taxonium-component/dist/SplitVcfTabixAdapter-DGOmPVtX.js

React component for exploring large phylogenetic trees in the browser

import { T as d } from "./tabixIndexedFile-B-0sKywF.js";
import "./unzip-ASAuJ12U.js";
import { V as g, a as h } from "./index-DYYPI5hS.js";
import { B as m } from "./index-BnQfM3Nw.js";
import { a4 as p, u } from "./JBrowsePanel-uJIA-L6s.js";
import { r as x } from "./rxjs-BnZkaVAs.js";
class F extends m.BaseFeatureDataAdapter {
  async configurePre(e) {
    const t = this.getConf("indexType"), a = this.getConf("vcfGzLocationMap")[e], n = this.getConf("indexLocationMap")[e] || {
      uri: `${a.uri}.${t.toLowerCase()}`
    }, o = p.openLocation(a, this.pluginManager), s = t === "CSI", i = new d({
      filehandle: o,
      csiFilehandle: s ? p.openLocation(n, this.pluginManager) : void 0,
      tbiFilehandle: s ? void 0 : p.openLocation(n, this.pluginManager),
      chunkCacheSize: 50 * 2 ** 20
    });
    return {
      vcf: i,
      parser: new g({
        header: await i.getHeader()
      })
    };
  }
  async configure(e, t) {
    const { statusCallback: a = () => {
    } } = t || {};
    return u.updateStatus("Downloading index", a, () => this.configurePre(e));
  }
  async getRefNames() {
    return Object.keys(this.getConf("vcfGzLocationMap"));
  }
  getFeatures(e, t = {}) {
    return x.ObservableCreate(async (a) => {
      const { refName: n, start: o, end: s } = e, { statusCallback: i = () => {
      } } = t, { vcf: r, parser: c } = await this.configure(e.refName, t);
      await u.updateStatus("Downloading variants", i, () => r.getLines(n, o, s, {
        lineCallback: (l, f) => {
          a.next(new h({
            variant: c.parseLine(l),
            parser: c,
            id: `${this.id}-vcf-${f}`
          }));
        },
        ...t
      })), a.complete();
    }, t.stopToken);
  }
  async getSources() {
    const e = this.getConf("samplesTsvLocation"), t = Object.keys(this.getConf("vcfGzLocationMap"))[0];
    if (e.uri === "" || e.uri === "/path/to/samples.tsv") {
      const { parser: a } = await this.configure(t);
      return a.samples.map((n) => ({
        name: n
      }));
    } else {
      const n = (await u.fetchAndMaybeUnzipText(p.openLocation(e, this.pluginManager))).split(/\n|\r\n|\r/), o = n[0].split("	"), { parser: s } = await this.configure(t), i = new Set(s.samples);
      return n.slice(1).map((r) => {
        const c = r.split("	");
        return {
          name: c[0],
          ...Object.fromEntries(c.slice(1).map((l, f) => [o[f + 1], l]))
        };
      }).filter((r) => i.has(r.name));
    }
  }
}
export {
  F as default
};
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