@jbrowse/bandage-core 11.7.0 → 11.7.3
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 +58 -40
- package/dist/bubbles/bubbleHalos.js +5 -4
- package/dist/bubbles/classifyBubble.js +4 -3
- package/dist/bubbles/superbubbles.js +6 -5
- package/dist/chunks/{chunk-YEYQFNFQ.js → chunk-2T3V6Z3M.js} +1 -1
- package/dist/chunks/{chunk-6YRSOL4K.js → chunk-2US43KNG.js} +1 -1
- package/dist/chunks/{chunk-OYCQVJYY.js → chunk-33KUO34R.js} +1 -1
- package/dist/chunks/{chunk-KJDERUQF.js → chunk-4KOYS5WR.js} +44 -9
- package/dist/chunks/{chunk-NTKWT6XL.js → chunk-4SN7R4UF.js} +1 -1
- package/dist/chunks/{chunk-SIA75TEG.js → chunk-63XWYNID.js} +1 -1
- package/dist/chunks/{chunk-2XEAITWM.js → chunk-6RB5ZQ34.js} +1 -1
- package/dist/chunks/{chunk-ZHZRAYEM.js → chunk-AJQRKN3X.js} +1 -1
- package/dist/chunks/{chunk-SNF2MIEF.js → chunk-AWJJSA7D.js} +1 -1
- package/dist/chunks/{chunk-KZMSSPS6.js → chunk-BLDUBB7X.js} +1 -1
- package/dist/chunks/{chunk-IJCSW6MV.js → chunk-CL6ELLVF.js} +1 -1
- package/dist/chunks/{chunk-A7Q7RTWX.js → chunk-EPOPGV5G.js} +1 -1
- package/dist/chunks/{chunk-5ZQKQ24Z.js → chunk-F4CDC72I.js} +1 -1
- package/dist/chunks/{chunk-BW2NMXRV.js → chunk-GD6RUZU5.js} +1 -1
- package/dist/chunks/{chunk-GZ36HNPJ.js → chunk-IHM43Y7B.js} +1 -1
- package/dist/chunks/{chunk-DTEXQ65J.js → chunk-K4KVAMEF.js} +1 -1
- package/dist/chunks/{chunk-C6E6HXP5.js → chunk-KMLATBNT.js} +2 -2
- package/dist/chunks/{chunk-56L6R6D2.js → chunk-LH436HS2.js} +1 -1
- package/dist/chunks/{chunk-T3H5ELLA.js → chunk-N73RA4DR.js} +1 -1
- package/dist/chunks/{chunk-DV5B5UU7.js → chunk-P276TWPM.js} +6 -2
- package/dist/chunks/{chunk-HELOUO6K.js → chunk-PKGPSTRW.js} +1 -1
- package/dist/chunks/{chunk-KA4F3N55.js → chunk-QJC63NFR.js} +2 -2
- package/dist/chunks/{chunk-QCOVHLJO.js → chunk-QLLKALSH.js} +1 -1
- package/dist/chunks/{chunk-HERVZPWA.js → chunk-QXBQDHKL.js} +11 -11
- package/dist/chunks/{chunk-SVPR7IZO.js → chunk-SG7VQB4F.js} +1 -1
- package/dist/chunks/{chunk-EH5JZETS.js → chunk-T3MEG5D3.js} +7 -7
- package/dist/chunks/chunk-TLWXLNLY.js +124 -0
- package/dist/chunks/{chunk-WWIUC4N4.js → chunk-UTDMFVC7.js} +7 -7
- package/dist/chunks/{chunk-DD5EZG3T.js → chunk-VNF236GG.js} +1 -1
- package/dist/chunks/{chunk-JGHZ3N34.js → chunk-VXKL2ZLR.js} +2 -2
- package/dist/chunks/{chunk-VO6FKNZE.js → chunk-W5YRBEWQ.js} +1 -1
- package/dist/chunks/{chunk-YER6TUXV.js → chunk-XKPXOIWD.js} +2 -2
- package/dist/chunks/{chunk-65YCFVS4.js → chunk-XTCIKBWM.js} +1 -1
- package/dist/chunks/{chunk-DUREQSOJ.js → chunk-Z4HXW6ZH.js} +2 -2
- package/dist/chunks/{chunk-3PZSBNLI.js → chunk-ZZZ6NVLW.js} +19 -14
- package/dist/cli/figure.js +24 -23
- package/dist/cli/fold.js +5 -4
- package/dist/deletionEdges.js +2 -1
- package/dist/figure.js +21 -20
- package/dist/figureData.js +18 -17
- package/dist/figureScene.js +13 -12
- package/dist/figureSettings.js +5 -4
- package/dist/foldVariants.js +1 -1
- package/dist/graphLabels.js +3 -2
- package/dist/index.js +33 -32
- package/dist/labelLayout.js +7 -6
- package/dist/layout/forceCache.js +5 -4
- package/dist/layout/orientToReference.js +3 -1
- package/dist/layout/trimToWindow.js +9 -101
- package/dist/layout/tubeMapLayout.js +5 -4
- package/dist/layout/walkRowDraw.js +7 -6
- package/dist/layout/walkStrip.js +8 -7
- package/dist/layoutModes.js +6 -5
- package/dist/pathColors.js +4 -3
- package/dist/pipeline.js +4 -3
- package/dist/referenceStrip.js +7 -6
- package/dist/renderer/GeometryBuilder.js +6 -5
- package/dist/tubeMap/axis.js +4 -3
- package/dist/tubeMap/bundle.js +6 -5
- package/dist/tubeMap/coarsen.js +6 -5
- package/dist/tubeMap/deviations.js +7 -6
- package/dist/tubeMap/genes.js +5 -4
- package/dist/tubeMap/nodeColors.js +7 -6
- package/dist/types/deletionEdges.d.ts +1 -1
- package/dist/types/foldVariants.d.ts +3 -1
- package/dist/types/layout/trimToWindow.d.ts +1 -0
- package/dist/types/types.d.ts +5 -0
- package/dist/types/version.d.ts +1 -1
- package/dist/util/SpatialIndex.js +4 -3
- package/dist/util/edgeCurves.js +3 -2
- package/dist/util/hitDetection.js +5 -4
- package/dist/version.js +1 -1
- package/dist/viewport.js +5 -4
- package/dist/walkEncoding.js +7 -6
- package/dist/walkHighlight.js +8 -7
- package/dist/walkKey.js +4 -3
- package/package.json +1 -1
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import {
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pathOrigin,
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trimOrigins
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PathVisitsBuilder
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} from "./chunk-ZPZ7GNBT.js";
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import {
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isBackbone,
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overlapsWindow
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// src/layout/trimToWindow.ts
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function trimToWindow(graph, window) {
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const inWindow = new Set(
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);
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(span, i) => span?.first === 0 && span.last === paths[i].nodeIds.length - 1
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)) {
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return graph;
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}
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const kept = /* @__PURE__ */ new Set();
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const trimmed = [];
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const stretches = /* @__PURE__ */ new Map();
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paths.forEach((path, i) => {
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const nodeIds = path.nodeIds.slice(span.first, span.last + 1);
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kept.add(id);
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}
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trimmed.push({ ...path, nodeIds });
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stretches.set(path.name, { first: span.first, nodeIds });
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return {
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...graph,
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nodes: graph.nodes.filter((n) => kept.has(n.id)),
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edges: graph.edges.filter((e) => kept.has(e.from) && kept.has(e.to)),
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paths: trimmed,
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pathVisits: graph.pathVisits && trimVisits(
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graph.pathVisits,
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paths,
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spans,
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new Map(graph.nodes.map((n) => [n.id, n.name]))
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anchorPaths: trimOrigins(graph, stretches)
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function trimVisits(visits, paths, spans, nameOf) {
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segment,
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visits.paths[origin],
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visits.start[at],
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visits.reversed[at] === 1
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function clipToWindow(graph, window, reachBp) {
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const [start, end] = overlapsWindow(node, window) ? [Math.max(from, window.start), Math.min(to, window.end)] : to <= window.start ? [Math.max(from, to - reachBp), to] : [from, Math.min(to, from + reachBp)];
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export {
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CHANGED
|
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7
|
} from "../chunks/chunk-O4EGE27I.js";
|
|
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|
import {
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|
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|
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CHANGED
|
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3
|
deletionDrawing,
|
|
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|
deletionEdges,
|
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5
|
edgeCurvesOf
|
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CHANGED
|
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|
|
|
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1
|
import {
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|
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|
figureSvg
|
|
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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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|
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package/dist/figureData.js
CHANGED
|
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|
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|
laidOutGraph,
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|
walkLayers
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+
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import "./chunks/chunk-JKJWSY4V.js";
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-
import "./chunks/chunk-
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+
import "./chunks/chunk-P276TWPM.js";
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+
import "./chunks/chunk-TLWXLNLY.js";
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import "./chunks/chunk-3YBP46PB.js";
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import "./chunks/chunk-VACK24HF.js";
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import "./chunks/chunk-CPMHA4W5.js";
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package/dist/figureScene.js
CHANGED
|
@@ -1,23 +1,23 @@
|
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1
1
|
import {
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|
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2
|
figureScene
|
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-
} from "./chunks/chunk-
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+
} from "./chunks/chunk-UTDMFVC7.js";
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import "./chunks/chunk-LOCJN3BZ.js";
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-
import "./chunks/chunk-
|
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-
import "./chunks/chunk-
|
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-
import "./chunks/chunk-
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5
|
+
import "./chunks/chunk-Z4HXW6ZH.js";
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|
+
import "./chunks/chunk-6RB5ZQ34.js";
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+
import "./chunks/chunk-VXKL2ZLR.js";
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|
import "./chunks/chunk-G2FD7S3C.js";
|
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|
-
import "./chunks/chunk-
|
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+
import "./chunks/chunk-SG7VQB4F.js";
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import "./chunks/chunk-GQZVR5DW.js";
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-
import "./chunks/chunk-
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+
import "./chunks/chunk-33KUO34R.js";
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import "./chunks/chunk-SENPGW4O.js";
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import "./chunks/chunk-BXE3SBBN.js";
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import "./chunks/chunk-G7SG4XMK.js";
|
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|
-
import "./chunks/chunk-
|
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+
import "./chunks/chunk-GD6RUZU5.js";
|
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|
import "./chunks/chunk-ZANALBSX.js";
|
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-
import "./chunks/chunk-
|
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-
import "./chunks/chunk-
|
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+
import "./chunks/chunk-4SN7R4UF.js";
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+
import "./chunks/chunk-XKPXOIWD.js";
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|
import "./chunks/chunk-OPPVSPEF.js";
|
|
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-
import "./chunks/chunk-
|
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+
import "./chunks/chunk-ZZZ6NVLW.js";
|
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|
import "./chunks/chunk-CKUVEHSS.js";
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22
|
import "./chunks/chunk-VPE4AYP7.js";
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23
|
import "./chunks/chunk-TUMJNAOL.js";
|
|
@@ -28,14 +28,15 @@ import "./chunks/chunk-VX656OAZ.js";
|
|
|
28
28
|
import "./chunks/chunk-5ORP7EFJ.js";
|
|
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|
import "./chunks/chunk-VSSIYQYF.js";
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|
import "./chunks/chunk-LG2UK4MB.js";
|
|
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|
-
import "./chunks/chunk-
|
|
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|
+
import "./chunks/chunk-N73RA4DR.js";
|
|
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32
|
import "./chunks/chunk-HMXCN6PG.js";
|
|
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33
|
import "./chunks/chunk-AB35TJST.js";
|
|
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34
|
import "./chunks/chunk-2VMKQKVO.js";
|
|
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35
|
import "./chunks/chunk-HKYXWZQS.js";
|
|
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36
|
import "./chunks/chunk-34BOZKIE.js";
|
|
37
37
|
import "./chunks/chunk-JKJWSY4V.js";
|
|
38
|
-
import "./chunks/chunk-
|
|
38
|
+
import "./chunks/chunk-P276TWPM.js";
|
|
39
|
+
import "./chunks/chunk-TLWXLNLY.js";
|
|
39
40
|
import "./chunks/chunk-3YBP46PB.js";
|
|
40
41
|
import "./chunks/chunk-VACK24HF.js";
|
|
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42
|
import "./chunks/chunk-CPMHA4W5.js";
|
package/dist/figureSettings.js
CHANGED
|
@@ -1,10 +1,10 @@
|
|
|
1
1
|
import {
|
|
2
2
|
FIGURE_DEFAULTS,
|
|
3
3
|
figureSpecSettings
|
|
4
|
-
} from "./chunks/chunk-
|
|
5
|
-
import "./chunks/chunk-
|
|
4
|
+
} from "./chunks/chunk-4SN7R4UF.js";
|
|
5
|
+
import "./chunks/chunk-XKPXOIWD.js";
|
|
6
6
|
import "./chunks/chunk-OPPVSPEF.js";
|
|
7
|
-
import "./chunks/chunk-
|
|
7
|
+
import "./chunks/chunk-ZZZ6NVLW.js";
|
|
8
8
|
import "./chunks/chunk-CKUVEHSS.js";
|
|
9
9
|
import "./chunks/chunk-VPE4AYP7.js";
|
|
10
10
|
import "./chunks/chunk-TUMJNAOL.js";
|
|
@@ -17,7 +17,8 @@ import "./chunks/chunk-LG2UK4MB.js";
|
|
|
17
17
|
import "./chunks/chunk-2VMKQKVO.js";
|
|
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18
|
import "./chunks/chunk-HKYXWZQS.js";
|
|
19
19
|
import "./chunks/chunk-34BOZKIE.js";
|
|
20
|
-
import "./chunks/chunk-
|
|
20
|
+
import "./chunks/chunk-P276TWPM.js";
|
|
21
|
+
import "./chunks/chunk-TLWXLNLY.js";
|
|
21
22
|
import "./chunks/chunk-3YBP46PB.js";
|
|
22
23
|
import "./chunks/chunk-VACK24HF.js";
|
|
23
24
|
import "./chunks/chunk-CPMHA4W5.js";
|