@genome-spy/app 0.40.0 → 0.42.0

package/package.json

@@ -7,7 +7,7 @@
   },
   "contributors": [],
   "license": "MIT",
-  "version": "0.40.0",
+  "version": "0.42.0",
   "main": "dist/index.js",
   "type": "module",
   "files": [
@@ -29,7 +29,7 @@
     "@fortawesome/fontawesome-free": "^6.4.2",
     "@fortawesome/fontawesome-svg-core": "^6.4.2",
     "@fortawesome/free-solid-svg-icons": "^6.4.2",
-    "@genome-spy/core": "^0.40.0",
+    "@genome-spy/core": "^0.42.0",
     "@reduxjs/toolkit": "^1.8.4",
     "idb": "^7.1.1",
     "lit": "^3.1.0",
@@ -39,5 +39,5 @@
     "redux-undo": "^1.0.1",
     "snarkdown": "^2.0.0"
   },
-  "gitHead": "74d4f6721b31c1916051f868e95be7d83d8d6369"
+  "gitHead": "59a4384ba903ee1b81212593e872ea61accc729d"
 }

package/dist/index-Cbz74kpR.js

@@ -1,638 +0,0 @@
-import { _ as J, L as K } from "./index-LD6yPc3X.js";
-import { L as N } from "./__vite-browser-external-ENoMJThg.js";
-import "./index-1QVesMzU.js";
-import { u as z, L as G, a as Q } from "./long-Veu0zKh9.js";
-import "./_commonjsHelpers-QtkX90xp.js";
-function H(a) {
-  if (a.greaterThan(Number.MAX_SAFE_INTEGER) || a.lessThan(Number.MIN_SAFE_INTEGER))
-    throw new Error("integer overflow");
-  return a.toNumber();
-}
-class W extends Error {
-}
-function L(a) {
-  if (a && a.aborted) {
-    if (typeof DOMException < "u")
-      throw new DOMException("aborted", "AbortError");
-    {
-      const e = new W("aborted");
-      throw e.code = "ERR_ABORTED", e;
-    }
-  }
-}
-function Z(a, e) {
-  return e.minv.blockPosition - a.maxv.blockPosition < 65e3 && e.maxv.blockPosition - a.minv.blockPosition < 5e6;
-}
-function j(a, e) {
-  const t = [];
-  let n = null;
-  return a.length === 0 ? a : (a.sort(function(r, i) {
-    const o = r.minv.blockPosition - i.minv.blockPosition;
-    return o !== 0 ? o : r.minv.dataPosition - i.minv.dataPosition;
-  }), a.forEach((r) => {
-    (!e || r.maxv.compareTo(e) > 0) && (n === null ? (t.push(r), n = r) : Z(n, r) ? r.maxv.compareTo(n.maxv) > 0 && (n.maxv = r.maxv) : (t.push(r), n = r));
-  }), t);
-}
-class R {
-  constructor(e, t) {
-    this.blockPosition = e, this.dataPosition = t;
-  }
-  toString() {
-    return `${this.blockPosition}:${this.dataPosition}`;
-  }
-  compareTo(e) {
-    return this.blockPosition - e.blockPosition || this.dataPosition - e.dataPosition;
-  }
-  static min(...e) {
-    let t, n = 0;
-    for (; !t; n += 1)
-      t = e[n];
-    for (; n < e.length; n += 1)
-      t.compareTo(e[n]) > 0 && (t = e[n]);
-    return t;
-  }
-}
-function v(a, e = 0, t = !1) {
-  if (t)
-    throw new Error("big-endian virtual file offsets not implemented");
-  return new R(a[e + 7] * 1099511627776 + a[e + 6] * 4294967296 + a[e + 5] * 16777216 + a[e + 4] * 65536 + a[e + 3] * 256 + a[e + 2], a[e + 1] << 8 | a[e]);
-}
-class P {
-  /**
-   * @param {VirtualOffset} minv
-   * @param {VirtualOffset} maxv
-   * @param {number} bin
-   * @param {number} [fetchedSize]
-   */
-  constructor(e, t, n, r = void 0) {
-    this.minv = e, this.maxv = t, this.bin = n, this._fetchedSize = r;
-  }
-  toUniqueString() {
-    return `${this.minv}..${this.maxv} (bin ${this.bin}, fetchedSize ${this.fetchedSize()})`;
-  }
-  toString() {
-    return this.toUniqueString();
-  }
-  compareTo(e) {
-    return this.minv.compareTo(e.minv) || this.maxv.compareTo(e.maxv) || this.bin - e.bin;
-  }
-  fetchedSize() {
-    return this._fetchedSize !== void 0 ? this._fetchedSize : this.maxv.blockPosition + 65536 - this.minv.blockPosition;
-  }
-}
-class X {
-  constructor({ filehandle: e, renameRefSeqs: t = (n) => n }) {
-    this.filehandle = e, this.renameRefSeq = t;
-  }
-  async getMetadata(e = {}) {
-    const { indices: t, ...n } = await this.parse(e);
-    return n;
-  }
-  _findFirstData(e, t) {
-    return e ? e.compareTo(t) > 0 ? t : e : t;
-  }
-  async parse(e = {}) {
-    return this.parseP || (this.parseP = this._parse(e).catch((t) => {
-      throw this.parseP = void 0, t;
-    })), this.parseP;
-  }
-  async hasRefSeq(e, t = {}) {
-    return !!((await this.parse(t)).indices[e] || {}).binIndex;
-  }
-}
-const ee = 21578324, O = 14;
-function te(a, e) {
-  return a += 1, e -= 1, [
-    [0, 0],
-    [1 + (a >> 26), 1 + (e >> 26)],
-    [9 + (a >> 23), 9 + (e >> 23)],
-    [73 + (a >> 20), 73 + (e >> 20)],
-    [585 + (a >> 17), 585 + (e >> 17)],
-    [4681 + (a >> 14), 4681 + (e >> 14)]
-  ];
-}
-class A extends X {
-  async lineCount(e, t = {}) {
-    const n = await this.parse(t);
-    if (!n)
-      return -1;
-    const r = n.refNameToId[e];
-    if (!n.indices[r])
-      return -1;
-    const { stats: o } = n.indices[r];
-    return o ? o.lineCount : -1;
-  }
-  // fetch and parse the index
-  async _parse(e = {}) {
-    const t = await this.filehandle.readFile(e), n = await z(t);
-    if (L(e.signal), n.readUInt32LE(0) !== ee)
-      throw new Error("Not a TBI file");
-    const r = n.readInt32LE(4), i = n.readInt32LE(8), o = i & 65536 ? "zero-based-half-open" : "1-based-closed", u = {
-      0: "generic",
-      1: "SAM",
-      2: "VCF"
-    }[i & 15];
-    if (!u)
-      throw new Error(`invalid Tabix preset format flags ${i}`);
-    const c = {
-      ref: n.readInt32LE(12),
-      start: n.readInt32LE(16),
-      end: n.readInt32LE(20)
-    }, h = n.readInt32LE(24), f = 5, l = ((1 << (f + 1) * 3) - 1) / 7, I = 2 ** (14 + f * 3), x = h ? String.fromCharCode(h) : null, w = n.readInt32LE(28), b = n.readInt32LE(32), { refNameToId: m, refIdToName: p } = this._parseNameBytes(n.slice(36, 36 + b));
-    let d = 36 + b, g;
-    return {
-      indices: new Array(r).fill(0).map(() => {
-        const E = n.readInt32LE(d);
-        d += 4;
-        const k = {};
-        let $;
-        for (let C = 0; C < E; C += 1) {
-          const y = n.readUInt32LE(d);
-          if (d += 4, y > l + 1)
-            throw new Error("tabix index contains too many bins, please use a CSI index");
-          if (y === l + 1) {
-            const S = n.readInt32LE(d);
-            d += 4, S === 2 && ($ = this.parsePseudoBin(n, d)), d += 16 * S;
-          } else {
-            const S = n.readInt32LE(d);
-            d += 4;
-            const M = new Array(S);
-            for (let B = 0; B < S; B += 1) {
-              const V = v(n, d), Y = v(n, d + 8);
-              d += 16, g = this._findFirstData(g, V), M[B] = new P(V, Y, y);
-            }
-            k[y] = M;
-          }
-        }
-        const F = n.readInt32LE(d);
-        d += 4;
-        const _ = new Array(F);
-        for (let C = 0; C < F; C += 1)
-          _[C] = v(n, d), d += 8, g = this._findFirstData(g, _[C]);
-        return { binIndex: k, linearIndex: _, stats: $ };
-      }),
-      metaChar: x,
-      maxBinNumber: l,
-      maxRefLength: I,
-      skipLines: w,
-      firstDataLine: g,
-      columnNumbers: c,
-      coordinateType: o,
-      format: u,
-      refIdToName: p,
-      refNameToId: m,
-      maxBlockSize: 65536
-    };
-  }
-  parsePseudoBin(e, t) {
-    return { lineCount: H(G.fromBytesLE(e.slice(t + 16, t + 24), !0)) };
-  }
-  _parseNameBytes(e) {
-    let t = 0, n = 0;
-    const r = [], i = {};
-    for (let o = 0; o < e.length; o += 1)
-      if (!e[o]) {
-        if (n < o) {
-          let s = e.toString("utf8", n, o);
-          s = this.renameRefSeq(s), r[t] = s, i[s] = t;
-        }
-        n = o + 1, t += 1;
-      }
-    return { refNameToId: i, refIdToName: r };
-  }
-  async blocksForRange(e, t, n, r = {}) {
-    t < 0 && (t = 0);
-    const i = await this.parse(r);
-    if (!i)
-      return [];
-    const o = i.refNameToId[e], s = i.indices[o];
-    if (!s)
-      return [];
-    (s.linearIndex.length ? s.linearIndex[t >> O >= s.linearIndex.length ? s.linearIndex.length - 1 : t >> O] : new R(0, 0)) || console.warn("querying outside of possible tabix range");
-    const c = te(t, n), h = [];
-    for (const [w, b] of c)
-      for (let m = w; m <= b; m++)
-        if (s.binIndex[m]) {
-          const p = s.binIndex[m];
-          for (let d = 0; d < p.length; ++d)
-            h.push(new P(p[d].minv, p[d].maxv, m));
-        }
-    const f = s.linearIndex.length;
-    let l = null;
-    const I = Math.min(t >> 14, f - 1), x = Math.min(n >> 14, f - 1);
-    for (let w = I; w <= x; ++w) {
-      const b = s.linearIndex[w];
-      b && (!l || b.compareTo(l) < 0) && (l = b);
-    }
-    return j(h, l);
-  }
-}
-const ne = 21582659, ie = 38359875;
-function re(a, e) {
-  return a * 2 ** e;
-}
-function q(a, e) {
-  return Math.floor(a / 2 ** e);
-}
-class U extends X {
-  constructor(e) {
-    super(e), this.maxBinNumber = 0, this.depth = 0, this.minShift = 0;
-  }
-  async lineCount(e, t = {}) {
-    const n = await this.parse(t);
-    if (!n)
-      return -1;
-    const r = n.refNameToId[e];
-    if (!n.indices[r])
-      return -1;
-    const { stats: o } = n.indices[r];
-    return o ? o.lineCount : -1;
-  }
-  async indexCov() {
-    throw new Error("CSI indexes do not support indexcov");
-  }
-  parseAuxData(e, t) {
-    const n = e.readInt32LE(t), r = n & 65536 ? "zero-based-half-open" : "1-based-closed", i = { 0: "generic", 1: "SAM", 2: "VCF" }[n & 15];
-    if (!i)
-      throw new Error(`invalid Tabix preset format flags ${n}`);
-    const o = {
-      ref: e.readInt32LE(t + 4),
-      start: e.readInt32LE(t + 8),
-      end: e.readInt32LE(t + 12)
-    }, s = e.readInt32LE(t + 16), u = s ? String.fromCharCode(s) : null, c = e.readInt32LE(t + 20), h = e.readInt32LE(t + 24), { refIdToName: f, refNameToId: l } = this._parseNameBytes(e.slice(t + 28, t + 28 + h));
-    return {
-      refIdToName: f,
-      refNameToId: l,
-      skipLines: c,
-      metaChar: u,
-      columnNumbers: o,
-      format: i,
-      coordinateType: r
-    };
-  }
-  _parseNameBytes(e) {
-    let t = 0, n = 0;
-    const r = [], i = {};
-    for (let o = 0; o < e.length; o += 1)
-      if (!e[o]) {
-        if (n < o) {
-          let s = e.toString("utf8", n, o);
-          s = this.renameRefSeq(s), r[t] = s, i[s] = t;
-        }
-        n = o + 1, t += 1;
-      }
-    return { refNameToId: i, refIdToName: r };
-  }
-  // fetch and parse the index
-  async _parse(e = {}) {
-    const t = await z(await this.filehandle.readFile(e));
-    let n;
-    if (t.readUInt32LE(0) === ne)
-      n = 1;
-    else if (t.readUInt32LE(0) === ie)
-      n = 2;
-    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 r = 2 ** (this.minShift + this.depth * 3), i = t.readInt32LE(12), o = i && i >= 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 + i);
-    let u, c = 16 + i + 4;
-    const h = new Array(s).fill(0).map(() => {
-      const f = t.readInt32LE(c);
-      c += 4;
-      const l = {};
-      let I;
-      for (let x = 0; x < f; x += 1) {
-        const w = t.readUInt32LE(c);
-        if (w > this.maxBinNumber)
-          I = this.parsePseudoBin(t, c + 4), c += 4 + 8 + 4 + 16 + 16;
-        else {
-          const b = v(t, c + 4);
-          u = this._findFirstData(u, b);
-          const m = t.readInt32LE(c + 12);
-          c += 16;
-          const p = new Array(m);
-          for (let d = 0; d < m; d += 1) {
-            const g = v(t, c), T = v(t, c + 8);
-            c += 16, p[d] = new P(g, T, w);
-          }
-          l[w] = p;
-        }
-      }
-      return { binIndex: l, stats: I };
-    });
-    return {
-      ...o,
-      csi: !0,
-      refCount: s,
-      maxBlockSize: 65536,
-      firstDataLine: u,
-      csiVersion: n,
-      indices: h,
-      depth: this.depth,
-      maxBinNumber: this.maxBinNumber,
-      maxRefLength: r
-    };
-  }
-  parsePseudoBin(e, t) {
-    return { lineCount: H(G.fromBytesLE(e.slice(t + 28, t + 36), !0)) };
-  }
-  async blocksForRange(e, t, n, r = {}) {
-    t < 0 && (t = 0);
-    const i = await this.parse(r);
-    if (!i)
-      return [];
-    const o = i.refNameToId[e], s = i.indices[o];
-    if (!s)
-      return [];
-    const u = this.reg2bins(t, n), c = [];
-    for (const [h, f] of u)
-      for (let l = h; l <= f; l++)
-        if (s.binIndex[l]) {
-          const I = s.binIndex[l];
-          for (let x = 0; x < I.length; ++x)
-            c.push(new P(I[x].minv, I[x].maxv, l));
-        }
-    return j(c, new R(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, r = 0, i = this.minShift + this.depth * 3;
-    const o = [];
-    for (; n <= this.depth; i -= 3, r += re(1, n * 3), n += 1) {
-      const s = r + q(e, i), u = r + q(t, i);
-      if (u - s + o.length > this.maxBinNumber)
-        throw new Error(`query ${e}-${t} is too large for current binning scheme (shift ${this.minShift}, depth ${this.depth}), try a smaller query or a coarser index binning scheme`);
-      o.push([s, u]);
-    }
-    return o;
-  }
-}
-const D = typeof TextDecoder < "u" ? new TextDecoder("utf-8") : void 0;
-function oe(a) {
-  return new Promise((e) => setTimeout(e, a));
-}
-class fe {
-  /**
-   * @param {object} args
-   * @param {string} [args.path]
-   * @param {filehandle} [args.filehandle]
-   * @param {string} [args.tbiPath]
-   * @param {filehandle} [args.tbiFilehandle]
-   * @param {string} [args.csiPath]
-   * @param {filehandle} [args.csiFilehandle]
-   * @param {number} [args.yieldTime] yield to main thread after N milliseconds if reading features is taking a long time to avoid hanging main thread
-   * @param {function} [args.renameRefSeqs] optional function with sig `string => string` to transform
-   * reference sequence names for the purpose of indexing and querying. note that the data that is returned is
-   * not altered, just the names of the reference sequences that are used for querying.
-   */
-  constructor({ path: e, filehandle: t, tbiPath: n, tbiFilehandle: r, csiPath: i, csiFilehandle: o, yieldTime: s = 500, chunkSizeLimit: u = 5e7, renameRefSeqs: c = (f) => f, chunkCacheSize: h = 5 * 2 ** 20 }) {
-    if (t)
-      this.filehandle = t;
-    else if (e)
-      this.filehandle = new N(e);
-    else
-      throw new TypeError("must provide either filehandle or path");
-    if (r)
-      this.index = new A({
-        filehandle: r,
-        renameRefSeqs: c
-      });
-    else if (o)
-      this.index = new U({
-        filehandle: o,
-        renameRefSeqs: c
-      });
-    else if (n)
-      this.index = new A({
-        filehandle: new N(n),
-        renameRefSeqs: c
-      });
-    else if (i)
-      this.index = new U({
-        filehandle: new N(i),
-        renameRefSeqs: c
-      });
-    else if (e)
-      this.index = new A({
-        filehandle: new N(`${e}.tbi`),
-        renameRefSeqs: c
-      });
-    else
-      throw new TypeError("must provide one of tbiFilehandle, tbiPath, csiFilehandle, or csiPath");
-    this.chunkSizeLimit = u, this.renameRefSeq = c, this.yieldTime = s, this.chunkCache = new J({
-      cache: new K({ maxSize: Math.floor(h / 65536) }),
-      fill: (f, l) => this.readChunk(f, { signal: l })
-    });
-  }
-  /**
-   * @param refName name of the reference sequence
-   * @param start start of the region (in 0-based half-open coordinates)
-   * @param end end of the region (in 0-based half-open coordinates)
-   * @param opts callback called for each line in the region. can also pass a object param containing obj.lineCallback, obj.signal, etc
-   * @returns promise that is resolved when the whole read is finished, rejected on error
-   */
-  async getLines(e, t, n, r) {
-    let i, o = {}, s;
-    if (typeof r > "u")
-      throw new TypeError("line callback must be provided");
-    if (typeof r == "function" ? s = r : (o = r, s = r.lineCallback), e === void 0)
-      throw new TypeError("must provide a reference sequence name");
-    if (!s)
-      throw new TypeError("line callback must be provided");
-    const u = await this.index.getMetadata(o);
-    if (L(i), t || (t = 0), n || (n = u.maxRefLength), !(t <= n))
-      throw new TypeError("invalid start and end coordinates. start must be less than or equal to end");
-    if (t === n)
-      return;
-    const c = await this.index.blocksForRange(e, t, n, o);
-    L(i);
-    for (let f = 0; f < c.length; f += 1) {
-      const l = c[f].fetchedSize();
-      if (l > this.chunkSizeLimit)
-        throw new Error(`Too much data. Chunk size ${l.toLocaleString()} bytes exceeds chunkSizeLimit of ${this.chunkSizeLimit.toLocaleString()}.`);
-    }
-    let h = Date.now();
-    for (let f = 0; f < c.length; f += 1) {
-      let l;
-      const I = c[f], { buffer: x, cpositions: w, dpositions: b } = await this.chunkCache.get(I.toString(), I);
-      L(i);
-      let m = 0, p = 0;
-      for (; m < x.length; ) {
-        const d = x.indexOf(`
-`, m);
-        if (d === -1)
-          break;
-        const g = x.slice(m, d), T = (D == null ? void 0 : D.decode(g)) || g.toString();
-        if (b) {
-          for (; m + I.minv.dataPosition >= b[p++]; )
-            ;
-          p--;
-        }
-        const { startCoordinate: E, overlaps: k } = this.checkLine(u, e, t, n, T);
-        if (l !== void 0 && E !== void 0 && l > E)
-          throw new Error(`Lines not sorted by start coordinate (${l} > ${E}), this file is not usable with Tabix.`);
-        if (l = E, k)
-          s(
-            T.trim(),
-            // 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
-            //
-            // 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[p] * 256 + (m - b[p]) + I.minv.dataPosition + 1
-          );
-        else if (E !== void 0 && E >= n)
-          return;
-        this.yieldTime && h - Date.now() > this.yieldTime && (h = Date.now(), L(i), await oe(1)), m = d + 1;
-      }
-    }
-  }
-  async getMetadata(e = {}) {
-    return this.index.getMetadata(e);
-  }
-  /**
-   * get a buffer containing the "header" region of
-   * the file, which are the bytes up to the first
-   * non-meta line
-   */
-  async getHeaderBuffer(e = {}) {
-    const { firstDataLine: t, metaChar: n, maxBlockSize: r } = await this.getMetadata(e);
-    L(e.signal);
-    const i = ((t == null ? void 0 : t.blockPosition) || 0) + r;
-    let o = await this._readRegion(0, i, e);
-    L(e.signal);
-    try {
-      o = await z(o);
-    } catch (s) {
-      throw console.error(s), new Error(
-        //@ts-ignore
-        `error decompressing block ${s.code} at 0 (length ${i}) ${s}`
-      );
-    }
-    if (n) {
-      let s = -1;
-      const u = `
-`.charCodeAt(0), c = n.charCodeAt(0);
-      for (let h = 0; h < o.length && !(h === s + 1 && o[h] !== c); h += 1)
-        o[h] === u && (s = h);
-      o = o.slice(0, s + 1);
-    }
-    return o;
-  }
-  /**
-   * get a string containing the "header" region of the
-   * file, is the portion up to the first non-meta line
-   *
-   * @returns {Promise} for a string
-   */
-  async getHeader(e = {}) {
-    return (await this.getHeaderBuffer(e)).toString("utf8");
-  }
-  /**
-   * get an array of reference sequence names, in the order in which
-   * they occur in the file. reference sequence renaming is not applied
-   * to these names.
-   */
-  async getReferenceSequenceNames(e = {}) {
-    return (await this.getMetadata(e)).refIdToName;
-  }
-  /**
-   * @param {object} metadata metadata object from the parsed index,
-   * containing columnNumbers, metaChar, and format
-   * @param {string} regionRefName
-   * @param {number} regionStart region start coordinate (0-based-half-open)
-   * @param {number} regionEnd region end coordinate (0-based-half-open)
-   * @param {array[string]} line
-   * @returns {object} like `{startCoordinate, overlaps}`. overlaps is boolean,
-   * true if line is a data line that overlaps the given region
-   */
-  checkLine(e, t, n, r, i) {
-    const { columnNumbers: o, metaChar: s, coordinateType: u, format: c } = e;
-    if (i.charAt(0) === s)
-      return { overlaps: !1 };
-    let { ref: h, start: f, end: l } = o;
-    h || (h = 0), f || (f = 0), l || (l = 0), c === "VCF" && (l = 8);
-    const I = Math.max(h, f, l);
-    let x = 1, w = 0, b = "", m = -1 / 0;
-    for (let p = 0; p < i.length + 1; p += 1)
-      if (i[p] === "	" || p === i.length) {
-        if (x === h) {
-          if (this.renameRefSeq(i.slice(w, p)) !== t)
-            return { overlaps: !1 };
-        } else if (x === f) {
-          if (m = parseInt(i.slice(w, p), 10), u === "1-based-closed" && (m -= 1), m >= r)
-            return { startCoordinate: m, overlaps: !1 };
-          if ((l === 0 || l === f) && m + 1 <= n)
-            return { startCoordinate: m, overlaps: !1 };
-        } else if (c === "VCF" && x === 4)
-          b = i.slice(w, p);
-        else if (x === l) {
-          let d;
-          if (c === "VCF" ? d = this._getVcfEnd(m, b, i.slice(w, p)) : d = parseInt(i.slice(w, p), 10), d <= n)
-            return { overlaps: !1 };
-        }
-        if (w = p + 1, x += 1, x > I)
-          break;
-      }
-    return { startCoordinate: m, overlaps: !0 };
-  }
-  _getVcfEnd(e, t, n) {
-    let r = e + t.length;
-    const i = n.indexOf("SVTYPE=TRA") !== -1;
-    if (n[0] !== "." && !i) {
-      let o = ";";
-      for (let s = 0; s < n.length; s += 1) {
-        if (o === ";" && n.slice(s, s + 4) === "END=") {
-          let u = n.indexOf(";", s);
-          u === -1 && (u = n.length), r = parseInt(n.slice(s + 4, u), 10);
-          break;
-        }
-        o = n[s];
-      }
-    } else if (i)
-      return e + 1;
-    return r;
-  }
-  /**
-   * return the approximate number of data lines in the given reference sequence
-   * @param refSeq reference sequence name
-   * @returns number of data lines present on that reference sequence
-   */
-  async lineCount(e, t = {}) {
-    return this.index.lineCount(e, t);
-  }
-  async _readRegion(e, t, n = {}) {
-    const r = Buffer.alloc(t), { bytesRead: i, buffer: o } = await this.filehandle.read(r, 0, t, e, n);
-    return o.slice(0, i);
-  }
-  /**
-   * read and uncompress the data in a chunk (composed of one or more
-   * contiguous bgzip blocks) of the file
-   */
-  async readChunk(e, t = {}) {
-    const n = await this._readRegion(e.minv.blockPosition, e.fetchedSize(), t);
-    try {
-      return Q(n, e);
-    } catch (r) {
-      throw new Error(`error decompressing c ${e.toString()} ${r}`);
-    }
-  }
-}
-export {
-  U as CSI,
-  A as TBI,
-  fe as TabixIndexedFile
-};