
12
  import "../chunks/chunk-OPPVSPEF.js";
13
13
  import "../chunks/chunk-VPE4AYP7.js";
14
14
  import "../chunks/chunk-PUG7LXDF.js";
15
- import "../chunks/chunk-QXAB2FLJ.js";
15
+ import "../chunks/chunk-IW6CYVX2.js";
16
16
  import "../chunks/chunk-QYBZZI5H.js";
17
17
  import "../chunks/chunk-PSMKPSO4.js";
18
18
  import "../chunks/chunk-CDLPYR5O.js";
19
- import "../chunks/chunk-EMUUNWRU.js";
19
+ import "../chunks/chunk-M6LK4GII.js";
20
20
  import "../chunks/chunk-RAEABQNW.js";
21
21
  import "../chunks/chunk-ES2N6V56.js";
22
22
  import "../chunks/chunk-G45YY72K.js";
package/dist/figure.js CHANGED
@@ -1,41 +1,41 @@
1
1
  import {
2
2
  figureSvg
3
- } from "./chunks/chunk-FFFYXMOP.js";
3
+ } from "./chunks/chunk-CFPER2S2.js";
4
4
  import "./chunks/chunk-47DYCZOK.js";
5
- import "./chunks/chunk-WI7ZHJ27.js";
5
+ import "./chunks/chunk-RPDXZLCG.js";
6
6
  import "./chunks/chunk-WBCOREDZ.js";
7
7
  import "./chunks/chunk-4BYTEJGW.js";
8
- import "./chunks/chunk-VZNKA3K2.js";
8
+ import "./chunks/chunk-XYP6WL2N.js";
9
9
  import "./chunks/chunk-3S3YVOJ7.js";
10
10
  import "./chunks/chunk-BUBZ32IC.js";
11
- import "./chunks/chunk-DCJC32QW.js";
11
+ import "./chunks/chunk-ZIUKZUPJ.js";
12
12
  import "./chunks/chunk-DRG4236Y.js";
13
13
  import "./chunks/chunk-FP4H7SFT.js";
14
14
  import "./chunks/chunk-MLSWIMZO.js";
15
15
  import "./chunks/chunk-NNODIW4U.js";
16
16
  import "./chunks/chunk-LOCJN3BZ.js";
17
- import "./chunks/chunk-KY4LV2Z6.js";
18
- import "./chunks/chunk-QORSYW7J.js";
19
- import "./chunks/chunk-QIVPRZ4H.js";
20
- import "./chunks/chunk-VOWI544A.js";
17
+ import "./chunks/chunk-MZIOBJZB.js";
18
+ import "./chunks/chunk-L5WF4ZPS.js";
19
+ import "./chunks/chunk-R456ME6J.js";
20
+ import "./chunks/chunk-ALDGONEI.js";
21
21
  import "./chunks/chunk-2LQ5BWT7.js";
22
- import "./chunks/chunk-NP356MC2.js";
22
+ import "./chunks/chunk-SBMJNRTV.js";
23
23
  import "./chunks/chunk-G2FD7S3C.js";
24
24
  import "./chunks/chunk-WFB5TXRA.js";
25
- import "./chunks/chunk-3XE3OUEN.js";
26
- import "./chunks/chunk-A647OH7N.js";
27
- import "./chunks/chunk-REE4GUDM.js";
25
+ import "./chunks/chunk-C7MZJSPT.js";
26
+ import "./chunks/chunk-RIPAA7OK.js";
27
+ import "./chunks/chunk-TWRLC3KK.js";
28
28
  import "./chunks/chunk-PBENCR5L.js";
29
- import "./chunks/chunk-MSX3BDO4.js";
29
+ import "./chunks/chunk-XTCNEKO5.js";
30
30
  import "./chunks/chunk-IGVV37VI.js";
31
31
  import "./chunks/chunk-OPPVSPEF.js";
32
32
  import "./chunks/chunk-VPE4AYP7.js";
33
33
  import "./chunks/chunk-PUG7LXDF.js";
34
- import "./chunks/chunk-QXAB2FLJ.js";
34
+ import "./chunks/chunk-IW6CYVX2.js";
35
35
  import "./chunks/chunk-QYBZZI5H.js";
36
36
  import "./chunks/chunk-PSMKPSO4.js";
37
37
  import "./chunks/chunk-CDLPYR5O.js";
38
- import "./chunks/chunk-EMUUNWRU.js";
38
+ import "./chunks/chunk-M6LK4GII.js";
39
39
  import "./chunks/chunk-RAEABQNW.js";
40
40
  import "./chunks/chunk-ES2N6V56.js";
41
41
  import "./chunks/chunk-RAKOB6IV.js";