@jbrowse/bandage-core 11.15.0 → 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.
- package/dist/bubbles/bubbleHalos.js +4 -4
- package/dist/bubbles/classifyBubble.js +3 -3
- package/dist/bubbles/superbubbles.js +5 -5
- package/dist/chunks/{chunk-BDS5VZYZ.js → chunk-2BSGQKF3.js} +1 -1
- package/dist/chunks/{chunk-H2TSYHOA.js → chunk-42MMT5QM.js} +1 -1
- package/dist/chunks/{chunk-XBX3HSC7.js → chunk-47R7GMU3.js} +7 -7
- package/dist/chunks/{chunk-TEFNVUGD.js → chunk-54CX2MCH.js} +1 -1
- package/dist/chunks/{chunk-2AVTTUP2.js → chunk-5LTWXDXK.js} +2 -2
- package/dist/chunks/{chunk-S6E3PMH7.js → chunk-7KVA7TFI.js} +1 -1
- package/dist/chunks/{chunk-P2GJBFNA.js → chunk-AGUBPT45.js} +1 -1
- package/dist/chunks/{chunk-EOB4Y3EM.js → chunk-BDMISSNR.js} +1 -1
- package/dist/chunks/{chunk-EIMRD6L7.js → chunk-CIMRLDRO.js} +1 -1
- package/dist/chunks/{chunk-JUYPCLF4.js → chunk-DTBQNR7P.js} +9 -9
- package/dist/chunks/{chunk-VQ353UDK.js → chunk-EHEIS3TE.js} +1 -1
- package/dist/chunks/{chunk-AURNOR27.js → chunk-ENBFQH7Y.js} +1 -1
- package/dist/chunks/{chunk-RVIRKMQI.js → chunk-FKMZG7HI.js} +27 -10
- package/dist/chunks/{chunk-DOCI5O5R.js → chunk-G3R7LUOS.js} +2 -2
- package/dist/chunks/{chunk-ZHCQOC67.js → chunk-GZ2F2CDT.js} +1 -1
- package/dist/chunks/{chunk-NWEVR2OQ.js → chunk-HYVIQS4D.js} +1 -1
- package/dist/chunks/{chunk-N65FW7LX.js → chunk-IWPINV4U.js} +35 -13
- package/dist/chunks/{chunk-TUMJNAOL.js → chunk-MSVYSCAH.js} +2 -0
- package/dist/chunks/{chunk-IZKM4NY7.js → chunk-OKH32P3Z.js} +1 -1
- package/dist/chunks/{chunk-3GORESBG.js → chunk-OMQWCVOJ.js} +2 -0
- package/dist/chunks/{chunk-K4RGSISK.js → chunk-OND5MXTK.js} +1 -1
- package/dist/chunks/{chunk-OYBYCF2O.js → chunk-PIPNW3VY.js} +1 -1
- package/dist/chunks/{chunk-MB4UWYDG.js → chunk-PL6X2IJC.js} +2 -2
- package/dist/chunks/{chunk-4JDO7ZLN.js → chunk-QWLCHMNS.js} +1 -1
- package/dist/chunks/{chunk-SZYFZNCO.js → chunk-RATN62M3.js} +1 -1
- package/dist/chunks/{chunk-QL673EK5.js → chunk-STUG7I25.js} +1 -1
- package/dist/chunks/{chunk-RT4U3DH3.js → chunk-TICU3HMJ.js} +1 -1
- package/dist/chunks/{chunk-I53QYITQ.js → chunk-TK2ANC2S.js} +1 -1
- package/dist/chunks/{chunk-TQ26XEFL.js → chunk-U6TXPLFJ.js} +2 -2
- package/dist/chunks/{chunk-7YSIP3O2.js → chunk-WTWO2IPM.js} +1 -1
- package/dist/chunks/{chunk-5SW3PTHO.js → chunk-XESCKKKT.js} +1 -1
- package/dist/chunks/chunk-XWH4LB56.js +115 -0
- package/dist/chunks/{chunk-VNCHWWLG.js → chunk-Y5BPNRFM.js} +1 -1
- package/dist/chunks/{chunk-OKPSS5PG.js → chunk-ZZUSCQVT.js} +1 -1
- package/dist/cli/figure.js +24 -24
- package/dist/cli/fold.js +3 -3
- package/dist/deletionEdges.js +3 -1
- package/dist/figure.js +21 -21
- package/dist/figureData.js +18 -18
- package/dist/figureScene.js +13 -13
- package/dist/figureSettings.js +4 -4
- package/dist/gfa/gfaConverter.js +1 -1
- package/dist/graphLabels.js +2 -2
- package/dist/index.js +47 -35
- package/dist/labelLayout.js +6 -6
- package/dist/layout/forceCache.js +4 -4
- package/dist/layout/tubeMapLayout.js +4 -4
- package/dist/layout/walkRowDraw.js +7 -7
- package/dist/layout/walkStrip.js +8 -8
- package/dist/layoutModes.js +5 -5
- package/dist/nodeWidths.js +14 -3
- package/dist/pathColors.js +3 -3
- package/dist/pipeline.js +3 -3
- package/dist/referenceStrip.js +7 -7
- package/dist/renderer/GeometryBuilder.js +6 -6
- package/dist/tubeMap/axis.js +3 -3
- package/dist/tubeMap/bundle.js +5 -5
- package/dist/tubeMap/coarsen.js +5 -5
- package/dist/tubeMap/deviations.js +6 -6
- package/dist/tubeMap/genes.js +4 -4
- package/dist/tubeMap/nodeColors.js +7 -7
- package/dist/types/deletionEdges.d.ts +1 -0
- package/dist/types/figureData.d.ts +13 -0
- package/dist/types/figureScene.d.ts +1 -1
- package/dist/types/index.d.ts +2 -2
- package/dist/types/nodeWidths.d.ts +13 -1
- package/dist/types/types.d.ts +1 -0
- package/dist/types/version.d.ts +1 -1
- package/dist/util/SpatialIndex.js +3 -3
- package/dist/util/edgeCurves.js +2 -2
- package/dist/util/hitDetection.js +4 -4
- package/dist/version.js +1 -1
- package/dist/viewport.js +4 -4
- package/dist/walkEncoding.js +7 -7
- package/dist/walkHighlight.js +8 -8
- package/dist/walkKey.js +3 -3
- package/package.json +1 -1
- package/dist/chunks/chunk-ZANALBSX.js +0 -65
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import {
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panSNHaplotype
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} from "./chunk-2JL2JVZ2.js";
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// src/nodeWidths.ts
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var NODE_WIDTHS = [
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{
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value: "depth",
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label: "By depth",
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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."
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},
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{
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value: "frequency",
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label: "By frequency",
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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."
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},
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{
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value: "uniform",
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label: "Uniform",
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description: "Every node the same thickness."
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}
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];
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var MIN_FACTOR = 0.3;
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var MAX_FACTOR = 3;
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var MIN_FREQUENCY_FACTOR = 0.05;
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function meanDepth(graph) {
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let weighted = 0;
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let length = 0;
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for (const node of graph.nodes) {
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weighted += node.depth * node.length;
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length += node.length;
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}
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return length > 0 ? weighted / length : 0;
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}
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function haplotypeOf(path) {
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return path.sample === void 0 ? panSNHaplotype(path.name) ?? path.name : `${path.sample}#${path.haplotype ?? 0}`;
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}
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function haplotypeCount(graph) {
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return new Set((graph.paths ?? []).map(haplotypeOf)).size;
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}
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function nodeFrequency(node, haplotypes) {
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return node.frequency ?? (haplotypes > 0 ? node.depth / haplotypes : void 0);
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}
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function withFrequencies(graph, frequencies) {
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if (!frequencies) {
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return graph;
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}
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const nodes = graph.nodes.map((node) => {
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const frequency = frequencies[node.name];
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return frequency === void 0 ? node : { ...node, frequency };
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});
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return { ...graph, nodes };
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}
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function widthNorm(graph, nodeWidth) {
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return nodeWidth === "depth" ? meanDepth(graph) : nodeWidth === "frequency" ? haplotypeCount(graph) : 0;
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}
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function frequencyFactor(f) {
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return Math.min(MAX_FACTOR, Math.max(MIN_FREQUENCY_FACTOR, f));
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}
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function frequencyWidthFactor(node, haplotypes) {
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const f = nodeFrequency(node, haplotypes);
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return f === void 0 ? 1 : frequencyFactor(f);
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}
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function frequencyKey(contigThickness) {
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return [1, 0.5, 0.1].map((f) => ({
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label: `${f * 100}%`,
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widthPx: contigThickness * frequencyFactor(f)
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}));
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}
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function depthWidthFactor(node, mean) {
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if (!(mean > 0) || !(node.depth > 0)) {
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return 1;
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}
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return Math.min(
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MAX_FACTOR,
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Math.max(MIN_FACTOR, Math.sqrt(node.depth / mean))
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);
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}
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function nodeWidthPx(node, contigThickness, nodeWidth, norm) {
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return contigThickness * (nodeWidth === "depth" ? depthWidthFactor(node, norm) : nodeWidth === "frequency" ? frequencyWidthFactor(node, norm) : 1);
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}
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function maxNodeWidthPx(contigThickness, nodeWidth) {
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return contigThickness * (nodeWidth === "uniform" ? 1 : MAX_FACTOR);
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}
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var MIN_WALK_LANE_PX = 4;
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function walkLaneWidthPx(width, lanes) {
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return Math.max(width / lanes, MIN_WALK_LANE_PX);
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}
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function nodeInk(graph, nodeById, contigThickness, nodeWidth, lanes = 0) {
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const norm = graph ? widthNorm(graph, nodeWidth) : 0;
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const reach = (width) => lanes > 0 ? walkLaneWidthPx(width, lanes) * lanes / 2 : width / 2;
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return {
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maxHalfWidthPx: reach(maxNodeWidthPx(contigThickness, nodeWidth)),
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halfWidthPx: (id) => {
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const node = nodeById?.get(id);
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return reach(
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node ? nodeWidthPx(node, contigThickness, nodeWidth, norm) : contigThickness
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);
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}
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};
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}
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export {
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NODE_WIDTHS,
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meanDepth,
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haplotypeCount,
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nodeFrequency,
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withFrequencies,
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widthNorm,
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frequencyKey,
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nodeWidthPx,
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maxNodeWidthPx,
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walkLaneWidthPx,
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nodeInk
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};
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package/dist/cli/figure.js
CHANGED
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} from "../chunks/chunk-FKMZG7HI.js";
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LAYOUT_ENGINE_VALUES,
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isLayoutEngineKind
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} from "../chunks/chunk-CO6RGQAD.js";
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LAYOUT_MODES
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} from "../chunks/chunk-54CX2MCH.js";
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figureSvg
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package/dist/cli/fold.js
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CHANGED
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CHANGED
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import {
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figureSvg
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|
import "./chunks/chunk-5ORP7EFJ.js";
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|
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|
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CHANGED
|
@@ -3,11 +3,11 @@ import {
|
|
|
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3
|
gfaFigureData,
|
|
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4
|
laidOutGraph,
|
|
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|
walkLayers
|
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|
-
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|
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|
+
} from "./chunks/chunk-FKMZG7HI.js";
|
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|
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|
import "./chunks/chunk-CNWAVRLF.js";
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|
import "./chunks/chunk-LLTISBAA.js";
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|
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18
|
import "./chunks/chunk-ZKSC7QVE.js";
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|
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|
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|
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|
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|
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import "./chunks/chunk-5ORP7EFJ.js";
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CHANGED
|
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1
|
import {
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|
figureScene
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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/figureSettings.js
CHANGED
|
@@ -1,13 +1,13 @@
|
|
|
1
1
|
import {
|
|
2
2
|
FIGURE_DEFAULTS,
|
|
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|
figureSpecSettings
|
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|
-
} from "./chunks/chunk-
|
|
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|
-
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|
|
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|
+
} from "./chunks/chunk-XESCKKKT.js";
|
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|
+
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|
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|
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|
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|
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|
import "./chunks/chunk-VPE4AYP7.js";
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|
+
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|
import "./chunks/chunk-QYBZZI5H.js";
|
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|
import "./chunks/chunk-CFXXFHRK.js";
|
|
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13
|
import "./chunks/chunk-7L7MN2OM.js";
|
|
@@ -17,7 +17,7 @@ import "./chunks/chunk-LG2UK4MB.js";
|
|
|
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17
|
import "./chunks/chunk-HNNP5QUN.js";
|
|
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|
import "./chunks/chunk-HKYXWZQS.js";
|
|
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|
import "./chunks/chunk-34BOZKIE.js";
|
|
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|
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import "./chunks/chunk-
|
|
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|
+
import "./chunks/chunk-OMQWCVOJ.js";
|
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|
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|
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|
|
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|
import "./chunks/chunk-JJV2GT2Z.js";
|
package/dist/gfa/gfaConverter.js
CHANGED
package/dist/graphLabels.js
CHANGED
|
@@ -6,11 +6,11 @@ import {
|
|
|
6
6
|
placeSizeLabels,
|
|
7
7
|
rowLabelBox,
|
|
8
8
|
sizeLabelCandidates
|
|
9
|
-
} from "./chunks/chunk-
|
|
9
|
+
} from "./chunks/chunk-ENBFQH7Y.js";
|
|
10
10
|
import "./chunks/chunk-HMXCN6PG.js";
|
|
11
11
|
import "./chunks/chunk-AB35TJST.js";
|
|
12
12
|
import "./chunks/chunk-HNNP5QUN.js";
|
|
13
|
-
import "./chunks/chunk-
|
|
13
|
+
import "./chunks/chunk-OMQWCVOJ.js";
|
|
14
14
|
import "./chunks/chunk-TLWXLNLY.js";
|
|
15
15
|
import "./chunks/chunk-3YBP46PB.js";
|
|
16
16
|
import "./chunks/chunk-JJV2GT2Z.js";
|