@genome-spy/core 0.65.0 → 0.67.0

package/dist/bundle/index-DhcU-Gk-.js

@@ -1,1487 +0,0 @@
-import { L as D } from "./index-BhtHKLUo.js";
-import { I as z, Z as G } from "./inflate-DRgHi_KK.js";
-import { LocalFile as B, RemoteFile as T } from "./browser-txUcLy2H.js";
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-    return this.toUniqueString();
-  }
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-  }
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-  }
-}
-class H {
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-  const n = c[e] | c[e + 1] << 8 | c[e + 2] << 16 | c[e + 3] << 24;
-  return ((c[e + 4] | c[e + 5] << 8 | c[e + 6] << 16 | c[e + 7] << 24) >>> 0) * te + (n >>> 0);
-}
-function re(c, e) {
-  return e.minv.blockPosition - c.maxv.blockPosition < 65e3 && e.maxv.blockPosition - c.minv.blockPosition < 5e6;
-}
-function se(c = {}) {
-  return "aborted" in c ? { signal: c } : c;
-}
-function j(c, e) {
-  const n = [];
-  let t;
-  if (c.length === 0)
-    return c;
-  c.sort((r, a) => {
-    const s = r.minv.blockPosition - a.minv.blockPosition;
-    return s === 0 ? r.minv.dataPosition - a.minv.dataPosition : s;
-  });
-  for (const r of c)
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-  return n;
-}
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-  return {
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-  };
-}
-function F(c, e) {
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-}
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-          o += String.fromCharCode(c[i]);
-        o = e(o), r[n] = o, a[o] = n;
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-    }
-  return { refNameToId: a, refIdToName: r };
-}
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-  for (const r of c)
-    e += r.length;
-  const n = new Uint8Array(e);
-  let t = 0;
-  for (const r of c)
-    n.set(r, t), t += r.length;
-  return n;
-}
-async function oe(c) {
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-  for await (const n of c)
-    for (const t of n)
-      e.push(t);
-  return e;
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-    return this.blockPosition - e.blockPosition || this.dataPosition - e.dataPosition;
-  }
-}
-function C(c, e = 0, n = !1) {
-  if (n)
-    throw new Error("big-endian virtual file offsets not implemented");
-  return new W(c[e + 7] * 1099511627776 + c[e + 6] * 4294967296 + c[e + 5] * 16777216 + c[e + 4] * 65536 + c[e + 3] * 256 + c[e + 2], c[e + 1] << 8 | c[e]);
-}
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-function fe(c, e) {
-  return c - c % e;
-}
-function de(c, e) {
-  return c - c % e + e;
-}
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-  return e -= 1, [
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-    [1 + (c >> 26), 1 + (e >> 26)],
-    [9 + (c >> 23), 9 + (e >> 23)],
-    [73 + (c >> 20), 73 + (e >> 20)],
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-    [4681 + (c >> 14), 4681 + (e >> 14)]
-  ];
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-  }
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-    if (t.getUint32(0, !0) !== ce)
-      throw new Error("Not a BAI file");
-    const r = t.getInt32(4, !0), s = ((1 << (5 + 1) * 3) - 1) / 7;
-    let o = 8, i;
-    const f = [];
-    for (let b = 0; b < r; b++) {
-      f.push(o);
-      const h = t.getInt32(o, !0);
-      o += 4;
-      for (let u = 0; u < h; u += 1) {
-        const l = t.getUint32(o, !0);
-        if (o += 4, l === s + 1)
-          o += 4, o += 32;
-        else {
-          if (l > s + 1)
-            throw new Error("bai index contains too many bins, please use CSI");
-          {
-            const m = t.getInt32(o, !0);
-            o += 4;
-            for (let y = 0; y < m; y++)
-              o += 8, o += 8;
-          }
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-      }
-      const g = t.getInt32(o, !0);
-      o += 4;
-      const w = new Array(g);
-      for (let u = 0; u < g; u++) {
-        const l = C(n, o);
-        o += 8, i = F(i, l), w[u] = l;
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-    });
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-      if (h === void 0)
-        return;
-      const g = t.getInt32(h, !0);
-      let w;
-      h += 4;
-      const u = {};
-      for (let y = 0; y < g; y += 1) {
-        const _ = t.getUint32(h, !0);
-        if (h += 4, _ === s + 1)
-          h += 4, w = Q(n, h + 16), h += 32;
-        else {
-          if (_ > s + 1)
-            throw new Error("bai index contains too many bins, please use CSI");
-          {
-            const p = t.getInt32(h, !0);
-            h += 4;
-            const I = new Array(p);
-            for (let P = 0; P < p; P++) {
-              const S = C(n, h);
-              h += 8;
-              const k = C(n, h);
-              h += 8, i = F(i, S), I[P] = new N(S, k, _);
-            }
-            u[_] = I;
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-      h += 4;
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-      for (let y = 0; y < l; y++) {
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-        h += 8, i = F(i, _), m[y] = _;
-      }
-      return {
-        binIndex: u,
-        linearIndex: m,
-        stats: w
-      };
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-    return {
-      bai: !0,
-      firstDataLine: i,
-      maxBlockSize: 65536,
-      indices: (b) => {
-        if (!d.has(b)) {
-          const h = x(b);
-          return h && d.set(b, h), h;
-        }
-        return d.get(b);
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-      refCount: r
-    };
-  }
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-    if (!i)
-      return [];
-    const { linearIndex: f = [], stats: d } = i;
-    if (f.length === 0)
-      return [];
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-    if (x > (f.length - 1) * 16384)
-      throw new Error("query outside of range of linear index");
-    let w = f[b / 16384].blockPosition;
-    for (let u = b / 16384, l = 0; u < x / 16384; u++, l++)
-      h[l] = {
-        score: f[u + 1].blockPosition - w,
-        start: u * 16384,
-        end: u * 16384 + 16384
-      }, w = f[u + 1].blockPosition;
-    return h.map((u) => ({
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-      score: u.score * ((d == null ? void 0 : d.lineCount) || 0) / g
-    }));
-  }
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-    const x = Math.min(n >> 14, f - 1), b = Math.min(t >> 14, f - 1);
-    for (let h = x; h <= b; ++h) {
-      const g = s.linearIndex[h];
-      g && (!d || g.compareTo(d) < 0) && (d = g);
-    }
-    return j(i, d);
-  }
-  async parse(e = {}) {
-    return this.setupP || (this.setupP = this._parse(e).catch((n) => {
-      throw this.setupP = void 0, n;
-    })), this.setupP;
-  }
-  async hasRefSeq(e, n = {}) {
-    var r;
-    return !!((r = (await this.parse(n)).indices(e)) != null && r.binIndex);
-  }
-}
-function ue(c) {
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-  for (const n of c)
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-  return e;
-}
-function Y(c, e) {
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-  let t = 0;
-  for (const r of c)
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-  return n;
-}
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-    do {
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-      if (t = new z(void 0), { strm: e } = t, t.push(s, G), t.err)
-        throw new Error(t.msg);
-      n += e.next_in;
-      const o = t.result;
-      r.push(o), a += o.length;
-    } while (e.avail_in);
-    return Y(r, a);
-  } catch (e) {
-    throw /incorrect header check/.exec(`${e}`) ? new Error("problem decompressing block: incorrect gzip header check") : e;
-  }
-}
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-    let s = r.blockPosition, o = r.dataPosition;
-    const i = [], f = [], d = [];
-    let x = 0, b = !1, h = 0;
-    do {
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-      let u, l;
-      const m = n == null ? void 0 : n.get(w);
-      if (m)
-        u = m.buffer, l = m.nextIn, b = !0;
-      else {
-        const p = new z(void 0);
-        if ({ strm: t } = p, p.push(g, G), p.err)
-          throw new Error(p.msg);
-        u = p.result, l = t.next_in, b = !1, n == null || n.set(w, { buffer: u, nextIn: l });
-      }
-      i.push(u);
-      let y = u.length;
-      f.push(s), d.push(o), i.length === 1 && r.dataPosition && (i[0] = i[0].subarray(r.dataPosition), y = i[0].length);
-      const _ = s;
-      if (s += l, o += y, _ >= a.blockPosition) {
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-        break;
-      }
-      h += y, x++;
-    } while (b ? s < c.length + r.blockPosition : (
-      // eslint-disable-next-line @typescript-eslint/no-unnecessary-type-assertion
-      t.avail_in
-    ));
-    return {
-      buffer: Y(i, h),
-      cpositions: f,
-      dpositions: d
-    };
-  } catch (t) {
-    throw /incorrect header check/.exec(`${t}`) ? new Error("problem decompressing block: incorrect gzip header check") : t;
-  }
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-}, be = 21582659, ge = 38359875;
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-    return ((a = (r = (await this.parse(n)).indices(e)) == null ? void 0 : r.stats) == null ? void 0 : a.lineCount) || 0;
-  }
-  async indexCov() {
-    return [];
-  }
-  parseAuxData(e, n) {
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-    if (!s)
-      throw new Error(`invalid Tabix preset format flags ${r}`);
-    const o = {
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-      start: t.getInt32(n + 8, !0),
-      end: t.getInt32(n + 12, !0)
-    }, i = t.getInt32(n + 16, !0), f = i ? String.fromCharCode(i) : "", d = t.getInt32(n + 20, !0), x = t.getInt32(n + 24, !0);
-    return {
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-      coordinateType: a,
-      metaValue: i,
-      metaChar: f,
-      skipLines: d,
-      format: s,
-      formatFlags: r,
-      ...ie(e.subarray(n + 28, n + 28 + x), this.renameRefSeq)
-    };
-  }
-  // fetch and parse the index
-  async _parse(e) {
-    const n = await this.filehandle.readFile(e), t = await V(n), r = new DataView(t.buffer);
-    let a;
-    const s = r.getUint32(0, !0);
-    if (s === be)
-      a = 1;
-    else if (s === ge)
-      a = 2;
-    else
-      throw new Error(`Not a CSI file ${s}`);
-    this.minShift = r.getInt32(4, !0), this.depth = r.getInt32(8, !0), this.maxBinNumber = ((1 << (this.depth + 1) * 3) - 1) / 7;
-    const o = this.maxBinNumber, i = r.getInt32(12, !0), f = i >= 30 ? this.parseAuxData(t, 16) : void 0, d = r.getInt32(16 + i, !0);
-    let x = 16 + i + 4, b;
-    const h = [];
-    for (let u = 0; u < d; u++) {
-      h.push(x);
-      const l = r.getInt32(x, !0);
-      x += 4;
-      for (let m = 0; m < l; m++) {
-        const y = r.getUint32(x, !0);
-        if (x += 4, y > this.maxBinNumber)
-          x += 44;
-        else {
-          x += 8;
-          const _ = r.getInt32(x, !0);
-          x += 4;
-          for (let p = 0; p < _; p += 1) {
-            const I = C(t, x);
-            x += 8, x += 8, b = F(b, I);
-          }
-        }
-      }
-    }
-    const g = new D({
-      maxSize: 5
-    });
-    function w(u) {
-      let l = h[u];
-      if (l === void 0)
-        return;
-      const m = r.getInt32(l, !0);
-      l += 4;
-      const y = {};
-      let _;
-      for (let p = 0; p < m; p++) {
-        const I = r.getUint32(l, !0);
-        if (l += 4, I > o)
-          _ = Q(t, l + 28), l += 44;
-        else {
-          b = F(b, C(t, l)), l += 8;
-          const P = r.getInt32(l, !0);
-          l += 4;
-          const S = new Array(P);
-          for (let k = 0; k < P; k += 1) {
-            const X = C(t, l);
-            l += 8;
-            const ee = C(t, l);
-            l += 8, S[k] = new N(X, ee, I);
-          }
-          y[I] = S;
-        }
-      }
-      return {
-        binIndex: y,
-        stats: _
-      };
-    }
-    return {
-      csiVersion: a,
-      firstDataLine: b,
-      indices: (u) => {
-        if (!g.has(u)) {
-          const l = w(u);
-          return l && g.set(u, l), l;
-        }
-        return g.get(u);
-      },
-      refCount: d,
-      csi: !0,
-      maxBlockSize: 65536,
-      ...f
-    };
-  }
-  async blocksForRange(e, n, t, r = {}) {
-    n < 0 && (n = 0);
-    const s = (await this.parse(r)).indices(e);
-    if (!s)
-      return [];
-    const o = this.reg2bins(n, t);
-    if (o.length === 0)
-      return [];
-    const i = [];
-    for (const [f, d] of o)
-      for (let x = f; x <= d; x++)
-        if (s.binIndex[x]) {
-          const b = s.binIndex[x];
-          for (const h of b)
-            i.push(h);
-        }
-    return j(i, new W(0, 0));
-  }
-  /**
-   * calculate the list of bins that may overlap with region [beg,end)
-   * (zero-based half-open)
-   */
-  reg2bins(e, n) {
-    e -= 1, e < 1 && (e = 1), n > 2 ** 50 && (n = 2 ** 34), n -= 1;
-    let t = 0, r = 0, a = this.minShift + this.depth * 3;
-    const s = [];
-    for (; t <= this.depth; a -= 3, r += we(1, t * 3), t += 1) {
-      const o = r + O(e, a), i = r + O(n, a);
-      if (i - o + s.length > this.maxBinNumber)
-        throw new Error(`query ${e}-${n} is too large for current binning scheme (shift ${this.minShift}, depth ${this.depth}), try a smaller query or a coarser index binning scheme`);
-      s.push([o, i]);
-    }
-    return s;
-  }
-  async parse(e = {}) {
-    return this.setupP || (this.setupP = this._parse(e).catch((n) => {
-      throw this.setupP = void 0, n;
-    })), this.setupP;
-  }
-  async hasRefSeq(e, n = {}) {
-    var r;
-    return !!((r = (await this.parse(n)).indices(e)) != null && r.binIndex);
-  }
-}
-class me {
-  read() {
-    throw new Error("never called");
-  }
-  stat() {
-    throw new Error("never called");
-  }
-  readFile() {
-    throw new Error("never called");
-  }
-  close() {
-    throw new Error("never called");
-  }
-}
-const A = {
-  //  the read is paired in sequencing, no matter whether it is mapped in a pair
-  BAM_FPAIRED: 1,
-  //  the read is mapped in a proper pair
-  BAM_FPROPER_PAIR: 2,
-  //  the read itself is unmapped; conflictive with BAM_FPROPER_PAIR
-  BAM_FUNMAP: 4,
-  //  the mate is unmapped
-  BAM_FMUNMAP: 8,
-  //  the read is mapped to the reverse strand
-  BAM_FREVERSE: 16,
-  //  the mate is mapped to the reverse strand
-  BAM_FMREVERSE: 32,
-  //  this is read1
-  BAM_FREAD1: 64,
-  //  this is read2
-  BAM_FREAD2: 128,
-  //  not primary alignment
-  BAM_FSECONDARY: 256,
-  //  QC failure
-  BAM_FQCFAIL: 512,
-  //  optical or PCR duplicate
-  BAM_FDUP: 1024,
-  //  supplementary alignment
-  BAM_FSUPPLEMENTARY: 2048
-}, v = "=ACMGRSVTWYHKDBN".split(""), ye = [
-  77,
-  73,
-  68,
-  78,
-  83,
-  72,
-  80,
-  61,
-  88,
-  63,
-  63,
-  63,
-  63,
-  63,
-  63,
-  63
-], _e = 1, pe = 3, K = 4, Ae = 5, Ie = 1 << _e | 1 << K | 1 << Ae;
-class R {
-  constructor(e) {
-    this.bytes = e.bytes, this.fileOffset = e.fileOffset, this._dataView = new DataView(this.bytes.byteArray.buffer);
-  }
-  get byteArray() {
-    return this.bytes.byteArray;
-  }
-  get flags() {
-    return (this._dataView.getInt32(this.bytes.start + 16, !0) & 4294901760) >> 16;
-  }
-  get ref_id() {
-    return this._dataView.getInt32(this.bytes.start + 4, !0);
-  }
-  get start() {
-    return this._dataView.getInt32(this.bytes.start + 8, !0);
-  }
-  get end() {
-    return this.start + this.length_on_ref;
-  }
-  get id() {
-    return this.fileOffset;
-  }
-  get mq() {
-    const e = (this.bin_mq_nl & 65280) >> 8;
-    return e === 255 ? void 0 : e;
-  }
-  get score() {
-    return this.mq;
-  }
-  get qual() {
-    if (this.isSegmentUnmapped())
-      return;
-    const e = this.b0 + this.read_name_length + this.num_cigar_bytes + this.num_seq_bytes;
-    return this.byteArray.subarray(e, e + this.seq_length);
-  }
-  get strand() {
-    return this.isReverseComplemented() ? -1 : 1;
-  }
-  get b0() {
-    return this.bytes.start + 36;
-  }
-  get name() {
-    let e = "";
-    for (let n = 0; n < this.read_name_length - 1; n++)
-      e += String.fromCharCode(this.byteArray[this.b0 + n]);
-    return e;
-  }
-  get tags() {
-    let e = this.b0 + this.read_name_length + this.num_cigar_bytes + this.num_seq_bytes + this.seq_length;
-    const n = this.bytes.end, t = {};
-    for (; e < n; ) {
-      const r = String.fromCharCode(this.byteArray[e]) + String.fromCharCode(this.byteArray[e + 1]), a = String.fromCharCode(this.byteArray[e + 2]);
-      switch (e += 3, a) {
-        case "A":
-          t[r] = String.fromCharCode(this.byteArray[e]), e += 1;
-          break;
-        case "i":
-          t[r] = this._dataView.getInt32(e, !0), e += 4;
-          break;
-        case "I":
-          t[r] = this._dataView.getUint32(e, !0), e += 4;
-          break;
-        case "c":
-          t[r] = this._dataView.getInt8(e), e += 1;
-          break;
-        case "C":
-          t[r] = this._dataView.getUint8(e), e += 1;
-          break;
-        case "s":
-          t[r] = this._dataView.getInt16(e, !0), e += 2;
-          break;
-        case "S":
-          t[r] = this._dataView.getUint16(e, !0), e += 2;
-          break;
-        case "f":
-          t[r] = this._dataView.getFloat32(e, !0), e += 4;
-          break;
-        case "Z":
-        case "H": {
-          const s = [];
-          for (; e <= n; ) {
-            const o = this.byteArray[e++];
-            if (o !== 0)
-              s.push(String.fromCharCode(o));
-            else
-              break;
-          }
-          t[r] = s.join("");
-          break;
-        }
-        case "B": {
-          const s = this.byteArray[e++], o = String.fromCharCode(s), i = this._dataView.getInt32(e, !0);
-          e += 4;
-          const f = this.byteArray.byteOffset + e;
-          if (o === "i") {
-            if (f % 4 === 0)
-              t[r] = new Int32Array(this.byteArray.buffer, f, i);
-            else {
-              const d = this.byteArray.slice(e, e + (i << 2));
-              t[r] = new Int32Array(d.buffer, d.byteOffset, i);
-            }
-            e += i << 2;
-          } else if (o === "I") {
-            if (f % 4 === 0)
-              t[r] = new Uint32Array(this.byteArray.buffer, f, i);
-            else {
-              const d = this.byteArray.slice(e, e + (i << 2));
-              t[r] = new Uint32Array(d.buffer, d.byteOffset, i);
-            }
-            e += i << 2;
-          } else if (o === "s") {
-            if (f % 2 === 0)
-              t[r] = new Int16Array(this.byteArray.buffer, f, i);
-            else {
-              const d = this.byteArray.slice(e, e + (i << 1));
-              t[r] = new Int16Array(d.buffer, d.byteOffset, i);
-            }
-            e += i << 1;
-          } else if (o === "S") {
-            if (f % 2 === 0)
-              t[r] = new Uint16Array(this.byteArray.buffer, f, i);
-            else {
-              const d = this.byteArray.slice(e, e + (i << 1));
-              t[r] = new Uint16Array(d.buffer, d.byteOffset, i);
-            }
-            e += i << 1;
-          } else if (o === "c")
-            t[r] = new Int8Array(this.byteArray.buffer, f, i), e += i;
-          else if (o === "C")
-            t[r] = new Uint8Array(this.byteArray.buffer, f, i), e += i;
-          else if (o === "f") {
-            if (f % 4 === 0)
-              t[r] = new Float32Array(this.byteArray.buffer, f, i);
-            else {
-              const d = this.byteArray.slice(e, e + (i << 2));
-              t[r] = new Float32Array(d.buffer, d.byteOffset, i);
-            }
-            e += i << 2;
-          }
-          break;
-        }
-        default:
-          console.error("Unknown BAM tag type", a);
-          break;
-      }
-    }
-    return t;
-  }
-  /**
-   * @returns {boolean} true if the read is paired, regardless of whether both
-   * segments are mapped
-   */
-  isPaired() {
-    return !!(this.flags & A.BAM_FPAIRED);
-  }
-  /** @returns {boolean} true if the read is paired, and both segments are mapped */
-  isProperlyPaired() {
-    return !!(this.flags & A.BAM_FPROPER_PAIR);
-  }
-  /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
-  isSegmentUnmapped() {
-    return !!(this.flags & A.BAM_FUNMAP);
-  }
-  /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
-  isMateUnmapped() {
-    return !!(this.flags & A.BAM_FMUNMAP);
-  }
-  /** @returns {boolean} true if the read is mapped to the reverse strand */
-  isReverseComplemented() {
-    return !!(this.flags & A.BAM_FREVERSE);
-  }
-  /** @returns {boolean} true if the mate is mapped to the reverse strand */
-  isMateReverseComplemented() {
-    return !!(this.flags & A.BAM_FMREVERSE);
-  }
-  /** @returns {boolean} true if this is read number 1 in a pair */
-  isRead1() {
-    return !!(this.flags & A.BAM_FREAD1);
-  }
-  /** @returns {boolean} true if this is read number 2 in a pair */
-  isRead2() {
-    return !!(this.flags & A.BAM_FREAD2);
-  }
-  /** @returns {boolean} true if this is a secondary alignment */
-  isSecondary() {
-    return !!(this.flags & A.BAM_FSECONDARY);
-  }
-  /** @returns {boolean} true if this read has failed QC checks */
-  isFailedQc() {
-    return !!(this.flags & A.BAM_FQCFAIL);
-  }
-  /** @returns {boolean} true if the read is an optical or PCR duplicate */
-  isDuplicate() {
-    return !!(this.flags & A.BAM_FDUP);
-  }
-  /** @returns {boolean} true if this is a supplementary alignment */
-  isSupplementary() {
-    return !!(this.flags & A.BAM_FSUPPLEMENTARY);
-  }
-  get cigarAndLength() {
-    if (this.isSegmentUnmapped())
-      return {
-        length_on_ref: 0,
-        NUMERIC_CIGAR: new Uint32Array(0)
-      };
-    const e = this.num_cigar_ops;
-    let n = this.b0 + this.read_name_length;
-    const t = this._dataView.getInt32(n, !0), r = t >> 4;
-    if ((t & 15) === K && r === this.seq_length) {
-      n += 4;
-      const s = this._dataView.getInt32(n, !0), o = s >> 4;
-      return (s & 15) !== pe && console.warn("CG tag with no N tag"), {
-        NUMERIC_CIGAR: this.tags.CG,
-        length_on_ref: o
-      };
-    } else {
-      const s = this.byteArray.byteOffset + n, o = s % 4 === 0 ? new Uint32Array(this.byteArray.buffer, s, e) : new Uint32Array(this.byteArray.slice(n, n + (e << 2)).buffer, 0, e);
-      let i = 0;
-      for (let f = 0; f < e; ++f) {
-        const d = o[f];
-        1 << (d & 15) & Ie || (i += d >> 4);
-      }
-      return {
-        NUMERIC_CIGAR: o,
-        length_on_ref: i
-      };
-    }
-  }
-  get length_on_ref() {
-    return this.cigarAndLength.length_on_ref;
-  }
-  get NUMERIC_CIGAR() {
-    return this.cigarAndLength.NUMERIC_CIGAR;
-  }
-  get CIGAR() {
-    const e = this.NUMERIC_CIGAR;
-    let n = "";
-    for (let t = 0, r = e.length; t < r; t++) {
-      const a = e[t], s = a >> 4, o = ye[a & 15];
-      n += s + String.fromCharCode(o);
-    }
-    return n;
-  }
-  get num_cigar_ops() {
-    return this.flag_nc & 65535;
-  }
-  get num_cigar_bytes() {
-    return this.num_cigar_ops << 2;
-  }
-  get read_name_length() {
-    return this.bin_mq_nl & 255;
-  }
-  get num_seq_bytes() {
-    return this.seq_length + 1 >> 1;
-  }
-  get NUMERIC_SEQ() {
-    const e = this.b0 + this.read_name_length + this.num_cigar_bytes, n = this.byteArray.subarray(e, e + this.num_seq_bytes);
-    return new Uint8Array(n.buffer, n.byteOffset, this.num_seq_bytes);
-  }
-  get seq() {
-    const e = this.NUMERIC_SEQ, n = this.seq_length, t = new Array(n);
-    let r = 0;
-    const a = n >> 1;
-    for (let s = 0; s < a; ++s) {
-      const o = e[s];
-      t[r++] = v[(o & 240) >> 4], t[r++] = v[o & 15];
-    }
-    if (r < n) {
-      const s = e[a];
-      t[r] = v[(s & 240) >> 4];
-    }
-    return t.join("");
-  }
-  // adapted from igv.js
-  get pair_orientation() {
-    if (!this.isSegmentUnmapped() && !this.isMateUnmapped() && this.ref_id === this.next_refid) {
-      const e = this.isReverseComplemented() ? "R" : "F", n = this.isMateReverseComplemented() ? "R" : "F";
-      let t = " ", r = " ";
-      this.isRead1() ? (t = "1", r = "2") : this.isRead2() && (t = "2", r = "1");
-      const a = [];
-      return this.template_length > 0 ? (a[0] = e, a[1] = t, a[2] = n, a[3] = r) : (a[2] = e, a[3] = t, a[0] = n, a[1] = r), a.join("");
-    }
-  }
-  get bin_mq_nl() {
-    return this._dataView.getInt32(this.bytes.start + 12, !0);
-  }
-  get flag_nc() {
-    return this._dataView.getInt32(this.bytes.start + 16, !0);
-  }
-  get seq_length() {
-    return this._dataView.getInt32(this.bytes.start + 20, !0);
-  }
-  get next_refid() {
-    return this._dataView.getInt32(this.bytes.start + 24, !0);
-  }
-  get next_pos() {
-    return this._dataView.getInt32(this.bytes.start + 28, !0);
-  }
-  get template_length() {
-    return this._dataView.getInt32(this.bytes.start + 32, !0);
-  }
-  seqAt(e) {
-    if (e < this.seq_length) {
-      const n = e >> 1, t = this.byteArray[this.b0 + this.read_name_length + this.num_cigar_bytes + n];
-      return e % 2 === 0 ? v[(t & 240) >> 4] : v[t & 15];
-    } else
-      return;
-  }
-  toJSON() {
-    const e = {};
-    for (const n of Object.keys(this))
-      n.startsWith("_") || n === "bytes" || (e[n] = this[n]);
-    return e;
-  }
-}
-function M(c, e) {
-  const n = Object.getOwnPropertyDescriptor(c.prototype, e);
-  if (!n)
-    throw new Error("OH NO, NO PROPERTY DESCRIPTOR");
-  const t = n.get;
-  if (!t)
-    throw new Error("OH NO, NOT A GETTER");
-  Object.defineProperty(c.prototype, e, {
-    get() {
-      const r = t.call(this);
-      return Object.defineProperty(this, e, { value: r }), r;
-    }
-  });
-}
-M(R, "tags");
-M(R, "cigarAndLength");
-M(R, "seq");
-M(R, "qual");
-M(R, "end");
-function Z(c) {
-  const e = c.split(/\r?\n/), n = [];
-  for (const t of e) {
-    const [r, ...a] = t.split(/\t/);
-    r && n.push({
-      tag: r.slice(1),
-      data: a.map((s) => {
-        const o = s.indexOf(":"), i = s.slice(0, o), f = s.slice(o + 1);
-        return { tag: i, value: f };
-      })
-    });
-  }
-  return n;
-}
-const J = 21840194, Ce = 65536;
-class Pe {
-  constructor({ bamFilehandle: e, bamPath: n, bamUrl: t, baiPath: r, baiFilehandle: a, baiUrl: s, csiPath: o, csiFilehandle: i, csiUrl: f, htsget: d, renameRefSeqs: x = (b) => b }) {
-    if (this.htsget = !1, this.cache = new D({
-      maxSize: 1e3
-    }), this.renameRefSeq = x, e)
-      this.bam = e;
-    else if (n)
-      this.bam = new B(n);
-    else if (t)
-      this.bam = new T(t);
-    else if (d)
-      this.htsget = !0, this.bam = new me();
-    else
-      throw new Error("unable to initialize bam");
-    if (i)
-      this.index = new U({ filehandle: i });
-    else if (o)
-      this.index = new U({ filehandle: new B(o) });
-    else if (f)
-      this.index = new U({ filehandle: new T(f) });
-    else if (a)
-      this.index = new E({ filehandle: a });
-    else if (r)
-      this.index = new E({ filehandle: new B(r) });
-    else if (s)
-      this.index = new E({ filehandle: new T(s) });
-    else if (n)
-      this.index = new E({ filehandle: new B(`${n}.bai`) });
-    else if (t)
-      this.index = new E({ filehandle: new T(`${t}.bai`) });
-    else if (d)
-      this.htsget = !0;
-    else
-      throw new Error("unable to infer index format");
-  }
-  async getHeaderPre(e) {
-    const n = se(e);
-    if (!this.index)
-      return;
-    const t = await this.index.parse(n), r = t.firstDataLine === void 0 ? await this.bam.readFile() : (
-      // the logic indexData.firstDataLine is a virtualOffset telling us
-      // where the data is. It is in the middle of a virtualOffset
-      // (provided by the bgzip block offset at blockPosition + the
-      // virtualOffset dataPosition, so we add one extra blockLen to make
-      // sure we consume the full header)
-      await this.bam.read(t.firstDataLine.blockPosition + Ce, 0)
-    ), a = await V(r), s = new DataView(a.buffer);
-    if (s.getInt32(0, !0) !== J)
-      throw new Error("Not a BAM file");
-    const o = s.getInt32(4, !0), i = new TextDecoder("utf8");
-    this.header = i.decode(a.subarray(8, 8 + o));
-    const { chrToIndex: f, indexToChr: d } = this._parseRefSeqs(a, o + 8);
-    return this.chrToIndex = f, this.indexToChr = d, Z(this.header);
-  }
-  getHeader(e) {
-    return this.headerP || (this.headerP = this.getHeaderPre(e).catch((n) => {
-      throw this.headerP = void 0, n;
-    })), this.headerP;
-  }
-  async getHeaderText(e = {}) {
-    return await this.getHeader(e), this.header;
-  }
-  _parseRefSeqs(e, n) {
-    const t = new DataView(e.buffer), r = t.getInt32(n, !0);
-    let a = n + 4;
-    const s = {}, o = [], i = new TextDecoder("utf8");
-    for (let f = 0; f < r; f += 1) {
-      if (a + 8 > e.length)
-        throw new Error(`Insufficient data for reference sequences: need more than ${e.length} bytes`);
-      const d = t.getInt32(a, !0), x = this.renameRefSeq(i.decode(e.subarray(a + 4, a + 4 + d - 1))), b = t.getInt32(a + d + 4, !0);
-      s[x] = f, o.push({ refName: x, length: b }), a = a + 8 + d;
-    }
-    return { chrToIndex: s, indexToChr: o };
-  }
-  async getRecordsForRange(e, n, t, r) {
-    return oe(this.streamRecordsForRange(e, n, t, r));
-  }
-  async *streamRecordsForRange(e, n, t, r) {
-    var o;
-    await this.getHeader(r);
-    const a = (o = this.chrToIndex) == null ? void 0 : o[e];
-    if (a === void 0 || !this.index)
-      return;
-    const s = await this.index.blocksForRange(a, n - 1, t, r);
-    yield* this._fetchChunkFeatures(s, a, n, t, r);
-  }
-  async *_fetchChunkFeatures(e, n, t, r, a = {}) {
-    const { viewAsPairs: s } = a, o = [];
-    let i = !1;
-    for (const f of e) {
-      const { data: d, cpositions: x, dpositions: b } = await this._readChunk({
-        chunk: f,
-        opts: a
-      }), h = await this.readBamFeatures(d, x, b, f, n, t, r), g = [];
-      for (const w of h)
-        if (w.ref_id === n)
-          if (w.start >= r) {
-            i = !0;
-            break;
-          } else w.end >= t && g.push(w);
-      if (o.push(g), yield g, i)
-        break;
-    }
-    s && (yield this.fetchPairs(n, o, a));
-  }
-  async fetchPairs(e, n, t) {
-    const { pairAcrossChr: r, maxInsertSize: a = 2e5 } = t, s = {}, o = {};
-    for (const b of n) {
-      const h = {};
-      for (const g of b) {
-        const w = g.name, u = g.id;
-        h[w] || (h[w] = 0), h[w]++, o[u] = 1;
-      }
-      for (const [g, w] of Object.entries(h))
-        w === 1 && (s[g] = !0);
-    }
-    const i = [];
-    for (const b of n)
-      for (const h of b) {
-        const g = h.name, w = h.start, u = h.next_pos, l = h.next_refid;
-        this.index && s[g] && (r || l === e && Math.abs(w - u) < a) && i.push(this.index.blocksForRange(l, u, u + 1, t));
-      }
-    const f = /* @__PURE__ */ new Map(), d = await Promise.all(i);
-    for (const b of d.flat())
-      f.has(b.toString()) || f.set(b.toString(), b);
-    return (await Promise.all([...f.values()].map(async (b) => {
-      const { data: h, cpositions: g, dpositions: w, chunk: u } = await this._readChunk({
-        chunk: b,
-        opts: t
-      }), l = [];
-      for (const m of await this.readBamFeatures(h, g, w, u))
-        s[m.name] && !o[m.id] && l.push(m);
-      return l;
-    }))).flat();
-  }
-  async _readChunk({ chunk: e, opts: n }) {
-    const t = await this.bam.read(e.fetchedSize(), e.minv.blockPosition, n), { buffer: r, cpositions: a, dpositions: s } = await le(t, e, this.cache);
-    return { data: r, cpositions: a, dpositions: s, chunk: e };
-  }
-  async readBamFeatures(e, n, t, r, a, s, o) {
-    let i = 0;
-    const f = [];
-    let d = 0;
-    const x = new DataView(e.buffer), b = t.length > 0, h = n.length > 0, g = a !== void 0 && s !== void 0 && o !== void 0;
-    for (; i + 4 < e.length; ) {
-      const w = x.getInt32(i, !0), u = i + 4 + w - 1;
-      if (b) {
-        for (; i + r.minv.dataPosition >= t[d++]; )
-          ;
-        d--;
-      }
-      if (u < e.length) {
-        if (g && i + 12 < e.length && !this._shouldIncludeFeature(x, i, a, o)) {
-          i = u + 1;
-          continue;
-        }
-        const l = new R({
-          bytes: {
-            byteArray: e,
-            start: i,
-            end: u
-          },
-          fileOffset: h ? n[d] * 256 + (i - t[d]) + r.minv.dataPosition + 1 : xe(e.subarray(i, u)) >>> 0
-        });
-        f.push(l);
-      }
-      i = u + 1;
-    }
-    return f;
-  }
-  _shouldIncludeFeature(e, n, t, r) {
-    const a = e.getInt32(n + 4, !0), s = e.getInt32(n + 8, !0);
-    return a === t && s < r;
-  }
-  async hasRefSeq(e) {
-    var t, r;
-    const n = (t = this.chrToIndex) == null ? void 0 : t[e];
-    return n === void 0 ? !1 : (r = this.index) == null ? void 0 : r.hasRefSeq(n);
-  }
-  async lineCount(e) {
-    var t;
-    const n = (t = this.chrToIndex) == null ? void 0 : t[e];
-    return n === void 0 || !this.index ? 0 : this.index.lineCount(n);
-  }
-  async indexCov(e, n, t) {
-    var a;
-    if (!this.index)
-      return [];
-    await this.index.parse();
-    const r = (a = this.chrToIndex) == null ? void 0 : a[e];
-    return r === void 0 ? [] : this.index.indexCov(r, n, t);
-  }
-  async blocksForRange(e, n, t, r) {
-    var s;
-    if (!this.index)
-      return [];
-    await this.index.parse();
-    const a = (s = this.chrToIndex) == null ? void 0 : s[e];
-    return a === void 0 ? [] : this.index.blocksForRange(a, n, t, r);
-  }
-}
-async function L(c, e) {
-  const n = await Promise.all(c.map(async (t) => {
-    const { url: r, headers: a } = t;
-    if (r.startsWith("data:")) {
-      const s = await fetch(r);
-      if (!s.ok)
-        throw new Error("failed to decode base64");
-      const o = await s.arrayBuffer();
-      return new Uint8Array(o);
-    } else {
-      const { referer: s, ...o } = a, i = await fetch(r, {
-        ...e,
-        headers: { ...e == null ? void 0 : e.headers, ...o }
-      });
-      if (!i.ok)
-        throw new Error(`HTTP ${i.status} fetching ${r}: ${await i.text()}`);
-      return new Uint8Array(await i.arrayBuffer());
-    }
-  }));
-  return ae(await Promise.all(n.map((t) => V(t))));
-}
-class Ee extends Pe {
-  constructor(e) {
-    super({ htsget: !0 }), this.baseUrl = e.baseUrl, this.trackId = e.trackId;
-  }
-  async *streamRecordsForRange(e, n, t, r) {
-    var i;
-    const s = `${`${this.baseUrl}/${this.trackId}`}?referenceName=${e}&start=${n}&end=${t}&format=BAM`, o = (i = this.chrToIndex) == null ? void 0 : i[e];
-    if (o === void 0)
-      yield [];
-    else {
-      const f = await fetch(s, { ...r });
-      if (!f.ok)
-        throw new Error(`HTTP ${f.status} fetching ${s}: ${await f.text()}`);
-      const d = await f.json(), x = await L(d.htsget.urls.slice(1), r);
-      yield* this._fetchChunkFeatures([
-        // fake stuff to pretend to be a Chunk
-        {
-          buffer: x,
-          _fetchedSize: void 0,
-          bin: 0,
-          compareTo() {
-            return 0;
-          },
-          toUniqueString() {
-            return `${e}_${n}_${t}`;
-          },
-          fetchedSize() {
-            return 0;
-          },
-          minv: {
-            dataPosition: 0,
-            blockPosition: 0,
-            compareTo: () => 0
-          },
-          maxv: {
-            dataPosition: Number.MAX_SAFE_INTEGER,
-            blockPosition: 0,
-            compareTo: () => 0
-          },
-          toString() {
-            return `${e}_${n}_${t}`;
-          }
-        }
-      ], o, n, t, r);
-    }
-  }
-  async _readChunk({ chunk: e }) {
-    if (!e.buffer)
-      throw new Error("expected chunk.buffer in htsget");
-    return {
-      data: e.buffer,
-      cpositions: [],
-      dpositions: [],
-      chunk: e
-    };
-  }
-  async getHeader(e = {}) {
-    const n = `${this.baseUrl}/${this.trackId}?referenceName=na&class=header`, t = await fetch(n, e);
-    if (!t.ok)
-      throw new Error(`HTTP ${t.status} fetching ${n}: ${await t.text()}`);
-    const r = await t.json(), a = await L(r.htsget.urls, e), s = new DataView(a.buffer);
-    if (s.getInt32(0, !0) !== J)
-      throw new Error("Not a BAM file");
-    const o = s.getInt32(4, !0), f = new TextDecoder("utf8").decode(a.subarray(8, 8 + o)), d = Z(f), x = [], b = {}, h = d.filter((g) => g.tag === "SQ");
-    for (const [g, w] of h.entries()) {
-      let u = "", l = 0;
-      for (const m of w.data)
-        m.tag === "SN" ? u = m.value : m.tag === "LN" && (l = +m.value);
-      b[u] = g, x[g] = { refName: u, length: l };
-    }
-    return this.chrToIndex = b, this.indexToChr = x, d;
-  }
-}
-export {
-  E as BAI,
-  Pe as BamFile,
-  R as BamRecord,
-  U as CSI,
-  Ee as HtsgetFile
-};