@genome-spy/app 0.58.0 → 0.58.1

package/dist/{index-Dec7VcMU.js → index-DKe9Bhvi.js}

@@ -1,7 +1,7 @@
 import { A as J, L as K } from "./index-CCJIjehY.js";
 import { b as Q } from "./index-BftNdA0O.js";
-import { L as B } from "./__vite-browser-external-C--ziKoh.js";
-import { R as A } from "./remoteFile-BuaqFGWk.js";
+import { L as R } from "./__vite-browser-external-C--ziKoh.js";
+import { R as F } from "./remoteFile-BuaqFGWk.js";
 import { u as $, L as H, a as Z } from "./long-BviWyoZx.js";
 function j(o) {
   if (o.greaterThan(Number.MAX_SAFE_INTEGER) || o.lessThan(Number.MIN_SAFE_INTEGER))
@@ -10,7 +10,7 @@ function j(o) {
 }
 class ee extends Error {
 }
-function L(o) {
+function _(o) {
   if (o && o.aborted) {
     if (typeof DOMException < "u")
       throw new DOMException("aborted", "AbortError");
@@ -26,9 +26,9 @@ function te(o, e) {
 function X(o, e) {
   const t = [];
   let n = null;
-  return o.length === 0 ? o : (o.sort(function(i, a) {
-    const r = i.minv.blockPosition - a.minv.blockPosition;
-    return r !== 0 ? r : i.minv.dataPosition - a.minv.dataPosition;
+  return o.length === 0 ? o : (o.sort(function(i, s) {
+    const a = i.minv.blockPosition - s.minv.blockPosition;
+    return a !== 0 ? a : i.minv.dataPosition - s.minv.dataPosition;
   }), o.forEach((i) => {
     (!e || i.maxv.compareTo(e) > 0) && (n === null ? (t.push(i), n = i) : te(n, i) ? i.maxv.compareTo(n.maxv) > 0 && (n.maxv = i.maxv) : (t.push(i), n = i));
   }), t);
@@ -98,73 +98,73 @@ function ie(o, e) {
     [4681 + (o >> 14), 4681 + (e >> 14)]
   ];
 }
-class k extends W {
+class y extends W {
   async lineCount(e, t = {}) {
     const n = await this.parse(t), i = n.refNameToId[e];
     if (i === void 0 || !n.indices[i])
       return -1;
-    const { stats: r } = n.indices[i];
-    return r ? r.lineCount : -1;
+    const { stats: a } = n.indices[i];
+    return a ? a.lineCount : -1;
   }
   // fetch and parse the index
   async _parse(e = {}) {
     const t = await this.filehandle.readFile(e), n = await $(t);
-    if (L(e.signal), n.readUInt32LE(0) !== ne)
+    if (_(e.signal), n.readUInt32LE(0) !== ne)
       throw new Error("Not a TBI file");
-    const i = n.readInt32LE(4), a = n.readInt32LE(8), r = a & 65536 ? "zero-based-half-open" : "1-based-closed", d = {
+    const i = n.readInt32LE(4), s = n.readInt32LE(8), a = s & 65536 ? "zero-based-half-open" : "1-based-closed", f = {
       0: "generic",
       1: "SAM",
       2: "VCF"
-    }[a & 15];
-    if (!d)
-      throw new Error(`invalid Tabix preset format flags ${a}`);
-    const l = {
+    }[s & 15];
+    if (!f)
+      throw new Error(`invalid Tabix preset format flags ${s}`);
+    const d = {
       ref: n.readInt32LE(12),
       start: n.readInt32LE(16),
       end: n.readInt32LE(20)
-    }, u = n.readInt32LE(24), c = 5, f = ((1 << (c + 1) * 3) - 1) / 7, I = 2 ** (14 + c * 3), w = u ? String.fromCharCode(u) : null, m = n.readInt32LE(28), b = n.readInt32LE(32), { refNameToId: p, refIdToName: x } = this._parseNameBytes(n.slice(36, 36 + b));
-    let h = 36 + b, g;
+    }, u = n.readInt32LE(24), h = 5, c = ((1 << (h + 1) * 3) - 1) / 7, b = 2 ** (14 + h * 3), I = u ? String.fromCharCode(u) : null, m = n.readInt32LE(28), w = n.readInt32LE(32), { refNameToId: x, refIdToName: p } = this._parseNameBytes(n.slice(36, 36 + w));
+    let l = 36 + w, g;
     return {
       indices: new Array(i).fill(0).map(() => {
-        const y = n.readInt32LE(h);
-        h += 4;
-        const S = {};
-        let E;
-        for (let v = 0; v < y; v += 1) {
-          const _ = n.readUInt32LE(h);
-          if (h += 4, _ > f + 1)
+        const E = n.readInt32LE(l);
+        l += 4;
+        const v = {};
+        let N;
+        for (let C = 0; C < E; C += 1) {
+          const A = n.readUInt32LE(l);
+          if (l += 4, A > c + 1)
             throw new Error("tabix index contains too many bins, please use a CSI index");
-          if (_ === f + 1) {
-            const N = n.readInt32LE(h);
-            h += 4, N === 2 && (E = this.parsePseudoBin(n, h)), h += 16 * N;
+          if (A === c + 1) {
+            const k = n.readInt32LE(l);
+            l += 4, k === 2 && (N = this.parsePseudoBin(n, l)), l += 16 * k;
           } else {
-            const N = n.readInt32LE(h);
-            h += 4;
-            const O = new Array(N);
-            for (let F = 0; F < N; F += 1) {
-              const q = T(n, h), Y = T(n, h + 8);
-              h += 16, g = this._findFirstData(g, q), O[F] = new D(q, Y, _);
+            const k = n.readInt32LE(l);
+            l += 4;
+            const O = new Array(k);
+            for (let M = 0; M < k; M += 1) {
+              const q = T(n, l), Y = T(n, l + 8);
+              l += 16, g = this._findFirstData(g, q), O[M] = new D(q, Y, A);
             }
-            S[_] = O;
+            v[A] = O;
           }
         }
-        const P = n.readInt32LE(h);
-        h += 4;
-        const R = new Array(P);
-        for (let v = 0; v < P; v += 1)
-          R[v] = T(n, h), h += 8, g = this._findFirstData(g, R[v]);
-        return { binIndex: S, linearIndex: R, stats: E };
+        const B = n.readInt32LE(l);
+        l += 4;
+        const L = new Array(B);
+        for (let C = 0; C < B; C += 1)
+          L[C] = T(n, l), l += 8, g = this._findFirstData(g, L[C]);
+        return { binIndex: v, linearIndex: L, stats: N };
       }),
-      metaChar: w,
-      maxBinNumber: f,
-      maxRefLength: I,
+      metaChar: I,
+      maxBinNumber: c,
+      maxRefLength: b,
       skipLines: m,
       firstDataLine: g,
-      columnNumbers: l,
-      coordinateType: r,
-      format: d,
-      refIdToName: x,
-      refNameToId: p,
+      columnNumbers: d,
+      coordinateType: a,
+      format: f,
+      refIdToName: p,
+      refNameToId: x,
       maxBlockSize: 65536
     };
   }
@@ -173,40 +173,40 @@ class k extends W {
   }
   _parseNameBytes(e) {
     let t = 0, n = 0;
-    const i = [], a = {};
-    for (let r = 0; r < e.length; r += 1)
-      if (!e[r]) {
-        if (n < r) {
-          let s = e.toString("utf8", n, r);
-          s = this.renameRefSeq(s), i[t] = s, a[s] = t;
+    const i = [], s = {};
+    for (let a = 0; a < e.length; a += 1)
+      if (!e[a]) {
+        if (n < a) {
+          let r = e.toString("utf8", n, a);
+          r = this.renameRefSeq(r), i[t] = r, s[r] = t;
         }
-        n = r + 1, t += 1;
+        n = a + 1, t += 1;
       }
-    return { refNameToId: a, refIdToName: i };
+    return { refNameToId: s, refIdToName: i };
   }
   async blocksForRange(e, t, n, i = {}) {
     t < 0 && (t = 0);
-    const a = await this.parse(i), r = a.refNameToId[e];
-    if (r === void 0)
+    const s = await this.parse(i), a = s.refNameToId[e];
+    if (a === void 0)
       return [];
-    const s = a.indices[r];
-    if (!s)
+    const r = s.indices[a];
+    if (!r)
       return [];
-    (s.linearIndex.length ? s.linearIndex[t >> U >= s.linearIndex.length ? s.linearIndex.length - 1 : t >> U] : new V(0, 0)) || console.warn("querying outside of possible tabix range");
-    const l = ie(t, n), u = [];
-    for (const [m, b] of l)
-      for (let p = m; p <= b; p++)
-        if (s.binIndex[p])
-          for (const x of s.binIndex[p])
-            u.push(new D(x.minv, x.maxv, p));
-    const c = s.linearIndex.length;
-    let f = null;
-    const I = Math.min(t >> 14, c - 1), w = Math.min(n >> 14, c - 1);
-    for (let m = I; m <= w; ++m) {
-      const b = s.linearIndex[m];
-      b && (!f || b.compareTo(f) < 0) && (f = b);
+    (r.linearIndex.length ? r.linearIndex[t >> U >= r.linearIndex.length ? r.linearIndex.length - 1 : t >> U] : new V(0, 0)) || console.warn("querying outside of possible tabix range");
+    const d = ie(t, n), u = [];
+    for (const [m, w] of d)
+      for (let x = m; x <= w; x++)
+        if (r.binIndex[x])
+          for (const p of r.binIndex[x])
+            u.push(new D(p.minv, p.maxv, x));
+    const h = r.linearIndex.length;
+    let c = null;
+    const b = Math.min(t >> 14, h - 1), I = Math.min(n >> 14, h - 1);
+    for (let m = b; m <= I; ++m) {
+      const w = r.linearIndex[m];
+      w && (!c || w.compareTo(c) < 0) && (c = w);
     }
-    return X(u, f);
+    return X(u, c);
   }
 }
 const re = 21582659, se = 38359875;
@@ -216,7 +216,7 @@ function ae(o, e) {
 function G(o, e) {
   return Math.floor(o / 2 ** e);
 }
-class M extends W {
+class z extends W {
   constructor(e) {
     super(e), this.maxBinNumber = 0, this.depth = 0, this.minShift = 0;
   }
@@ -224,43 +224,43 @@ class M extends W {
     const n = await this.parse(t), i = n.refNameToId[e];
     if (i === void 0 || !n.indices[i])
       return -1;
-    const { stats: r } = n.indices[i];
-    return r ? r.lineCount : -1;
+    const { stats: a } = n.indices[i];
+    return a ? a.lineCount : -1;
   }
   indexCov() {
     throw new Error("CSI indexes do not support indexcov");
   }
   parseAuxData(e, t) {
-    const n = e.readInt32LE(t), i = n & 65536 ? "zero-based-half-open" : "1-based-closed", a = { 0: "generic", 1: "SAM", 2: "VCF" }[n & 15];
-    if (!a)
+    const n = e.readInt32LE(t), i = n & 65536 ? "zero-based-half-open" : "1-based-closed", s = { 0: "generic", 1: "SAM", 2: "VCF" }[n & 15];
+    if (!s)
       throw new Error(`invalid Tabix preset format flags ${n}`);
-    const r = {
+    const a = {
       ref: e.readInt32LE(t + 4),
       start: e.readInt32LE(t + 8),
       end: e.readInt32LE(t + 12)
-    }, s = e.readInt32LE(t + 16), d = s ? String.fromCharCode(s) : null, l = e.readInt32LE(t + 20), u = e.readInt32LE(t + 24), { refIdToName: c, refNameToId: f } = this._parseNameBytes(e.slice(t + 28, t + 28 + u));
+    }, r = e.readInt32LE(t + 16), f = r ? String.fromCharCode(r) : null, d = e.readInt32LE(t + 20), u = e.readInt32LE(t + 24), { refIdToName: h, refNameToId: c } = this._parseNameBytes(e.slice(t + 28, t + 28 + u));
     return {
-      refIdToName: c,
-      refNameToId: f,
-      skipLines: l,
-      metaChar: d,
-      columnNumbers: r,
-      format: a,
+      refIdToName: h,
+      refNameToId: c,
+      skipLines: d,
+      metaChar: f,
+      columnNumbers: a,
+      format: s,
       coordinateType: i
     };
   }
   _parseNameBytes(e) {
     let t = 0, n = 0;
-    const i = [], a = {};
-    for (let r = 0; r < e.length; r += 1)
-      if (!e[r]) {
-        if (n < r) {
-          let s = e.toString("utf8", n, r);
-          s = this.renameRefSeq(s), i[t] = s, a[s] = t;
+    const i = [], s = {};
+    for (let a = 0; a < e.length; a += 1)
+      if (!e[a]) {
+        if (n < a) {
+          let r = e.toString("utf8", n, a);
+          r = this.renameRefSeq(r), i[t] = r, s[r] = t;
         }
-        n = r + 1, t += 1;
+        n = a + 1, t += 1;
       }
-    return { refNameToId: a, refIdToName: i };
+    return { refNameToId: s, refIdToName: i };
   }
   // fetch and parse the index
   async _parse(e = {}) {
@@ -273,45 +273,45 @@ class M extends W {
     else
       throw new Error("Not a CSI file");
     this.minShift = t.readInt32LE(4), this.depth = t.readInt32LE(8), this.maxBinNumber = ((1 << (this.depth + 1) * 3) - 1) / 7;
-    const i = 2 ** (this.minShift + this.depth * 3), a = t.readInt32LE(12), r = a && a >= 30 ? this.parseAuxData(t, 16) : {
+    const i = 2 ** (this.minShift + this.depth * 3), s = t.readInt32LE(12), a = s && s >= 30 ? this.parseAuxData(t, 16) : {
       refIdToName: [],
       refNameToId: {},
       metaChar: null,
       columnNumbers: { ref: 0, start: 1, end: 2 },
       coordinateType: "zero-based-half-open",
       format: "generic"
-    }, s = t.readInt32LE(16 + a);
-    let d, l = 16 + a + 4;
-    const u = new Array(s).fill(0).map(() => {
-      const c = t.readInt32LE(l);
-      l += 4;
-      const f = {};
-      let I;
-      for (let w = 0; w < c; w += 1) {
-        const m = t.readUInt32LE(l);
+    }, r = t.readInt32LE(16 + s);
+    let f, d = 16 + s + 4;
+    const u = new Array(r).fill(0).map(() => {
+      const h = t.readInt32LE(d);
+      d += 4;
+      const c = {};
+      let b;
+      for (let I = 0; I < h; I += 1) {
+        const m = t.readUInt32LE(d);
         if (m > this.maxBinNumber)
-          I = this.parsePseudoBin(t, l + 4), l += 48;
+          b = this.parsePseudoBin(t, d + 4), d += 48;
         else {
-          const b = T(t, l + 4);
-          d = this._findFirstData(d, b);
-          const p = t.readInt32LE(l + 12);
-          l += 16;
-          const x = new Array(p);
-          for (let h = 0; h < p; h += 1) {
-            const g = T(t, l), C = T(t, l + 8);
-            l += 16, x[h] = new D(g, C, m);
+          const w = T(t, d + 4);
+          f = this._findFirstData(f, w);
+          const x = t.readInt32LE(d + 12);
+          d += 16;
+          const p = new Array(x);
+          for (let l = 0; l < x; l += 1) {
+            const g = T(t, d), P = T(t, d + 8);
+            d += 16, p[l] = new D(g, P, m);
           }
-          f[m] = x;
+          c[m] = p;
         }
       }
-      return { binIndex: f, stats: I };
+      return { binIndex: c, stats: b };
     });
     return {
-      ...r,
+      ...a,
       csi: !0,
-      refCount: s,
+      refCount: r,
       maxBlockSize: 65536,
-      firstDataLine: d,
+      firstDataLine: f,
       csiVersion: n,
       indices: u,
       depth: this.depth,
@@ -324,40 +324,40 @@ class M extends W {
   }
   async blocksForRange(e, t, n, i = {}) {
     t < 0 && (t = 0);
-    const a = await this.parse(i), r = a.refNameToId[e];
-    if (r === void 0)
+    const s = await this.parse(i), a = s.refNameToId[e];
+    if (a === void 0)
       return [];
-    const s = a.indices[r];
-    if (!s)
+    const r = s.indices[a];
+    if (!r)
       return [];
-    const d = this.reg2bins(t, n), l = [];
-    for (const [u, c] of d)
-      for (let f = u; f <= c; f++)
-        if (s.binIndex[f])
-          for (const I of s.binIndex[f])
-            l.push(new D(I.minv, I.maxv, f));
-    return X(l, new V(0, 0));
+    const f = this.reg2bins(t, n), d = [];
+    for (const [u, h] of f)
+      for (let c = u; c <= h; c++)
+        if (r.binIndex[c])
+          for (const b of r.binIndex[c])
+            d.push(new D(b.minv, b.maxv, c));
+    return X(d, new V(0, 0));
   }
   /**
    * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
    */
   reg2bins(e, t) {
     e -= 1, e < 1 && (e = 1), t > 2 ** 50 && (t = 2 ** 34), t -= 1;
-    let n = 0, i = 0, a = this.minShift + this.depth * 3;
-    const r = [];
-    for (; n <= this.depth; a -= 3, i += ae(1, n * 3), n += 1) {
-      const s = i + G(e, a), d = i + G(t, a);
-      if (d - s + r.length > this.maxBinNumber)
+    let n = 0, i = 0, s = this.minShift + this.depth * 3;
+    const a = [];
+    for (; n <= this.depth; s -= 3, i += ae(1, n * 3), n += 1) {
+      const r = i + G(e, s), f = i + G(t, s);
+      if (f - r + a.length > this.maxBinNumber)
         throw new Error(`query ${e}-${t} is too large for current binning scheme (shift ${this.minShift}, depth ${this.depth}), try a smaller query or a coarser index binning scheme`);
-      r.push([s, d]);
+      a.push([r, f]);
     }
-    return r;
+    return a;
   }
 }
-const z = typeof TextDecoder < "u" ? new TextDecoder("utf8") : void 0;
 function oe(o) {
-  return new Promise((e) => setTimeout(e, o));
+  return /^[\u0000-\u007F]*$/.test(o);
 }
+const S = typeof TextDecoder < "u" ? new TextDecoder("utf8") : void 0;
 class ue {
   /**
    * @param {object} args
@@ -374,65 +374,68 @@ class ue {
    *
    * @param {filehandle} [args.csiFilehandle]
    *
-   * @param {number} [args.yieldTime] yield to main thread after N milliseconds
-   * if reading features is taking a long time to avoid hanging main thread
+   * @param {url} [args.url]
+   *
+   * @param {csiUrl} [args.csiUrl]
+   *
+   * @param {tbiUrl} [args.tbiUrl]
    *
    * @param {function} [args.renameRefSeqs] optional function with sig `string
    * => string` to transform reference sequence names for the purpose of
    * indexing and querying. note that the data that is returned is not altered,
    * just the names of the reference sequences that are used for querying.
    */
-  constructor({ path: e, filehandle: t, url: n, tbiPath: i, tbiUrl: a, tbiFilehandle: r, csiPath: s, csiUrl: d, csiFilehandle: l, yieldTime: u = 500, renameRefSeqs: c = (I) => I, chunkCacheSize: f = 5 * 2 ** 20 }) {
+  constructor({ path: e, filehandle: t, url: n, tbiPath: i, tbiUrl: s, tbiFilehandle: a, csiPath: r, csiUrl: f, csiFilehandle: d, renameRefSeqs: u = (c) => c, chunkCacheSize: h = 5 * 2 ** 20 }) {
     if (t)
       this.filehandle = t;
     else if (e)
-      this.filehandle = new B(e);
+      this.filehandle = new R(e);
     else if (n)
-      this.filehandle = new A(n);
+      this.filehandle = new F(n);
     else
       throw new TypeError("must provide either filehandle or path");
-    if (r)
-      this.index = new k({
-        filehandle: r,
-        renameRefSeqs: c
+    if (a)
+      this.index = new y({
+        filehandle: a,
+        renameRefSeqs: u
       });
-    else if (l)
-      this.index = new M({
-        filehandle: l,
-        renameRefSeqs: c
+    else if (d)
+      this.index = new z({
+        filehandle: d,
+        renameRefSeqs: u
       });
     else if (i)
-      this.index = new k({
-        filehandle: new B(i),
-        renameRefSeqs: c
+      this.index = new y({
+        filehandle: new R(i),
+        renameRefSeqs: u
       });
-    else if (s)
-      this.index = new M({
-        filehandle: new B(s),
-        renameRefSeqs: c
+    else if (r)
+      this.index = new z({
+        filehandle: new R(r),
+        renameRefSeqs: u
       });
     else if (e)
-      this.index = new k({
-        filehandle: new B(`${e}.tbi`),
-        renameRefSeqs: c
+      this.index = new y({
+        filehandle: new R(`${e}.tbi`),
+        renameRefSeqs: u
       });
-    else if (d)
-      this.index = new M({
-        filehandle: new A(d)
+    else if (f)
+      this.index = new z({
+        filehandle: new F(f)
       });
-    else if (a)
-      this.index = new k({
-        filehandle: new A(a)
+    else if (s)
+      this.index = new y({
+        filehandle: new F(s)
       });
     else if (n)
-      this.index = new k({
-        filehandle: new A(`${n}.tbi`)
+      this.index = new y({
+        filehandle: new F(`${n}.tbi`)
       });
     else
       throw new TypeError("must provide one of tbiFilehandle, tbiPath, csiFilehandle, csiPath, tbiUrl, csiUrl");
-    this.renameRefSeq = c, this.yieldTime = u, this.chunkCache = new J({
-      cache: new K({ maxSize: Math.floor(f / 65536) }),
-      fill: (I, w) => this.readChunk(I, { signal: w })
+    this.renameRefSeq = u, this.chunkCache = new J({
+      cache: new K({ maxSize: Math.floor(h / 65536) }),
+      fill: (c, b) => this.readChunk(c, { signal: b })
     });
   }
   /**
@@ -449,54 +452,62 @@ class ue {
    * rejected on error
    */
   async getLines(e, t, n, i) {
-    var a;
-    let r, s = {}, d;
-    typeof i == "function" ? d = i : (s = i, d = i.lineCallback, r = i.signal);
-    const l = await this.index.getMetadata(s);
-    L(r);
-    const u = t ?? 0, c = n ?? l.maxRefLength;
-    if (!(u <= c))
+    var s, a;
+    let r, f = {}, d;
+    typeof i == "function" ? d = i : (f = i, d = i.lineCallback, r = i.signal);
+    const u = await this.index.getMetadata(f);
+    _(r);
+    const h = t ?? 0, c = n ?? u.maxRefLength;
+    if (!(h <= c))
       throw new TypeError("invalid start and end coordinates. start must be less than or equal to end");
-    if (u === c)
+    if (h === c)
       return;
-    const f = await this.index.blocksForRange(e, u, c, s);
-    L(r);
-    let I = Date.now();
-    for (const w of f) {
-      let m;
-      const { buffer: b, cpositions: p, dpositions: x } = await this.chunkCache.get(w.toString(), w, r);
-      L(r);
-      let h = 0, g = 0;
-      for (; h < b.length; ) {
-        const C = b.indexOf(`
-`, h);
-        if (C === -1)
-          break;
-        const y = b.slice(h, C), S = (a = z == null ? void 0 : z.decode(y)) !== null && a !== void 0 ? a : y.toString();
+    const b = await this.index.blocksForRange(e, h, c, f);
+    _(r);
+    for (const I of b) {
+      const { buffer: m, cpositions: w, dpositions: x } = await this.chunkCache.get(I.toString(), I, r);
+      _(r);
+      let p = 0, l = 0;
+      const g = (s = S == null ? void 0 : S.decode(m)) !== null && s !== void 0 ? s : m.toString(), P = m.length < 5e8 && oe(g);
+      for (; p < g.length; ) {
+        let E, v;
+        if (P) {
+          if (v = g.indexOf(`
+`, p), v === -1)
+            break;
+          E = g.slice(p, v);
+        } else {
+          if (v = m.indexOf(`
+`, p), v === -1)
+            break;
+          const L = m.slice(p, v);
+          E = (a = S == null ? void 0 : S.decode(L)) !== null && a !== void 0 ? a : L.toString();
+        }
         if (x) {
-          for (; h + w.minv.dataPosition >= x[g++]; )
+          for (; p + I.minv.dataPosition >= x[l++]; )
             ;
-          g--;
+          l--;
         }
-        const { startCoordinate: E, overlaps: P } = this.checkLine(l, e, u, c, S);
-        if (m !== void 0 && E !== void 0 && m > E)
-          throw new Error(`Lines not sorted by start coordinate (${m} > ${E}), this file is not usable with Tabix.`);
-        if (m = E, P)
+        const { startCoordinate: N, overlaps: B } = this.checkLine(u, e, h, c, E);
+        if (B)
           d(
-            S.trim(),
-            // cpositions[pos] refers to actual file offset of a bgzip block boundaries
+            E,
+            // cpositions[pos] refers to actual file offset of a bgzip block
+            // boundaries
             //
-            // we multiply by (1 <<8) in order to make sure each block has a "unique"
-            // address space so that data in that block could never overlap
+            // we multiply by (1 <<8) in order to make sure each block has a
+            // "unique" address space so that data in that block could never
+            // overlap
             //
-            // then the blockStart-dpositions is an uncompressed file offset from
-            // that bgzip block boundary, and since the cpositions are multiplied by
-            // (1 << 8) these uncompressed offsets get a unique space
-            p[g] * 256 + (h - x[g]) + w.minv.dataPosition + 1
+            // then the blockStart-dpositions is an uncompressed file offset
+            // from that bgzip block boundary, and since the cpositions are
+            // multiplied by (1 << 8) these uncompressed offsets get a unique
+            // space
+            w[l] * 256 + (p - x[l]) + I.minv.dataPosition + 1
           );
-        else if (E !== void 0 && E >= c)
+        else if (N !== void 0 && N >= c)
           return;
-        this.yieldTime && I - Date.now() > this.yieldTime && (I = Date.now(), L(r), await oe(1)), h = C + 1;
+        p = v + 1;
       }
     }
   }
@@ -509,16 +520,16 @@ class ue {
    */
   async getHeaderBuffer(e = {}) {
     const { firstDataLine: t, metaChar: n, maxBlockSize: i } = await this.getMetadata(e);
-    L(e.signal);
-    const a = ((t == null ? void 0 : t.blockPosition) || 0) + i, r = await this._readRegion(0, a, e), s = await $(r);
+    _(e.signal);
+    const s = ((t == null ? void 0 : t.blockPosition) || 0) + i, a = await this._readRegion(0, s, e), r = await $(a);
     if (n) {
-      let d = -1;
-      const l = 10, u = n.charCodeAt(0);
-      for (let c = 0; c < s.length && !(c === d + 1 && s[c] !== u); c += 1)
-        s[c] === l && (d = c);
-      return s.slice(0, d + 1);
+      let f = -1;
+      const d = 10, u = n.charCodeAt(0);
+      for (let h = 0; h < r.length && !(h === f + 1 && r[h] !== u); h += 1)
+        r[h] === d && (f = h);
+      return r.subarray(0, f + 1);
     }
-    return s;
+    return r;
   }
   /**
    * get a string containing the "header" region of the file, is the portion up
@@ -551,47 +562,61 @@ class ue {
    * @returns {object} like `{startCoordinate, overlaps}`. overlaps is boolean,
    * true if line is a data line that overlaps the given region
    */
-  checkLine(e, t, n, i, a) {
-    const { columnNumbers: r, metaChar: s, coordinateType: d, format: l } = e;
-    if (s && a.startsWith(s))
+  checkLine(e, t, n, i, s) {
+    const { columnNumbers: a, metaChar: r, coordinateType: f, format: d } = e;
+    if (r && s.startsWith(r))
       return { overlaps: !1 };
-    let { ref: u, start: c, end: f } = r;
-    u || (u = 0), c || (c = 0), f || (f = 0), l === "VCF" && (f = 8);
-    const I = Math.max(u, c, f);
-    let w = 1, m = 0, b = "", p = -1 / 0;
-    for (let x = 0; x < a.length + 1; x += 1)
-      if (a[x] === "	" || x === a.length) {
-        if (w === u) {
-          if (this.renameRefSeq(a.slice(m, x)) !== t)
-            return { overlaps: !1 };
-        } else if (w === c) {
-          if (p = parseInt(a.slice(m, x), 10), d === "1-based-closed" && (p -= 1), p >= i)
-            return { startCoordinate: p, overlaps: !1 };
-          if ((f === 0 || f === c) && p + 1 <= n)
-            return { startCoordinate: p, overlaps: !1 };
-        } else if (l === "VCF" && w === 4)
-          b = a.slice(m, x);
-        else if (w === f && (l === "VCF" ? this._getVcfEnd(p, b, a.slice(m, x)) : parseInt(a.slice(m, x), 10)) <= n)
-          return { overlaps: !1 };
-        if (m = x + 1, w += 1, w > I)
+    let { ref: u, start: h, end: c } = a;
+    u || (u = 0), h || (h = 0), c || (c = 0), d === "VCF" && (c = 8);
+    const b = Math.max(u, h, c);
+    let I = 1, m = 0, w = "", x = -1 / 0;
+    const p = s.length;
+    for (let l = 0; l < p + 1; l++)
+      if (s[l] === "	" || l === p) {
+        if (I === u) {
+          if (this.renameRefSeq(s.slice(m, l)) !== t)
+            return {
+              overlaps: !1
+            };
+        } else if (I === h) {
+          if (x = parseInt(s.slice(m, l), 10), f === "1-based-closed" && (x -= 1), x >= i)
+            return {
+              startCoordinate: x,
+              overlaps: !1
+            };
+          if ((c === 0 || c === h) && x + 1 <= n)
+            return {
+              startCoordinate: x,
+              overlaps: !1
+            };
+        } else if (d === "VCF" && I === 4)
+          w = s.slice(m, l);
+        else if (I === c && (d === "VCF" ? this._getVcfEnd(x, w, s.slice(m, l)) : Number.parseInt(s.slice(m, l), 10)) <= n)
+          return {
+            overlaps: !1
+          };
+        if (m = l + 1, I += 1, I > b)
           break;
       }
-    return { startCoordinate: p, overlaps: !0 };
+    return {
+      startCoordinate: x,
+      overlaps: !0
+    };
   }
   _getVcfEnd(e, t, n) {
     let i = e + t.length;
-    const a = n.includes("SVTYPE=TRA");
-    if (n[0] !== "." && !a) {
-      let r = ";";
-      for (let s = 0; s < n.length; s += 1) {
-        if (r === ";" && n.slice(s, s + 4) === "END=") {
-          let d = n.indexOf(";", s);
-          d === -1 && (d = n.length), i = parseInt(n.slice(s + 4, d), 10);
+    const s = n.includes("SVTYPE=TRA");
+    if (n[0] !== "." && !s) {
+      let a = ";";
+      for (let r = 0; r < n.length; r += 1) {
+        if (a === ";" && n.slice(r, r + 4) === "END=") {
+          let f = n.indexOf(";", r);
+          f === -1 && (f = n.length), i = parseInt(n.slice(r + 4, f), 10);
           break;
         }
-        r = n[s];
+        a = n[r];
       }
-    } else if (a)
+    } else if (s)
       return e + 1;
     return i;
   }
@@ -607,8 +632,8 @@ class ue {
     return this.index.lineCount(e, t);
   }
   async _readRegion(e, t, n = {}) {
-    const i = Q.Buffer.alloc(t), { bytesRead: a, buffer: r } = await this.filehandle.read(i, 0, t, e, n);
-    return r.slice(0, a);
+    const i = Q.Buffer.alloc(t), { bytesRead: s, buffer: a } = await this.filehandle.read(i, 0, t, e, n);
+    return a.subarray(0, s);
   }
   /**
    * read and uncompress the data in a chunk (composed of one or more
@@ -620,7 +645,7 @@ class ue {
   }
 }
 export {
-  M as CSI,
-  k as TBI,
+  z as CSI,
+  y as TBI,
   ue as TabixIndexedFile
 };