@jbrowse/bandage-core 7.2.0 → 7.3.0

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 (46) hide show
  1. package/dist/chunks/{chunk-MH5IA57M.js → chunk-36UKA6RQ.js} +1 -1
  2. package/dist/chunks/{chunk-QMJ4J5PT.js → chunk-45J7P6YW.js} +36 -37
  3. package/dist/chunks/{chunk-EXSXBIMH.js → chunk-5N5YRRFE.js} +1 -1
  4. package/dist/chunks/{chunk-E7FWQQHP.js → chunk-7GBL7SJY.js} +15 -4
  5. package/dist/chunks/{chunk-Y7UR3MDE.js → chunk-AGJZ5RDC.js} +1 -1
  6. package/dist/chunks/{chunk-4FQTTG5F.js → chunk-AYOSNXLQ.js} +1 -1
  7. package/dist/chunks/{chunk-TQ7VCGJR.js → chunk-C4IUUTAB.js} +1 -1
  8. package/dist/chunks/chunk-CBBDB3UC.js +27 -0
  9. package/dist/chunks/{chunk-S73EYTZA.js → chunk-ERHAGG72.js} +1 -1
  10. package/dist/chunks/{chunk-KREASK3Z.js → chunk-HPIZNWF7.js} +4 -4
  11. package/dist/chunks/{chunk-JKXE6CIP.js → chunk-IW6K4VHZ.js} +4 -4
  12. package/dist/chunks/chunk-K5SIJGAE.js +12 -0
  13. package/dist/chunks/{chunk-CNQSHEBS.js → chunk-O7QXUXGZ.js} +1 -1
  14. package/dist/chunks/{chunk-UGD6ZMOF.js → chunk-RCPGXIWA.js} +6 -7
  15. package/dist/chunks/{chunk-EPWYRSHH.js → chunk-SGAMPIKO.js} +22 -0
  16. package/dist/chunks/{chunk-VST5SR4C.js → chunk-W7R55CIZ.js} +1 -1
  17. package/dist/chunks/{chunk-VECR253P.js → chunk-Z3OHBOEA.js} +1 -1
  18. package/dist/cli/figure.js +47 -58
  19. package/dist/figure.js +24 -24
  20. package/dist/figureSettings.js +25 -0
  21. package/dist/index.js +122 -106
  22. package/dist/layout/tubeMapLayout.js +4 -4
  23. package/dist/layout/walkRowDraw.js +8 -8
  24. package/dist/layout/walkRowLayout.js +1 -1
  25. package/dist/layout/walkStrip.js +9 -9
  26. package/dist/layoutModes.js +8 -8
  27. package/dist/layoutQualities.js +6 -0
  28. package/dist/pathColors.js +7 -5
  29. package/dist/pipeline.js +6 -2
  30. package/dist/referenceRampCss.js +6 -6
  31. package/dist/referenceStrip.js +6 -6
  32. package/dist/renderer/GeometryBuilder.js +5 -5
  33. package/dist/tubeMap/coarsen.js +5 -5
  34. package/dist/tubeMap/nodeColors.js +6 -6
  35. package/dist/types/figure.d.ts +1 -0
  36. package/dist/types/figureSettings.d.ts +15 -0
  37. package/dist/types/index.d.ts +6 -1
  38. package/dist/types/layoutQualities.d.ts +17 -0
  39. package/dist/types/pathColors.d.ts +4 -0
  40. package/dist/types/pipeline.d.ts +2 -0
  41. package/dist/types/version.d.ts +1 -1
  42. package/dist/version.js +1 -1
  43. package/dist/viewport.js +3 -3
  44. package/dist/walkEncoding.js +6 -6
  45. package/dist/walkHighlight.js +7 -7
  46. package/package.json +1 -1
@@ -1,7 +1,7 @@
1
1
  import {
2
2
  encodedColor,
3
3
  resolveEncoding
4
- } from "./chunk-TQ7VCGJR.js";
4
+ } from "./chunk-C4IUUTAB.js";
5
5
  import {
6
6
  pathOrigin
7
7
  } from "./chunk-ST2IBUAN.js";
@@ -1,19 +1,19 @@
1
+ import {
2
+ stripGeneGaps,
3
+ walkStripFrame,
4
+ walkStripLabelsTree
5
+ } from "./chunk-HPIZNWF7.js";
1
6
  import {
2
7
  Canvas2DRenderer
3
8
  } from "./chunk-CH3DLBUT.js";
4
9
  import {
5
10
  svgCanvas
6
11
  } from "./chunk-47DYCZOK.js";
7
- import {
8
- stripGeneGaps,
9
- walkStripFrame,
10
- walkStripLabelsTree
11
- } from "./chunk-KREASK3Z.js";
12
12
  import {
13
13
  walkRowsKey,
14
14
  walkRowsKeyTree,
15
15
  walkRowsTree
16
- } from "./chunk-UGD6ZMOF.js";
16
+ } from "./chunk-RCPGXIWA.js";
17
17
  import {
18
18
  EXON_COLOR,
19
19
  exonOutlineTree,
@@ -22,35 +22,33 @@ import {
22
22
  import {
23
23
  genePins
24
24
  } from "./chunk-BUBZ32IC.js";
25
- import {
26
- version
27
- } from "./chunk-S73EYTZA.js";
28
- import {
29
- axisScaleOf
30
- } from "./chunk-Y7UR3MDE.js";
31
25
  import {
32
26
  facetLifts,
33
27
  walkLift
34
- } from "./chunk-MH5IA57M.js";
35
- import {
36
- encodingStops
37
- } from "./chunk-TQ7VCGJR.js";
28
+ } from "./chunk-36UKA6RQ.js";
38
29
  import {
39
30
  rangeText,
40
31
  walkKey
41
32
  } from "./chunk-2LQ5BWT7.js";
42
33
  import {
43
- FIT_PADDING,
44
- drawingBounds,
45
- fitTransform
46
- } from "./chunk-EPWYRSHH.js";
34
+ version
35
+ } from "./chunk-ERHAGG72.js";
36
+ import {
37
+ axisScaleOf
38
+ } from "./chunk-AGJZ5RDC.js";
39
+ import {
40
+ encodingStops
41
+ } from "./chunk-C4IUUTAB.js";
47
42
  import {
48
43
  buildGeometry,
49
44
  computeReferenceRamp
50
- } from "./chunk-VST5SR4C.js";
45
+ } from "./chunk-W7R55CIZ.js";
51
46
  import {
52
47
  nodeInk
53
48
  } from "./chunk-PBENCR5L.js";
49
+ import {
50
+ referenceLabel
51
+ } from "./chunk-RAKOB6IV.js";
54
52
  import {
55
53
  geneLabelCandidates
56
54
  } from "./chunk-GJMC3PGM.js";
@@ -61,8 +59,9 @@ import {
61
59
  walkRowsExtent
62
60
  } from "./chunk-3JANT2SW.js";
63
61
  import {
64
- pathLegend
65
- } from "./chunk-E7FWQQHP.js";
62
+ pathLegend,
63
+ walkLabelsOf
64
+ } from "./chunk-7GBL7SJY.js";
66
65
  import {
67
66
  LABEL_CHAR_PX,
68
67
  LABEL_PAD,
@@ -73,13 +72,6 @@ import {
73
72
  import {
74
73
  resolveColorScheme
75
74
  } from "./chunk-JKJWSY4V.js";
76
- import {
77
- deletionDrawing,
78
- deletionEdges
79
- } from "./chunk-N6FECAXP.js";
80
- import {
81
- ROW_HEIGHT_PX
82
- } from "./chunk-CPMHA4W5.js";
83
75
  import {
84
76
  serializeEl
85
77
  } from "./chunk-NNODIW4U.js";
@@ -92,8 +84,17 @@ import {
92
84
  facetSettingOf
93
85
  } from "./chunk-6SBUFFTB.js";
94
86
  import {
95
- referenceLabel
96
- } from "./chunk-RAKOB6IV.js";
87
+ FIT_PADDING,
88
+ drawingBounds,
89
+ fitTransform
90
+ } from "./chunk-SGAMPIKO.js";
91
+ import {
92
+ deletionDrawing,
93
+ deletionEdges
94
+ } from "./chunk-N6FECAXP.js";
95
+ import {
96
+ ROW_HEIGHT_PX
97
+ } from "./chunk-CPMHA4W5.js";
97
98
 
98
99
  // src/figure.ts
99
100
  var FONT = 'font-family="Helvetica, Arial, sans-serif" font-size="11"';
@@ -174,11 +175,8 @@ function figureSvg(graph, layout, o = {}) {
174
175
  const lift = layers.length > 0 && !layout.tubeMap ? walkLift(graph, layers, walkRamp) : void 0;
175
176
  const facet = facetSettingOf(o.facet);
176
177
  const panels = facet.field && lift && lift.walks.length > 1 ? facetLifts(graph, lift, layers, walkRamp) : void 0;
177
- const labels = new Map(
178
- (graph.paths?.length ? pathLegend(graph.paths) : []).map((p) => [
179
- p.name,
180
- p.label
181
- ])
178
+ const labels = walkLabelsOf(
179
+ graph.paths?.length ? pathLegend(graph.paths) : []
182
180
  );
183
181
  const labelOf = (name) => labels.get(name) ?? name;
184
182
  const referenceName = o.referenceName ?? referenceLabel(graph, region);
@@ -279,6 +277,7 @@ function figureSvg(graph, layout, o = {}) {
279
277
  connectorThickness: o.connectorThickness ?? 2,
280
278
  drawPaths: false,
281
279
  nodeWidth,
280
+ linearLayout: o.linearLayout,
282
281
  highlight,
283
282
  axis,
284
283
  referenceRamp,
@@ -2,7 +2,7 @@ import {
2
2
  LIFT_BACKDROP_CSS,
3
3
  computeColorSchemeRange,
4
4
  getNodeColor
5
- } from "./chunk-VST5SR4C.js";
5
+ } from "./chunk-W7R55CIZ.js";
6
6
  import {
7
7
  abgrToCssRgba
8
8
  } from "./chunk-UMNCCYBN.js";
@@ -1,9 +1,9 @@
1
- import {
2
- pathOrigin
3
- } from "./chunk-ST2IBUAN.js";
4
1
  import {
5
2
  groupDigits
6
3
  } from "./chunk-3ZZSX5HN.js";
4
+ import {
5
+ pathOrigin
6
+ } from "./chunk-ST2IBUAN.js";
7
7
  import {
8
8
  isGenericSample
9
9
  } from "./chunk-BPLIXMH7.js";
@@ -68,6 +68,16 @@ function pathLegend(paths, colors) {
68
68
  color: colors?.[i] ?? pathCssColor(i, paths.length)
69
69
  }));
70
70
  }
71
+ function walkLabelsOf(entries) {
72
+ const seen = /* @__PURE__ */ new Map();
73
+ return new Map(
74
+ [...entries].sort((a, b) => a.label.localeCompare(b.label)).map((e) => {
75
+ const n = (seen.get(e.label) ?? 0) + 1;
76
+ seen.set(e.label, n);
77
+ return [e.name, n > 1 ? `${e.label} (${n})` : e.label];
78
+ })
79
+ );
80
+ }
71
81
 
72
82
  export {
73
83
  nameHue,
@@ -78,5 +88,6 @@ export {
78
88
  pathColorsLegible,
79
89
  pathCssColor,
80
90
  pathGreyCssColor,
81
- pathLegend
91
+ pathLegend,
92
+ walkLabelsOf
82
93
  };
@@ -1,6 +1,6 @@
1
1
  import {
2
2
  clampZoom
3
- } from "./chunk-EPWYRSHH.js";
3
+ } from "./chunk-SGAMPIKO.js";
4
4
 
5
5
  // src/viewport.ts
6
6
  function axisScaleOf(scale, pixelRows) {
@@ -7,7 +7,7 @@ import {
7
7
  import {
8
8
  pathCssColor,
9
9
  pathGreyCssColor
10
- } from "./chunk-E7FWQQHP.js";
10
+ } from "./chunk-7GBL7SJY.js";
11
11
  import {
12
12
  pathOrigin
13
13
  } from "./chunk-ST2IBUAN.js";
@@ -2,7 +2,7 @@ import {
2
2
  REFERENCE_RAMP_ALT_COLOR,
3
3
  REFERENCE_RAMP_MAX_HUE,
4
4
  hslToRgb
5
- } from "./chunk-VST5SR4C.js";
5
+ } from "./chunk-W7R55CIZ.js";
6
6
  import {
7
7
  packAbgr
8
8
  } from "./chunk-UMNCCYBN.js";
@@ -0,0 +1,27 @@
1
+ import {
2
+ ENGINE_DEFAULTS
3
+ } from "./chunk-SGAMPIKO.js";
4
+
5
+ // src/figureSettings.ts
6
+ var FIGURE_DEFAULTS = {
7
+ ...ENGINE_DEFAULTS,
8
+ colorScheme: "auto",
9
+ nodeWidth: "depth",
10
+ contigThickness: 6,
11
+ connectorThickness: 2
12
+ };
13
+ function figureSpecSettings(s) {
14
+ const defaults = FIGURE_DEFAULTS;
15
+ const out = {};
16
+ for (const [k, v] of Object.entries(s)) {
17
+ if (v !== void 0 && v !== defaults[k]) {
18
+ out[k] = v;
19
+ }
20
+ }
21
+ return out;
22
+ }
23
+
24
+ export {
25
+ FIGURE_DEFAULTS,
26
+ figureSpecSettings
27
+ };
@@ -1,5 +1,5 @@
1
1
  // src/version.ts
2
- var version = "7.2.0";
2
+ var version = "7.3.0";
3
3
 
4
4
  export {
5
5
  version
@@ -2,16 +2,16 @@ import {
2
2
  alongRow,
3
3
  boxesGenes,
4
4
  rowPitch
5
- } from "./chunk-UGD6ZMOF.js";
6
- import {
7
- pathOrigin
8
- } from "./chunk-ST2IBUAN.js";
5
+ } from "./chunk-RCPGXIWA.js";
9
6
  import {
10
7
  LABEL_CHAR_PX
11
8
  } from "./chunk-AB35TJST.js";
12
9
  import {
13
10
  el
14
11
  } from "./chunk-NNODIW4U.js";
12
+ import {
13
+ pathOrigin
14
+ } from "./chunk-ST2IBUAN.js";
15
15
 
16
16
  // src/layout/walkStrip.ts
17
17
  var PAD_PX = 6;
@@ -1,11 +1,11 @@
1
+ import {
2
+ sampleRowLayout
3
+ } from "./chunk-LOEA5IHZ.js";
1
4
  import {
2
5
  hasTubeMapPaths,
3
6
  tubeMapLayout,
4
7
  tubeMapReferenceLayout
5
- } from "./chunk-4FQTTG5F.js";
6
- import {
7
- sampleRowLayout
8
- } from "./chunk-LOEA5IHZ.js";
8
+ } from "./chunk-AYOSNXLQ.js";
9
9
  import {
10
10
  anchoredLayout
11
11
  } from "./chunk-L3O7AWLI.js";
@@ -0,0 +1,12 @@
1
+ // src/layoutQualities.ts
2
+ var LAYOUT_QUALITIES = [
3
+ { value: 0, label: "Fastest" },
4
+ { value: 1, label: "Fast" },
5
+ { value: 2, label: "Default" },
6
+ { value: 3, label: "Fine" },
7
+ { value: 4, label: "Best" }
8
+ ];
9
+
10
+ export {
11
+ LAYOUT_QUALITIES
12
+ };
@@ -1,7 +1,7 @@
1
1
  import {
2
2
  computeColorSchemeRange,
3
3
  getNodeColor
4
- } from "./chunk-VST5SR4C.js";
4
+ } from "./chunk-W7R55CIZ.js";
5
5
  import {
6
6
  abgrToCssRgba
7
7
  } from "./chunk-UMNCCYBN.js";
@@ -3,19 +3,19 @@ import {
3
3
  RAMP_GRADIENT_STOPS,
4
4
  rampHueCss,
5
5
  rampStops
6
- } from "./chunk-VECR253P.js";
6
+ } from "./chunk-Z3OHBOEA.js";
7
7
  import {
8
8
  REFERENCE_RAMP_ALT_CSS
9
- } from "./chunk-VST5SR4C.js";
9
+ } from "./chunk-W7R55CIZ.js";
10
10
  import {
11
11
  LABEL_CHAR_PX
12
12
  } from "./chunk-AB35TJST.js";
13
- import {
14
- ROW_HEIGHT_PX
15
- } from "./chunk-CPMHA4W5.js";
16
13
  import {
17
14
  el
18
15
  } from "./chunk-NNODIW4U.js";
16
+ import {
17
+ ROW_HEIGHT_PX
18
+ } from "./chunk-CPMHA4W5.js";
19
19
 
20
20
  // src/layout/walkRowDraw.ts
21
21
  var ON_REFERENCE = "#2f8fd6";
@@ -25,7 +25,6 @@ var GENE_INK = "#1c1c22";
25
25
  var BAR_PX = 12;
26
26
  var GAP_PX = 4;
27
27
  var LABELLED_ROW_PX = 12;
28
- var READOUT_ROW_PX = 14;
29
28
  var MIN_TILED_BAR_PX = 6;
30
29
  var MIN_TILE_PX = 3;
31
30
  function kb(bp) {
@@ -278,7 +277,7 @@ function rowPitch(count, room, minRowPx = 0) {
278
277
  rowPx,
279
278
  barPx: rowPx <= 3 ? rowPx : Math.max(3, Math.round(rowPx * 0.6)),
280
279
  labelled: rowPx >= LABELLED_ROW_PX,
281
- readouts: rowPx >= READOUT_ROW_PX
280
+ readouts: rowPx >= LABELLED_ROW_PX
282
281
  };
283
282
  }
284
283
  function coalesceRuns(runs, pxPerBp) {
@@ -54,6 +54,26 @@ function loadGraph(text, name, opts = {}) {
54
54
  }
55
55
  return graph;
56
56
  }
57
+ var ENGINE_DEFAULTS = {
58
+ engine: "fmmm",
59
+ quality: 2,
60
+ linearLayout: false,
61
+ bubbleSpread: "auto",
62
+ spacing: 1,
63
+ componentSeparation: 1,
64
+ showDeletionEdges: true
65
+ };
66
+ function engineSettingsOf(s = {}) {
67
+ return {
68
+ engine: s.engine ?? ENGINE_DEFAULTS.engine,
69
+ quality: s.quality ?? ENGINE_DEFAULTS.quality,
70
+ linearLayout: s.linearLayout ?? ENGINE_DEFAULTS.linearLayout,
71
+ bubbleSpread: s.bubbleSpread ?? ENGINE_DEFAULTS.bubbleSpread,
72
+ spacing: s.spacing ?? ENGINE_DEFAULTS.spacing,
73
+ componentSeparation: s.componentSeparation ?? ENGINE_DEFAULTS.componentSeparation,
74
+ showDeletionEdges: s.showDeletionEdges ?? ENGINE_DEFAULTS.showDeletionEdges
75
+ };
76
+ }
57
77
  var COMPONENT_SEPARATION = 15;
58
78
  function engineRequest(graph, scaling, settings) {
59
79
  const anchored = graph.nodes.some(isBackbone);
@@ -210,6 +230,8 @@ function drawingBounds(layout, opts = {}) {
210
230
 
211
231
  export {
212
232
  loadGraph,
233
+ ENGINE_DEFAULTS,
234
+ engineSettingsOf,
213
235
  engineRequest,
214
236
  engineKey,
215
237
  forceLayout,
@@ -15,7 +15,7 @@ import {
15
15
  PATH_SATURATION,
16
16
  nameHue,
17
17
  pathHueAt
18
- } from "./chunk-E7FWQQHP.js";
18
+ } from "./chunk-7GBL7SJY.js";
19
19
  import {
20
20
  referenceMidpoints
21
21
  } from "./chunk-ES2N6V56.js";
@@ -1,6 +1,6 @@
1
1
  import {
2
2
  REFERENCE_RAMP_MAX_HUE
3
- } from "./chunk-VST5SR4C.js";
3
+ } from "./chunk-W7R55CIZ.js";
4
4
 
5
5
  // src/referenceRampCss.ts
6
6
  function rampHueCss(hue) {
@@ -4,6 +4,15 @@ import {
4
4
  genesFromGff3Lines,
5
5
  genesFromText
6
6
  } from "../chunks/chunk-BXEPA4KS.js";
7
+ import {
8
+ HPRC_GBZ,
9
+ cutGbzRegion,
10
+ haplotypeIndexBeside,
11
+ openGbz,
12
+ parseRegion
13
+ } from "../chunks/chunk-73RSLGZT.js";
14
+ import "../chunks/chunk-LTUWJKHD.js";
15
+ import "../chunks/chunk-WSIFAZU7.js";
7
16
  import {
8
17
  LAYOUT_ENGINE_VALUES,
9
18
  isLayoutEngineKind,
@@ -11,89 +20,81 @@ import {
11
20
  } from "../chunks/chunk-6EJIU6IA.js";
12
21
  import "../chunks/chunk-UNOE2NDN.js";
13
22
  import "../chunks/chunk-LYJ4US66.js";
23
+ import "../chunks/chunk-7XHHVYG7.js";
14
24
  import {
15
25
  LAYOUT_MODES,
16
26
  layoutModeByValue
17
- } from "../chunks/chunk-JKXE6CIP.js";
18
- import "../chunks/chunk-4FQTTG5F.js";
19
- import "../chunks/chunk-TEDQJPMI.js";
27
+ } from "../chunks/chunk-IW6K4VHZ.js";
20
28
  import "../chunks/chunk-LOEA5IHZ.js";
29
+ import "../chunks/chunk-AYOSNXLQ.js";
30
+ import "../chunks/chunk-TEDQJPMI.js";
21
31
  import "../chunks/chunk-L3O7AWLI.js";
22
32
  import "../chunks/chunk-TZFWUT2C.js";
33
+ import "../chunks/chunk-C44YRP5F.js";
23
34
  import "../chunks/chunk-RVS2QCOX.js";
24
35
  import "../chunks/chunk-HNQPEMYE.js";
25
- import "../chunks/chunk-C44YRP5F.js";
26
- import "../chunks/chunk-7XHHVYG7.js";
27
36
  import {
28
37
  figureSvg
29
- } from "../chunks/chunk-QMJ4J5PT.js";
38
+ } from "../chunks/chunk-45J7P6YW.js";
39
+ import "../chunks/chunk-HPIZNWF7.js";
30
40
  import "../chunks/chunk-CH3DLBUT.js";
31
41
  import "../chunks/chunk-4BYTEJGW.js";
32
42
  import "../chunks/chunk-47DYCZOK.js";
33
- import "../chunks/chunk-KREASK3Z.js";
34
43
  import {
35
44
  genesOnRow,
36
45
  placeRowGenes
37
- } from "../chunks/chunk-UGD6ZMOF.js";
46
+ } from "../chunks/chunk-RCPGXIWA.js";
38
47
  import "../chunks/chunk-3S3YVOJ7.js";
39
48
  import "../chunks/chunk-BUBZ32IC.js";
40
- import "../chunks/chunk-S73EYTZA.js";
41
- import "../chunks/chunk-Y7UR3MDE.js";
42
- import "../chunks/chunk-MH5IA57M.js";
43
- import "../chunks/chunk-TQ7VCGJR.js";
49
+ import "../chunks/chunk-36UKA6RQ.js";
44
50
  import "../chunks/chunk-2LQ5BWT7.js";
45
- import {
46
- forceLayout,
47
- loadGraph
48
- } from "../chunks/chunk-EPWYRSHH.js";
49
- import "../chunks/chunk-PUG7LXDF.js";
50
- import "../chunks/chunk-IGVV37VI.js";
51
- import "../chunks/chunk-72N5DJHZ.js";
52
- import "../chunks/chunk-QYBZZI5H.js";
53
- import "../chunks/chunk-CDLPYR5O.js";
54
- import "../chunks/chunk-VECR253P.js";
55
- import "../chunks/chunk-VST5SR4C.js";
51
+ import "../chunks/chunk-Z3OHBOEA.js";
52
+ import "../chunks/chunk-ERHAGG72.js";
53
+ import "../chunks/chunk-AGJZ5RDC.js";
54
+ import "../chunks/chunk-C4IUUTAB.js";
55
+ import "../chunks/chunk-W7R55CIZ.js";
56
56
  import "../chunks/chunk-UMNCCYBN.js";
57
57
  import "../chunks/chunk-PBENCR5L.js";
58
+ import {
59
+ featuresOnBackbone,
60
+ graphBackbone,
61
+ refNameBinding
62
+ } from "../chunks/chunk-RAKOB6IV.js";
58
63
  import "../chunks/chunk-GJMC3PGM.js";
59
64
  import "../chunks/chunk-FP4H7SFT.js";
60
65
  import "../chunks/chunk-MLSWIMZO.js";
61
66
  import "../chunks/chunk-WFB5TXRA.js";
62
- import "../chunks/chunk-JVLURPFW.js";
63
67
  import "../chunks/chunk-3JANT2SW.js";
64
68
  import {
65
69
  filterSamples,
66
70
  walkRows
67
71
  } from "../chunks/chunk-SZNZ2T6D.js";
68
- import "../chunks/chunk-E7FWQQHP.js";
69
- import "../chunks/chunk-ES2N6V56.js";
70
- import "../chunks/chunk-ST2IBUAN.js";
72
+ import "../chunks/chunk-7GBL7SJY.js";
71
73
  import "../chunks/chunk-3ZZSX5HN.js";
72
74
  import "../chunks/chunk-AB35TJST.js";
75
+ import "../chunks/chunk-JKJWSY4V.js";
76
+ import "../chunks/chunk-NNODIW4U.js";
77
+ import "../chunks/chunk-6SBUFFTB.js";
78
+ import {
79
+ engineSettingsOf,
80
+ forceLayout,
81
+ loadGraph
82
+ } from "../chunks/chunk-SGAMPIKO.js";
83
+ import "../chunks/chunk-PUG7LXDF.js";
84
+ import "../chunks/chunk-IGVV37VI.js";
85
+ import "../chunks/chunk-72N5DJHZ.js";
86
+ import "../chunks/chunk-QYBZZI5H.js";
87
+ import "../chunks/chunk-CDLPYR5O.js";
88
+ import "../chunks/chunk-JVLURPFW.js";
89
+ import "../chunks/chunk-ES2N6V56.js";
90
+ import "../chunks/chunk-ST2IBUAN.js";
91
+ import "../chunks/chunk-BPLIXMH7.js";
73
92
  import "../chunks/chunk-TAMCZHLW.js";
74
93
  import "../chunks/chunk-UVBGRJQX.js";
75
94
  import "../chunks/chunk-6JEWNXCQ.js";
76
- import "../chunks/chunk-JKJWSY4V.js";
77
95
  import "../chunks/chunk-N6FECAXP.js";
78
96
  import "../chunks/chunk-2CVHXFK7.js";
79
97
  import "../chunks/chunk-CPMHA4W5.js";
80
- import "../chunks/chunk-NNODIW4U.js";
81
- import "../chunks/chunk-6SBUFFTB.js";
82
- import {
83
- HPRC_GBZ,
84
- cutGbzRegion,
85
- haplotypeIndexBeside,
86
- openGbz,
87
- parseRegion
88
- } from "../chunks/chunk-73RSLGZT.js";
89
- import "../chunks/chunk-LTUWJKHD.js";
90
- import "../chunks/chunk-WSIFAZU7.js";
91
- import {
92
- featuresOnBackbone,
93
- graphBackbone,
94
- refNameBinding
95
- } from "../chunks/chunk-RAKOB6IV.js";
96
- import "../chunks/chunk-BPLIXMH7.js";
97
98
  import "../chunks/chunk-FYQWPEEY.js";
98
99
 
99
100
  // src/cli/figure.ts
@@ -241,19 +242,7 @@ async function renderSpec(spec, base) {
241
242
  const graph = loadGraph(source.text, source.name, {
242
243
  referencePath: spec.referencePath
243
244
  });
244
- const layout = layoutModeByValue(spec.layout ?? "force").run(graph, source.region) ?? (await forceLayout(
245
- graph,
246
- {
247
- quality: spec.quality ?? 2,
248
- linearLayout: false,
249
- bubbleSpread: spec.bubbleSpread ?? "auto",
250
- engine: spec.engine,
251
- spacing: spec.spacing,
252
- componentSeparation: spec.componentSeparation,
253
- showDeletionEdges: spec.showDeletionEdges
254
- },
255
- layoutEngine
256
- )).result;
245
+ const layout = layoutModeByValue(spec.layout ?? "force").run(graph, source.region) ?? (await forceLayout(graph, engineSettingsOf(spec), layoutEngine)).result;
257
246
  const bars = spec.walkStrip ? walkRows(graph, source.region) : void 0;
258
247
  const stripRows = bars && {
259
248
  ...bars,
package/dist/figure.js CHANGED
@@ -1,51 +1,51 @@
1
1
  import {
2
2
  figureSvg
3
- } from "./chunks/chunk-QMJ4J5PT.js";
3
+ } from "./chunks/chunk-45J7P6YW.js";
4
+ import "./chunks/chunk-HPIZNWF7.js";
4
5
  import "./chunks/chunk-CH3DLBUT.js";
5
6
  import "./chunks/chunk-4BYTEJGW.js";
6
7
  import "./chunks/chunk-47DYCZOK.js";
7
- import "./chunks/chunk-KREASK3Z.js";
8
- import "./chunks/chunk-UGD6ZMOF.js";
8
+ import "./chunks/chunk-RCPGXIWA.js";
9
9
  import "./chunks/chunk-3S3YVOJ7.js";
10
10
  import "./chunks/chunk-BUBZ32IC.js";
11
- import "./chunks/chunk-S73EYTZA.js";
12
- import "./chunks/chunk-Y7UR3MDE.js";
13
- import "./chunks/chunk-MH5IA57M.js";
14
- import "./chunks/chunk-TQ7VCGJR.js";
11
+ import "./chunks/chunk-36UKA6RQ.js";
15
12
  import "./chunks/chunk-2LQ5BWT7.js";
16
- import "./chunks/chunk-EPWYRSHH.js";
17
- import "./chunks/chunk-PUG7LXDF.js";
18
- import "./chunks/chunk-IGVV37VI.js";
19
- import "./chunks/chunk-72N5DJHZ.js";
20
- import "./chunks/chunk-QYBZZI5H.js";
21
- import "./chunks/chunk-CDLPYR5O.js";
22
- import "./chunks/chunk-VECR253P.js";
23
- import "./chunks/chunk-VST5SR4C.js";
13
+ import "./chunks/chunk-Z3OHBOEA.js";
14
+ import "./chunks/chunk-ERHAGG72.js";
15
+ import "./chunks/chunk-AGJZ5RDC.js";
16
+ import "./chunks/chunk-C4IUUTAB.js";
17
+ import "./chunks/chunk-W7R55CIZ.js";
24
18
  import "./chunks/chunk-UMNCCYBN.js";
25
19
  import "./chunks/chunk-PBENCR5L.js";
20
+ import "./chunks/chunk-RAKOB6IV.js";
26
21
  import "./chunks/chunk-GJMC3PGM.js";
27
22
  import "./chunks/chunk-FP4H7SFT.js";
28
23
  import "./chunks/chunk-MLSWIMZO.js";
29
24
  import "./chunks/chunk-WFB5TXRA.js";
30
- import "./chunks/chunk-JVLURPFW.js";
31
25
  import "./chunks/chunk-3JANT2SW.js";
32
26
  import "./chunks/chunk-SZNZ2T6D.js";
33
- import "./chunks/chunk-E7FWQQHP.js";
34
- import "./chunks/chunk-ES2N6V56.js";
35
- import "./chunks/chunk-ST2IBUAN.js";
27
+ import "./chunks/chunk-7GBL7SJY.js";
36
28
  import "./chunks/chunk-3ZZSX5HN.js";
37
29
  import "./chunks/chunk-AB35TJST.js";
30
+ import "./chunks/chunk-JKJWSY4V.js";
31
+ import "./chunks/chunk-NNODIW4U.js";
32
+ import "./chunks/chunk-6SBUFFTB.js";
33
+ import "./chunks/chunk-SGAMPIKO.js";
34
+ import "./chunks/chunk-PUG7LXDF.js";
35
+ import "./chunks/chunk-IGVV37VI.js";
36
+ import "./chunks/chunk-72N5DJHZ.js";
37
+ import "./chunks/chunk-QYBZZI5H.js";
38
+ import "./chunks/chunk-CDLPYR5O.js";
39
+ import "./chunks/chunk-JVLURPFW.js";
40
+ import "./chunks/chunk-ES2N6V56.js";
41
+ import "./chunks/chunk-ST2IBUAN.js";
42
+ import "./chunks/chunk-BPLIXMH7.js";
38
43
  import "./chunks/chunk-TAMCZHLW.js";
39
44
  import "./chunks/chunk-UVBGRJQX.js";
40
45
  import "./chunks/chunk-6JEWNXCQ.js";
41
- import "./chunks/chunk-JKJWSY4V.js";
42
46
  import "./chunks/chunk-N6FECAXP.js";
43
47
  import "./chunks/chunk-2CVHXFK7.js";
44
48
  import "./chunks/chunk-CPMHA4W5.js";
45
- import "./chunks/chunk-NNODIW4U.js";
46
- import "./chunks/chunk-6SBUFFTB.js";
47
- import "./chunks/chunk-RAKOB6IV.js";
48
- import "./chunks/chunk-BPLIXMH7.js";
49
49
  import "./chunks/chunk-FYQWPEEY.js";
50
50
  export {
51
51
  figureSvg