taxonium-component/dist/BedGraphTabixAdapter-B6CVKBe0.js

React component for exploring large phylogenetic trees in the browser

import { T as S } from "./tabixIndexedFile-B-0sKywF.js";
import "./unzip-ASAuJ12U.js";
import { B as $ } from "./index-BnQfM3Nw.js";
import { a4 as p, u as y } from "./JBrowsePanel-uJIA-L6s.js";
import { r as F } from "./rxjs-BnZkaVAs.js";
class z extends $.BaseFeatureDataAdapter {
  async configurePre() {
    const e = this.pluginManager, n = this.getConf("bedGraphGzLocation"), s = this.getConf(["index", "location"]), o = this.getConf(["index", "indexType"]), t = p.openLocation(n, e), a = o === "CSI", i = new S({
      filehandle: t,
      csiFilehandle: a ? p.openLocation(s, e) : void 0,
      tbiFilehandle: a ? void 0 : p.openLocation(s, e),
      chunkCacheSize: 50 * 2 ** 20
    }), u = this.getConf("columnNames"), c = await i.getHeader();
    return {
      columnNames: u,
      bedGraph: i,
      header: c
    };
  }
  async configure() {
    return this.configured || (this.configured = this.configurePre().catch((e) => {
      throw this.configured = void 0, e;
    })), this.configured;
  }
  async getNames() {
    const { bedGraph: e, columnNames: n } = await this.configure();
    if (n.length)
      return n;
    const t = (await e.getHeader()).split(/\n|\r\n|\r/).filter((a) => !!a).at(-1);
    return t != null && t.includes("	") ? t.slice(1).split("	").map((a) => a.trim()) : void 0;
  }
  async getRefNames(e = {}) {
    const { bedGraph: n } = await this.configure();
    return n.getReferenceSequenceNames(e);
  }
  async getHeader() {
    const { bedGraph: e } = await this.configure();
    return e.getHeader();
  }
  getFeatures(e, n = {}) {
    return F.ObservableCreate(async (s) => {
      var o;
      const { bedGraph: t } = await this.configure(), a = await t.getMetadata(), { columnNumbers: i } = a, u = i.ref - 1, c = i.start - 1, d = i.end - 1, f = c === d, w = ((o = await this.getNames()) === null || o === void 0 ? void 0 : o.slice(f ? 2 : 3)) || [];
      await t.getLines(e.refName, e.start + (f ? -1 : 0), e.end, {
        lineCallback: (m, x) => {
          const l = m.split("	"), G = l[u], h = +l[c], g = +(f ? h + 1 : l[d]), b = l.slice(d + 1);
          if (Number.isNaN(h) || Number.isNaN(g))
            throw new Error(`start/end NaN on line "${m}", with colStart:${c} and colEnd:${d}. run "tabix -p bed" to ensure bed preset`);
          for (let r = 0; r < b.length; r++) {
            const C = `${this.id}-${x}-${r}`, N = Math.abs(+b[r]), E = w[r] || `col${r}`;
            N && s.next(new y.SimpleFeature({
              id: C,
              data: {
                refName: G,
                start: h,
                end: g,
                score: N,
                source: E
              }
            }));
          }
        },
        ...n
      }), s.complete();
    });
  }
}
export {
  z as default
};
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