@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.
- package/README.md +3 -0
- package/dist/bubbles/popBubble.js +2 -2
- package/dist/bubbles/superbubbles.js +3 -3
- package/dist/chunks/{chunk-IFOZFVZK.js → chunk-4R6QNG23.js} +2 -2
- package/dist/chunks/{chunk-KJYSOHVN.js → chunk-5BGP5Z64.js} +1 -1
- package/dist/chunks/{chunk-VOWI544A.js → chunk-ALDGONEI.js} +1 -1
- package/dist/chunks/{chunk-3XE3OUEN.js → chunk-C7MZJSPT.js} +1 -1
- package/dist/chunks/{chunk-FFFYXMOP.js → chunk-CFPER2S2.js} +10 -10
- package/dist/chunks/{chunk-CFNFT4RA.js → chunk-CRTD2SBP.js} +1 -1
- package/dist/chunks/{chunk-IM4SJUPO.js → chunk-DK5P2YOL.js} +2 -2
- package/dist/chunks/{chunk-BEWLQADP.js → chunk-FNGIQF43.js} +1 -1
- package/dist/chunks/{chunk-OEPCRURR.js → chunk-GNTTI6LA.js} +1 -1
- package/dist/chunks/{chunk-HQ2AHRMH.js → chunk-IUDJKOLB.js} +1 -1
- package/dist/chunks/{chunk-QXAB2FLJ.js → chunk-IW6CYVX2.js} +1 -1
- package/dist/chunks/{chunk-QORSYW7J.js → chunk-L5WF4ZPS.js} +1 -1
- package/dist/chunks/{chunk-EMUUNWRU.js → chunk-M6LK4GII.js} +7 -1
- package/dist/chunks/{chunk-ZR7A7DKQ.js → chunk-MVFDSFV2.js} +1 -1
- package/dist/chunks/{chunk-KY4LV2Z6.js → chunk-MZIOBJZB.js} +1 -1
- package/dist/chunks/{chunk-FG762CCP.js → chunk-PKFMP65V.js} +2 -2
- package/dist/chunks/{chunk-QIVPRZ4H.js → chunk-R456ME6J.js} +2 -2
- package/dist/chunks/{chunk-A647OH7N.js → chunk-RIPAA7OK.js} +1 -1
- package/dist/chunks/{chunk-WI7ZHJ27.js → chunk-RPDXZLCG.js} +2 -2
- package/dist/chunks/{chunk-NP356MC2.js → chunk-SBMJNRTV.js} +1 -1
- package/dist/chunks/{chunk-4QTNXTGW.js → chunk-T6V4KI2L.js} +1 -1
- package/dist/chunks/{chunk-REE4GUDM.js → chunk-TWRLC3KK.js} +1 -1
- package/dist/chunks/{chunk-AZJF2PZE.js → chunk-VIERZJO2.js} +7 -7
- package/dist/chunks/{chunk-MSX3BDO4.js → chunk-XTCNEKO5.js} +2 -2
- package/dist/chunks/{chunk-VZNKA3K2.js → chunk-XYP6WL2N.js} +7 -3
- package/dist/chunks/{chunk-B4645SM2.js → chunk-YPYWYPHX.js} +3 -3
- package/dist/chunks/{chunk-DCJC32QW.js → chunk-ZIUKZUPJ.js} +1 -1
- package/dist/cli/figure.js +17 -17
- package/dist/cli/fold.js +4 -4
- package/dist/figure.js +15 -15
- package/dist/figureData.js +14 -14
- package/dist/figureSettings.js +4 -4
- package/dist/foldVariants.js +1 -1
- package/dist/gfa/gfaConverter.js +2 -2
- package/dist/index.js +26 -26
- package/dist/layout/forceCache.js +4 -4
- package/dist/layout/trimToWindow.js +1 -1
- package/dist/layout/tubeMapLayout.js +3 -3
- package/dist/layout/walkRowDraw.js +5 -5
- package/dist/layout/walkRowLayout.js +3 -3
- package/dist/layout/walkRows.js +2 -2
- package/dist/layout/walkStrip.js +6 -6
- package/dist/layoutModes.js +6 -6
- package/dist/pathAnchoring.js +1 -1
- package/dist/pathColors.js +2 -2
- package/dist/pipeline.js +3 -3
- package/dist/referenceRampCss.js +4 -4
- package/dist/referenceStrip.js +4 -4
- package/dist/renderer/GeometryBuilder.js +3 -3
- package/dist/tubeMap/bundle.js +4 -4
- package/dist/tubeMap/coarsen.js +3 -3
- package/dist/tubeMap/draw.js +2 -2
- package/dist/tubeMap/nodeColors.js +4 -4
- package/dist/types/version.d.ts +1 -1
- package/dist/version.js +1 -1
- package/dist/viewport.js +4 -4
- package/dist/walkEncoding.js +4 -4
- package/dist/walkHighlight.js +5 -5
- package/package.json +1 -1
package/README.md
CHANGED
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@@ -25,6 +25,9 @@ npm install @jbrowse/bandage-core
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and the `bandage-figure` CLI makes one from a JSON spec with no browser:
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`npx -p @jbrowse/bandage-core bandage-figure spec.json -o figure.svg`. See
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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
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reference, so a graph track draws a whole chromosome. See
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[docs/coarse-tier.md](docs/coarse-tier.md)
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- Figure data: `figureData` returns what `figureSvg` would paint as columnar
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tables, for another graphics system to draw;
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[ggbandage](https://github.com/GMOD/ggbandage) draws them in ggplot2
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@@ -1,7 +1,7 @@
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import {
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bubbleSubgraph
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} from "../chunks/chunk-
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import "../chunks/chunk-
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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";
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@@ -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-
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} from "../chunks/chunk-FNGIQF43.js";
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import "../chunks/chunk-CLOP7UVD.js";
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import "../chunks/chunk-
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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-
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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";
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@@ -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-
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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";
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} from "./chunk-HNQPEMYE.js";
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import {
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walkRowLayout
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} from "./chunk-
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} from "./chunk-C7MZJSPT.js";
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import {
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isBackbone,
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isOffReference
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stripGeneGaps,
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walkStripFrame,
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walkStripLabelsTree
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} from "./chunk-
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} from "./chunk-RPDXZLCG.js";
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import {
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Canvas2DRenderer
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} from "./chunk-WBCOREDZ.js";
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walkRowsKey,
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walkRowsKeyTree,
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walkRowsTree
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} from "./chunk-
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} from "./chunk-XYP6WL2N.js";
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import {
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EXON_COLOR,
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exonOutlineTree,
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} from "./chunk-LOCJN3BZ.js";
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import {
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version
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} from "./chunk-
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} from "./chunk-MZIOBJZB.js";
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import {
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axisScaleOf
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} from "./chunk-
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} from "./chunk-L5WF4ZPS.js";
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import {
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facetLifts,
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walkLift
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} from "./chunk-
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} from "./chunk-R456ME6J.js";
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import {
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encodingStops
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} from "./chunk-
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} from "./chunk-ALDGONEI.js";
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import {
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rangeText,
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walkKey
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import {
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buildGeometry,
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computeReferenceRamp
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} from "./chunk-
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} from "./chunk-SBMJNRTV.js";
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import {
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walkRowLabels,
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walkRowsExtent
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} from "./chunk-
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} from "./chunk-C7MZJSPT.js";
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import {
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walkLabelsOf
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} from "./chunk-
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} from "./chunk-TWRLC3KK.js";
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import {
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nodeInk
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} from "./chunk-PBENCR5L.js";
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FIT_PADDING,
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fitTransform
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} from "./chunk-
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} from "./chunk-XTCNEKO5.js";
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import {
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// src/pathAnchoring.ts
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var RANGE_SUFFIX = /:(\d+)-\d+$/;
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var VG_FRAGMENT = /^([^#]*#[^#]*#[^#[]*)#(\d+)(?:\[(\d+)-\d+\])?$/;
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var VG_SUBRANGE = /\[(\d+)-\d+\]$/;
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function pathOrigin(pathName) {
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const
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const fragment = VG_FRAGMENT.exec(pathName);
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if (fragment) {
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return { name: fragment[1], start: +fragment[2] + +(fragment[3] ?? 0) };
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@@ -42,7 +46,7 @@ function walkRowReadout(row, reference, unit, call) {
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42
46
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const called = call ? ` \xB7 called ${kb(call.bp)}${call.spanningReads === 0 ? " \xB7 no spanning read" : ""}` : "";
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if (complete) {
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const delta = bp - reference.bp;
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45
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-
const against = delta === 0 ? "" : ` (${
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+
const against = delta === 0 ? "" : ` (${signedLength(delta)})`;
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return `${kb(bp)}${units(bp, unit)}${against}${outside}${called}`;
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}
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const region = unit ? "repeat" : "window";
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@@ -173,7 +173,7 @@ function nearestOutside(i, side, links, allele, dist, nodes) {
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let best;
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for (const link of links[i]) {
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const j = link.other;
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-
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].
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|
+
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)) {
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best = j;
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}
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}
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@@ -183,7 +183,7 @@ function distancesFromBackbone(nodes, links) {
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const dist = new Float64Array(nodes.length).fill(Infinity);
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const pred = new Int32Array(nodes.length).fill(-1);
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const heap = new MinHeap(
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-
([da, a], [db, b]) => da - db || cmp(nodes[a].
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+
([da, a], [db, b]) => da - db || cmp(nodes[a].name, nodes[b].name)
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);
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nodes.forEach((node, i) => {
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if (isBackbone(node)) {
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@@ -205,7 +205,7 @@ function distancesFromBackbone(nodes, links) {
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dist[other] = d;
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pred[other] = i;
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heap.push([d, other]);
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-
} else if (d === dist[other] && cmp(nodes[i].
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+
} else if (d === dist[other] && cmp(nodes[i].name, nodes[pred[other]].name) < 0) {
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pred[other] = i;
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}
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}
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package/dist/cli/figure.js
CHANGED
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@@ -6,18 +6,18 @@ import {
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6
6
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} from "../chunks/chunk-BXEPA4KS.js";
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import {
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figureSvg
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-
} from "../chunks/chunk-
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+
} from "../chunks/chunk-CFPER2S2.js";
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import "../chunks/chunk-47DYCZOK.js";
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-
import "../chunks/chunk-
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+
import "../chunks/chunk-RPDXZLCG.js";
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import "../chunks/chunk-WBCOREDZ.js";
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import "../chunks/chunk-4BYTEJGW.js";
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import {
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genesOnRow,
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placeRowGenes
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-
} from "../chunks/chunk-
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+
} from "../chunks/chunk-XYP6WL2N.js";
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import "../chunks/chunk-3S3YVOJ7.js";
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import "../chunks/chunk-BUBZ32IC.js";
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-
import "../chunks/chunk-
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+
import "../chunks/chunk-ZIUKZUPJ.js";
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import "../chunks/chunk-DRG4236Y.js";
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import "../chunks/chunk-FP4H7SFT.js";
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import "../chunks/chunk-MLSWIMZO.js";
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@@ -30,9 +30,9 @@ import {
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import {
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LAYOUT_MODES,
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|
layoutModeByValue
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-
} from "../chunks/chunk-
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+
} from "../chunks/chunk-4R6QNG23.js";
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import "../chunks/chunk-LOEA5IHZ.js";
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-
import "../chunks/chunk-
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+
import "../chunks/chunk-DK5P2YOL.js";
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import "../chunks/chunk-CWFNEKST.js";
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import "../chunks/chunk-L3O7AWLI.js";
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import "../chunks/chunk-TZFWUT2C.js";
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@@ -50,35 +50,35 @@ import {
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import "../chunks/chunk-Q7LYHGGQ.js";
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import "../chunks/chunk-WSIFAZU7.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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-
import "../chunks/chunk-
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+
import "../chunks/chunk-MZIOBJZB.js";
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+
import "../chunks/chunk-L5WF4ZPS.js";
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+
import "../chunks/chunk-R456ME6J.js";
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+
import "../chunks/chunk-ALDGONEI.js";
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import "../chunks/chunk-2LQ5BWT7.js";
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-
import "../chunks/chunk-
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+
import "../chunks/chunk-SBMJNRTV.js";
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import "../chunks/chunk-G2FD7S3C.js";
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|
import "../chunks/chunk-WFB5TXRA.js";
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-
import "../chunks/chunk-
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+
import "../chunks/chunk-C7MZJSPT.js";
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|
import {
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|
filterSamples,
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|
walkRows
|
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|
-
} from "../chunks/chunk-
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|
-
import "../chunks/chunk-
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|
+
} from "../chunks/chunk-RIPAA7OK.js";
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|
+
import "../chunks/chunk-TWRLC3KK.js";
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|
import "../chunks/chunk-PBENCR5L.js";
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import {
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69
|
engineSettingsOf,
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70
70
|
forceLayout,
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|
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71
|
loadGraph
|
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72
|
-
} from "../chunks/chunk-
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|
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|
+
} from "../chunks/chunk-XTCNEKO5.js";
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|
import "../chunks/chunk-IGVV37VI.js";
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import "../chunks/chunk-OPPVSPEF.js";
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import "../chunks/chunk-VPE4AYP7.js";
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import "../chunks/chunk-PUG7LXDF.js";
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-
import "../chunks/chunk-
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+
import "../chunks/chunk-IW6CYVX2.js";
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|
import "../chunks/chunk-QYBZZI5H.js";
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import "../chunks/chunk-PSMKPSO4.js";
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|
import "../chunks/chunk-CDLPYR5O.js";
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-
import "../chunks/chunk-
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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-ES2N6V56.js";
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84
|
import {
|
package/dist/cli/fold.js
CHANGED
|
@@ -4,19 +4,19 @@ import {
|
|
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4
4
|
} from "../chunks/chunk-B4YH42OP.js";
|
|
5
5
|
import {
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|
6
6
|
foldVariants
|
|
7
|
-
} from "../chunks/chunk-
|
|
7
|
+
} from "../chunks/chunk-YPYWYPHX.js";
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|
8
8
|
import {
|
|
9
9
|
loadGraph
|
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10
|
-
} from "../chunks/chunk-
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10
|
+
} from "../chunks/chunk-XTCNEKO5.js";
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11
|
import "../chunks/chunk-IGVV37VI.js";
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import "../chunks/chunk-OPPVSPEF.js";
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import "../chunks/chunk-VPE4AYP7.js";
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import "../chunks/chunk-PUG7LXDF.js";
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-
import "../chunks/chunk-
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+
import "../chunks/chunk-IW6CYVX2.js";
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import "../chunks/chunk-QYBZZI5H.js";
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import "../chunks/chunk-PSMKPSO4.js";
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|
import "../chunks/chunk-CDLPYR5O.js";
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-
import "../chunks/chunk-
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+
import "../chunks/chunk-M6LK4GII.js";
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20
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import "../chunks/chunk-RAEABQNW.js";
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21
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import "../chunks/chunk-ES2N6V56.js";
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22
|
import "../chunks/chunk-G45YY72K.js";
|
package/dist/figure.js
CHANGED
|
@@ -1,41 +1,41 @@
|
|
|
1
1
|
import {
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|
2
2
|
figureSvg
|
|
3
|
-
} from "./chunks/chunk-
|
|
3
|
+
} from "./chunks/chunk-CFPER2S2.js";
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4
4
|
import "./chunks/chunk-47DYCZOK.js";
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|
5
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-
import "./chunks/chunk-
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5
|
+
import "./chunks/chunk-RPDXZLCG.js";
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6
|
import "./chunks/chunk-WBCOREDZ.js";
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7
|
import "./chunks/chunk-4BYTEJGW.js";
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8
|
-
import "./chunks/chunk-
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|
8
|
+
import "./chunks/chunk-XYP6WL2N.js";
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9
|
import "./chunks/chunk-3S3YVOJ7.js";
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|
import "./chunks/chunk-BUBZ32IC.js";
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-
import "./chunks/chunk-
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|
+
import "./chunks/chunk-ZIUKZUPJ.js";
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|
import "./chunks/chunk-DRG4236Y.js";
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|
import "./chunks/chunk-FP4H7SFT.js";
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import "./chunks/chunk-MLSWIMZO.js";
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|
import "./chunks/chunk-NNODIW4U.js";
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16
|
import "./chunks/chunk-LOCJN3BZ.js";
|
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|
-
import "./chunks/chunk-
|
|
18
|
-
import "./chunks/chunk-
|
|
19
|
-
import "./chunks/chunk-
|
|
20
|
-
import "./chunks/chunk-
|
|
17
|
+
import "./chunks/chunk-MZIOBJZB.js";
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|
18
|
+
import "./chunks/chunk-L5WF4ZPS.js";
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|
+
import "./chunks/chunk-R456ME6J.js";
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|
+
import "./chunks/chunk-ALDGONEI.js";
|
|
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21
|
import "./chunks/chunk-2LQ5BWT7.js";
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|
-
import "./chunks/chunk-
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|
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|
+
import "./chunks/chunk-SBMJNRTV.js";
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|
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23
|
import "./chunks/chunk-G2FD7S3C.js";
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|
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24
|
import "./chunks/chunk-WFB5TXRA.js";
|
|
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|
-
import "./chunks/chunk-
|
|
26
|
-
import "./chunks/chunk-
|
|
27
|
-
import "./chunks/chunk-
|
|
25
|
+
import "./chunks/chunk-C7MZJSPT.js";
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|
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|
+
import "./chunks/chunk-RIPAA7OK.js";
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|
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|
+
import "./chunks/chunk-TWRLC3KK.js";
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|
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28
|
import "./chunks/chunk-PBENCR5L.js";
|
|
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|
-
import "./chunks/chunk-
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|
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|
+
import "./chunks/chunk-XTCNEKO5.js";
|
|
30
30
|
import "./chunks/chunk-IGVV37VI.js";
|
|
31
31
|
import "./chunks/chunk-OPPVSPEF.js";
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|
32
32
|
import "./chunks/chunk-VPE4AYP7.js";
|
|
33
33
|
import "./chunks/chunk-PUG7LXDF.js";
|
|
34
|
-
import "./chunks/chunk-
|
|
34
|
+
import "./chunks/chunk-IW6CYVX2.js";
|
|
35
35
|
import "./chunks/chunk-QYBZZI5H.js";
|
|
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|
import "./chunks/chunk-PSMKPSO4.js";
|
|
37
37
|
import "./chunks/chunk-CDLPYR5O.js";
|
|
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|
-
import "./chunks/chunk-
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|
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|
+
import "./chunks/chunk-M6LK4GII.js";
|
|
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39
|
import "./chunks/chunk-RAEABQNW.js";
|
|
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40
|
import "./chunks/chunk-ES2N6V56.js";
|
|
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41
|
import "./chunks/chunk-RAKOB6IV.js";
|