taxonium-component/dist/HtsgetBamAdapter-BL-voECU.js

React component for exploring large phylogenetic trees in the browser

import "./remoteFile-H_6BTCFF.js";
import { u as p } from "./unzip-NIBF0hze.js";
import { B as A, a as I, p as k, c as y, b as x } from "./BamAdapter-lVmrDAGd.js";
async function $(l, e) {
  const r = await Promise.all(l.map(async (t) => {
    const { url: a, headers: i } = t;
    if (a.startsWith("data:")) {
      const s = await fetch(a);
      if (!s.ok)
        throw new Error("failed to decode base64");
      const n = await s.arrayBuffer();
      return new Uint8Array(n);
    } else {
      const { referer: s, ...n } = i, o = await fetch(a, {
        ...e,
        headers: { ...e == null ? void 0 : e.headers, ...n }
      });
      if (!o.ok)
        throw new Error(`HTTP ${o.status} fetching ${a}: ${await o.text()}`);
      return new Uint8Array(await o.arrayBuffer());
    }
  }));
  return y(await Promise.all(r.map((t) => p(t))));
}
class B extends A {
  constructor(e) {
    super({ htsget: !0 }), this.baseUrl = e.baseUrl, this.trackId = e.trackId;
  }
  async *streamRecordsForRange(e, r, t, a) {
    var o;
    const s = `${`${this.baseUrl}/${this.trackId}`}?referenceName=${e}&start=${r}&end=${t}&format=BAM`, n = (o = this.chrToIndex) == null ? void 0 : o[e];
    if (n === void 0)
      yield [];
    else {
      const c = await fetch(s, { ...a });
      if (!c.ok)
        throw new Error(`HTTP ${c.status} fetching ${s}: ${await c.text()}`);
      const d = await c.json(), f = await $(d.htsget.urls.slice(1), a);
      yield* this._fetchChunkFeatures([
        // fake stuff to pretend to be a Chunk
        {
          buffer: f,
          _fetchedSize: void 0,
          bin: 0,
          compareTo() {
            return 0;
          },
          toUniqueString() {
            return `${e}_${r}_${t}`;
          },
          fetchedSize() {
            return 0;
          },
          minv: {
            dataPosition: 0,
            blockPosition: 0,
            compareTo: () => 0
          },
          maxv: {
            dataPosition: Number.MAX_SAFE_INTEGER,
            blockPosition: 0,
            compareTo: () => 0
          },
          toString() {
            return `${e}_${r}_${t}`;
          }
        }
      ], n, r, t, a);
    }
  }
  // @ts-expect-error
  async _readChunk({ chunk: e }) {
    if (!e.buffer)
      throw new Error("expected chunk.buffer in htsget");
    return {
      data: e.buffer,
      cpositions: [],
      dpositions: [],
      chunk: e
    };
  }
  async getHeader(e = {}) {
    const r = `${this.baseUrl}/${this.trackId}?referenceName=na&class=header`, t = await fetch(r, e);
    if (!t.ok)
      throw new Error(`HTTP ${t.status} fetching ${r}: ${await t.text()}`);
    const a = await t.json(), i = await $(a.htsget.urls, e), s = new DataView(i.buffer);
    if (s.getInt32(0, !0) !== I)
      throw new Error("Not a BAM file");
    const n = s.getInt32(4, !0), c = new TextDecoder("utf8").decode(i.subarray(8, 8 + n)), d = k(c), f = [], g = {}, m = d.filter((u) => u.tag === "SQ");
    for (const [u, T] of m.entries()) {
      let w = "", b = 0;
      for (const h of T.data)
        h.tag === "SN" ? w = h.value : h.tag === "LN" && (b = +h.value);
      g[w] = u, f[u] = { refName: w, length: b };
    }
    return this.chrToIndex = g, this.indexToChr = f, d;
  }
}
class N extends x {
  async configurePre() {
    const e = this.getConf("htsgetBase"), r = this.getConf("htsgetTrackId"), t = new B({
      baseUrl: e,
      trackId: r
    }), a = this.getConf("sequenceAdapter");
    if (a && this.getSubAdapter) {
      const i = await this.getSubAdapter(a);
      return {
        bam: t,
        sequenceAdapter: i.dataAdapter
      };
    }
    return { bam: t };
  }
}
export {
  N as default
};
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