@genome-spy/core 0.64.0 → 0.65.0

package/dist/bundle/index-B03-Om4z.js

@@ -1,274 +0,0 @@
-import { L as g } from "./__vite-browser-external-C--ziKoh.js";
-import { b as w } from "./index-BftNdA0O.js";
-import { L as _, u as b } from "./long-B-FASCSo.js";
-const m = 1;
-class I {
-  constructor({ filehandle: e, path: t }) {
-    if (e)
-      this.filehandle = e;
-    else if (t)
-      this.filehandle = new g(t);
-    else
-      throw new TypeError("either filehandle or path must be defined");
-  }
-  _readLongWithOverflow(e, t = 0, s = !0) {
-    const n = _.fromBytesLE(e.slice(t, t + 8), s);
-    if (n.greaterThan(Number.MAX_SAFE_INTEGER) || n.lessThan(Number.MIN_SAFE_INTEGER))
-      throw new TypeError("integer overflow");
-    return n.toNumber();
-  }
-  _getIndex() {
-    return this.index || (this.index = this._readIndex()), this.index;
-  }
-  async _readIndex() {
-    let e = w.Buffer.allocUnsafe(8);
-    await this.filehandle.read(e, 0, 8, 0);
-    const t = this._readLongWithOverflow(e, 0, !0);
-    if (!t)
-      return [[0, 0]];
-    const s = new Array(t + 1);
-    s[0] = [0, 0];
-    const n = 8 * 2 * t;
-    if (n > Number.MAX_SAFE_INTEGER)
-      throw new TypeError("integer overflow");
-    e = w.Buffer.allocUnsafe(n), await this.filehandle.read(e, 0, n, 8);
-    for (let r = 0; r < t; r += 1) {
-      const i = this._readLongWithOverflow(e, r * 16), l = this._readLongWithOverflow(e, r * 16 + 8);
-      s[r + 1] = [i, l];
-    }
-    return s;
-  }
-  async getLastBlock() {
-    const e = await this._getIndex();
-    if (e.length)
-      return e[e.length - 1];
-  }
-  async getRelevantBlocksForRead(e, t) {
-    const s = t + e;
-    if (e === 0)
-      return [];
-    const n = await this._getIndex(), r = [], i = (h, u) => {
-      const p = h[m], E = u ? u[m] : 1 / 0;
-      return p <= t && E > t ? 0 : p < t ? -1 : 1;
-    };
-    let l = 0, f = n.length - 1, a = Math.floor(n.length / 2), d = i(n[a], n[a + 1]);
-    for (; d !== 0; )
-      d > 0 ? f = a - 1 : d < 0 && (l = a + 1), a = Math.ceil((f - l) / 2) + l, d = i(n[a], n[a + 1]);
-    r.push(n[a]);
-    let c = a + 1;
-    for (; c < n.length && (r.push(n[c]), !(n[c][m] >= s)); c += 1)
-      ;
-    return r[r.length - 1][m] < s && r.push([]), r;
-  }
-}
-class y {
-  constructor({ filehandle: e, path: t, gziFilehandle: s, gziPath: n }) {
-    if (e)
-      this.filehandle = e;
-    else if (t)
-      this.filehandle = new g(t);
-    else
-      throw new TypeError("either filehandle or path must be defined");
-    if (!s && !n && !t)
-      throw new TypeError("either gziFilehandle or gziPath must be defined");
-    this.gzi = new I({
-      filehandle: s,
-      path: !s && !n && t ? n : `${t}.gzi`
-    });
-  }
-  async stat() {
-    const e = await this.filehandle.stat();
-    return Object.assign(e, {
-      size: await this.getUncompressedFileSize(),
-      blocks: void 0,
-      blksize: void 0
-    });
-  }
-  async getUncompressedFileSize() {
-    const [, e] = await this.gzi.getLastBlock(), { size: t } = await this.filehandle.stat(), s = w.Buffer.allocUnsafe(4), { bytesRead: n } = await this.filehandle.read(s, 0, 4, t - 28 - 4);
-    if (n !== 4)
-      throw new Error("read error");
-    const r = s.readUInt32LE(0);
-    return e + r;
-  }
-  async _readAndUncompressBlock(e, [t], [s]) {
-    let n = s;
-    n || (n = (await this.filehandle.stat()).size);
-    const r = n - t;
-    return await this.filehandle.read(e, 0, r, t), await b(e.slice(0, r));
-  }
-  async read(e, t, s, n) {
-    const r = await this.gzi.getRelevantBlocksForRead(s, n), i = w.Buffer.allocUnsafe(32768 * 2);
-    let l = t, f = 0;
-    for (let a = 0; a < r.length - 1; a += 1) {
-      const d = await this._readAndUncompressBlock(i, r[a], r[a + 1]), [, c] = r[a], h = c >= n ? 0 : n - c, u = Math.min(n + s, c + d.length) - c;
-      h >= 0 && h < d.length && (d.copy(e, l, h, u), l += u - h, f += u - h);
-    }
-    return { bytesRead: f, buffer: e };
-  }
-}
-function x(o, e) {
-  return o.offset + o.lineBytes * Math.floor(e / o.lineLength) + e % o.lineLength;
-}
-async function S(o, e) {
-  const t = await o.readFile(e);
-  if (!(t != null && t.length))
-    throw new Error("No data read from FASTA index (FAI) file");
-  let s = 0, n;
-  const r = t.toString("utf8").split(/\r?\n/).filter((i) => /\S/.test(i)).map((i) => i.split("	")).filter((i) => i[0] !== "").map((i) => ((!n || n.name !== i[0]) && (n = { name: i[0], id: s }, s += 1), {
-    id: n.id,
-    name: i[0],
-    length: +i[1],
-    start: 0,
-    end: +i[1],
-    offset: +i[2],
-    lineLength: +i[3],
-    lineBytes: +i[4]
-  }));
-  return {
-    name: Object.fromEntries(r.map((i) => [i.name, i])),
-    id: Object.fromEntries(r.map((i) => [i.id, i]))
-  };
-}
-class B {
-  constructor({ fasta: e, fai: t, path: s, faiPath: n }) {
-    if (e)
-      this.fasta = e;
-    else if (s)
-      this.fasta = new g(s);
-    else
-      throw new Error("Need to pass filehandle for fasta or path to localfile");
-    if (t)
-      this.fai = t;
-    else if (n)
-      this.fai = new g(n);
-    else if (s)
-      this.fai = new g(`${s}.fai`);
-    else
-      throw new Error("Need to pass filehandle for  or path to localfile");
-  }
-  async _getIndexes(e) {
-    return this.indexes || (this.indexes = S(this.fai, e)), this.indexes;
-  }
-  /**
-   * @returns {array[string]} 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)).name);
-  }
-  /**
-   * @returns {array[string]} 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 = {}, s = await this._getIndexes(e);
-    for (const n of Object.values(s.id))
-      t[n.name] = n.length;
-    return t;
-  }
-  /**
-   * @returns {array[string]} 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) {
-    var s;
-    return (s = (await this._getIndexes(t)).name[e]) === null || s === void 0 ? void 0 : s.length;
-  }
-  /**
-   *
-   * @param {string} name
-   * @returns {Promise[boolean]} true if the file contains the given reference sequence name
-   */
-  async hasReferenceSequence(e, t) {
-    return !!(await this._getIndexes(t)).name[e];
-  }
-  /**
-   *
-   * @param {number} seqId
-   * @param {number} min
-   * @param {number} max
-   */
-  async getResiduesById(e, t, s, n) {
-    const r = (await this._getIndexes(n)).id[e];
-    if (r)
-      return this._fetchFromIndexEntry(r, t, s, n);
-  }
-  /**
-   * @param {string} seqName
-   * @param {number} min
-   * @param {number} max
-   */
-  async getResiduesByName(e, t, s, n) {
-    const r = (await this._getIndexes(n)).name[e];
-    if (r)
-      return this._fetchFromIndexEntry(r, t, s, n);
-  }
-  //alias for getResiduesByName
-  async getSequence(e, t, s, n) {
-    return this.getResiduesByName(e, t, s, n);
-  }
-  async _fetchFromIndexEntry(e, t = 0, s, n) {
-    let r = s;
-    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 i = x(e, t), l = x(e, r) - i, f = w.Buffer.allocUnsafe(l);
-    return await this.fasta.read(f, 0, l, i, n), f.toString("utf8").replace(/\s+/g, "");
-  }
-}
-class v extends B {
-  constructor({ fasta: e, path: t, fai: s, faiPath: n, gzi: r, gziPath: i }) {
-    super({ fasta: e, path: t, fai: s, faiPath: n }), e && r ? this.fasta = new y({
-      filehandle: e,
-      gziFilehandle: r
-    }) : t && i && (this.fasta = new y({ path: t, gziPath: i }));
-  }
-}
-function F(o) {
-  return o.split(">").filter((e) => /\S/.test(e)).map((e) => {
-    const [t, ...s] = e.split(`
-`), [n, ...r] = t.split(" "), i = s.join("").replace(/\s/g, "");
-    return {
-      id: n,
-      description: r.join(" "),
-      sequence: i
-    };
-  });
-}
-class O {
-  constructor({ fasta: e, path: t }) {
-    if (e)
-      this.fasta = e;
-    else if (t)
-      this.fasta = new g(t);
-    else
-      throw new Error("Need to pass fasta or path");
-    this.data = this.fasta.readFile().then((s) => {
-      const n = s.toString("utf8");
-      return F(n);
-    });
-  }
-  async fetch(e, t, s) {
-    const r = (await this.data).find((l) => l.id === e), i = s - t;
-    if (!r)
-      throw new Error(`no sequence with id ${e} exists`);
-    return r.sequence.slice(t, i);
-  }
-  async getSequenceNames() {
-    return (await this.data).map((t) => t.id);
-  }
-}
-export {
-  v as BgzipIndexedFasta,
-  O as FetchableSmallFasta,
-  B as IndexedFasta,
-  F as parseSmallFasta
-};

package/dist/bundle/index-BftNdA0O.js

@@ -1,27 +0,0 @@
-import { g as i } from "./_commonjsHelpers-DjF3Plf2.js";
-import { r as s } from "./index-DnIkxb0L.js";
-function u(t, n) {
-  for (var o = 0; o < n.length; o++) {
-    const e = n[o];
-    if (typeof e != "string" && !Array.isArray(e)) {
-      for (const r in e)
-        if (r !== "default" && !(r in t)) {
-          const f = Object.getOwnPropertyDescriptor(e, r);
-          f && Object.defineProperty(t, r, f.get ? f : {
-            enumerable: !0,
-            get: () => e[r]
-          });
-        }
-    }
-  }
-  return Object.freeze(Object.defineProperty(t, Symbol.toStringTag, { value: "Module" }));
-}
-var a = s();
-const c = /* @__PURE__ */ i(a), l = /* @__PURE__ */ u({
-  __proto__: null,
-  default: c
-}, [a]);
-export {
-  a as b,
-  l as i
-};