@genome-spy/app 0.51.0 → 0.53.0

package/dist/{index-C8lYPtq_.js → index-B5cesONJ.js}

@@ -18,12 +18,12 @@ function Sr(c, f) {
 var V = {}, j = {};
 j.byteLength = Nr;
 j.toByteArray = kr;
-j.fromByteArray = Pr;
+j.fromByteArray = $r;
 var _ = [], R = [], Lr = typeof Uint8Array < "u" ? Uint8Array : Array, H = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/";
 for (var k = 0, br = H.length; k < br; ++k)
   _[k] = H[k], R[H.charCodeAt(k)] = k;
-R["-".charCodeAt(0)] = 62;
-R["_".charCodeAt(0)] = 63;
+R[45] = 62;
+R[95] = 63;
 function hr(c) {
   var f = c.length;
   if (f % 4 > 0)
@@ -49,14 +49,14 @@ function kr(c) {
 function Dr(c) {
   return _[c >> 18 & 63] + _[c >> 12 & 63] + _[c >> 6 & 63] + _[c & 63];
 }
-function $r(c, f, s) {
+function Pr(c, f, s) {
   for (var w, y = [], l = f; l < s; l += 3)
     w = (c[l] << 16 & 16711680) + (c[l + 1] << 8 & 65280) + (c[l + 2] & 255), y.push(Dr(w));
   return y.join("");
 }
-function Pr(c) {
+function $r(c) {
   for (var f, s = c.length, w = s % 3, y = [], l = 16383, p = 0, o = s - w; p < o; p += l)
-    y.push($r(c, p, p + l > o ? o : p + l));
+    y.push(Pr(c, p, p + l > o ? o : p + l));
   return w === 1 ? (f = c[s - 1], y.push(
     _[f >> 2] + _[f << 4 & 63] + "=="
   )) : w === 2 && (f = (c[s - 2] << 8) + c[s - 1], y.push(
@@ -81,12 +81,12 @@ X.read = function(c, f, s, w, y) {
   return (A ? -1 : 1) * p * Math.pow(2, l - w);
 };
 X.write = function(c, f, s, w, y, l) {
-  var p, o, B, T = l * 8 - y - 1, I = (1 << T) - 1, F = I >> 1, S = y === 23 ? Math.pow(2, -24) - Math.pow(2, -77) : 0, A = w ? 0 : l - 1, D = w ? 1 : -1, $ = f < 0 || f === 0 && 1 / f < 0 ? 1 : 0;
+  var p, o, B, T = l * 8 - y - 1, I = (1 << T) - 1, F = I >> 1, S = y === 23 ? Math.pow(2, -24) - Math.pow(2, -77) : 0, A = w ? 0 : l - 1, D = w ? 1 : -1, P = f < 0 || f === 0 && 1 / f < 0 ? 1 : 0;
   for (f = Math.abs(f), isNaN(f) || f === 1 / 0 ? (o = isNaN(f) ? 1 : 0, p = I) : (p = Math.floor(Math.log(f) / Math.LN2), f * (B = Math.pow(2, -p)) < 1 && (p--, B *= 2), p + F >= 1 ? f += S / B : f += S * Math.pow(2, 1 - F), f * B >= 2 && (p++, B /= 2), p + F >= I ? (o = 0, p = I) : p + F >= 1 ? (o = (f * B - 1) * Math.pow(2, y), p = p + F) : (o = f * Math.pow(2, F - 1) * Math.pow(2, y), p = 0)); y >= 8; c[s + A] = o & 255, A += D, o /= 256, y -= 8)
     ;
   for (p = p << y | o, T += y; T > 0; c[s + A] = p & 255, A += D, p /= 256, T -= 8)
     ;
-  c[s + A - D] |= $ * 128;
+  c[s + A - D] |= P * 128;
 };
 /*!
  * The buffer module from node.js, for the browser.
@@ -151,7 +151,7 @@ X.write = function(c, f, s, w, y, l) {
         "The first argument must be one of type string, Buffer, ArrayBuffer, Array, or Array-like Object. Received type " + typeof i
       );
     if (C(i, ArrayBuffer) || i && C(i.buffer, ArrayBuffer) || typeof SharedArrayBuffer < "u" && (C(i, SharedArrayBuffer) || i && C(i.buffer, SharedArrayBuffer)))
-      return $(i, r, t);
+      return P(i, r, t);
     if (typeof i == "number")
       throw new TypeError(
         'The "value" argument must not be of type number. Received type number'
@@ -208,11 +208,11 @@ X.write = function(c, f, s, w, y, l) {
   function D(i) {
     if (C(i, Uint8Array)) {
       const r = new Uint8Array(i);
-      return $(r.buffer, r.byteOffset, r.byteLength);
+      return P(r.buffer, r.byteOffset, r.byteLength);
     }
     return A(i);
   }
-  function $(i, r, t) {
+  function P(i, r, t) {
     if (r < 0 || i.byteLength < r)
       throw new RangeError('"offset" is outside of buffer bounds');
     if (i.byteLength < r + (t || 0))
@@ -664,13 +664,13 @@ X.write = function(c, f, s, w, y, l) {
   }, o.prototype.readBigUInt64LE = L(function(r) {
     r = r >>> 0, M(r, "offset");
     const t = this[r], n = this[r + 7];
-    (t === void 0 || n === void 0) && P(r, this.length - 8);
+    (t === void 0 || n === void 0) && $(r, this.length - 8);
     const e = t + this[++r] * 2 ** 8 + this[++r] * 2 ** 16 + this[++r] * 2 ** 24, u = this[++r] + this[++r] * 2 ** 8 + this[++r] * 2 ** 16 + n * 2 ** 24;
     return BigInt(e) + (BigInt(u) << BigInt(32));
   }), o.prototype.readBigUInt64BE = L(function(r) {
     r = r >>> 0, M(r, "offset");
     const t = this[r], n = this[r + 7];
-    (t === void 0 || n === void 0) && P(r, this.length - 8);
+    (t === void 0 || n === void 0) && $(r, this.length - 8);
     const e = t * 2 ** 24 + this[++r] * 2 ** 16 + this[++r] * 2 ** 8 + this[++r], u = this[++r] * 2 ** 24 + this[++r] * 2 ** 16 + this[++r] * 2 ** 8 + n;
     return (BigInt(e) << BigInt(32)) + BigInt(u);
   }), o.prototype.readIntLE = function(r, t, n) {
@@ -702,13 +702,13 @@ X.write = function(c, f, s, w, y, l) {
   }, o.prototype.readBigInt64LE = L(function(r) {
     r = r >>> 0, M(r, "offset");
     const t = this[r], n = this[r + 7];
-    (t === void 0 || n === void 0) && P(r, this.length - 8);
+    (t === void 0 || n === void 0) && $(r, this.length - 8);
     const e = this[r + 4] + this[r + 5] * 2 ** 8 + this[r + 6] * 2 ** 16 + (n << 24);
     return (BigInt(e) << BigInt(32)) + BigInt(t + this[++r] * 2 ** 8 + this[++r] * 2 ** 16 + this[++r] * 2 ** 24);
   }), o.prototype.readBigInt64BE = L(function(r) {
     r = r >>> 0, M(r, "offset");
     const t = this[r], n = this[r + 7];
-    (t === void 0 || n === void 0) && P(r, this.length - 8);
+    (t === void 0 || n === void 0) && $(r, this.length - 8);
     const e = (t << 24) + // Overflow
     this[++r] * 2 ** 16 + this[++r] * 2 ** 8 + this[++r];
     return (BigInt(e) << BigInt(32)) + BigInt(this[++r] * 2 ** 24 + this[++r] * 2 ** 16 + this[++r] * 2 ** 8 + n);
@@ -932,13 +932,13 @@ X.write = function(c, f, s, w, y, l) {
     return `${i.slice(0, t)}${r}`;
   }
   function Ir(i, r, t) {
-    M(r, "offset"), (i[r] === void 0 || i[r + t] === void 0) && P(r, i.length - (t + 1));
+    M(r, "offset"), (i[r] === void 0 || i[r + t] === void 0) && $(r, i.length - (t + 1));
   }
   function or(i, r, t, n, e, u) {
     if (i > t || i < r) {
       const h = typeof r == "bigint" ? "n" : "";
       let a;
-      throw u > 3 ? r === 0 || r === BigInt(0) ? a = `>= 0${h} and < 2${h} ** ${(u + 1) * 8}${h}` : a = `>= -(2${h} ** ${(u + 1) * 8 - 1}${h}) and < 2 ** ${(u + 1) * 8 - 1}${h}` : a = `>= ${r}${h} and <= ${t}${h}`, new N.ERR_OUT_OF_RANGE("value", a, i);
+      throw r === 0 || r === BigInt(0) ? a = `>= 0${h} and < 2${h} ** ${(u + 1) * 8}${h}` : a = `>= -(2${h} ** ${(u + 1) * 8 - 1}${h}) and < 2 ** ${(u + 1) * 8 - 1}${h}`, new N.ERR_OUT_OF_RANGE("value", a, i);
     }
     Ir(n, e, u);
   }
@@ -946,10 +946,10 @@ X.write = function(c, f, s, w, y, l) {
     if (typeof i != "number")
       throw new N.ERR_INVALID_ARG_TYPE(r, "number", i);
   }
-  function P(i, r, t) {
-    throw Math.floor(i) !== i ? (M(i, t), new N.ERR_OUT_OF_RANGE(t || "offset", "an integer", i)) : r < 0 ? new N.ERR_BUFFER_OUT_OF_BOUNDS() : new N.ERR_OUT_OF_RANGE(
-      t || "offset",
-      `>= ${t ? 1 : 0} and <= ${r}`,
+  function $(i, r, t) {
+    throw Math.floor(i) !== i ? (M(i, t), new N.ERR_OUT_OF_RANGE("offset", "an integer", i)) : r < 0 ? new N.ERR_BUFFER_OUT_OF_BOUNDS() : new N.ERR_OUT_OF_RANGE(
+      "offset",
+      `>= 0 and <= ${r}`,
       i
     );
   }

package/dist/index-BJLu48Hz.js

@@ -0,0 +1,274 @@
+import { L as g } from "./__vite-browser-external-C--ziKoh.js";
+import { b as m } from "./index-B5cesONJ.js";
+import { L as E, u as _ } from "./long-D4tVjLLz.js";
+const w = 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 = E.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 = m.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 = m.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[w], x = u ? u[w] : 1 / 0;
+      return p <= t && x > 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][w] >= s)); c += 1)
+      ;
+    return r[r.length - 1][w] < 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 = m.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 _(e.slice(0, r));
+  }
+  async read(e, t, s, n) {
+    const r = await this.gzi.getRelevantBlocksForRead(s, n), i = m.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 b(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 && 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), n = Object.values(s.id);
+    for (let r = 0; r < n.length; r += 1)
+      t[n[r].name] = n[r].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 = b(e, t), l = b(e, r) - i, f = Buffer.allocUnsafe(l);
+    return await this.fasta.read(f, 0, l, i, n), f.toString("utf8").replace(/\s+/g, "");
+  }
+}
+class O 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 k {
+  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.substr(t, i);
+  }
+  async getSequenceNames() {
+    return (await this.data).map((t) => t.id);
+  }
+}
+export {
+  O as BgzipIndexedFasta,
+  k as FetchableSmallFasta,
+  B as IndexedFasta,
+  F as parseSmallFasta
+};