taxonium-component/dist/VcfAdapter-D41_2-cN.js

React component for exploring large phylogenetic trees in the browser

import { I as y } from "./main-D1zX1xg0.js";
import { V as F, a as M } from "./index-DYYPI5hS.js";
import { B as T } from "./index-BnQfM3Nw.js";
import { a4 as v, u as w } from "./JBrowsePanel-uJIA-L6s.js";
import { r as C } from "./rxjs-BnZkaVAs.js";
class L extends T.BaseFeatureDataAdapter {
  constructor() {
    super(...arguments), this.calculatedIntervalTreeMap = {};
  }
  async getHeader() {
    const { header: t } = await this.setup();
    return t;
  }
  async getMetadata() {
    const { parser: t } = await this.setup();
    return t.getMetadata();
  }
  async setupP(t) {
    const { statusCallback: n = () => {
    } } = t || {}, s = v.openLocation(this.getConf("vcfLocation"), this.pluginManager), a = await w.fetchAndMaybeUnzip(s, t), o = [], c = {};
    let e = 0;
    const l = new TextDecoder("utf8");
    let u = 0;
    for (; e < a.length; ) {
      const i = a.indexOf(10, e), h = i === -1 ? a.subarray(e) : a.subarray(e, i), r = l.decode(h).trim();
      if (r)
        if (r.startsWith("#"))
          o.push(r);
        else {
          const m = r.indexOf("	"), p = r.slice(0, m);
          c[p] || (c[p] = []), c[p].push(r);
        }
      u++ % 1e4 === 0 && n(`Loading ${w.getProgressDisplayStr(e, a.length)}`), e = i + 1;
    }
    const f = o.join(`
`), d = new F({ header: f }), x = Object.fromEntries(Object.entries(c).map(([i, h]) => [
      i,
      (r) => {
        if (!this.calculatedIntervalTreeMap[i]) {
          r == null || r("Parsing VCF data");
          let m = 0;
          const p = new y();
          for (const b of h) {
            const g = new M({
              variant: d.parseLine(b),
              parser: d,
              id: `${this.id}-${i}-${m++}`
            });
            p.insert([g.get("start"), g.get("end")], g);
          }
          this.calculatedIntervalTreeMap[i] = p;
        }
        return this.calculatedIntervalTreeMap[i];
      }
    ]));
    return {
      header: f,
      parser: d,
      intervalTreeMap: x
    };
  }
  async setup() {
    return this.vcfFeatures || (this.vcfFeatures = this.setupP().catch((t) => {
      throw this.vcfFeatures = void 0, t;
    })), this.vcfFeatures;
  }
  async getRefNames(t = {}) {
    const { intervalTreeMap: n } = await this.setup();
    return Object.keys(n);
  }
  getFeatures(t, n = {}) {
    return C.ObservableCreate(async (s) => {
      var a;
      try {
        const { start: o, end: c, refName: e } = t, { intervalTreeMap: l } = await this.setup();
        for (const u of ((a = l[e]) === null || a === void 0 ? void 0 : a.call(l, n.statusCallback).search([
          o,
          c
        ])) || [])
          s.next(u);
        s.complete();
      } catch (o) {
        s.error(o);
      }
    }, n.stopToken);
  }
  async getSources() {
    const t = this.getConf("samplesTsvLocation");
    if (t.uri === "" || t.uri === "/path/to/samples.tsv") {
      const { parser: n } = await this.setup();
      return n.samples.map((s) => ({
        name: s
      }));
    } else {
      const s = (await v.openLocation(t).readFile("utf8")).split(/\n|\r\n|\r/), a = s[0].split("	"), { parser: o } = await this.setup(), c = new Set(o.samples);
      return s.slice(1).map((e) => {
        const l = e.split("	");
        return {
          name: l[0],
          ...Object.fromEntries(l.slice(1).map((u, f) => [a[f + 1], u]))
        };
      }).filter((e) => c.has(e.name));
    }
  }
}
L.capabilities = ["getFeatures", "getRefNames"];
export {
  L as default
};
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