@genome-spy/core 0.73.0 → 0.75.0

package/dist/bundle/index-GDOuv_D5.js

@@ -1,266 +0,0 @@
-import { LocalFile as d } from "./browser-0iNU5Wit.js";
-import { I as y, Z as _ } from "./inflate-GtwLkvSP.js";
-const g = 65536, I = g * g;
-function u(i, e = 0) {
-  const t = i[e] | i[e + 1] << 8 | i[e + 2] << 16 | i[e + 3] << 24;
-  return ((i[e + 4] | i[e + 5] << 8 | i[e + 6] << 16 | i[e + 7] << 24) >>> 0) * I + (t >>> 0);
-}
-const f = 1;
-function w(i, e, t) {
-  const n = e[f], s = t ? t[f] : 1 / 0;
-  return n <= i && s > i ? 0 : n < i ? -1 : 1;
-}
-class b {
-  filehandle;
-  index;
-  constructor({ filehandle: e }) {
-    this.filehandle = e;
-  }
-  _getIndex() {
-    return this.index || (this.index = this._readIndex().catch((e) => {
-      throw this.index = void 0, e;
-    })), this.index;
-  }
-  async _readIndex() {
-    const e = await this.filehandle.read(8, 0), t = u(e);
-    if (!t)
-      return [[0, 0]];
-    const n = new Array(t + 1);
-    n[0] = [0, 0];
-    const s = 16 * t;
-    if (s > Number.MAX_SAFE_INTEGER)
-      throw new TypeError("integer overflow");
-    const r = await this.filehandle.read(s, 8);
-    for (let a = 0; a < t; a += 1) {
-      const o = u(r, a * 16), c = u(r, a * 16 + 8);
-      n[a + 1] = [o, c];
-    }
-    return n;
-  }
-  async getLastBlock() {
-    return (await this._getIndex()).at(-1);
-  }
-  async getRelevantBlocksForRead(e, t) {
-    const n = t + e;
-    if (e === 0)
-      return [];
-    const s = await this._getIndex(), r = [];
-    let a = 0, o = s.length - 1, c = Math.floor(s.length / 2), l = w(t, s[c], s[c + 1]);
-    for (; l !== 0; )
-      l > 0 ? o = c - 1 : l < 0 && (a = c + 1), c = Math.ceil((o - a) / 2) + a, l = w(t, s[c], s[c + 1]);
-    r.push(s[c]);
-    let h = c + 1;
-    for (; h < s.length && (r.push(s[h]), !(s[h][f] >= n)); h += 1)
-      ;
-    return r[r.length - 1][f] < n && r.push([]), r;
-  }
-}
-function F(i) {
-  let e = 0;
-  for (const t of i)
-    e += t.length;
-  return e;
-}
-function x(i, e) {
-  const t = new Uint8Array(e ?? F(i));
-  let n = 0;
-  for (const s of i)
-    t.set(s, n), n += s.length;
-  return t;
-}
-async function S(i) {
-  try {
-    let e, t = 0, n;
-    const s = [];
-    let r = 0;
-    do {
-      const a = i.subarray(t);
-      if (n = new y(void 0), { strm: e } = n, n.push(a, _), n.err)
-        throw new Error(n.msg);
-      t += e.next_in;
-      const o = n.result;
-      s.push(o), r += o.length;
-    } while (e.avail_in);
-    return x(s, r);
-  } catch (e) {
-    throw /incorrect header check/.exec(`${e}`) ? new Error("problem decompressing block: incorrect gzip header check") : e;
-  }
-}
-class m {
-  filehandle;
-  gzi;
-  constructor({ filehandle: e, gziFilehandle: t }) {
-    this.filehandle = e, this.gzi = new b({
-      filehandle: t
-    });
-  }
-  async _readAndUncompressBlock(e, t) {
-    let n = t;
-    n || (n = (await this.filehandle.stat()).size);
-    const s = n - e, r = await this.filehandle.read(s, e);
-    return S(r);
-  }
-  async read(e, t) {
-    const n = await this.gzi.getRelevantBlocksForRead(e, t), s = [];
-    for (let r = 0; r < n.length - 1; r += 1) {
-      const a = await this._readAndUncompressBlock(n[r][0], n[r + 1][0]), [, o] = n[r], c = o >= t ? 0 : t - o, l = Math.min(t + e, o + a.length) - o;
-      c >= 0 && c < a.length && s.push(a.subarray(c, l));
-    }
-    return x(s);
-  }
-}
-function p(i, e) {
-  return i.offset + i.lineBytes * Math.floor(e / i.lineLength) + e % i.lineLength;
-}
-async function B(i, e = {}) {
-  const t = new TextDecoder("utf8");
-  return Object.fromEntries(t.decode(await i.readFile(e)).split(/\r?\n/).map((n) => n.trim()).filter((n) => !!n).map((n) => n.split("	")).map((n) => {
-    if (n[0]?.startsWith(">"))
-      throw new Error("found > in sequence name, might have supplied FASTA file for the FASTA index");
-    return [
-      n[0],
-      {
-        name: n[0],
-        length: +n[1],
-        start: 0,
-        end: +n[1],
-        offset: +n[2],
-        lineLength: +n[3],
-        lineBytes: +n[4]
-      }
-    ];
-  }));
-}
-class E {
-  constructor({ fasta: e, fai: t, path: n, faiPath: s }) {
-    if (e)
-      this.fasta = e;
-    else if (n)
-      this.fasta = new d(n);
-    else
-      throw new Error("Need to pass filehandle for fasta or path to localfile");
-    if (t)
-      this.fai = t;
-    else if (s)
-      this.fai = new d(s);
-    else if (n)
-      this.fai = new d(`${n}.fai`);
-    else
-      throw new Error("Need to pass filehandle for  or path to localfile");
-  }
-  async _getIndexes(e) {
-    return this.indexes || (this.indexes = B(this.fai, e).catch((t) => {
-      throw this.indexes = void 0, t;
-    })), this.indexes;
-  }
-  /**
-   * @returns array of string sequence names that are present in the index, in
-   * which the array index indicates the sequence ID, and the value is the
-   * sequence name
-   */
-  async getSequenceNames(e) {
-    return Object.keys(await this._getIndexes(e));
-  }
-  /**
-   * @returns array of string sequence names that are present in the index, in
-   * which the array index indicates the sequence ID, and the value is the
-   * sequence name
-   */
-  async getSequenceSizes(e) {
-    const t = {}, n = await this._getIndexes(e);
-    for (const s of Object.values(n))
-      t[s.name] = s.length;
-    return t;
-  }
-  /**
-   * @returns array of string sequence names that are present in the index, in
-   * which the array index indicates the sequence ID, and the value is the
-   * sequence name
-   */
-  async getSequenceSize(e, t) {
-    return (await this._getIndexes(t))[e]?.length;
-  }
-  /**
-   * @param name
-   *
-   * @returns true if the file contains the given reference sequence name
-   */
-  async hasReferenceSequence(e, t) {
-    return !!(await this._getIndexes(t))[e];
-  }
-  /**
-   * @param seqName
-   * @param min
-   * @param max
-   */
-  async getResiduesByName(e, t, n, s) {
-    const r = (await this._getIndexes(s))[e];
-    return r ? this._fetchFromIndexEntry(r, t, n, s) : void 0;
-  }
-  //alias for getResiduesByName
-  async getSequence(e, t, n, s) {
-    return this.getResiduesByName(e, t, n, s);
-  }
-  async _fetchFromIndexEntry(e, t = 0, n, s) {
-    let r = n;
-    if (t < 0)
-      throw new TypeError("regionStart cannot be less than 0");
-    if ((r === void 0 || r > e.length) && (r = e.length), t >= r)
-      return "";
-    const a = p(e, t), o = p(e, r) - a, l = new TextDecoder("utf8").decode(await this.fasta.read(o, a, s)).replace(/\s+/g, "");
-    if (/[^\x20-\x7e]/.test(l.slice(0, 1e3)))
-      throw new Error("Non-ASCII characters detected in sequence. The file may be gzip compressed. Use BgzipIndexedFasta for bgzip files, or decompress the file.");
-    return l;
-  }
-}
-class A extends E {
-  constructor({ fasta: e, path: t, fai: n, faiPath: s, gzi: r, gziPath: a }) {
-    super({ fasta: e, path: t, fai: n, faiPath: s }), e && r ? this.fasta = new m({
-      filehandle: e,
-      gziFilehandle: r
-    }) : t && a && (this.fasta = new m({
-      filehandle: new d(t),
-      gziFilehandle: new d(a)
-    }));
-  }
-}
-function k(i) {
-  return i.split(">").filter((e) => /\S/.test(e)).map((e) => {
-    const [t, ...n] = e.split(`
-`), [s, ...r] = t.split(" "), a = n.join("").replace(/\s/g, "");
-    return {
-      id: s,
-      description: r.join(" "),
-      sequence: a
-    };
-  });
-}
-class q {
-  constructor({ fasta: e, path: t }) {
-    if (e)
-      this.fasta = e;
-    else if (t)
-      this.fasta = new d(t);
-    else
-      throw new Error("Need to pass fasta or path");
-    this.data = this.fasta.readFile().then((n) => {
-      const r = new TextDecoder("utf8").decode(n);
-      return k(r);
-    });
-  }
-  async fetch(e, t, n) {
-    const r = (await this.data).find((o) => o.id === e), a = n - t;
-    if (!r)
-      throw new Error(`no sequence with id ${e} exists`);
-    return r.sequence.slice(t, a);
-  }
-  async getSequenceNames() {
-    return (await this.data).map((t) => t.id);
-  }
-}
-export {
-  A as BgzipIndexedFasta,
-  q as FetchableSmallFasta,
-  E as IndexedFasta,
-  k as parseSmallFasta
-};