@jbrowse/bandage-core 11.16.0 → 11.17.0

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 (45) hide show
  1. package/dist/chunks/{chunk-NIB2A2UZ.js → chunk-42MMT5QM.js} +1 -1
  2. package/dist/chunks/{chunk-F3254CLY.js → chunk-47R7GMU3.js} +4 -4
  3. package/dist/chunks/{chunk-3KGUENAV.js → chunk-5LTWXDXK.js} +1 -1
  4. package/dist/chunks/{chunk-JWXSEGEA.js → chunk-BDMISSNR.js} +1 -1
  5. package/dist/chunks/{chunk-7UR5EXC2.js → chunk-CIMRLDRO.js} +1 -1
  6. package/dist/chunks/{chunk-72JZSR4B.js → chunk-DTBQNR7P.js} +7 -7
  7. package/dist/chunks/{chunk-KMYMAPQ3.js → chunk-FKMZG7HI.js} +22 -9
  8. package/dist/chunks/{chunk-U7JDTZSK.js → chunk-GZ2F2CDT.js} +1 -1
  9. package/dist/chunks/{chunk-SR6LCQ5U.js → chunk-IWPINV4U.js} +10 -10
  10. package/dist/chunks/{chunk-TUMJNAOL.js → chunk-MSVYSCAH.js} +2 -0
  11. package/dist/chunks/{chunk-Z5T6EOPF.js → chunk-OND5MXTK.js} +1 -1
  12. package/dist/chunks/{chunk-5KQRVX4N.js → chunk-PIPNW3VY.js} +1 -1
  13. package/dist/chunks/{chunk-WRSI6VK7.js → chunk-PL6X2IJC.js} +2 -2
  14. package/dist/chunks/{chunk-BMO5MVPB.js → chunk-STUG7I25.js} +1 -1
  15. package/dist/chunks/{chunk-CF2AXV5I.js → chunk-XESCKKKT.js} +1 -1
  16. package/dist/chunks/chunk-XWH4LB56.js +115 -0
  17. package/dist/chunks/{chunk-ZB5ADQYK.js → chunk-ZZUSCQVT.js} +1 -1
  18. package/dist/cli/figure.js +14 -14
  19. package/dist/cli/fold.js +2 -2
  20. package/dist/figure.js +13 -13
  21. package/dist/figureData.js +11 -11
  22. package/dist/figureScene.js +8 -8
  23. package/dist/figureSettings.js +3 -3
  24. package/dist/gfa/gfaConverter.js +1 -1
  25. package/dist/index.js +28 -18
  26. package/dist/layout/forceCache.js +3 -3
  27. package/dist/layout/walkRowDraw.js +3 -3
  28. package/dist/layout/walkStrip.js +4 -4
  29. package/dist/nodeWidths.js +14 -3
  30. package/dist/pipeline.js +2 -2
  31. package/dist/referenceStrip.js +3 -3
  32. package/dist/renderer/GeometryBuilder.js +2 -2
  33. package/dist/tubeMap/nodeColors.js +3 -3
  34. package/dist/types/figureData.d.ts +11 -0
  35. package/dist/types/figureScene.d.ts +1 -1
  36. package/dist/types/index.d.ts +1 -1
  37. package/dist/types/nodeWidths.d.ts +13 -1
  38. package/dist/types/types.d.ts +1 -0
  39. package/dist/types/version.d.ts +1 -1
  40. package/dist/version.js +1 -1
  41. package/dist/viewport.js +3 -3
  42. package/dist/walkEncoding.js +3 -3
  43. package/dist/walkHighlight.js +4 -4
  44. package/package.json +1 -1
  45. package/dist/chunks/chunk-ZANALBSX.js +0 -65
@@ -1,5 +1,5 @@
1
1
  // src/version.ts
2
- var version = "11.16.0";
2
+ var version = "11.17.0";
3
3
 
4
4
  export {
5
5
  version
@@ -4,11 +4,11 @@ import {
4
4
  import {
5
5
  facetLifts,
6
6
  walkLift
7
- } from "./chunk-WRSI6VK7.js";
7
+ } from "./chunk-PL6X2IJC.js";
8
8
  import {
9
9
  buildGeometry,
10
10
  computeReferenceRamp
11
- } from "./chunk-72JZSR4B.js";
11
+ } from "./chunk-DTBQNR7P.js";
12
12
  import {
13
13
  walkKey
14
14
  } from "./chunk-OKH32P3Z.js";
@@ -21,10 +21,10 @@ import {
21
21
  } from "./chunk-EHEIS3TE.js";
22
22
  import {
23
23
  FIGURE_DEFAULTS
24
- } from "./chunk-CF2AXV5I.js";
24
+ } from "./chunk-XESCKKKT.js";
25
25
  import {
26
26
  drawingBounds
27
- } from "./chunk-3KGUENAV.js";
27
+ } from "./chunk-5LTWXDXK.js";
28
28
  import {
29
29
  referenceLabel
30
30
  } from "./chunk-5ORP7EFJ.js";
@@ -14,7 +14,7 @@ import {
14
14
  } from "./chunk-VPE4AYP7.js";
15
15
  import {
16
16
  convertGFAToGraph
17
- } from "./chunk-TUMJNAOL.js";
17
+ } from "./chunk-MSVYSCAH.js";
18
18
  import {
19
19
  parseGFA
20
20
  } from "./chunk-CFXXFHRK.js";
@@ -1,7 +1,7 @@
1
1
  import {
2
2
  REFERENCE_RAMP_ALT_COLOR,
3
3
  hslToRgb
4
- } from "./chunk-72JZSR4B.js";
4
+ } from "./chunk-DTBQNR7P.js";
5
5
  import {
6
6
  packAbgr
7
7
  } from "./chunk-G2FD7S3C.js";
@@ -1,7 +1,7 @@
1
1
  import {
2
2
  engineKey,
3
3
  forceLayout
4
- } from "./chunk-3KGUENAV.js";
4
+ } from "./chunk-5LTWXDXK.js";
5
5
 
6
6
  // src/layout/forceCache.ts
7
7
  var DEFAULT_SIZE = 4;
@@ -29,10 +29,10 @@ import {
29
29
  pathHueAt
30
30
  } from "./chunk-EHEIS3TE.js";
31
31
  import {
32
- meanDepth,
33
32
  nodeWidthPx,
34
- walkLaneWidthPx
35
- } from "./chunk-ZANALBSX.js";
33
+ walkLaneWidthPx,
34
+ widthNorm
35
+ } from "./chunk-XWH4LB56.js";
36
36
  import {
37
37
  referenceMidpoints
38
38
  } from "./chunk-L4DBSRA2.js";
@@ -515,7 +515,7 @@ function buildGeometry(options) {
515
515
  hiddenEdges,
516
516
  version = 0
517
517
  } = options;
518
- const depthNorm = nodeWidth === "depth" ? meanDepth(graph) : 0;
518
+ const widthScale = widthNorm(graph, nodeWidth);
519
519
  const busiest = edgeWidth === "walks" ? busiestEdge(graph) : 0;
520
520
  const scale = axis.scaleX;
521
521
  const worldPerScreenPx = 1 / Math.max(scale, MIN_SCALE_FOR_OFFSET);
@@ -618,7 +618,7 @@ function buildGeometry(options) {
618
618
  if (width === void 0) {
619
619
  const node = nodeById.get(id);
620
620
  width = walkLaneWidthPx(
621
- node ? nodeWidthPx(node, contigThickness, nodeWidth, depthNorm) : contigThickness,
621
+ node ? nodeWidthPx(node, contigThickness, nodeWidth, widthScale) : contigThickness,
622
622
  liftedWalks.length
623
623
  );
624
624
  laneWidths.set(id, width);
@@ -697,7 +697,7 @@ function buildGeometry(options) {
697
697
  const plainEdgeColor = isDeletion ? EDGE_DELETION_COLOR : EDGE_DEFAULT_COLOR;
698
698
  const edgeColor = !highlight || onWalk ? plainEdgeColor : fadeAbgr(plainEdgeColor, FADED_ALPHA);
699
699
  const toNode = nodeById.get(edge.to);
700
- const intoHalfWidth = (toNode ? nodeWidthPx(toNode, contigThickness, nodeWidth, depthNorm) : contigThickness) / 2;
700
+ const intoHalfWidth = (toNode ? nodeWidthPx(toNode, contigThickness, nodeWidth, widthScale) : contigThickness) / 2;
701
701
  const inView = (curves) => !viewportBounds || isBezierInBounds(curves, viewportBounds);
702
702
  const dashesOf = (curves) => dashSpans(curves, DELETION_DASH_PX / scale, yToX, viewportBounds);
703
703
  const stroke = (curves, thickness, color) => {
@@ -882,7 +882,7 @@ function buildGeometry(options) {
882
882
  colorRange
883
883
  );
884
884
  const color = faded ? fadeAbgr(own, FADED_ALPHA) : own;
885
- const width = nodeWidthPx(node, contigThickness, nodeWidth, depthNorm);
885
+ const width = nodeWidthPx(node, contigThickness, nodeWidth, widthScale);
886
886
  const nodeThickness = width / 2;
887
887
  const start = nodeStrokes.length;
888
888
  const slots = nodePathSlots.get(nodeId);
@@ -12,19 +12,19 @@ import {
12
12
  } from "./chunk-HEYIAMTC.js";
13
13
  import {
14
14
  version
15
- } from "./chunk-NIB2A2UZ.js";
15
+ } from "./chunk-42MMT5QM.js";
16
16
  import {
17
17
  axisScaleOf
18
- } from "./chunk-ZB5ADQYK.js";
18
+ } from "./chunk-ZZUSCQVT.js";
19
19
  import {
20
20
  figureScene
21
- } from "./chunk-F3254CLY.js";
21
+ } from "./chunk-47R7GMU3.js";
22
22
  import {
23
23
  fadedKey
24
- } from "./chunk-WRSI6VK7.js";
24
+ } from "./chunk-PL6X2IJC.js";
25
25
  import {
26
26
  encodingStops
27
- } from "./chunk-JWXSEGEA.js";
27
+ } from "./chunk-BDMISSNR.js";
28
28
  import {
29
29
  laneSlideAt,
30
30
  passesKey,
@@ -36,15 +36,21 @@ import {
36
36
  abgrGreen,
37
37
  abgrRed
38
38
  } from "./chunk-G2FD7S3C.js";
39
+ import {
40
+ frequencyKey,
41
+ haplotypeCount,
42
+ nodeFrequency,
43
+ withFrequencies
44
+ } from "./chunk-XWH4LB56.js";
39
45
  import {
40
46
  FIGURE_DEFAULTS
41
- } from "./chunk-CF2AXV5I.js";
47
+ } from "./chunk-XESCKKKT.js";
42
48
  import {
43
49
  engineSettingsOf,
44
50
  fitTransform,
45
51
  forceLayout,
46
52
  loadGraph
47
- } from "./chunk-3KGUENAV.js";
53
+ } from "./chunk-5LTWXDXK.js";
48
54
  import {
49
55
  referencePositions
50
56
  } from "./chunk-L4DBSRA2.js";
@@ -308,6 +314,7 @@ function figureData(graph, layout, o = {}) {
308
314
  }
309
315
  const startsOf = referenceVisitStarts(graph);
310
316
  const positions = referencePositions(graph);
317
+ const haplotypes = haplotypeCount(graph);
311
318
  return {
312
319
  meta: {
313
320
  generator: `@jbrowse/bandage-core@${version}`,
@@ -330,7 +337,9 @@ function figureData(graph, layout, o = {}) {
330
337
  graph,
331
338
  lift,
332
339
  lift.walks.length === 1 ? labelOf(lift.walks[0].name) : "these walks"
333
- ) : null
340
+ ) : null,
341
+ // the widths a key shows where nodes are as wide as their frequency
342
+ frequencyKey: o.nodeWidth === "frequency" ? frequencyKey(o.contigThickness ?? FIGURE_DEFAULTS.contigThickness) : null
334
343
  },
335
344
  panels: {
336
345
  panel: panels.map((p) => p.name),
@@ -350,6 +359,7 @@ function figureData(graph, layout, o = {}) {
350
359
  name: graph.nodes.map((n) => n.name),
351
360
  length: graph.nodes.map((n) => n.length),
352
361
  depth: graph.nodes.map((n) => n.depth),
362
+ frequency: graph.nodes.map((n) => nodeFrequency(n, haplotypes) ?? null),
353
363
  backbone: graph.nodes.map((n) => isBackbone(n)),
354
364
  referenceVisits: graph.nodes.map(
355
365
  (n) => isBackbone(n) ? startsOf(n).length : 0
@@ -363,7 +373,10 @@ function figureData(graph, layout, o = {}) {
363
373
  };
364
374
  }
365
375
  async function laidOutGraph(text, name, region, spec) {
366
- const graph = loadGraph(text, name, { referencePath: spec.referencePath });
376
+ const graph = withFrequencies(
377
+ loadGraph(text, name, { referencePath: spec.referencePath }),
378
+ spec.frequencies
379
+ );
367
380
  const layout = layoutModeByValue(spec.layout ?? "force").run(graph, region) ?? (await forceLayout(graph, engineSettingsOf(spec), layoutEngine)).result;
368
381
  return { graph, layout };
369
382
  }
@@ -1,7 +1,7 @@
1
1
  import {
2
2
  computeColorSchemeRange,
3
3
  getNodeColor
4
- } from "./chunk-72JZSR4B.js";
4
+ } from "./chunk-DTBQNR7P.js";
5
5
  import {
6
6
  abgrToCssRgba
7
7
  } from "./chunk-G2FD7S3C.js";
@@ -5,7 +5,7 @@ import {
5
5
  stripGeneGaps,
6
6
  walkStripFrame,
7
7
  walkStripLabelsTree
8
- } from "./chunk-BMO5MVPB.js";
8
+ } from "./chunk-STUG7I25.js";
9
9
  import {
10
10
  Canvas2DRenderer
11
11
  } from "./chunk-4DMSPNYV.js";
@@ -13,7 +13,7 @@ import {
13
13
  walkRowsKey,
14
14
  walkRowsKeyTree,
15
15
  walkRowsTree
16
- } from "./chunk-5KQRVX4N.js";
16
+ } from "./chunk-PIPNW3VY.js";
17
17
  import {
18
18
  EXON_COLOR,
19
19
  exonOutlineTree,
@@ -30,19 +30,19 @@ import {
30
30
  } from "./chunk-HEYIAMTC.js";
31
31
  import {
32
32
  version
33
- } from "./chunk-NIB2A2UZ.js";
33
+ } from "./chunk-42MMT5QM.js";
34
34
  import {
35
35
  axisScaleOf
36
- } from "./chunk-ZB5ADQYK.js";
36
+ } from "./chunk-ZZUSCQVT.js";
37
37
  import {
38
38
  figureScene
39
- } from "./chunk-F3254CLY.js";
39
+ } from "./chunk-47R7GMU3.js";
40
40
  import {
41
41
  fadedKey
42
- } from "./chunk-WRSI6VK7.js";
42
+ } from "./chunk-PL6X2IJC.js";
43
43
  import {
44
44
  encodingStops
45
- } from "./chunk-JWXSEGEA.js";
45
+ } from "./chunk-BDMISSNR.js";
46
46
  import {
47
47
  THREAD_PX,
48
48
  passesKey,
@@ -56,14 +56,14 @@ import {
56
56
  } from "./chunk-VCUOYVLC.js";
57
57
  import {
58
58
  nodeInk
59
- } from "./chunk-ZANALBSX.js";
59
+ } from "./chunk-XWH4LB56.js";
60
60
  import {
61
61
  FIGURE_DEFAULTS
62
- } from "./chunk-CF2AXV5I.js";
62
+ } from "./chunk-XESCKKKT.js";
63
63
  import {
64
64
  FIT_PADDING,
65
65
  fitTransform
66
- } from "./chunk-3KGUENAV.js";
66
+ } from "./chunk-5LTWXDXK.js";
67
67
  import {
68
68
  LABEL_CHAR_PX,
69
69
  LABEL_PAD,
@@ -75,11 +75,13 @@ function statedDepth({ tags, length }) {
75
75
  return positive(tags.dp) ?? positive(tags.DP) ?? (count !== void 0 && length > 0 ? count / length : void 0);
76
76
  }
77
77
  function makeNode(gfaNode, strand, depth) {
78
+ const frequency = gfaNode.tags.AF;
78
79
  return {
79
80
  id: `${gfaNode.id}${strand}`,
80
81
  name: gfaNode.id,
81
82
  length: gfaNode.length,
82
83
  depth,
84
+ ...typeof frequency === "number" && frequency >= 0 ? { frequency } : {},
83
85
  stable: stableCoordinate(gfaNode),
84
86
  samples: carriedSamples(gfaNode)
85
87
  };
@@ -2,7 +2,7 @@ import {
2
2
  LIFT_BACKDROP_CSS,
3
3
  computeColorSchemeRange,
4
4
  getNodeColor
5
- } from "./chunk-72JZSR4B.js";
5
+ } from "./chunk-DTBQNR7P.js";
6
6
  import {
7
7
  abgrToCssRgba
8
8
  } from "./chunk-G2FD7S3C.js";
@@ -1,6 +1,6 @@
1
1
  import {
2
2
  REFERENCE_RAMP_ALT_CSS
3
- } from "./chunk-72JZSR4B.js";
3
+ } from "./chunk-DTBQNR7P.js";
4
4
  import {
5
5
  RAMP_GRADIENT_CSS,
6
6
  RAMP_GRADIENT_STOPS,
@@ -2,10 +2,10 @@ import {
2
2
  encodedColor,
3
3
  resolveEncoding,
4
4
  splitFamilies
5
- } from "./chunk-JWXSEGEA.js";
5
+ } from "./chunk-BDMISSNR.js";
6
6
  import {
7
7
  rampFraction
8
- } from "./chunk-72JZSR4B.js";
8
+ } from "./chunk-DTBQNR7P.js";
9
9
  import {
10
10
  gapParts
11
11
  } from "./chunk-LG2UK4MB.js";
@@ -3,7 +3,7 @@ import {
3
3
  boxesGenes,
4
4
  rowPitch,
5
5
  rowSpan
6
- } from "./chunk-5KQRVX4N.js";
6
+ } from "./chunk-PIPNW3VY.js";
7
7
  import {
8
8
  READOUT_ROOM,
9
9
  longestBar
@@ -1,6 +1,6 @@
1
1
  import {
2
2
  ENGINE_DEFAULTS
3
- } from "./chunk-3KGUENAV.js";
3
+ } from "./chunk-5LTWXDXK.js";
4
4
 
5
5
  // src/figureSettings.ts
6
6
  var FIGURE_DEFAULTS = {
@@ -0,0 +1,115 @@
1
+ import {
2
+ panSNHaplotype
3
+ } from "./chunk-2JL2JVZ2.js";
4
+
5
+ // src/nodeWidths.ts
6
+ var NODE_WIDTHS = [
7
+ {
8
+ value: "depth",
9
+ label: "By depth",
10
+ description: "Thicker the more paths carry a node, on the square root of its depth against the mean. A graph with one depth everywhere draws uniform."
11
+ },
12
+ {
13
+ value: "frequency",
14
+ label: "By frequency",
15
+ description: "As wide as the share of haplotypes that pass a node, or its AF tag: full width at 100%, half at 50%, and wider where a haplotype passes it more than once."
16
+ },
17
+ {
18
+ value: "uniform",
19
+ label: "Uniform",
20
+ description: "Every node the same thickness."
21
+ }
22
+ ];
23
+ var MIN_FACTOR = 0.3;
24
+ var MAX_FACTOR = 3;
25
+ var MIN_FREQUENCY_FACTOR = 0.05;
26
+ function meanDepth(graph) {
27
+ let weighted = 0;
28
+ let length = 0;
29
+ for (const node of graph.nodes) {
30
+ weighted += node.depth * node.length;
31
+ length += node.length;
32
+ }
33
+ return length > 0 ? weighted / length : 0;
34
+ }
35
+ function haplotypeOf(path) {
36
+ return path.sample === void 0 ? panSNHaplotype(path.name) ?? path.name : `${path.sample}#${path.haplotype ?? 0}`;
37
+ }
38
+ function haplotypeCount(graph) {
39
+ return new Set((graph.paths ?? []).map(haplotypeOf)).size;
40
+ }
41
+ function nodeFrequency(node, haplotypes) {
42
+ return node.frequency ?? (haplotypes > 0 ? node.depth / haplotypes : void 0);
43
+ }
44
+ function withFrequencies(graph, frequencies) {
45
+ if (!frequencies) {
46
+ return graph;
47
+ }
48
+ const nodes = graph.nodes.map((node) => {
49
+ const frequency = frequencies[node.name];
50
+ return frequency === void 0 ? node : { ...node, frequency };
51
+ });
52
+ return { ...graph, nodes };
53
+ }
54
+ function widthNorm(graph, nodeWidth) {
55
+ return nodeWidth === "depth" ? meanDepth(graph) : nodeWidth === "frequency" ? haplotypeCount(graph) : 0;
56
+ }
57
+ function frequencyFactor(f) {
58
+ return Math.min(MAX_FACTOR, Math.max(MIN_FREQUENCY_FACTOR, f));
59
+ }
60
+ function frequencyWidthFactor(node, haplotypes) {
61
+ const f = nodeFrequency(node, haplotypes);
62
+ return f === void 0 ? 1 : frequencyFactor(f);
63
+ }
64
+ function frequencyKey(contigThickness) {
65
+ return [1, 0.5, 0.1].map((f) => ({
66
+ label: `${f * 100}%`,
67
+ widthPx: contigThickness * frequencyFactor(f)
68
+ }));
69
+ }
70
+ function depthWidthFactor(node, mean) {
71
+ if (!(mean > 0) || !(node.depth > 0)) {
72
+ return 1;
73
+ }
74
+ return Math.min(
75
+ MAX_FACTOR,
76
+ Math.max(MIN_FACTOR, Math.sqrt(node.depth / mean))
77
+ );
78
+ }
79
+ function nodeWidthPx(node, contigThickness, nodeWidth, norm) {
80
+ return contigThickness * (nodeWidth === "depth" ? depthWidthFactor(node, norm) : nodeWidth === "frequency" ? frequencyWidthFactor(node, norm) : 1);
81
+ }
82
+ function maxNodeWidthPx(contigThickness, nodeWidth) {
83
+ return contigThickness * (nodeWidth === "uniform" ? 1 : MAX_FACTOR);
84
+ }
85
+ var MIN_WALK_LANE_PX = 4;
86
+ function walkLaneWidthPx(width, lanes) {
87
+ return Math.max(width / lanes, MIN_WALK_LANE_PX);
88
+ }
89
+ function nodeInk(graph, nodeById, contigThickness, nodeWidth, lanes = 0) {
90
+ const norm = graph ? widthNorm(graph, nodeWidth) : 0;
91
+ const reach = (width) => lanes > 0 ? walkLaneWidthPx(width, lanes) * lanes / 2 : width / 2;
92
+ return {
93
+ maxHalfWidthPx: reach(maxNodeWidthPx(contigThickness, nodeWidth)),
94
+ halfWidthPx: (id) => {
95
+ const node = nodeById?.get(id);
96
+ return reach(
97
+ node ? nodeWidthPx(node, contigThickness, nodeWidth, norm) : contigThickness
98
+ );
99
+ }
100
+ };
101
+ }
102
+
103
+ export {
104
+ NODE_WIDTHS,
105
+ meanDepth,
106
+ haplotypeCount,
107
+ nodeFrequency,
108
+ withFrequencies,
109
+ widthNorm,
110
+ frequencyKey,
111
+ nodeWidthPx,
112
+ maxNodeWidthPx,
113
+ walkLaneWidthPx,
114
+ nodeInk
115
+ };
@@ -1,6 +1,6 @@
1
1
  import {
2
2
  clampZoom
3
- } from "./chunk-3KGUENAV.js";
3
+ } from "./chunk-5LTWXDXK.js";
4
4
 
5
5
  // src/viewport.ts
6
6
  function axisScaleOf(scale, pixelRows) {
@@ -9,7 +9,7 @@ import "../chunks/chunk-EQDQ7P4Y.js";
9
9
  import {
10
10
  laidOutGraph,
11
11
  walkLayers
12
- } from "../chunks/chunk-KMYMAPQ3.js";
12
+ } from "../chunks/chunk-FKMZG7HI.js";
13
13
  import {
14
14
  LAYOUT_ENGINE_VALUES,
15
15
  isLayoutEngineKind
@@ -36,27 +36,27 @@ import "../chunks/chunk-ZKSC7QVE.js";
36
36
  import "../chunks/chunk-HNWJ4B7S.js";
37
37
  import {
38
38
  figureSvg
39
- } from "../chunks/chunk-SR6LCQ5U.js";
39
+ } from "../chunks/chunk-IWPINV4U.js";
40
40
  import "../chunks/chunk-V4YML3GR.js";
41
- import "../chunks/chunk-BMO5MVPB.js";
41
+ import "../chunks/chunk-STUG7I25.js";
42
42
  import "../chunks/chunk-4DMSPNYV.js";
43
43
  import "../chunks/chunk-RBCE2OQH.js";
44
44
  import {
45
45
  genesOnRow,
46
46
  placeRowGenes
47
- } from "../chunks/chunk-5KQRVX4N.js";
47
+ } from "../chunks/chunk-PIPNW3VY.js";
48
48
  import "../chunks/chunk-JSUCGZ6K.js";
49
49
  import "../chunks/chunk-U6TXPLFJ.js";
50
50
  import "../chunks/chunk-QWLCHMNS.js";
51
51
  import "../chunks/chunk-WTWO2IPM.js";
52
52
  import "../chunks/chunk-HEYIAMTC.js";
53
- import "../chunks/chunk-NIB2A2UZ.js";
54
- import "../chunks/chunk-ZB5ADQYK.js";
55
- import "../chunks/chunk-F3254CLY.js";
53
+ import "../chunks/chunk-42MMT5QM.js";
54
+ import "../chunks/chunk-ZZUSCQVT.js";
55
+ import "../chunks/chunk-47R7GMU3.js";
56
56
  import "../chunks/chunk-LOCJN3BZ.js";
57
- import "../chunks/chunk-WRSI6VK7.js";
58
- import "../chunks/chunk-JWXSEGEA.js";
59
- import "../chunks/chunk-72JZSR4B.js";
57
+ import "../chunks/chunk-PL6X2IJC.js";
58
+ import "../chunks/chunk-BDMISSNR.js";
59
+ import "../chunks/chunk-DTBQNR7P.js";
60
60
  import "../chunks/chunk-YUIKEUKY.js";
61
61
  import "../chunks/chunk-G2FD7S3C.js";
62
62
  import "../chunks/chunk-OKH32P3Z.js";
@@ -69,14 +69,14 @@ import {
69
69
  } from "../chunks/chunk-C3KAPREU.js";
70
70
  import "../chunks/chunk-LODKC7PJ.js";
71
71
  import "../chunks/chunk-EHEIS3TE.js";
72
- import "../chunks/chunk-ZANALBSX.js";
73
- import "../chunks/chunk-CF2AXV5I.js";
74
- import "../chunks/chunk-3KGUENAV.js";
72
+ import "../chunks/chunk-XWH4LB56.js";
73
+ import "../chunks/chunk-XESCKKKT.js";
74
+ import "../chunks/chunk-5LTWXDXK.js";
75
75
  import "../chunks/chunk-OPPVSPEF.js";
76
76
  import "../chunks/chunk-NAYS472K.js";
77
77
  import "../chunks/chunk-4FRX2SPT.js";
78
78
  import "../chunks/chunk-VPE4AYP7.js";
79
- import "../chunks/chunk-TUMJNAOL.js";
79
+ import "../chunks/chunk-MSVYSCAH.js";
80
80
  import "../chunks/chunk-QYBZZI5H.js";
81
81
  import "../chunks/chunk-CFXXFHRK.js";
82
82
  import "../chunks/chunk-7L7MN2OM.js";
package/dist/cli/fold.js CHANGED
@@ -10,12 +10,12 @@ import {
10
10
  } from "../chunks/chunk-4BYGFDQB.js";
11
11
  import {
12
12
  loadGraph
13
- } from "../chunks/chunk-3KGUENAV.js";
13
+ } from "../chunks/chunk-5LTWXDXK.js";
14
14
  import "../chunks/chunk-OPPVSPEF.js";
15
15
  import "../chunks/chunk-NAYS472K.js";
16
16
  import "../chunks/chunk-4FRX2SPT.js";
17
17
  import "../chunks/chunk-VPE4AYP7.js";
18
- import "../chunks/chunk-TUMJNAOL.js";
18
+ import "../chunks/chunk-MSVYSCAH.js";
19
19
  import "../chunks/chunk-QYBZZI5H.js";
20
20
  import "../chunks/chunk-CFXXFHRK.js";
21
21
  import "../chunks/chunk-7L7MN2OM.js";
package/dist/figure.js CHANGED
@@ -1,23 +1,23 @@
1
1
  import {
2
2
  figureSvg
3
- } from "./chunks/chunk-SR6LCQ5U.js";
3
+ } from "./chunks/chunk-IWPINV4U.js";
4
4
  import "./chunks/chunk-V4YML3GR.js";
5
- import "./chunks/chunk-BMO5MVPB.js";
5
+ import "./chunks/chunk-STUG7I25.js";
6
6
  import "./chunks/chunk-4DMSPNYV.js";
7
7
  import "./chunks/chunk-RBCE2OQH.js";
8
- import "./chunks/chunk-5KQRVX4N.js";
8
+ import "./chunks/chunk-PIPNW3VY.js";
9
9
  import "./chunks/chunk-JSUCGZ6K.js";
10
10
  import "./chunks/chunk-U6TXPLFJ.js";
11
11
  import "./chunks/chunk-QWLCHMNS.js";
12
12
  import "./chunks/chunk-WTWO2IPM.js";
13
13
  import "./chunks/chunk-HEYIAMTC.js";
14
- import "./chunks/chunk-NIB2A2UZ.js";
15
- import "./chunks/chunk-ZB5ADQYK.js";
16
- import "./chunks/chunk-F3254CLY.js";
14
+ import "./chunks/chunk-42MMT5QM.js";
15
+ import "./chunks/chunk-ZZUSCQVT.js";
16
+ import "./chunks/chunk-47R7GMU3.js";
17
17
  import "./chunks/chunk-LOCJN3BZ.js";
18
- import "./chunks/chunk-WRSI6VK7.js";
19
- import "./chunks/chunk-JWXSEGEA.js";
20
- import "./chunks/chunk-72JZSR4B.js";
18
+ import "./chunks/chunk-PL6X2IJC.js";
19
+ import "./chunks/chunk-BDMISSNR.js";
20
+ import "./chunks/chunk-DTBQNR7P.js";
21
21
  import "./chunks/chunk-YUIKEUKY.js";
22
22
  import "./chunks/chunk-G2FD7S3C.js";
23
23
  import "./chunks/chunk-OKH32P3Z.js";
@@ -27,14 +27,14 @@ import "./chunks/chunk-VCUOYVLC.js";
27
27
  import "./chunks/chunk-C3KAPREU.js";
28
28
  import "./chunks/chunk-LODKC7PJ.js";
29
29
  import "./chunks/chunk-EHEIS3TE.js";
30
- import "./chunks/chunk-ZANALBSX.js";
31
- import "./chunks/chunk-CF2AXV5I.js";
32
- import "./chunks/chunk-3KGUENAV.js";
30
+ import "./chunks/chunk-XWH4LB56.js";
31
+ import "./chunks/chunk-XESCKKKT.js";
32
+ import "./chunks/chunk-5LTWXDXK.js";
33
33
  import "./chunks/chunk-OPPVSPEF.js";
34
34
  import "./chunks/chunk-NAYS472K.js";
35
35
  import "./chunks/chunk-4FRX2SPT.js";
36
36
  import "./chunks/chunk-VPE4AYP7.js";
37
- import "./chunks/chunk-TUMJNAOL.js";
37
+ import "./chunks/chunk-MSVYSCAH.js";
38
38
  import "./chunks/chunk-QYBZZI5H.js";
39
39
  import "./chunks/chunk-CFXXFHRK.js";
40
40
  import "./chunks/chunk-7L7MN2OM.js";
@@ -3,7 +3,7 @@ import {
3
3
  gfaFigureData,
4
4
  laidOutGraph,
5
5
  walkLayers
6
- } from "./chunks/chunk-KMYMAPQ3.js";
6
+ } from "./chunks/chunk-FKMZG7HI.js";
7
7
  import "./chunks/chunk-CO6RGQAD.js";
8
8
  import "./chunks/chunk-54CX2MCH.js";
9
9
  import "./chunks/chunk-3JDGPLCL.js";
@@ -18,13 +18,13 @@ import "./chunks/chunk-FNDNSDKW.js";
18
18
  import "./chunks/chunk-ZKSC7QVE.js";
19
19
  import "./chunks/chunk-HNWJ4B7S.js";
20
20
  import "./chunks/chunk-HEYIAMTC.js";
21
- import "./chunks/chunk-NIB2A2UZ.js";
22
- import "./chunks/chunk-ZB5ADQYK.js";
23
- import "./chunks/chunk-F3254CLY.js";
21
+ import "./chunks/chunk-42MMT5QM.js";
22
+ import "./chunks/chunk-ZZUSCQVT.js";
23
+ import "./chunks/chunk-47R7GMU3.js";
24
24
  import "./chunks/chunk-LOCJN3BZ.js";
25
- import "./chunks/chunk-WRSI6VK7.js";
26
- import "./chunks/chunk-JWXSEGEA.js";
27
- import "./chunks/chunk-72JZSR4B.js";
25
+ import "./chunks/chunk-PL6X2IJC.js";
26
+ import "./chunks/chunk-BDMISSNR.js";
27
+ import "./chunks/chunk-DTBQNR7P.js";
28
28
  import "./chunks/chunk-YUIKEUKY.js";
29
29
  import "./chunks/chunk-G2FD7S3C.js";
30
30
  import "./chunks/chunk-OKH32P3Z.js";
@@ -34,14 +34,14 @@ import "./chunks/chunk-VCUOYVLC.js";
34
34
  import "./chunks/chunk-C3KAPREU.js";
35
35
  import "./chunks/chunk-LODKC7PJ.js";
36
36
  import "./chunks/chunk-EHEIS3TE.js";
37
- import "./chunks/chunk-ZANALBSX.js";
38
- import "./chunks/chunk-CF2AXV5I.js";
39
- import "./chunks/chunk-3KGUENAV.js";
37
+ import "./chunks/chunk-XWH4LB56.js";
38
+ import "./chunks/chunk-XESCKKKT.js";
39
+ import "./chunks/chunk-5LTWXDXK.js";
40
40
  import "./chunks/chunk-OPPVSPEF.js";
41
41
  import "./chunks/chunk-NAYS472K.js";
42
42
  import "./chunks/chunk-4FRX2SPT.js";
43
43
  import "./chunks/chunk-VPE4AYP7.js";
44
- import "./chunks/chunk-TUMJNAOL.js";
44
+ import "./chunks/chunk-MSVYSCAH.js";
45
45
  import "./chunks/chunk-QYBZZI5H.js";
46
46
  import "./chunks/chunk-CFXXFHRK.js";
47
47
  import "./chunks/chunk-7L7MN2OM.js";