@jbrowse/bandage-core 9.10.0 → 10.0.0
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/popBubble.js +3 -2
- package/dist/bubbles/superbubbles.js +4 -3
- package/dist/chunks/{chunk-Q6UIUY6X.js → chunk-33T67FPZ.js} +1 -1
- package/dist/chunks/{chunk-TOVOJNT7.js → chunk-3APK25GI.js} +1 -1
- package/dist/chunks/{chunk-A6PSWTLX.js → chunk-4QTNXTGW.js} +1 -1
- package/dist/chunks/{chunk-5GZEPPEW.js → chunk-BEWLQADP.js} +1 -1
- package/dist/chunks/{chunk-2VTM3DHG.js → chunk-CDPYXHVR.js} +1 -1
- package/dist/chunks/{chunk-K5NYTPLC.js → chunk-DCJC32QW.js} +1 -1
- package/dist/chunks/{chunk-IZI7KIVX.js → chunk-E5UEYZWK.js} +1 -1
- package/dist/chunks/{chunk-IGJCTPFB.js → chunk-EMUUNWRU.js} +52 -43
- package/dist/chunks/{chunk-PIN7ZMTZ.js → chunk-EU6FBTQF.js} +4 -4
- 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-FUUJ76KD.js → chunk-ICXMWYOA.js} +5 -5
- package/dist/chunks/{chunk-CXKZYLYS.js → chunk-IM4SJUPO.js} +12 -22
- package/dist/chunks/{chunk-6PYZYBBF.js → chunk-KAN2WTG5.js} +1 -1
- package/dist/chunks/{chunk-BDWQQK33.js → chunk-KJYSOHVN.js} +1 -1
- 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-PT37VS5B.js → chunk-OOLNLCIO.js} +1 -1
- package/dist/chunks/{chunk-OA7RIMZ2.js → chunk-PSMKPSO4.js} +89 -22
- package/dist/chunks/{chunk-NGODVSCA.js → chunk-Q6IOQP4J.js} +8 -8
- 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-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-2FLBFVMO.js → chunk-RJXPPYA7.js} +13 -13
- package/dist/chunks/{chunk-KYY5363X.js → chunk-VOWI544A.js} +1 -1
- package/dist/chunks/{chunk-FJZ2TB46.js → chunk-VZNKA3K2.js} +2 -2
- package/dist/chunks/{chunk-HRAU4VTB.js → chunk-W4GZCVUK.js} +6 -6
- package/dist/chunks/{chunk-DMH4NL2M.js → chunk-WI7ZHJ27.js} +2 -2
- package/dist/cli/figure.js +24 -23
- package/dist/cli/fold.js +6 -5
- package/dist/figure.js +19 -18
- package/dist/figureData.js +20 -19
- package/dist/figureSettings.js +7 -6
- 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 +57 -47
- package/dist/layout/forceCache.js +7 -6
- 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/layoutModes.js +8 -7
- package/dist/pathAnchoring.js +2 -1
- package/dist/pathColors.js +3 -2
- package/dist/pathVisits.js +8 -0
- package/dist/pipeline.js +6 -5
- 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 +4 -3
- 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 +2 -1
- package/dist/types/layout/deletionRoutes.d.ts +1 -1
- 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 +7 -6
- package/dist/walkEncoding.js +5 -4
- package/dist/walkHighlight.js +6 -5
- package/package.json +1 -1
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import {
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wellKnownSample
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} from "./chunk-RAKOB6IV.js";
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import {
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gfaTables
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} from "./chunk-G45YY72K.js";
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import {
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panSNMatchesPrefix,
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panSNSample
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} from "./chunk-BPLIXMH7.js";
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// src/gbzWindow.ts
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import { isReverse, nodeId } from "@gmod/gbz-base";
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var NoReferenceSampleError = class extends Error {
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constructor(anchor, referenceSamples) {
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super(
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snarls: "contained",
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limit: 1e5
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};
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async function
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return "";
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}
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const subgraphs = await db.getSubgraphs({ ...opts, path: query, start, end, haplotypes: "all" }).catch((error) => {
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async function windowCuts(db, query, start, end, opts) {
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return db.getSubgraphs({ ...opts, path: query, start, end, haplotypes: "all" }).catch((error) => {
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}
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async function joinedGFA(db, subgraphs) {
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await Promise.all(subgraphs.map((subgraph) => subgraph.toGFA())),
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async function cutWindowGFA(db, query, start, end, opts) {
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return query ? joinedGFA(db, await windowCuts(db, query, start, end, opts)) : "";
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}
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async function cutWindowTables(db, query, start, end, opts) {
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return "";
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}
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const subgraphs = await windowCuts(db, query, start, end, opts);
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return compactTables(subgraphs[0].toCompactSubgraph());
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}
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const text = await joinedGFA(db, subgraphs);
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}
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function segmentIndex(ids, names) {
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let low = Infinity;
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let high = -Infinity;
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for (const id of ids) {
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high = Math.max(high, id);
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}
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const span = high - low + 1;
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const table = ids.length > 0 && span <= 16 * ids.length ? new Int32Array(span).fill(-1) : void 0;
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const extra = /* @__PURE__ */ new Map();
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ids.forEach((id, i) => {
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table[id - low] = i;
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extra.set(id, i);
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}
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});
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return (handle) => {
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const id = nodeId(handle);
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const tabled = table !== void 0 && id >= low && id <= high;
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const i = tabled ? table[id - low] : extra.get(id) ?? -1;
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return i;
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}
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if (tabled) {
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table[id - low] = names.length;
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extra.set(id, names.length);
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}
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names.push(String(id));
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return names.length - 1;
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};
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}
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var WALK_NAME = /^(.*)\[(\d+)-(\d+)\]$/;
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function compactTables(cut) {
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const names = Array.from(cut.nodeIds, String);
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const indexOf = segmentIndex(cut.nodeIds, names);
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const declared = cut.nodeIds.length;
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const linkCount = cut.edges.length / 2;
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const from = new Int32Array(linkCount);
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const to = new Int32Array(linkCount);
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const strands = new Uint8Array(linkCount);
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for (let k = 0; k < linkCount; k++) {
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const a = cut.edges[2 * k];
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const b = cut.edges[2 * k + 1];
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from[k] = indexOf(a);
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to[k] = indexOf(b);
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strands[k] = (isReverse(a) ? 1 : 0) | (isReverse(b) ? 2 : 0);
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}
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const walks = cut.paths.filter((path) => path.steps.length > 0);
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const offsets = new Int32Array(walks.length + 1);
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walks.forEach((walk, p) => {
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offsets[p + 1] = offsets[p] + walk.steps.length;
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});
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const steps = new Int32Array(offsets[walks.length]);
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const reversed = new Uint8Array(steps.length);
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const starts = new Float64Array(walks.length);
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const ends = new Float64Array(walks.length);
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const walkNames = walks.map((walk, p) => {
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const named = WALK_NAME.exec(walk.name);
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starts[p] = named ? +named[2] : 0;
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ends[p] = named ? +named[3] : -1;
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let at = offsets[p];
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for (const handle of walk.steps) {
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steps[at] = indexOf(handle);
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reversed[at++] = isReverse(handle) ? 1 : 0;
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}
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return named ? named[1] : walk.name;
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});
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return {
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nodes: {
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names,
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lengths: Int32Array.from(cut.nodeSequences, (s) => s.length),
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refs: new Int32Array(declared).fill(-1),
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starts: new Float64Array(declared),
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ranks: new Int32Array(declared),
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refNames: []
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},
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links: { from, to, strands },
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walks: {
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names: walkNames,
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starts,
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ends,
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offsets,
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steps,
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}
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};
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}
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export {
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};
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const a = slot < 0 ? -1 : visits.firstBy(slot, own);
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static from(entries) {
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// Paths' steps replayed in walk order against their visits: the k-th call
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replay() {
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const cursor = /* @__PURE__ */ new Map();
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return (slot, p) => {
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const key = slot * this.paths.length + p;
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let at = cursor.get(key) ?? this.offsets[slot];
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while (at < end && this.path[at] !== p) {
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this.start[i],
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strand(i) {
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return this.reversed[i] ? "-" : "+";
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}
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visit(i) {
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path: this.paths[p],
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sample: this.samples[p],
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start: this.start[i],
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strand: this.strand(i)
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*entries() {
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}
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const grown = new this.data.constructor(
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);
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grown.set(this.data);
|
|
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this.data = grown;
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}
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this.data[this.length++] = value;
|
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}
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};
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var PathVisitsBuilder = class {
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constructor() {
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this.segments = [];
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this.paths = [];
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this.samples = [];
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this.slot = new Column(new Int32Array(1024));
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this.path = new Column(new Int32Array(1024));
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this.start = new Column(new Float64Array(1024));
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this.reversed = new Column(new Uint8Array(1024));
|
|
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|
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}
|
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// a segment's place in iteration order, though it has no visits yet
|
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declare(segment) {
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let s = this.slots.get(segment);
|
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if (s === void 0) {
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this.slots.set(segment, s);
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this.segments.push(segment);
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}
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return s;
|
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}
|
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// a path's index, so a caller adding many of its visits names it once
|
|
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|
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pathOf(path, sample) {
|
|
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|
+
let p = this.pathIndex.get(path);
|
|
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|
+
if (p === void 0) {
|
|
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|
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p = this.paths.length;
|
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|
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this.pathIndex.set(path, p);
|
|
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this.paths.push(path);
|
|
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|
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this.samples.push(sample);
|
|
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|
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}
|
|
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|
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return p;
|
|
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|
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}
|
|
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|
+
add(segment, path, sample, start, reversed) {
|
|
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this.addAt(
|
|
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this.declare(segment),
|
|
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|
+
this.pathOf(path, sample),
|
|
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|
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start,
|
|
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|
+
reversed
|
|
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|
+
);
|
|
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|
+
}
|
|
185
|
+
addAt(slot, path, start, reversed) {
|
|
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|
+
this.slot.push(slot);
|
|
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|
+
this.path.push(path);
|
|
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|
+
this.start.push(start);
|
|
189
|
+
this.reversed.push(reversed ? 1 : 0);
|
|
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|
+
}
|
|
191
|
+
build() {
|
|
192
|
+
const n = this.slot.length;
|
|
193
|
+
const segments = this.segments.length;
|
|
194
|
+
const offsets = new Int32Array(segments + 1);
|
|
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|
+
const slot = this.slot.data;
|
|
196
|
+
for (let i = 0; i < n; i++) {
|
|
197
|
+
offsets[slot[i] + 1]++;
|
|
198
|
+
}
|
|
199
|
+
for (let s = 0; s < segments; s++) {
|
|
200
|
+
offsets[s + 1] += offsets[s];
|
|
201
|
+
}
|
|
202
|
+
const fill = offsets.slice(0, segments);
|
|
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|
+
const path = new Int32Array(n);
|
|
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|
+
const start = new Float64Array(n);
|
|
205
|
+
const reversed = new Uint8Array(n);
|
|
206
|
+
for (let i = 0; i < n; i++) {
|
|
207
|
+
const at = fill[slot[i]]++;
|
|
208
|
+
path[at] = this.path.data[i];
|
|
209
|
+
start[at] = this.start.data[i];
|
|
210
|
+
reversed[at] = this.reversed.data[i];
|
|
211
|
+
}
|
|
212
|
+
return new PathVisits({
|
|
213
|
+
segments: this.segments,
|
|
214
|
+
offsets,
|
|
215
|
+
path,
|
|
216
|
+
start,
|
|
217
|
+
reversed,
|
|
218
|
+
paths: this.paths,
|
|
219
|
+
samples: this.samples
|
|
220
|
+
});
|
|
221
|
+
}
|
|
222
|
+
};
|
|
223
|
+
|
|
224
|
+
export {
|
|
225
|
+
PathVisits,
|
|
226
|
+
PathVisitsBuilder
|
|
227
|
+
};
|
|
@@ -5,23 +5,23 @@ import {
|
|
|
5
5
|
stripGeneGaps,
|
|
6
6
|
walkStripFrame,
|
|
7
7
|
walkStripLabelsTree
|
|
8
|
-
} from "./chunk-
|
|
8
|
+
} from "./chunk-WI7ZHJ27.js";
|
|
9
9
|
import {
|
|
10
10
|
walkRowsKey,
|
|
11
11
|
walkRowsKeyTree,
|
|
12
12
|
walkRowsTree
|
|
13
|
-
} from "./chunk-
|
|
13
|
+
} from "./chunk-VZNKA3K2.js";
|
|
14
14
|
import {
|
|
15
15
|
Canvas2DRenderer
|
|
16
16
|
} from "./chunk-WBCOREDZ.js";
|
|
17
|
-
import {
|
|
18
|
-
genePins
|
|
19
|
-
} from "./chunk-BUBZ32IC.js";
|
|
20
17
|
import {
|
|
21
18
|
EXON_COLOR,
|
|
22
19
|
exonOutlineTree,
|
|
23
20
|
exonStretches
|
|
24
21
|
} from "./chunk-3S3YVOJ7.js";
|
|
22
|
+
import {
|
|
23
|
+
genePins
|
|
24
|
+
} from "./chunk-BUBZ32IC.js";
|
|
25
25
|
import {
|
|
26
26
|
geneLabelCandidates
|
|
27
27
|
} from "./chunk-DRG4236Y.js";
|
|
@@ -36,17 +36,17 @@ import {
|
|
|
36
36
|
} from "./chunk-LOCJN3BZ.js";
|
|
37
37
|
import {
|
|
38
38
|
version
|
|
39
|
-
} from "./chunk-
|
|
39
|
+
} from "./chunk-CDPYXHVR.js";
|
|
40
40
|
import {
|
|
41
41
|
axisScaleOf
|
|
42
|
-
} from "./chunk-
|
|
42
|
+
} from "./chunk-OOLNLCIO.js";
|
|
43
43
|
import {
|
|
44
44
|
facetLifts,
|
|
45
45
|
walkLift
|
|
46
|
-
} from "./chunk-
|
|
46
|
+
} from "./chunk-QIVPRZ4H.js";
|
|
47
47
|
import {
|
|
48
48
|
encodingStops
|
|
49
|
-
} from "./chunk-
|
|
49
|
+
} from "./chunk-VOWI544A.js";
|
|
50
50
|
import {
|
|
51
51
|
rangeText,
|
|
52
52
|
walkKey
|
|
@@ -54,15 +54,15 @@ import {
|
|
|
54
54
|
import {
|
|
55
55
|
buildGeometry,
|
|
56
56
|
computeReferenceRamp
|
|
57
|
-
} from "./chunk-
|
|
57
|
+
} from "./chunk-NP356MC2.js";
|
|
58
58
|
import {
|
|
59
59
|
walkRowLabels,
|
|
60
60
|
walkRowsExtent
|
|
61
|
-
} from "./chunk-
|
|
61
|
+
} from "./chunk-3APK25GI.js";
|
|
62
62
|
import {
|
|
63
63
|
pathLegend,
|
|
64
64
|
walkLabelsOf
|
|
65
|
-
} from "./chunk-
|
|
65
|
+
} from "./chunk-REE4GUDM.js";
|
|
66
66
|
import {
|
|
67
67
|
nodeInk
|
|
68
68
|
} from "./chunk-PBENCR5L.js";
|
|
@@ -70,7 +70,7 @@ import {
|
|
|
70
70
|
FIT_PADDING,
|
|
71
71
|
drawingBounds,
|
|
72
72
|
fitTransform
|
|
73
|
-
} from "./chunk-
|
|
73
|
+
} from "./chunk-W4GZCVUK.js";
|
|
74
74
|
import {
|
|
75
75
|
referenceLabel
|
|
76
76
|
} from "./chunk-RAKOB6IV.js";
|
|
@@ -3,13 +3,13 @@ import {
|
|
|
3
3
|
RAMP_GRADIENT_STOPS,
|
|
4
4
|
rampHueCss,
|
|
5
5
|
rampStops
|
|
6
|
-
} from "./chunk-
|
|
6
|
+
} from "./chunk-DCJC32QW.js";
|
|
7
7
|
import {
|
|
8
8
|
el
|
|
9
9
|
} from "./chunk-NNODIW4U.js";
|
|
10
10
|
import {
|
|
11
11
|
REFERENCE_RAMP_ALT_CSS
|
|
12
|
-
} from "./chunk-
|
|
12
|
+
} from "./chunk-NP356MC2.js";
|
|
13
13
|
import {
|
|
14
14
|
LABEL_CHAR_PX
|
|
15
15
|
} from "./chunk-AB35TJST.js";
|
|
@@ -9,13 +9,10 @@ import {
|
|
|
9
9
|
} from "./chunk-PUG7LXDF.js";
|
|
10
10
|
import {
|
|
11
11
|
convertGFAToGraph
|
|
12
|
-
} from "./chunk-
|
|
13
|
-
import {
|
|
14
|
-
gfaTables
|
|
15
|
-
} from "./chunk-G45YY72K.js";
|
|
12
|
+
} from "./chunk-QXAB2FLJ.js";
|
|
16
13
|
import {
|
|
17
14
|
graphFromTables
|
|
18
|
-
} from "./chunk-
|
|
15
|
+
} from "./chunk-PSMKPSO4.js";
|
|
19
16
|
import {
|
|
20
17
|
parseGFA
|
|
21
18
|
} from "./chunk-CDLPYR5O.js";
|
|
@@ -26,7 +23,10 @@ import {
|
|
|
26
23
|
} from "./chunk-JVLURPFW.js";
|
|
27
24
|
import {
|
|
28
25
|
anchorGraph
|
|
29
|
-
} from "./chunk-
|
|
26
|
+
} from "./chunk-EMUUNWRU.js";
|
|
27
|
+
import {
|
|
28
|
+
gfaTables
|
|
29
|
+
} from "./chunk-G45YY72K.js";
|
|
30
30
|
import {
|
|
31
31
|
mergeRuns,
|
|
32
32
|
splitRuns
|
|
@@ -2,13 +2,13 @@ import {
|
|
|
2
2
|
alongRow,
|
|
3
3
|
boxesGenes,
|
|
4
4
|
rowPitch
|
|
5
|
-
} from "./chunk-
|
|
5
|
+
} from "./chunk-VZNKA3K2.js";
|
|
6
6
|
import {
|
|
7
7
|
el
|
|
8
8
|
} from "./chunk-NNODIW4U.js";
|
|
9
9
|
import {
|
|
10
10
|
pathOrigin
|
|
11
|
-
} from "./chunk-
|
|
11
|
+
} from "./chunk-EMUUNWRU.js";
|
|
12
12
|
import {
|
|
13
13
|
LABEL_CHAR_PX
|
|
14
14
|
} from "./chunk-AB35TJST.js";
|
package/dist/cli/figure.js
CHANGED
|
@@ -6,18 +6,18 @@ import {
|
|
|
6
6
|
} from "../chunks/chunk-BXEPA4KS.js";
|
|
7
7
|
import {
|
|
8
8
|
figureSvg
|
|
9
|
-
} from "../chunks/chunk-
|
|
9
|
+
} from "../chunks/chunk-RJXPPYA7.js";
|
|
10
10
|
import "../chunks/chunk-47DYCZOK.js";
|
|
11
|
-
import "../chunks/chunk-
|
|
11
|
+
import "../chunks/chunk-WI7ZHJ27.js";
|
|
12
12
|
import {
|
|
13
13
|
genesOnRow,
|
|
14
14
|
placeRowGenes
|
|
15
|
-
} from "../chunks/chunk-
|
|
15
|
+
} from "../chunks/chunk-VZNKA3K2.js";
|
|
16
16
|
import "../chunks/chunk-WBCOREDZ.js";
|
|
17
17
|
import "../chunks/chunk-4BYTEJGW.js";
|
|
18
|
-
import "../chunks/chunk-BUBZ32IC.js";
|
|
19
18
|
import "../chunks/chunk-3S3YVOJ7.js";
|
|
20
|
-
import "../chunks/chunk-
|
|
19
|
+
import "../chunks/chunk-BUBZ32IC.js";
|
|
20
|
+
import "../chunks/chunk-DCJC32QW.js";
|
|
21
21
|
import "../chunks/chunk-DRG4236Y.js";
|
|
22
22
|
import "../chunks/chunk-FP4H7SFT.js";
|
|
23
23
|
import "../chunks/chunk-MLSWIMZO.js";
|
|
@@ -32,10 +32,10 @@ import "../chunks/chunk-LYJ4US66.js";
|
|
|
32
32
|
import {
|
|
33
33
|
LAYOUT_MODES,
|
|
34
34
|
layoutModeByValue
|
|
35
|
-
} from "../chunks/chunk-
|
|
36
|
-
import "../chunks/chunk-
|
|
37
|
-
import "../chunks/chunk-CXKZYLYS.js";
|
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