@jbrowse/bandage-core 9.10.0 → 10.0.1
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.
- package/README.md +20 -0
- package/dist/bubbles/popBubble.js +3 -2
- package/dist/bubbles/superbubbles.js +4 -3
- package/dist/chunks/{chunk-TOVOJNT7.js → chunk-3XE3OUEN.js} +1 -1
- package/dist/chunks/{chunk-A6PSWTLX.js → chunk-4QTNXTGW.js} +1 -1
- package/dist/chunks/chunk-A647OH7N.js +284 -0
- package/dist/chunks/{chunk-NGODVSCA.js → chunk-AZJF2PZE.js} +9 -9
- package/dist/chunks/{chunk-5GZEPPEW.js → chunk-BEWLQADP.js} +1 -1
- package/dist/chunks/{chunk-Q6UIUY6X.js → chunk-CFNFT4RA.js} +1 -1
- package/dist/chunks/{chunk-K5NYTPLC.js → chunk-DCJC32QW.js} +1 -1
- package/dist/chunks/{chunk-IGJCTPFB.js → chunk-EMUUNWRU.js} +52 -43
- package/dist/chunks/{chunk-2FLBFVMO.js → chunk-FFFYXMOP.js} +16 -16
- package/dist/chunks/{chunk-LZWSZRUY.js → chunk-FG762CCP.js} +3 -8
- package/dist/chunks/{chunk-73RSLGZT.js → chunk-FLFBYSJO.js} +1 -1
- package/dist/chunks/{chunk-VK6XMP6B.js → chunk-FLUQODT2.js} +1 -3
- package/dist/chunks/{chunk-PIN7ZMTZ.js → chunk-HQ2AHRMH.js} +1 -1
- package/dist/chunks/{chunk-FUUJ76KD.js → chunk-IFOZFVZK.js} +2 -2
- package/dist/chunks/{chunk-CXKZYLYS.js → chunk-IM4SJUPO.js} +12 -22
- package/dist/chunks/{chunk-BDWQQK33.js → chunk-KJYSOHVN.js} +1 -1
- package/dist/chunks/{chunk-2VTM3DHG.js → chunk-KY4LV2Z6.js} +1 -1
- package/dist/chunks/{chunk-HRAU4VTB.js → chunk-MSX3BDO4.js} +11 -11
- package/dist/chunks/{chunk-4IYP43W6.js → chunk-NP356MC2.js} +1 -1
- package/dist/chunks/{chunk-TFAFIRZB.js → chunk-OEPCRURR.js} +1 -1
- package/dist/chunks/{chunk-OA7RIMZ2.js → chunk-PSMKPSO4.js} +89 -22
- package/dist/chunks/{chunk-LTUWJKHD.js → chunk-Q7LYHGGQ.js} +114 -6
- package/dist/chunks/{chunk-MVMP6AGI.js → chunk-QIVPRZ4H.js} +12 -7
- package/dist/chunks/{chunk-PT37VS5B.js → chunk-QORSYW7J.js} +1 -1
- package/dist/chunks/{chunk-J7YKQ5YW.js → chunk-QXAB2FLJ.js} +1 -1
- package/dist/chunks/chunk-RAEABQNW.js +227 -0
- package/dist/chunks/{chunk-XZ2BLAA6.js → chunk-REE4GUDM.js} +1 -1
- package/dist/chunks/{chunk-KYY5363X.js → chunk-VOWI544A.js} +1 -1
- package/dist/chunks/{chunk-JVLURPFW.js → chunk-VPE4AYP7.js} +1 -2
- package/dist/chunks/{chunk-FJZ2TB46.js → chunk-VZNKA3K2.js} +2 -2
- package/dist/chunks/{chunk-DMH4NL2M.js → chunk-WI7ZHJ27.js} +2 -2
- package/dist/chunks/{chunk-IZI7KIVX.js → chunk-ZR7A7DKQ.js} +1 -1
- package/dist/cli/figure.js +27 -28
- package/dist/cli/fold.js +7 -6
- package/dist/figure.js +20 -19
- package/dist/figureData.js +21 -22
- package/dist/figureSettings.js +8 -7
- package/dist/gbzCut.js +3 -2
- package/dist/gbzWindow.js +6 -1
- package/dist/gfa/gfaConverter.js +3 -2
- package/dist/gfa/graphTables.js +2 -1
- package/dist/index.js +63 -54
- package/dist/layout/deletionRoutes.js +1 -3
- package/dist/layout/forceCache.js +8 -7
- package/dist/layout/trimToWindow.js +17 -23
- package/dist/layout/tubeMapLayout.js +4 -3
- package/dist/layout/walkRowDraw.js +6 -5
- package/dist/layout/walkRowLayout.js +4 -3
- package/dist/layout/walkRows.js +3 -2
- package/dist/layout/walkStrip.js +7 -6
- package/dist/layoutEngines.js +1 -5
- package/dist/layoutModes.js +7 -6
- package/dist/pathAnchoring.js +2 -1
- package/dist/pathColors.js +3 -2
- package/dist/pathVisits.js +8 -0
- package/dist/pipeline.js +7 -6
- package/dist/referenceRampCss.js +5 -4
- package/dist/referenceStrip.js +5 -4
- package/dist/renderer/GeometryBuilder.js +4 -3
- package/dist/tubeMap/bundle.js +5 -4
- package/dist/tubeMap/coarsen.js +15 -13
- package/dist/tubeMap/draw.js +3 -2
- package/dist/tubeMap/nodeColors.js +5 -4
- package/dist/types/gbzWindow.d.ts +15 -1
- package/dist/types/gfa/gfaConverter.d.ts +1 -1
- package/dist/types/index.d.ts +3 -2
- package/dist/types/layout/deletionRoutes.d.ts +1 -2
- package/dist/types/pathAnchoring.d.ts +3 -2
- package/dist/types/pathVisits.d.ts +64 -0
- package/dist/types/types.d.ts +2 -1
- package/dist/types/version.d.ts +1 -1
- package/dist/version.js +1 -1
- package/dist/viewport.js +8 -7
- package/dist/walkEncoding.js +5 -4
- package/dist/walkHighlight.js +6 -5
- package/package.json +2 -1
- package/dist/chunks/chunk-6PYZYBBF.js +0 -226
- package/dist/chunks/chunk-LYJ4US66.js +0 -664
- package/dist/chunks/chunk-Q6FRNVDU.js +0 -531
- package/dist/layout/stressEngine.js +0 -11
- package/dist/layout/stressPlacement.js +0 -7
- package/dist/types/layout/stressEngine.d.ts +0 -27
- package/dist/types/layout/stressPlacement.d.ts +0 -5
package/dist/gfa/graphTables.js
CHANGED
package/dist/index.js
CHANGED
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tubeMapMismatchAt,
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tubeMapPicture,
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tubeMapTrackAt
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} from "./chunks/chunk-
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} from "./chunks/chunk-HQ2AHRMH.js";
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import {
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tubeMapFrame,
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tubeMapNodeAt
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import "./chunks/chunk-XXT2JCAC.js";
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import {
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tubeMapNodeColors
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} from "./chunks/chunk-
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} from "./chunks/chunk-OEPCRURR.js";
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import {
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referenceKnots,
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warpX
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} from "./chunks/chunk-HK5Y2YWV.js";
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import {
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drawTubeMapRuler,
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referenceBoxes,
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rulerBoxes,
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tubeX
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bundleRoutes
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connectorAt,
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drawLitConnector,
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drawTubeMapConnectors,
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tubeMapConnectors
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import {
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drawTubeMapRuler,
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referenceBoxes,
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rulerBoxes,
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tubeX
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} from "./chunks/chunk-BPRXQ2SS.js";
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createForceLayoutCache
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} from "./chunks/chunk-
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} from "./chunks/chunk-CFNFT4RA.js";
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import {
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graphBubbles,
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superbubblesFromGraph
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} from "./chunks/chunk-
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bubbleSubgraph
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import {
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stripBlockAt
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import {
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|
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|
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|
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|
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|
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|
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|
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|
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|
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out.set(segment, [visit]);
|
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}
|
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|
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|
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|
|
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out.add(
|
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|
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|
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visits.paths[origin],
|
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|
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|
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|
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visits.start[at],
|
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|
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visits.reversed[at] === 1
|
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|
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);
|
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|
}
|
|
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|
});
|
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|
|
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|
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return out;
|
|
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|
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return out.build();
|
|
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|
}
|
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|
function clipToWindow(graph, window, reachBp) {
|
|
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|
const nodes = graph.nodes.map((node) => {
|
|
@@ -8,11 +8,12 @@ import {
|
|
|
8
8
|
tubeMapReferenceLayout,
|
|
9
9
|
tubeMapTracks,
|
|
10
10
|
tubeWidth
|
|
11
|
-
} from "../chunks/chunk-
|
|
11
|
+
} from "../chunks/chunk-IM4SJUPO.js";
|
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12
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|
import "../chunks/chunk-CWFNEKST.js";
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import "../chunks/chunk-C44YRP5F.js";
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|
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import "../chunks/chunk-
|
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import "../chunks/chunk-REE4GUDM.js";
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|
import "../chunks/chunk-3ZZSX5HN.js";
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|
import "../chunks/chunk-AB35TJST.js";
|
|
@@ -26,15 +26,16 @@ import {
|
|
|
26
26
|
walkRowsKey,
|
|
27
27
|
walkRowsKeyTree,
|
|
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|
walkRowsTree
|
|
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|
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} from "../chunks/chunk-
|
|
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|
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import "../chunks/chunk-
|
|
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|
+
} from "../chunks/chunk-VZNKA3K2.js";
|
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|
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|
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import "../chunks/chunk-
|
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|
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|
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|
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import "../chunks/chunk-
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|
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import "../chunks/chunk-RAEABQNW.js";
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|
import "../chunks/chunk-ES2N6V56.js";
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40
|
import "../chunks/chunk-BPLIXMH7.js";
|
|
40
41
|
import "../chunks/chunk-3ZZSX5HN.js";
|
|
@@ -2,9 +2,10 @@ import {
|
|
|
2
2
|
walkRowLabels,
|
|
3
3
|
walkRowLayout,
|
|
4
4
|
walkRowsExtent
|
|
5
|
-
} from "../chunks/chunk-
|
|
6
|
-
import "../chunks/chunk-
|
|
7
|
-
import "../chunks/chunk-
|
|
5
|
+
} from "../chunks/chunk-3XE3OUEN.js";
|
|
6
|
+
import "../chunks/chunk-A647OH7N.js";
|
|
7
|
+
import "../chunks/chunk-EMUUNWRU.js";
|
|
8
|
+
import "../chunks/chunk-RAEABQNW.js";
|
|
8
9
|
import "../chunks/chunk-BPLIXMH7.js";
|
|
9
10
|
import "../chunks/chunk-CPMHA4W5.js";
|
|
10
11
|
import "../chunks/chunk-FYQWPEEY.js";
|
package/dist/layout/walkRows.js
CHANGED
|
@@ -1,8 +1,9 @@
|
|
|
1
1
|
import {
|
|
2
2
|
filterSamples,
|
|
3
3
|
walkRows
|
|
4
|
-
} from "../chunks/chunk-
|
|
5
|
-
import "../chunks/chunk-
|
|
4
|
+
} from "../chunks/chunk-A647OH7N.js";
|
|
5
|
+
import "../chunks/chunk-EMUUNWRU.js";
|
|
6
|
+
import "../chunks/chunk-RAEABQNW.js";
|
|
6
7
|
import "../chunks/chunk-BPLIXMH7.js";
|
|
7
8
|
import "../chunks/chunk-FYQWPEEY.js";
|
|
8
9
|
export {
|
package/dist/layout/walkStrip.js
CHANGED
|
@@ -9,18 +9,19 @@ import {
|
|
|
9
9
|
walkStripApplies,
|
|
10
10
|
walkStripFrame,
|
|
11
11
|
walkStripLabelsTree
|
|
12
|
-
} from "../chunks/chunk-
|
|
12
|
+
} from "../chunks/chunk-WI7ZHJ27.js";
|
|
13
13
|
import {
|
|
14
14
|
LABELLED_ROW_PX
|
|
15
|
-
} from "../chunks/chunk-
|
|
16
|
-
import "../chunks/chunk-
|
|
15
|
+
} from "../chunks/chunk-VZNKA3K2.js";
|
|
16
|
+
import "../chunks/chunk-DCJC32QW.js";
|
|
17
17
|
import "../chunks/chunk-NNODIW4U.js";
|
|
18
|
-
import "../chunks/chunk-
|
|
18
|
+
import "../chunks/chunk-NP356MC2.js";
|
|
19
19
|
import "../chunks/chunk-G2FD7S3C.js";
|
|
20
20
|
import "../chunks/chunk-WFB5TXRA.js";
|
|
21
|
-
import "../chunks/chunk-
|
|
21
|
+
import "../chunks/chunk-REE4GUDM.js";
|
|
22
22
|
import "../chunks/chunk-PBENCR5L.js";
|
|
23
|
-
import "../chunks/chunk-
|
|
23
|
+
import "../chunks/chunk-EMUUNWRU.js";
|
|
24
|
+
import "../chunks/chunk-RAEABQNW.js";
|
|
24
25
|
import "../chunks/chunk-ES2N6V56.js";
|
|
25
26
|
import "../chunks/chunk-BPLIXMH7.js";
|
|
26
27
|
import "../chunks/chunk-3ZZSX5HN.js";
|
package/dist/layoutEngines.js
CHANGED
|
@@ -3,12 +3,8 @@ import {
|
|
|
3
3
|
LAYOUT_ENGINE_VALUES,
|
|
4
4
|
isLayoutEngineKind,
|
|
5
5
|
layoutEngine
|
|
6
|
-
} from "./chunks/chunk-
|
|
7
|
-
import "./chunks/chunk-Q6FRNVDU.js";
|
|
8
|
-
import "./chunks/chunk-LYJ4US66.js";
|
|
6
|
+
} from "./chunks/chunk-FLUQODT2.js";
|
|
9
7
|
import "./chunks/chunk-7XHHVYG7.js";
|
|
10
|
-
import "./chunks/chunk-JVLURPFW.js";
|
|
11
|
-
import "./chunks/chunk-FYQWPEEY.js";
|
|
12
8
|
export {
|
|
13
9
|
LAYOUT_ENGINES,
|
|
14
10
|
LAYOUT_ENGINE_VALUES,
|
package/dist/layoutModes.js
CHANGED
|
@@ -4,19 +4,20 @@ import {
|
|
|
4
4
|
LAYOUT_MODE_VALUES,
|
|
5
5
|
layoutModeByValue,
|
|
6
6
|
modeUsesLayoutEngine
|
|
7
|
-
} from "./chunks/chunk-
|
|
7
|
+
} from "./chunks/chunk-IFOZFVZK.js";
|
|
8
8
|
import "./chunks/chunk-LOEA5IHZ.js";
|
|
9
|
-
import "./chunks/chunk-
|
|
9
|
+
import "./chunks/chunk-IM4SJUPO.js";
|
|
10
10
|
import "./chunks/chunk-CWFNEKST.js";
|
|
11
11
|
import "./chunks/chunk-L3O7AWLI.js";
|
|
12
12
|
import "./chunks/chunk-TZFWUT2C.js";
|
|
13
13
|
import "./chunks/chunk-HNQPEMYE.js";
|
|
14
14
|
import "./chunks/chunk-C44YRP5F.js";
|
|
15
15
|
import "./chunks/chunk-RVS2QCOX.js";
|
|
16
|
-
import "./chunks/chunk-
|
|
17
|
-
import "./chunks/chunk-
|
|
18
|
-
import "./chunks/chunk-
|
|
19
|
-
import "./chunks/chunk-
|
|
16
|
+
import "./chunks/chunk-3XE3OUEN.js";
|
|
17
|
+
import "./chunks/chunk-A647OH7N.js";
|
|
18
|
+
import "./chunks/chunk-REE4GUDM.js";
|
|
19
|
+
import "./chunks/chunk-EMUUNWRU.js";
|
|
20
|
+
import "./chunks/chunk-RAEABQNW.js";
|
|
20
21
|
import "./chunks/chunk-ES2N6V56.js";
|
|
21
22
|
import "./chunks/chunk-BPLIXMH7.js";
|
|
22
23
|
import "./chunks/chunk-3ZZSX5HN.js";
|
package/dist/pathAnchoring.js
CHANGED
package/dist/pathColors.js
CHANGED
|
@@ -9,8 +9,9 @@ import {
|
|
|
9
9
|
pathHueAt,
|
|
10
10
|
pathLegend,
|
|
11
11
|
walkLabelsOf
|
|
12
|
-
} from "./chunks/chunk-
|
|
13
|
-
import "./chunks/chunk-
|
|
12
|
+
} from "./chunks/chunk-REE4GUDM.js";
|
|
13
|
+
import "./chunks/chunk-EMUUNWRU.js";
|
|
14
|
+
import "./chunks/chunk-RAEABQNW.js";
|
|
14
15
|
import "./chunks/chunk-BPLIXMH7.js";
|
|
15
16
|
import "./chunks/chunk-3ZZSX5HN.js";
|
|
16
17
|
import "./chunks/chunk-AB35TJST.js";
|
package/dist/pipeline.js
CHANGED
|
@@ -11,18 +11,19 @@ import {
|
|
|
11
11
|
forceLayout,
|
|
12
12
|
layoutExtent,
|
|
13
13
|
loadGraph
|
|
14
|
-
} from "./chunks/chunk-
|
|
14
|
+
} from "./chunks/chunk-MSX3BDO4.js";
|
|
15
15
|
import "./chunks/chunk-IGVV37VI.js";
|
|
16
16
|
import "./chunks/chunk-OPPVSPEF.js";
|
|
17
|
+
import "./chunks/chunk-VPE4AYP7.js";
|
|
17
18
|
import "./chunks/chunk-PUG7LXDF.js";
|
|
18
|
-
import "./chunks/chunk-
|
|
19
|
-
import "./chunks/chunk-G45YY72K.js";
|
|
20
|
-
import "./chunks/chunk-OA7RIMZ2.js";
|
|
19
|
+
import "./chunks/chunk-QXAB2FLJ.js";
|
|
21
20
|
import "./chunks/chunk-QYBZZI5H.js";
|
|
21
|
+
import "./chunks/chunk-PSMKPSO4.js";
|
|
22
22
|
import "./chunks/chunk-CDLPYR5O.js";
|
|
23
|
-
import "./chunks/chunk-
|
|
24
|
-
import "./chunks/chunk-
|
|
23
|
+
import "./chunks/chunk-EMUUNWRU.js";
|
|
24
|
+
import "./chunks/chunk-RAEABQNW.js";
|
|
25
25
|
import "./chunks/chunk-ES2N6V56.js";
|
|
26
|
+
import "./chunks/chunk-G45YY72K.js";
|
|
26
27
|
import "./chunks/chunk-BPLIXMH7.js";
|
|
27
28
|
import "./chunks/chunk-TAMCZHLW.js";
|
|
28
29
|
import "./chunks/chunk-UVBGRJQX.js";
|
package/dist/referenceRampCss.js
CHANGED
|
@@ -4,13 +4,14 @@ import {
|
|
|
4
4
|
rampHue,
|
|
5
5
|
rampHueCss,
|
|
6
6
|
rampStops
|
|
7
|
-
} from "./chunks/chunk-
|
|
8
|
-
import "./chunks/chunk-
|
|
7
|
+
} from "./chunks/chunk-DCJC32QW.js";
|
|
8
|
+
import "./chunks/chunk-NP356MC2.js";
|
|
9
9
|
import "./chunks/chunk-G2FD7S3C.js";
|
|
10
10
|
import "./chunks/chunk-WFB5TXRA.js";
|
|
11
|
-
import "./chunks/chunk-
|
|
11
|
+
import "./chunks/chunk-REE4GUDM.js";
|
|
12
12
|
import "./chunks/chunk-PBENCR5L.js";
|
|
13
|
-
import "./chunks/chunk-
|
|
13
|
+
import "./chunks/chunk-EMUUNWRU.js";
|
|
14
|
+
import "./chunks/chunk-RAEABQNW.js";
|
|
14
15
|
import "./chunks/chunk-ES2N6V56.js";
|
|
15
16
|
import "./chunks/chunk-BPLIXMH7.js";
|
|
16
17
|
import "./chunks/chunk-3ZZSX5HN.js";
|
package/dist/referenceStrip.js
CHANGED
|
@@ -7,13 +7,14 @@ import {
|
|
|
7
7
|
stripBlockAt,
|
|
8
8
|
stripOverhang,
|
|
9
9
|
stripPixels
|
|
10
|
-
} from "./chunks/chunk-
|
|
11
|
-
import "./chunks/chunk-
|
|
10
|
+
} from "./chunks/chunk-KJYSOHVN.js";
|
|
11
|
+
import "./chunks/chunk-NP356MC2.js";
|
|
12
12
|
import "./chunks/chunk-G2FD7S3C.js";
|
|
13
13
|
import "./chunks/chunk-WFB5TXRA.js";
|
|
14
|
-
import "./chunks/chunk-
|
|
14
|
+
import "./chunks/chunk-REE4GUDM.js";
|
|
15
15
|
import "./chunks/chunk-PBENCR5L.js";
|
|
16
|
-
import "./chunks/chunk-
|
|
16
|
+
import "./chunks/chunk-EMUUNWRU.js";
|
|
17
|
+
import "./chunks/chunk-RAEABQNW.js";
|
|
17
18
|
import "./chunks/chunk-ES2N6V56.js";
|
|
18
19
|
import "./chunks/chunk-BPLIXMH7.js";
|
|
19
20
|
import "./chunks/chunk-3ZZSX5HN.js";
|