@genome-spy/core 0.64.0 → 0.65.0

package/dist/bundle/index-CCe8rnZz.js

@@ -0,0 +1,716 @@
+import { A as te } from "./AbortablePromiseCache-CcuMrnn7.js";
+import { I as Y, Z } from "./inflate-DRgHi_KK.js";
+import { LocalFile as E, RemoteFile as D } from "./browser-txUcLy2H.js";
+import { L as H } from "./index-BhtHKLUo.js";
+function ne(s) {
+  let e = 0;
+  for (const t of s)
+    e += t.length;
+  return e;
+}
+function K(s, e) {
+  const t = new Uint8Array(e ?? ne(s));
+  let n = 0;
+  for (const i of s)
+    t.set(i, n), n += i.length;
+  return t;
+}
+async function V(s) {
+  try {
+    let e, t = 0, n;
+    const i = [];
+    let o = 0;
+    do {
+      const a = s.subarray(t);
+      if (n = new Y(void 0), { strm: e } = n, n.push(a, Z), n.err)
+        throw new Error(n.msg);
+      t += e.next_in;
+      const r = n.result;
+      i.push(r), o += r.length;
+    } while (e.avail_in);
+    return K(i, o);
+  } catch (e) {
+    throw /incorrect header check/.exec(`${e}`) ? new Error("problem decompressing block: incorrect gzip header check") : e;
+  }
+}
+async function ie(s, e, t) {
+  try {
+    let n;
+    const { minv: i, maxv: o } = e;
+    let a = i.blockPosition, r = i.dataPosition;
+    const l = [], m = [], c = [];
+    let u = 0, f = !1, g = 0;
+    do {
+      const b = s.subarray(a - i.blockPosition), I = a.toString();
+      let x, h;
+      const p = t == null ? void 0 : t.get(I);
+      if (p)
+        x = p.buffer, h = p.nextIn, f = !0;
+      else {
+        const d = new Y(void 0);
+        if ({ strm: n } = d, d.push(b, Z), d.err)
+          throw new Error(d.msg);
+        x = d.result, h = n.next_in, f = !1, t == null || t.set(I, { buffer: x, nextIn: h });
+      }
+      l.push(x);
+      let w = x.length;
+      m.push(a), c.push(r), l.length === 1 && i.dataPosition && (l[0] = l[0].subarray(i.dataPosition), w = l[0].length);
+      const k = a;
+      if (a += h, r += w, k >= o.blockPosition) {
+        l[u] = l[u].subarray(0, o.blockPosition === i.blockPosition ? o.dataPosition - i.dataPosition + 1 : o.dataPosition + 1), g += l[u].length, m.push(a), c.push(r);
+        break;
+      }
+      g += w, u++;
+    } while (f ? a < s.length + i.blockPosition : (
+      // eslint-disable-next-line @typescript-eslint/no-unnecessary-type-assertion
+      n.avail_in
+    ));
+    return {
+      buffer: K(l, g),
+      cpositions: m,
+      dpositions: c
+    };
+  } catch (n) {
+    throw /incorrect header check/.exec(`${n}`) ? new Error("problem decompressing block: incorrect gzip header check") : n;
+  }
+}
+class L {
+  constructor(e, t, n, i) {
+    this.minv = e, this.maxv = t, this.bin = n, this._fetchedSize = i;
+  }
+  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 = {}) {
+    var i;
+    return !!((i = (await this.parse(t)).indices[e]) != null && i.binIndex);
+  }
+  _parseNameBytes(e) {
+    let t = 0, n = 0;
+    const i = [], o = {}, a = new TextDecoder("utf8");
+    for (let r = 0; r < e.length; r += 1)
+      if (!e[r]) {
+        if (n < r) {
+          const l = this.renameRefSeq(a.decode(e.subarray(n, r)));
+          i[t] = l, o[l] = t;
+        }
+        n = r + 1, t += 1;
+      }
+    return {
+      refNameToId: o,
+      refIdToName: i
+    };
+  }
+}
+const W = 65536, re = W * W;
+function J(s, e = 0) {
+  const t = s[e] | s[e + 1] << 8 | s[e + 2] << 16 | s[e + 3] << 24;
+  return ((s[e + 4] | s[e + 5] << 8 | s[e + 6] << 16 | s[e + 7] << 24) >>> 0) * re + (t >>> 0);
+}
+class se extends Error {
+}
+function B(s) {
+  if (s && s.aborted)
+    if (typeof DOMException > "u") {
+      const e = new se("aborted");
+      throw e.code = "ERR_ABORTED", e;
+    } else
+      throw new DOMException("aborted", "AbortError");
+}
+function oe(s, e) {
+  return e.minv.blockPosition - s.maxv.blockPosition < 65e3 && e.maxv.blockPosition - s.minv.blockPosition < 5e6;
+}
+function Q(s, e) {
+  const t = [];
+  let n;
+  if (s.length === 0)
+    return s;
+  s.sort(function(i, o) {
+    const a = i.minv.blockPosition - o.minv.blockPosition;
+    return a === 0 ? i.minv.dataPosition - o.minv.dataPosition : a;
+  });
+  for (const i of s)
+    (!e || i.maxv.compareTo(e) > 0) && (n === void 0 ? (t.push(i), n = i) : oe(n, i) ? i.maxv.compareTo(n.maxv) > 0 && (n.maxv = i.maxv) : (t.push(i), n = i));
+  return t;
+}
+class $ {
+  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;
+  }
+}
+function T(s, e = 0) {
+  return new $(s[e + 7] * 1099511627776 + s[e + 6] * 4294967296 + s[e + 5] * 16777216 + s[e + 4] * 65536 + s[e + 3] * 256 + s[e + 2], s[e + 1] << 8 | s[e]);
+}
+const ae = 21582659, ce = 38359875, le = {
+  0: "generic",
+  1: "SAM",
+  2: "VCF"
+};
+function fe(s, e) {
+  return s * 2 ** e;
+}
+function G(s, e) {
+  return Math.floor(s / 2 ** e);
+}
+class R 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), i = n.refNameToId[e];
+    if (i === void 0 || !n.indices[i])
+      return -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 = new DataView(e.buffer), i = n.getInt32(t, !0), o = i & 65536 ? "zero-based-half-open" : "1-based-closed", a = le[i & 15];
+    if (!a)
+      throw new Error(`invalid Tabix preset format flags ${i}`);
+    const r = {
+      ref: n.getInt32(t + 4, !0),
+      start: n.getInt32(t + 8, !0),
+      end: n.getInt32(t + 12, !0)
+    }, l = n.getInt32(t + 16, !0), m = l ? String.fromCharCode(l) : void 0, c = n.getInt32(t + 20, !0), u = n.getInt32(t + 24, !0), { refIdToName: f, refNameToId: g } = this._parseNameBytes(e.subarray(t + 28, t + 28 + u));
+    return {
+      refIdToName: f,
+      refNameToId: g,
+      skipLines: c,
+      metaChar: m,
+      columnNumbers: r,
+      format: a,
+      coordinateType: o
+    };
+  }
+  async _parse(e = {}) {
+    const t = await V(await this.filehandle.readFile(e)), n = new DataView(t.buffer);
+    let i;
+    if (n.getUint32(0, !0) === ae)
+      i = 1;
+    else if (n.getUint32(0, !0) === ce)
+      i = 2;
+    else
+      throw new Error("Not a CSI file");
+    this.minShift = n.getInt32(4, !0), this.depth = n.getInt32(8, !0), this.maxBinNumber = ((1 << (this.depth + 1) * 3) - 1) / 7;
+    const o = 2 ** (this.minShift + this.depth * 3), a = n.getInt32(12, !0), r = a && a >= 30 ? this.parseAuxData(t, 16) : {
+      refIdToName: [],
+      refNameToId: {},
+      metaChar: void 0,
+      columnNumbers: { ref: 0, start: 1, end: 2 },
+      coordinateType: "zero-based-half-open",
+      format: "generic"
+    }, l = n.getInt32(16 + a, !0);
+    let m, c = 16 + a + 4;
+    const u = new Array(l).fill(0).map(() => {
+      const f = n.getInt32(c, !0);
+      c += 4;
+      const g = {};
+      let b;
+      for (let I = 0; I < f; I += 1) {
+        const x = n.getUint32(c, !0);
+        if (x > this.maxBinNumber)
+          b = this.parsePseudoBin(t, c + 4), c += 48;
+        else {
+          const h = T(t, c + 4);
+          m = this._findFirstData(m, h);
+          const p = n.getInt32(c + 12, !0);
+          c += 16;
+          const w = new Array(p);
+          for (let k = 0; k < p; k += 1) {
+            const d = T(t, c), C = T(t, c + 8);
+            c += 16, w[k] = new L(d, C, x);
+          }
+          g[x] = w;
+        }
+      }
+      return { binIndex: g, stats: b };
+    });
+    return {
+      ...r,
+      csi: !0,
+      refCount: l,
+      maxBlockSize: 65536,
+      firstDataLine: m,
+      csiVersion: i,
+      indices: u,
+      depth: this.depth,
+      maxBinNumber: this.maxBinNumber,
+      maxRefLength: o
+    };
+  }
+  parsePseudoBin(e, t) {
+    return {
+      lineCount: J(e, t + 28)
+    };
+  }
+  async blocksForRange(e, t, n, i = {}) {
+    t < 0 && (t = 0);
+    const o = await this.parse(i), a = o.refNameToId[e];
+    if (a === void 0)
+      return [];
+    const r = o.indices[a];
+    if (!r)
+      return [];
+    const l = this.reg2bins(t, n), m = [];
+    for (const [c, u] of l)
+      for (let f = c; f <= u; f++)
+        if (r.binIndex[f])
+          for (const g of r.binIndex[f])
+            m.push(new L(g.minv, g.maxv, f));
+    return Q(m, new $(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, o = this.minShift + this.depth * 3;
+    const a = [];
+    for (; n <= this.depth; o -= 3, i += fe(1, n * 3), n += 1) {
+      const r = i + G(e, o), l = i + G(t, o);
+      if (l - 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`);
+      a.push([r, l]);
+    }
+    return a;
+  }
+}
+const he = 21578324, j = 14;
+function de(s, e) {
+  return s += 1, e -= 1, [
+    [0, 0],
+    [1 + (s >> 26), 1 + (e >> 26)],
+    [9 + (s >> 23), 9 + (e >> 23)],
+    [73 + (s >> 20), 73 + (e >> 20)],
+    [585 + (s >> 17), 585 + (e >> 17)],
+    [4681 + (s >> 14), 4681 + (e >> 14)]
+  ];
+}
+class _ extends X {
+  async lineCount(e, t = {}) {
+    var a;
+    const n = await this.parse(t), i = n.refNameToId[e];
+    return i === void 0 || !n.indices[i] ? -1 : ((a = n.indices[i].stats) == null ? void 0 : a.lineCount) ?? -1;
+  }
+  // fetch and parse the index
+  async _parse(e = {}) {
+    const t = await this.filehandle.readFile(e), n = await V(t);
+    B(e.signal);
+    const i = new DataView(n.buffer);
+    if (i.getUint32(0, !0) !== he)
+      throw new Error("Not a TBI file");
+    const a = i.getUint32(4, !0), r = i.getUint32(8, !0), l = r & 65536 ? "zero-based-half-open" : "1-based-closed", c = {
+      0: "generic",
+      1: "SAM",
+      2: "VCF"
+    }[r & 15];
+    if (!c)
+      throw new Error(`invalid Tabix preset format flags ${r}`);
+    const u = {
+      ref: i.getInt32(12, !0),
+      start: i.getInt32(16, !0),
+      end: i.getInt32(20, !0)
+    }, f = i.getInt32(24, !0), g = 5, b = ((1 << (g + 1) * 3) - 1) / 7, I = 2 ** (14 + g * 3), x = f ? String.fromCharCode(f) : void 0, h = i.getInt32(28, !0), p = i.getInt32(32, !0), { refNameToId: w, refIdToName: k } = this._parseNameBytes(n.slice(36, 36 + p));
+    let d = 36 + p, C;
+    return {
+      indices: new Array(a).fill(0).map(() => {
+        const P = i.getInt32(d, !0);
+        d += 4;
+        const S = {};
+        let A;
+        for (let v = 0; v < P; v += 1) {
+          const F = i.getUint32(d, !0);
+          if (d += 4, F > b + 1)
+            throw new Error("tabix index contains too many bins, please use a CSI index");
+          if (F === b + 1) {
+            const N = i.getInt32(d, !0);
+            d += 4, N === 2 && (A = this.parsePseudoBin(n, d)), d += 16 * N;
+          } else {
+            const N = i.getInt32(d, !0);
+            d += 4;
+            const U = new Array(N);
+            for (let M = 0; M < N; M += 1) {
+              const q = T(n, d), ee = T(n, d + 8);
+              d += 16, C = this._findFirstData(C, q), U[M] = new L(q, ee, F);
+            }
+            S[F] = U;
+          }
+        }
+        const O = i.getInt32(d, !0);
+        d += 4;
+        const z = new Array(O);
+        for (let v = 0; v < O; v += 1)
+          z[v] = T(n, d), d += 8, C = this._findFirstData(C, z[v]);
+        return {
+          binIndex: S,
+          linearIndex: z,
+          stats: A
+        };
+      }),
+      metaChar: x,
+      maxBinNumber: b,
+      maxRefLength: I,
+      skipLines: h,
+      firstDataLine: C,
+      columnNumbers: u,
+      coordinateType: l,
+      format: c,
+      refIdToName: k,
+      refNameToId: w,
+      maxBlockSize: 65536
+    };
+  }
+  parsePseudoBin(e, t) {
+    return {
+      lineCount: J(e, t + 16)
+    };
+  }
+  async blocksForRange(e, t, n, i = {}) {
+    t < 0 && (t = 0);
+    const o = await this.parse(i), a = o.refNameToId[e];
+    if (a === void 0)
+      return [];
+    const r = o.indices[a];
+    if (!r)
+      return [];
+    (r.linearIndex.length > 0 ? r.linearIndex[t >> j >= r.linearIndex.length ? r.linearIndex.length - 1 : t >> j] : new $(0, 0)) || console.warn("querying outside of possible tabix range");
+    const m = de(t, n), c = [];
+    for (const [I, x] of m)
+      for (let h = I; h <= x; h++)
+        if (r.binIndex[h])
+          for (const p of r.binIndex[h])
+            c.push(new L(p.minv, p.maxv, h));
+    const u = r.linearIndex.length;
+    let f;
+    const g = Math.min(t >> 14, u - 1), b = Math.min(n >> 14, u - 1);
+    for (let I = g; I <= b; ++I) {
+      const x = r.linearIndex[I];
+      x && (!f || x.compareTo(f) < 0) && (f = x);
+    }
+    return Q(c, f);
+  }
+}
+class pe {
+  /**
+   * @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 {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: o, tbiFilehandle: a, csiPath: r, csiUrl: l, csiFilehandle: m, renameRefSeqs: c = (f) => f, chunkCacheSize: u = 5 * 2 ** 20 }) {
+    if (this.cache = new H({
+      maxSize: 1e3
+    }), t)
+      this.filehandle = t;
+    else if (e)
+      this.filehandle = new E(e);
+    else if (n)
+      this.filehandle = new D(n);
+    else
+      throw new TypeError("must provide either filehandle or path");
+    if (a)
+      this.index = new _({
+        filehandle: a,
+        renameRefSeqs: c
+      });
+    else if (m)
+      this.index = new R({
+        filehandle: m,
+        renameRefSeqs: c
+      });
+    else if (i)
+      this.index = new _({
+        filehandle: new E(i),
+        renameRefSeqs: c
+      });
+    else if (r)
+      this.index = new R({
+        filehandle: new E(r),
+        renameRefSeqs: c
+      });
+    else if (e)
+      this.index = new _({
+        filehandle: new E(`${e}.tbi`),
+        renameRefSeqs: c
+      });
+    else if (l)
+      this.index = new R({
+        filehandle: new D(l)
+      });
+    else if (o)
+      this.index = new _({
+        filehandle: new D(o)
+      });
+    else if (n)
+      this.index = new _({
+        filehandle: new D(`${n}.tbi`)
+      });
+    else
+      throw new TypeError("must provide one of tbiFilehandle, tbiPath, csiFilehandle, csiPath, tbiUrl, csiUrl");
+    this.renameRefSeq = c, this.chunkCache = new te({
+      cache: new H({ maxSize: Math.floor(u / 65536) }),
+      fill: (f, g) => this.readChunk(f, { signal: g })
+    });
+  }
+  /**
+   * @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
+   */
+  calculateFileOffset(e, t, n, i, o) {
+    return e[n] * 256 + (i - t[n]) + o + 1;
+  }
+  async getLines(e, t, n, i) {
+    let o, a = {}, r;
+    typeof i == "function" ? r = i : (a = i, r = i.lineCallback, o = i.signal);
+    const l = await this.index.getMetadata(a);
+    B(o);
+    const m = t ?? 0, c = n ?? l.maxRefLength;
+    if (!(m <= c))
+      throw new TypeError("invalid start and end coordinates. start must be less than or equal to end");
+    if (m === c)
+      return;
+    const u = await this.index.blocksForRange(e, m, c, a);
+    B(o);
+    const f = new TextDecoder("utf8");
+    for (const g of u) {
+      const { buffer: b, cpositions: I, dpositions: x } = await this.chunkCache.get(g.toString(), g, o);
+      B(o);
+      let h = 0, p = 0;
+      const w = f.decode(b);
+      if (b.length == w.length)
+        for (; h < w.length; ) {
+          const d = w.indexOf(`
+`, h);
+          if (d === -1)
+            break;
+          const C = w.slice(h, d);
+          if (x) {
+            const S = h + g.minv.dataPosition;
+            for (; p < x.length && S >= x[p]; )
+              p++;
+          }
+          const { startCoordinate: y, overlaps: P } = this.checkLine(l, e, m, c, C);
+          if (P)
+            r(C, this.calculateFileOffset(I, x, p, h, g.minv.dataPosition));
+          else if (y !== void 0 && y >= c)
+            return;
+          h = d + 1;
+        }
+      else
+        for (; h < b.length; ) {
+          const d = b.indexOf(10, h);
+          if (d === -1)
+            break;
+          const C = b.slice(h, d), y = f.decode(C);
+          if (x) {
+            const A = h + g.minv.dataPosition;
+            for (; p < x.length && A >= x[p]; )
+              p++;
+          }
+          const { startCoordinate: P, overlaps: S } = this.checkLine(l, e, m, c, y);
+          if (S)
+            r(y, this.calculateFileOffset(I, x, p, h, g.minv.dataPosition));
+          else if (P !== void 0 && P >= c)
+            return;
+          h = 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: i } = await this.getMetadata(e);
+    B(e.signal);
+    const o = ((t == null ? void 0 : t.blockPosition) || 0) + i, a = await this.filehandle.read(o, 0, e), r = await V(a);
+    if (n) {
+      let l = -1;
+      const m = 10, c = n.charCodeAt(0);
+      for (let u = 0, f = r.length; u < f; u++) {
+        const g = r[u];
+        if (u === l + 1 && g !== c)
+          break;
+        g === m && (l = u);
+      }
+      return r.subarray(0, l + 1);
+    }
+    return r;
+  }
+  /**
+   * 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 = {}) {
+    const t = new TextDecoder("utf8"), n = await this.getHeaderBuffer(e);
+    return t.decode(n);
+  }
+  /**
+   * 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, i, o) {
+    const { columnNumbers: a, metaChar: r, coordinateType: l, format: m } = e;
+    if (r && o.startsWith(r))
+      return { overlaps: !1 };
+    let { ref: c, start: u, end: f } = a;
+    c || (c = 0), u || (u = 0), f || (f = 0), m === "VCF" && (f = 8);
+    const g = Math.max(c, u, f);
+    let b = 1, I = 0, x = "", h = -1 / 0;
+    const p = o.length;
+    for (let w = 0; w < p + 1; w++)
+      if (o[w] === "	" || w === p) {
+        if (b === c) {
+          if (this.renameRefSeq(o.slice(I, w)) !== t)
+            return {
+              overlaps: !1
+            };
+        } else if (b === u) {
+          if (h = Number.parseInt(o.slice(I, w), 10), l === "1-based-closed" && (h -= 1), h >= i)
+            return {
+              startCoordinate: h,
+              overlaps: !1
+            };
+          if ((f === 0 || f === u) && // if we have no end, we assume the feature is 1 bp long
+          h + 1 <= n)
+            return {
+              startCoordinate: h,
+              overlaps: !1
+            };
+        } else if (m === "VCF" && b === 4)
+          x = o.slice(I, w);
+        else if (b === f && (m === "VCF" ? this._getVcfEnd(h, x, o.slice(I, w)) : Number.parseInt(o.slice(I, w), 10)) <= n)
+          return {
+            overlaps: !1
+          };
+        if (b === g)
+          break;
+        I = w + 1, b += 1;
+      }
+    return {
+      startCoordinate: h,
+      overlaps: !0
+    };
+  }
+  _getVcfEnd(e, t, n) {
+    let i = e + t.length;
+    const o = n.includes("SVTYPE=TRA");
+    if (n[0] !== "." && !o) {
+      const r = /(?:^|;)END=([^;]+)/.exec(n);
+      r && (i = Number.parseInt(r[1], 10));
+    } else if (o)
+      return e + 1;
+    return i;
+  }
+  /**
+   * 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);
+  }
+  /**
+   * 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.filehandle.read(e.fetchedSize(), e.minv.blockPosition, t);
+    return ie(n, e, this.cache);
+  }
+}
+export {
+  R as CSI,
+  _ as TBI,
+  pe as TabixIndexedFile
+};