@jbrowse/bandage-core 10.2.6 → 10.2.7
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/chunks/{chunk-HFVGGB3U.js → chunk-23YFB5BB.js} +2 -2
- package/dist/chunks/{chunk-BS4UZ44I.js → chunk-A7CFWFQS.js} +1 -1
- package/dist/chunks/{chunk-HNCXR2VS.js → chunk-AUFAPUO4.js} +1 -1
- package/dist/chunks/{chunk-YYMW5XOF.js → chunk-CG35S2S2.js} +1 -1
- package/dist/chunks/{chunk-WZNPX7Q6.js → chunk-EQ2NIFRH.js} +1 -1
- package/dist/chunks/{chunk-PSMKPSO4.js → chunk-OIV2GBAJ.js} +11 -15
- package/dist/chunks/{chunk-XBHMXTOR.js → chunk-QBHPHLAQ.js} +4 -4
- package/dist/chunks/{chunk-2QLLQJ72.js → chunk-QXUEF3AJ.js} +1 -1
- package/dist/chunks/{chunk-FB5RKZQY.js → chunk-VV6KGJ7M.js} +4 -4
- package/dist/cli/figure.js +8 -8
- package/dist/cli/fold.js +2 -2
- package/dist/figure.js +7 -7
- package/dist/figureData.js +7 -7
- package/dist/figureScene.js +4 -4
- package/dist/figureSettings.js +3 -3
- package/dist/gfa/graphTables.js +1 -1
- package/dist/index.js +9 -9
- package/dist/layout/forceCache.js +3 -3
- package/dist/pipeline.js +2 -2
- package/dist/types/gfa/graphTables.d.ts +3 -1
- package/dist/types/version.d.ts +1 -1
- package/dist/version.js +1 -1
- package/dist/viewport.js +3 -3
- package/package.json +1 -1
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@@ -18,10 +18,10 @@ import {
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} from "./chunk-3XSM4OZU.js";
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import {
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FIGURE_DEFAULTS
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} from "./chunk-
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} from "./chunk-AUFAPUO4.js";
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import {
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drawingBounds
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} from "./chunk-
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} from "./chunk-QXUEF3AJ.js";
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import {
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referenceLabel
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} from "./chunk-RAKOB6IV.js";
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@@ -8,7 +8,7 @@ import {
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// src/gfa/graphTables.ts
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function walkFields(panSN) {
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const [sample = "", haplotype = "", ...contig] = panSN.split("#");
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return { sample, haplotype, contig: contig.join("#") };
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return contig.length > 0 ? { sample, haplotype: +haplotype, contig: contig.join("#") } : void 0;
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}
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function namesByList(lists, names, listCount, pathNames) {
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const starts = new Int32Array(listCount + 1);
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@@ -161,8 +161,8 @@ function graphFromTables({ nodes: n, links: l, walks: w }, name = "Imported GFA"
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const blocks = [0];
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const pathSamples = [];
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for (const p of drawnWalks) {
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const
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const pathName = `${sample}#${
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const fields = walkFields(w.names[p]);
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const pathName = fields ? `${fields.sample}#${fields.haplotype}#${fields.contig}` : w.names[p];
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let named = nameIndex.get(pathName);
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if (named === void 0) {
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named = pathNames.length;
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@@ -199,14 +199,7 @@ function graphFromTables({ nodes: n, links: l, walks: w }, name = "Imported GFA"
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}
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prev = node;
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}
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paths.push({
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name: pathName,
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nodeIds,
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start,
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sample,
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haplotype: +haplotype,
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contig
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});
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paths.push({ name: pathName, nodeIds, start, ...fields });
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anchorPaths.push({
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name: pathName,
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sample: visitSample,
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@@ -260,13 +253,16 @@ function graphTablesGFA({ nodes, links, walks }) {
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);
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}
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for (let p = 0; p < walks.names.length; p++) {
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const
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const name = walks.names[p];
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const fields = walkFields(name);
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const start = walks.starts[p];
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const end = walks.ends[p];
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const steps = [];
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for (let s = walks.offsets[p]; s < walks.offsets[p + 1]; s++) {
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steps.push([names[walks.steps[s]], walks.reversed[s]]);
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}
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lines.push(
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`W ${sample} ${haplotype} ${contig} ${
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fields ? `W ${fields.sample} ${fields.haplotype} ${fields.contig} ${start} ${end} ${steps.map(([id, rev]) => (rev ? "<" : ">") + id).join("")}` : `P ${start === 0 ? name : `${name}:${start}-${end}`} ${steps.map(([id, rev]) => id + (rev ? "-" : "+")).join(",")} *`
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);
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}
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return lines.join("\n");
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import {
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version
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} from "./chunk-
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} from "./chunk-CG35S2S2.js";
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import {
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axisScaleOf
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} from "./chunk-
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} from "./chunk-A7CFWFQS.js";
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import {
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rangeText,
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walkKey
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} from "./chunk-4ETPXDO6.js";
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import {
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figureScene
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} from "./chunk-
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} from "./chunk-23YFB5BB.js";
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import {
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encodingStops
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} from "./chunk-VQC7KELB.js";
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import {
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FIT_PADDING,
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fitTransform
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} from "./chunk-
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} from "./chunk-QXUEF3AJ.js";
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import {
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LABEL_CHAR_PX,
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LABEL_PAD,
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import {
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} from "./chunk-
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} from "./chunk-CG35S2S2.js";
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axisScaleOf
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} from "./chunk-
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} from "./chunk-A7CFWFQS.js";
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import {
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walkKey
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} from "./chunk-4ETPXDO6.js";
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import {
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figureScene
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} from "./chunk-
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} from "./chunk-23YFB5BB.js";
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import {
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abgrAlpha,
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abgrBlue,
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fitTransform,
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forceLayout,
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loadGraph
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} from "./chunk-
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} from "./chunk-QXUEF3AJ.js";
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import {
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package/dist/cli/figure.js
CHANGED
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figureSvg
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} from "../chunks/chunk-
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} from "../chunks/chunk-QBHPHLAQ.js";
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import "../chunks/chunk-RUCH6ZFL.js";
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import "../chunks/chunk-WBSWROE6.js";
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import {
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import {
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walkLayers
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} from "../chunks/chunk-
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} from "../chunks/chunk-VV6KGJ7M.js";
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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-
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import "../chunks/chunk-
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import "../chunks/chunk-CG35S2S2.js";
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import "../chunks/chunk-A7CFWFQS.js";
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import "../chunks/chunk-
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import "../chunks/chunk-23YFB5BB.js";
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import "../chunks/chunk-QXUEF3AJ.js";
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package/dist/cli/fold.js
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package/dist/figure.js
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package/dist/figureScene.js
CHANGED
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import {
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figureScene
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} from "./chunks/chunk-23YFB5BB.js";
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import "./chunks/chunk-OPPVSPEF.js";
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CHANGED
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import {
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FIGURE_DEFAULTS,
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figureSpecSettings
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} from "./chunks/chunk-
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import "./chunks/chunk-
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} from "./chunks/chunk-AUFAPUO4.js";
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import "./chunks/chunk-
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package/dist/gfa/graphTables.js
CHANGED
package/dist/index.js
CHANGED
|
@@ -41,7 +41,7 @@ import {
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|
} from "./chunks/chunk-2ZT7ZF7A.js";
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import {
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createForceLayoutCache
|
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} from "./chunks/chunk-
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} from "./chunks/chunk-EQ2NIFRH.js";
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import {
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graphBubbles,
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superbubblesFromGraph
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} from "./chunks/chunk-AZFVORTC.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-QBHPHLAQ.js";
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import {
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svgCanvas
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} from "./chunks/chunk-RUCH6ZFL.js";
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import {
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|
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} from "./chunks/chunk-
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|
+
} from "./chunks/chunk-VV6KGJ7M.js";
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import {
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LAYOUT_ENGINES,
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layoutEngine
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|
@@ -201,7 +201,7 @@ import {
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version
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} from "./chunks/chunk-
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contains,
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} from "./chunks/chunk-
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} from "./chunks/chunk-A7CFWFQS.js";
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import {
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|
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|
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|
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|
@@ -262,7 +262,7 @@ import {
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import {
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|
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|
figureSpecSettings
|
|
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|
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} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-AUFAPUO4.js";
|
|
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|
import {
|
|
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|
ENGINE_DEFAULTS,
|
|
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FIT_PADDING,
|
|
@@ -275,7 +275,7 @@ import {
|
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|
forceLayout,
|
|
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|
layoutExtent,
|
|
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|
loadGraph
|
|
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} from "./chunks/chunk-
|
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|
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} from "./chunks/chunk-QXUEF3AJ.js";
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import {
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|
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graphFromTables,
|
|
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|
graphTablesGFA
|
|
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|
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} from "./chunks/chunk-
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|
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|
+
} from "./chunks/chunk-OIV2GBAJ.js";
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import {
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|
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PathVisits,
|
|
@@ -1,7 +1,7 @@
|
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1
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import {
|
|
2
2
|
createForceLayoutCache
|
|
3
|
-
} from "../chunks/chunk-
|
|
4
|
-
import "../chunks/chunk-
|
|
3
|
+
} from "../chunks/chunk-EQ2NIFRH.js";
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|
+
import "../chunks/chunk-QXUEF3AJ.js";
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|
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|
import "../chunks/chunk-IGVV37VI.js";
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7
|
import "../chunks/chunk-OPPVSPEF.js";
|
|
@@ -9,7 +9,7 @@ import "../chunks/chunk-VPE4AYP7.js";
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|
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import "../chunks/chunk-AR4BUBMU.js";
|
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|
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import "../chunks/chunk-
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|
+
import "../chunks/chunk-OIV2GBAJ.js";
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package/dist/pipeline.js
CHANGED
|
@@ -11,7 +11,7 @@ import {
|
|
|
11
11
|
forceLayout,
|
|
12
12
|
layoutExtent,
|
|
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13
|
loadGraph
|
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|
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} from "./chunks/chunk-
|
|
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|
+
} from "./chunks/chunk-QXUEF3AJ.js";
|
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|
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|
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import "./chunks/chunk-
|
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|
+
import "./chunks/chunk-OIV2GBAJ.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-ES2N6V56.js";
|
|
@@ -36,6 +36,8 @@ export interface GraphTables {
|
|
|
36
36
|
*/
|
|
37
37
|
export declare function graphFromTables({ nodes: n, links: l, walks: w }: GraphTables, name?: string): Graph;
|
|
38
38
|
/**
|
|
39
|
-
* The tables as GFA text: S lines in table order, then L lines, then W
|
|
39
|
+
* The tables as GFA text: S lines in table order, then L lines, then a W
|
|
40
|
+
* line per walk, or a P line for a walk whose name has fewer than three PanSN
|
|
41
|
+
* parts
|
|
40
42
|
*/
|
|
41
43
|
export declare function graphTablesGFA({ nodes, links, walks }: GraphTables): string;
|
package/dist/types/version.d.ts
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
export declare const version = "10.2.
|
|
1
|
+
export declare const version = "10.2.7";
|
package/dist/version.js
CHANGED
package/dist/viewport.js
CHANGED
|
@@ -5,8 +5,8 @@ import {
|
|
|
5
5
|
screenToLayout,
|
|
6
6
|
viewportOf,
|
|
7
7
|
zoomAbout
|
|
8
|
-
} from "./chunks/chunk-
|
|
9
|
-
import "./chunks/chunk-
|
|
8
|
+
} from "./chunks/chunk-A7CFWFQS.js";
|
|
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|
+
import "./chunks/chunk-QXUEF3AJ.js";
|
|
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|
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11
|
import "./chunks/chunk-IGVV37VI.js";
|
|
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12
|
import "./chunks/chunk-OPPVSPEF.js";
|
|
@@ -14,7 +14,7 @@ import "./chunks/chunk-VPE4AYP7.js";
|
|
|
14
14
|
import "./chunks/chunk-AR4BUBMU.js";
|
|
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15
|
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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-OIV2GBAJ.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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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/bandage-core",
|
|
3
|
-
"version": "10.2.
|
|
3
|
+
"version": "10.2.7",
|
|
4
4
|
"description": "Pangenome graph layout and drawing with no host: GFA in, the Bandage force-directed engine and reference-anchored layouts, a Canvas2D renderer, hit testing and labels out",
|
|
5
5
|
"license": "GPL-3.0-or-later",
|
|
6
6
|
"repository": {
|