@genome-spy/core 0.56.0 → 0.57.0

package/dist/bundle/{index-CjesiOz_.js → index-DutovjI-.js}

@@ -1,7 +1,7 @@
 import { L as g } from "./__vite-browser-external-C--ziKoh.js";
-import { b as m } from "./index-B6haPltu.js";
-import { L as E, u as _ } from "./long-BXK3UEks.js";
-const w = 1;
+import { b as w } from "./index-DluFz_0j.js";
+import { L as _, u as b } from "./long-DM5IWGqg.js";
+const m = 1;
 class I {
   constructor({ filehandle: e, path: t }) {
     if (e)
@@ -12,7 +12,7 @@ class I {
       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);
+    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();
@@ -21,7 +21,7 @@ class I {
     return this.index || (this.index = this._readIndex()), this.index;
   }
   async _readIndex() {
-    let e = m.Buffer.allocUnsafe(8);
+    let e = w.Buffer.allocUnsafe(8);
     await this.filehandle.read(e, 0, 8, 0);
     const t = this._readLongWithOverflow(e, 0, !0);
     if (!t)
@@ -31,7 +31,7 @@ class I {
     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);
+    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];
@@ -48,17 +48,17 @@ class I {
     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;
+      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][w] >= s)); c += 1)
+    for (; c < n.length && (r.push(n[c]), !(n[c][m] >= s)); c += 1)
       ;
-    return r[r.length - 1][w] < s && r.push([]), r;
+    return r[r.length - 1][m] < s && r.push([]), r;
   }
 }
 class y {
@@ -85,7 +85,7 @@ class y {
     });
   }
   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);
+    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);
@@ -95,10 +95,10 @@ class y {
     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));
+    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 = m.Buffer.allocUnsafe(32768 * 2);
+    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;
@@ -107,12 +107,12 @@ class y {
     return { bytesRead: f, buffer: e };
   }
 }
-function b(o, 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 && t.length))
+  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), {
@@ -166,9 +166,9 @@ class B {
    * 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;
+    const t = {}, s = await this._getIndexes(e);
+    for (const n of Object.values(s.id))
+      t[n.name] = n.length;
     return t;
   }
   /**
@@ -220,11 +220,11 @@ class B {
       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);
+    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 O extends B {
+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,
@@ -243,7 +243,7 @@ function F(o) {
     };
   });
 }
-class k {
+class O {
   constructor({ fasta: e, path: t }) {
     if (e)
       this.fasta = e;
@@ -260,15 +260,15 @@ class k {
     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);
+    return r.sequence.slice(t, i);
   }
   async getSequenceNames() {
     return (await this.data).map((t) => t.id);
   }
 }
 export {
-  O as BgzipIndexedFasta,
-  k as FetchableSmallFasta,
+  v as BgzipIndexedFasta,
+  O as FetchableSmallFasta,
   B as IndexedFasta,
   F as parseSmallFasta
 };