@genome-spy/core 0.63.0 → 0.65.0

package/dist/bundle/index-5ajWdKly.js

@@ -1,1319 +0,0 @@
-import { L as Y, u as P, a as Q } from "./long-B-FASCSo.js";
-import { b as y } from "./index-BftNdA0O.js";
-import { L as C } from "./__vite-browser-external-C--ziKoh.js";
-import { R as L } from "./remoteFile-BuaqFGWk.js";
-import { A as W, L as X } from "./index-CCJIjehY.js";
-class O {
-  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 E(o, e = 0, t = !1) {
-  if (t)
-    throw new Error("big-endian virtual file offsets not implemented");
-  return new O(o[e + 7] * 1099511627776 + o[e + 6] * 4294967296 + o[e + 5] * 16777216 + o[e + 4] * 65536 + o[e + 3] * 256 + o[e + 2], o[e + 1] << 8 | o[e]);
-}
-class F {
-  constructor(e, t, n, r) {
-    this.minv = e, this.maxv = t, this.bin = n, this._fetchedSize = r;
-  }
-  toUniqueString() {
-    return `${this.minv.toString()}..${this.maxv.toString()} (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;
-  }
-}
-function J(o) {
-  return new Promise((e) => setTimeout(e, o));
-}
-function K(o) {
-  if (o && o.aborted)
-    if (typeof DOMException > "u") {
-      const e = new Error("aborted");
-      throw e.code = "ERR_ABORTED", e;
-    } else
-      throw new DOMException("aborted", "AbortError");
-}
-function Z(o, e) {
-  return e.minv.blockPosition - o.maxv.blockPosition < 65e3 && e.maxv.blockPosition - o.minv.blockPosition < 5e6;
-}
-function ee(o = {}) {
-  return "aborted" in o ? { signal: o } : o;
-}
-function z(o, e) {
-  const t = [];
-  let n;
-  if (o.length === 0)
-    return o;
-  o.sort((r, s) => {
-    const i = r.minv.blockPosition - s.minv.blockPosition;
-    return i === 0 ? r.minv.dataPosition - s.minv.dataPosition : i;
-  });
-  for (const r of o)
-    (!e || r.maxv.compareTo(e) > 0) && (n === void 0 ? (t.push(r), n = r) : Z(n, r) ? r.maxv.compareTo(n.maxv) > 0 && (n.maxv = r.maxv) : (t.push(r), n = r));
-  return t;
-}
-function G(o, e) {
-  return {
-    lineCount: Y.fromBytesLE(Array.prototype.slice.call(o, e, e + 8), !0).toNumber()
-  };
-}
-function S(o, e) {
-  return o ? o.compareTo(e) > 0 ? e : o : e;
-}
-function te(o, e = (t) => t) {
-  let t = 0, n = 0;
-  const r = [], s = {};
-  for (let i = 0; i < o.length; i += 1)
-    if (!o[i]) {
-      if (n < i) {
-        let c = o.toString("utf8", n, i);
-        c = e(c), r[t] = c, s[c] = t;
-      }
-      n = i + 1, t += 1;
-    }
-  return { refNameToId: s, refIdToName: r };
-}
-class H {
-  /**
-   * @param {filehandle} filehandle
-   * @param {function} [renameRefSeqs]
-   */
-  constructor({ filehandle: e, renameRefSeq: t = (n) => n }) {
-    this.filehandle = e, this.renameRefSeq = t;
-  }
-}
-const ne = 21578050;
-function re(o, e) {
-  return o - o % e;
-}
-function se(o, e) {
-  return o - o % e + e;
-}
-function ie(o, e) {
-  return e -= 1, [
-    [0, 0],
-    [1 + (o >> 26), 1 + (e >> 26)],
-    [9 + (o >> 23), 9 + (e >> 23)],
-    [73 + (o >> 20), 73 + (e >> 20)],
-    [585 + (o >> 17), 585 + (e >> 17)],
-    [4681 + (o >> 14), 4681 + (e >> 14)]
-  ];
-}
-class v extends H {
-  async lineCount(e, t) {
-    var n, r;
-    return ((r = (n = (await this.parse(t)).indices[e]) === null || n === void 0 ? void 0 : n.stats) === null || r === void 0 ? void 0 : r.lineCount) || 0;
-  }
-  // fetch and parse the index
-  async _parse(e) {
-    const t = await this.filehandle.readFile(e);
-    if (t.readUInt32LE(0) !== ne)
-      throw new Error("Not a BAI file");
-    const n = t.readInt32LE(4), s = ((1 << (5 + 1) * 3) - 1) / 7;
-    let i = 8, c;
-    const a = new Array(n);
-    for (let d = 0; d < n; d++) {
-      const f = t.readInt32LE(i);
-      let h;
-      i += 4;
-      const l = {};
-      for (let b = 0; b < f; b += 1) {
-        const u = t.readUInt32LE(i);
-        if (i += 4, u === s + 1)
-          i += 4, h = G(t, i + 16), i += 32;
-        else {
-          if (u > s + 1)
-            throw new Error("bai index contains too many bins, please use CSI");
-          {
-            const g = t.readInt32LE(i);
-            i += 4;
-            const w = new Array(g);
-            for (let _ = 0; _ < g; _++) {
-              const I = E(t, i);
-              i += 8;
-              const M = E(t, i);
-              i += 8, c = S(c, I), w[_] = new F(I, M, u);
-            }
-            l[u] = w;
-          }
-        }
-      }
-      const x = t.readInt32LE(i);
-      i += 4;
-      const m = new Array(x);
-      for (let b = 0; b < x; b++) {
-        const u = E(t, i);
-        i += 8, c = S(c, u), m[b] = u;
-      }
-      a[d] = { binIndex: l, linearIndex: m, stats: h };
-    }
-    return {
-      bai: !0,
-      firstDataLine: c,
-      maxBlockSize: 65536,
-      indices: a,
-      refCount: n
-    };
-  }
-  async indexCov(e, t, n, r = {}) {
-    const i = t !== void 0, a = (await this.parse(r)).indices[e];
-    if (!a)
-      return [];
-    const { linearIndex: d = [], stats: f } = a;
-    if (d.length === 0)
-      return [];
-    const h = n === void 0 ? (d.length - 1) * 16384 : se(n, 16384), l = t === void 0 ? 0 : re(t, 16384), x = i ? new Array((h - l) / 16384) : new Array(d.length - 1), m = d[d.length - 1].blockPosition;
-    if (h > (d.length - 1) * 16384)
-      throw new Error("query outside of range of linear index");
-    let b = d[l / 16384].blockPosition;
-    for (let u = l / 16384, g = 0; u < h / 16384; u++, g++)
-      x[g] = {
-        score: d[u + 1].blockPosition - b,
-        start: u * 16384,
-        end: u * 16384 + 16384
-      }, b = d[u + 1].blockPosition;
-    return x.map((u) => ({
-      ...u,
-      score: u.score * ((f == null ? void 0 : f.lineCount) || 0) / m
-    }));
-  }
-  async blocksForRange(e, t, n, r = {}) {
-    t < 0 && (t = 0);
-    const s = await this.parse(r);
-    if (!s)
-      return [];
-    const i = s.indices[e];
-    if (!i)
-      return [];
-    const c = ie(t, n), a = [];
-    for (const [x, m] of c)
-      for (let b = x; b <= m; b++)
-        if (i.binIndex[b]) {
-          const u = i.binIndex[b];
-          for (const g of u)
-            a.push(new F(g.minv, g.maxv, b));
-        }
-    const d = i.linearIndex.length;
-    let f;
-    const h = Math.min(t >> 14, d - 1), l = Math.min(n >> 14, d - 1);
-    for (let x = h; x <= l; ++x) {
-      const m = i.linearIndex[x];
-      m && (!f || m.compareTo(f) < 0) && (f = m);
-    }
-    return z(a, f);
-  }
-  async parse(e = {}) {
-    return this.setupP || (this.setupP = this._parse(e).catch((t) => {
-      throw this.setupP = void 0, t;
-    })), this.setupP;
-  }
-  async hasRefSeq(e, t = {}) {
-    var n;
-    return !!(!((n = (await this.parse(t)).indices[e]) === null || n === void 0) && n.binIndex);
-  }
-}
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-];
-typeof Int32Array < "u" && (B = new Int32Array(B));
-const ae = (o, e) => {
-  let t = e === 0 ? 0 : ~~e ^ -1;
-  for (let n = 0; n < o.length; n++)
-    t = B[(t ^ o[n]) & 255] ^ t >>> 8;
-  return t ^ -1;
-}, N = (o, e) => y.Buffer.from(o, e);
-function oe(o, e) {
-  const t = (n, r) => e(N(n), r) >>> 0;
-  return t.signed = (n, r) => e(N(n), r), t.unsigned = t, t.model = o, t;
-}
-const ce = oe("crc-32", ae), de = 21582659, fe = 38359875;
-function he(o, e) {
-  return o * 2 ** e;
-}
-function q(o, e) {
-  return Math.floor(o / 2 ** e);
-}
-class T extends H {
-  constructor() {
-    super(...arguments), this.maxBinNumber = 0, this.depth = 0, this.minShift = 0;
-  }
-  async lineCount(e, t) {
-    var n, r;
-    return ((r = (n = (await this.parse(t)).indices[e]) === null || n === void 0 ? void 0 : n.stats) === null || r === void 0 ? void 0 : r.lineCount) || 0;
-  }
-  async indexCov() {
-    return [];
-  }
-  parseAuxData(e, t) {
-    const n = e.readInt32LE(t), r = 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 i = {
-      ref: e.readInt32LE(t + 4),
-      start: e.readInt32LE(t + 8),
-      end: e.readInt32LE(t + 12)
-    }, c = e.readInt32LE(t + 16), a = c ? String.fromCharCode(c) : "", d = e.readInt32LE(t + 20), f = e.readInt32LE(t + 24);
-    return {
-      columnNumbers: i,
-      coordinateType: r,
-      metaValue: c,
-      metaChar: a,
-      skipLines: d,
-      format: s,
-      formatFlags: n,
-      ...te(e.subarray(t + 28, t + 28 + f), this.renameRefSeq)
-    };
-  }
-  // fetch and parse the index
-  async _parse(e) {
-    const t = await this.filehandle.readFile(e), n = await P(t);
-    let r;
-    if (n.readUInt32LE(0) === de)
-      r = 1;
-    else if (n.readUInt32LE(0) === fe)
-      r = 2;
-    else
-      throw new Error("Not a CSI file");
-    this.minShift = n.readInt32LE(4), this.depth = n.readInt32LE(8), this.maxBinNumber = ((1 << (this.depth + 1) * 3) - 1) / 7;
-    const s = n.readInt32LE(12), i = s >= 30 ? this.parseAuxData(n, 16) : void 0, c = n.readInt32LE(16 + s);
-    let a = 16 + s + 4, d;
-    const f = new Array(c);
-    for (let h = 0; h < c; h++) {
-      const l = n.readInt32LE(a);
-      a += 4;
-      const x = {};
-      let m;
-      for (let b = 0; b < l; b++) {
-        const u = n.readUInt32LE(a);
-        if (a += 4, u > this.maxBinNumber)
-          m = G(n, a + 28), a += 44;
-        else {
-          d = S(d, E(n, a)), a += 8;
-          const g = n.readInt32LE(a);
-          a += 4;
-          const w = new Array(g);
-          for (let _ = 0; _ < g; _ += 1) {
-            const I = E(n, a);
-            a += 8;
-            const M = E(n, a);
-            a += 8, d = S(d, I), w[_] = new F(I, M, u);
-          }
-          x[u] = w;
-        }
-      }
-      f[h] = { binIndex: x, stats: m };
-    }
-    return {
-      csiVersion: r,
-      firstDataLine: d,
-      indices: f,
-      refCount: c,
-      csi: !0,
-      maxBlockSize: 65536,
-      ...i
-    };
-  }
-  async blocksForRange(e, t, n, r = {}) {
-    t < 0 && (t = 0);
-    const i = (await this.parse(r)).indices[e];
-    if (!i)
-      return [];
-    const c = this.reg2bins(t, n);
-    if (c.length === 0)
-      return [];
-    const a = [];
-    for (const [d, f] of c)
-      for (let h = d; h <= f; h++)
-        if (i.binIndex[h]) {
-          const l = i.binIndex[h];
-          for (const x of l)
-            a.push(x);
-        }
-    return z(a, new O(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, s = this.minShift + this.depth * 3;
-    const i = [];
-    for (; n <= this.depth; s -= 3, r += he(1, n * 3), n += 1) {
-      const c = r + q(e, s), a = r + q(t, s);
-      if (a - c + i.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`);
-      i.push([c, a]);
-    }
-    return i;
-  }
-  async parse(e = {}) {
-    return this.setupP || (this.setupP = this._parse(e).catch((t) => {
-      throw this.setupP = void 0, t;
-    })), this.setupP;
-  }
-  async hasRefSeq(e, t = {}) {
-    var n;
-    return !!(!((n = (await this.parse(t)).indices[e]) === null || n === void 0) && n.binIndex);
-  }
-}
-const p = {
-  //  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
-}, D = "=ACMGRSVTWYHKDBN".split(""), A = "MIDNSHP=X???????".split("");
-class R {
-  constructor(e) {
-    this.bytes = e.bytes, this.fileOffset = e.fileOffset;
-  }
-  get byteArray() {
-    return this.bytes.byteArray;
-  }
-  get flags() {
-    return (this.byteArray.readInt32LE(this.bytes.start + 16) & 4294901760) >> 16;
-  }
-  get ref_id() {
-    return this.byteArray.readInt32LE(this.bytes.start + 4);
-  }
-  get start() {
-    return this.byteArray.readInt32LE(this.bytes.start + 8);
-  }
-  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_ops * 4 + 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() {
-    return this.byteArray.toString("ascii", this.b0, this.b0 + this.read_name_length - 1);
-  }
-  get tags() {
-    const { byteArray: e } = this.bytes;
-    let t = this.b0 + this.read_name_length + this.num_cigar_ops * 4 + this.num_seq_bytes + this.seq_length;
-    const n = this.bytes.end, r = {};
-    for (; t < n; ) {
-      const s = String.fromCharCode(e[t], e[t + 1]), i = String.fromCharCode(e[t + 2]);
-      if (t += 3, i === "A")
-        r[s] = String.fromCharCode(e[t]), t += 1;
-      else if (i === "i")
-        r[s] = e.readInt32LE(t), t += 4;
-      else if (i === "I")
-        r[s] = e.readUInt32LE(t), t += 4;
-      else if (i === "c")
-        r[s] = e.readInt8(t), t += 1;
-      else if (i === "C")
-        r[s] = e.readUInt8(t), t += 1;
-      else if (i === "s")
-        r[s] = e.readInt16LE(t), t += 2;
-      else if (i === "S")
-        r[s] = e.readUInt16LE(t), t += 2;
-      else if (i === "f")
-        r[s] = e.readFloatLE(t), t += 4;
-      else if (i === "Z" || i === "H") {
-        const c = [];
-        for (; t <= n; ) {
-          const a = e[t++];
-          if (a !== 0)
-            c.push(String.fromCharCode(a));
-          else
-            break;
-        }
-        r[s] = c.join("");
-      } else if (i === "B") {
-        const c = e[t++], a = String.fromCharCode(c), d = e.readInt32LE(t);
-        if (t += 4, a === "i")
-          if (s === "CG") {
-            const f = [];
-            for (let h = 0; h < d; h++) {
-              const l = e.readInt32LE(t), x = l >> 4, m = A[l & 15];
-              f.push(x + m), t += 4;
-            }
-            r[s] = f.join("");
-          } else {
-            const f = [];
-            for (let h = 0; h < d; h++)
-              f.push(e.readInt32LE(t)), t += 4;
-            r[s] = f;
-          }
-        else if (a === "I")
-          if (s === "CG") {
-            const f = [];
-            for (let h = 0; h < d; h++) {
-              const l = e.readUInt32LE(t), x = l >> 4, m = A[l & 15];
-              f.push(x + m), t += 4;
-            }
-            r[s] = f.join("");
-          } else {
-            const f = [];
-            for (let h = 0; h < d; h++)
-              f.push(e.readUInt32LE(t)), t += 4;
-            r[s] = f;
-          }
-        else if (a === "s") {
-          const f = [];
-          for (let h = 0; h < d; h++)
-            f.push(e.readInt16LE(t)), t += 2;
-          r[s] = f;
-        } else if (a === "S") {
-          const f = [];
-          for (let h = 0; h < d; h++)
-            f.push(e.readUInt16LE(t)), t += 2;
-          r[s] = f;
-        } else if (a === "c") {
-          const f = [];
-          for (let h = 0; h < d; h++)
-            f.push(e.readInt8(t)), t += 1;
-          r[s] = f;
-        } else if (a === "C") {
-          const f = [];
-          for (let h = 0; h < d; h++)
-            f.push(e.readUInt8(t)), t += 1;
-          r[s] = f;
-        } else if (a === "f") {
-          const f = [];
-          for (let h = 0; h < d; h++)
-            f.push(e.readFloatLE(t)), t += 4;
-          r[s] = f;
-        }
-      } else {
-        console.error("Unknown BAM tag type", i);
-        break;
-      }
-    }
-    return r;
-  }
-  /**
-   * @returns {boolean} true if the read is paired, regardless of whether both
-   * segments are mapped
-   */
-  isPaired() {
-    return !!(this.flags & p.BAM_FPAIRED);
-  }
-  /** @returns {boolean} true if the read is paired, and both segments are mapped */
-  isProperlyPaired() {
-    return !!(this.flags & p.BAM_FPROPER_PAIR);
-  }
-  /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
-  isSegmentUnmapped() {
-    return !!(this.flags & p.BAM_FUNMAP);
-  }
-  /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
-  isMateUnmapped() {
-    return !!(this.flags & p.BAM_FMUNMAP);
-  }
-  /** @returns {boolean} true if the read is mapped to the reverse strand */
-  isReverseComplemented() {
-    return !!(this.flags & p.BAM_FREVERSE);
-  }
-  /** @returns {boolean} true if the mate is mapped to the reverse strand */
-  isMateReverseComplemented() {
-    return !!(this.flags & p.BAM_FMREVERSE);
-  }
-  /** @returns {boolean} true if this is read number 1 in a pair */
-  isRead1() {
-    return !!(this.flags & p.BAM_FREAD1);
-  }
-  /** @returns {boolean} true if this is read number 2 in a pair */
-  isRead2() {
-    return !!(this.flags & p.BAM_FREAD2);
-  }
-  /** @returns {boolean} true if this is a secondary alignment */
-  isSecondary() {
-    return !!(this.flags & p.BAM_FSECONDARY);
-  }
-  /** @returns {boolean} true if this read has failed QC checks */
-  isFailedQc() {
-    return !!(this.flags & p.BAM_FQCFAIL);
-  }
-  /** @returns {boolean} true if the read is an optical or PCR duplicate */
-  isDuplicate() {
-    return !!(this.flags & p.BAM_FDUP);
-  }
-  /** @returns {boolean} true if this is a supplementary alignment */
-  isSupplementary() {
-    return !!(this.flags & p.BAM_FSUPPLEMENTARY);
-  }
-  get cigarAndLength() {
-    if (this.isSegmentUnmapped())
-      return {
-        length_on_ref: 0,
-        CIGAR: ""
-      };
-    const e = this.num_cigar_ops;
-    let t = this.b0 + this.read_name_length;
-    const n = [];
-    let r = this.byteArray.readInt32LE(t), s = r >> 4, i = A[r & 15];
-    if (i === "S" && s === this.seq_length)
-      return t += 4, r = this.byteArray.readInt32LE(t), s = r >> 4, i = A[r & 15], i !== "N" && console.warn("CG tag with no N tag"), {
-        CIGAR: this.tags.CG,
-        length_on_ref: s
-      };
-    {
-      let c = 0;
-      for (let a = 0; a < e; ++a)
-        r = this.byteArray.readInt32LE(t), s = r >> 4, i = A[r & 15], n.push(s + i), i !== "H" && i !== "S" && i !== "I" && (c += s), t += 4;
-      return {
-        CIGAR: n.join(""),
-        length_on_ref: c
-      };
-    }
-  }
-  get length_on_ref() {
-    return this.cigarAndLength.length_on_ref;
-  }
-  get CIGAR() {
-    return this.cigarAndLength.CIGAR;
-  }
-  get num_cigar_ops() {
-    return this.flag_nc & 65535;
-  }
-  get read_name_length() {
-    return this.bin_mq_nl & 255;
-  }
-  get num_seq_bytes() {
-    return this.seq_length + 1 >> 1;
-  }
-  get seq() {
-    const { byteArray: e } = this.bytes, t = this.b0 + this.read_name_length + this.num_cigar_ops * 4, n = this.num_seq_bytes, r = this.seq_length, s = [];
-    let i = 0;
-    for (let c = 0; c < n; ++c) {
-      const a = e[t + c];
-      s.push(D[(a & 240) >> 4]), i++, i < r && (s.push(D[a & 15]), i++);
-    }
-    return s.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", t = this.isMateReverseComplemented() ? "R" : "F";
-      let n = " ", r = " ";
-      this.isRead1() ? (n = "1", r = "2") : this.isRead2() && (n = "2", r = "1");
-      const s = [];
-      return this.template_length > 0 ? (s[0] = e, s[1] = n, s[2] = t, s[3] = r) : (s[2] = e, s[3] = n, s[0] = t, s[1] = r), s.join("");
-    }
-  }
-  get bin_mq_nl() {
-    return this.byteArray.readInt32LE(this.bytes.start + 12);
-  }
-  get flag_nc() {
-    return this.byteArray.readInt32LE(this.bytes.start + 16);
-  }
-  get seq_length() {
-    return this.byteArray.readInt32LE(this.bytes.start + 20);
-  }
-  get next_refid() {
-    return this.byteArray.readInt32LE(this.bytes.start + 24);
-  }
-  get next_pos() {
-    return this.byteArray.readInt32LE(this.bytes.start + 28);
-  }
-  get template_length() {
-    return this.byteArray.readInt32LE(this.bytes.start + 32);
-  }
-  toJSON() {
-    const e = {};
-    for (const t of Object.keys(this))
-      t.startsWith("_") || t === "bytes" || (e[t] = this[t]);
-    return e;
-  }
-}
-function k(o, e) {
-  const t = Object.getOwnPropertyDescriptor(o.prototype, e);
-  if (!t)
-    throw new Error("OH NO, NO PROPERTY DESCRIPTOR");
-  const n = t.get;
-  if (!n)
-    throw new Error("OH NO, NOT A GETTER");
-  Object.defineProperty(o.prototype, e, {
-    get() {
-      const r = n.call(this);
-      return Object.defineProperty(this, e, { value: r }), r;
-    }
-  });
-}
-k(R, "tags");
-k(R, "cigarAndLength");
-k(R, "seq");
-k(R, "qual");
-function j(o) {
-  const e = o.split(/\r?\n/), t = [];
-  for (const n of e) {
-    const [r, ...s] = n.split(/\t/);
-    r && t.push({
-      tag: r.slice(1),
-      data: s.map((i) => {
-        const c = i.indexOf(":"), a = i.slice(0, c), d = i.slice(c + 1);
-        return { tag: a, value: d };
-      })
-    });
-  }
-  return t;
-}
-const V = 21840194, $ = 65536;
-async function le(o) {
-  let e = [];
-  for await (const t of o)
-    e = e.concat(t);
-  return e;
-}
-class xe {
-  read() {
-    throw new Error("never called");
-  }
-  stat() {
-    throw new Error("never called");
-  }
-  readFile() {
-    throw new Error("never called");
-  }
-  close() {
-    throw new Error("never called");
-  }
-}
-class ue {
-  constructor({ bamFilehandle: e, bamPath: t, bamUrl: n, baiPath: r, baiFilehandle: s, baiUrl: i, csiPath: c, csiFilehandle: a, csiUrl: d, htsget: f, yieldThreadTime: h = 100, renameRefSeqs: l = (x) => x }) {
-    if (this.htsget = !1, this.featureCache = new W({
-      cache: new X({
-        maxSize: 50
-      }),
-      fill: async (x, m) => {
-        const { chunk: b, opts: u } = x, { data: g, cpositions: w, dpositions: _ } = await this._readChunk({
-          chunk: b,
-          opts: { ...u, signal: m }
-        });
-        return this.readBamFeatures(g, w, _, b);
-      }
-    }), this.renameRefSeq = l, e)
-      this.bam = e;
-    else if (t)
-      this.bam = new C(t);
-    else if (n)
-      this.bam = new L(n);
-    else if (f)
-      this.htsget = !0, this.bam = new xe();
-    else
-      throw new Error("unable to initialize bam");
-    if (a)
-      this.index = new T({ filehandle: a });
-    else if (c)
-      this.index = new T({ filehandle: new C(c) });
-    else if (d)
-      this.index = new T({ filehandle: new L(d) });
-    else if (s)
-      this.index = new v({ filehandle: s });
-    else if (r)
-      this.index = new v({ filehandle: new C(r) });
-    else if (i)
-      this.index = new v({ filehandle: new L(i) });
-    else if (t)
-      this.index = new v({ filehandle: new C(`${t}.bai`) });
-    else if (n)
-      this.index = new v({ filehandle: new L(`${n}.bai`) });
-    else if (f)
-      this.htsget = !0;
-    else
-      throw new Error("unable to infer index format");
-    this.yieldThreadTime = h;
-  }
-  async getHeaderPre(e) {
-    const t = ee(e);
-    if (!this.index)
-      return;
-    const n = await this.index.parse(t), r = n.firstDataLine ? n.firstDataLine.blockPosition + 65535 : void 0;
-    let s;
-    if (r) {
-      const f = r + $, h = await this.bam.read(y.Buffer.alloc(f), 0, f, 0, t);
-      if (!h.bytesRead)
-        throw new Error("Error reading header");
-      s = h.buffer.subarray(0, Math.min(h.bytesRead, r));
-    } else
-      s = await this.bam.readFile(t);
-    const i = await P(s);
-    if (i.readInt32LE(0) !== V)
-      throw new Error("Not a BAM file");
-    const c = i.readInt32LE(4);
-    this.header = i.toString("utf8", 8, 8 + c);
-    const { chrToIndex: a, indexToChr: d } = await this._readRefSeqs(c + 8, 65535, t);
-    return this.chrToIndex = a, this.indexToChr = d, j(this.header);
-  }
-  getHeader(e) {
-    return this.headerP || (this.headerP = this.getHeaderPre(e).catch((t) => {
-      throw this.headerP = void 0, t;
-    })), this.headerP;
-  }
-  async getHeaderText(e = {}) {
-    return await this.getHeader(e), this.header;
-  }
-  // the full length of the refseq block is not given in advance so this grabs
-  // a chunk and doubles it if all refseqs haven't been processed
-  async _readRefSeqs(e, t, n) {
-    if (e > t)
-      return this._readRefSeqs(e, t * 2, n);
-    const r = t + $, { bytesRead: s, buffer: i } = await this.bam.read(y.Buffer.alloc(r), 0, t, 0, n);
-    if (!s)
-      throw new Error("Error reading refseqs from header");
-    const c = await P(i.subarray(0, Math.min(s, t))), a = c.readInt32LE(e);
-    let d = e + 4;
-    const f = {}, h = [];
-    for (let l = 0; l < a; l += 1) {
-      const x = c.readInt32LE(d), m = this.renameRefSeq(c.toString("utf8", d + 4, d + 4 + x - 1)), b = c.readInt32LE(d + x + 4);
-      if (f[m] = l, h.push({ refName: m, length: b }), d = d + 8 + x, d > c.length)
-        return console.warn(`BAM header is very big.  Re-fetching ${t} bytes.`), this._readRefSeqs(e, t * 2, n);
-    }
-    return { chrToIndex: f, indexToChr: h };
-  }
-  async getRecordsForRange(e, t, n, r) {
-    return le(this.streamRecordsForRange(e, t, n, r));
-  }
-  async *streamRecordsForRange(e, t, n, r) {
-    var s;
-    await this.getHeader(r);
-    const i = (s = this.chrToIndex) === null || s === void 0 ? void 0 : s[e];
-    if (i === void 0 || !this.index)
-      yield [];
-    else {
-      const c = await this.index.blocksForRange(i, t - 1, n, r);
-      yield* this._fetchChunkFeatures(c, i, t, n, r);
-    }
-  }
-  async *_fetchChunkFeatures(e, t, n, r, s = {}) {
-    const { viewAsPairs: i } = s, c = [];
-    let a = !1;
-    for (const d of e) {
-      const f = await this.featureCache.get(d.toString(), { chunk: d, opts: s }, s.signal), h = [];
-      for (const l of f)
-        if (l.ref_id === t)
-          if (l.start >= r) {
-            a = !0;
-            break;
-          } else l.end >= n && h.push(l);
-      if (c.push(h), yield h, a)
-        break;
-    }
-    K(s.signal), i && (yield this.fetchPairs(t, c, s));
-  }
-  async fetchPairs(e, t, n) {
-    const { pairAcrossChr: r, maxInsertSize: s = 2e5 } = n, i = {}, c = {};
-    t.map((l) => {
-      const x = {};
-      for (const m of l) {
-        const b = m.name, u = m.id;
-        x[b] || (x[b] = 0), x[b]++, c[u] = 1;
-      }
-      for (const [m, b] of Object.entries(x))
-        b === 1 && (i[m] = !0);
-    });
-    const a = [];
-    t.map((l) => {
-      for (const x of l) {
-        const m = x.name, b = x.start, u = x.next_pos, g = x.next_refid;
-        this.index && i[m] && (r || g === e && Math.abs(b - u) < s) && a.push(this.index.blocksForRange(g, u, u + 1, n));
-      }
-    });
-    const d = /* @__PURE__ */ new Map(), f = await Promise.all(a);
-    for (const l of f.flat())
-      d.has(l.toString()) || d.set(l.toString(), l);
-    return (await Promise.all([...d.values()].map(async (l) => {
-      const { data: x, cpositions: m, dpositions: b, chunk: u } = await this._readChunk({
-        chunk: l,
-        opts: n
-      }), g = [];
-      for (const w of await this.readBamFeatures(x, m, b, u))
-        i[w.name] && !c[w.id] && g.push(w);
-      return g;
-    }))).flat();
-  }
-  async _readRegion(e, t, n = {}) {
-    const { bytesRead: r, buffer: s } = await this.bam.read(y.Buffer.alloc(t), 0, t, e, n);
-    return s.subarray(0, Math.min(r, t));
-  }
-  async _readChunk({ chunk: e, opts: t }) {
-    const n = await this._readRegion(e.minv.blockPosition, e.fetchedSize(), t), { buffer: r, cpositions: s, dpositions: i } = await Q(n, e);
-    return { data: r, cpositions: s, dpositions: i, chunk: e };
-  }
-  async readBamFeatures(e, t, n, r) {
-    let s = 0;
-    const i = [];
-    let c = 0, a = +Date.now();
-    for (; s + 4 < e.length; ) {
-      const d = e.readInt32LE(s), f = s + 4 + d - 1;
-      if (n) {
-        for (; s + r.minv.dataPosition >= n[c++]; )
-          ;
-        c--;
-      }
-      if (f < e.length) {
-        const h = new R({
-          bytes: {
-            byteArray: e,
-            start: s,
-            end: f
-          },
-          // the below results in an automatically calculated file-offset based
-          // ID if the info for that is available, otherwise crc32 of the
-          // features
-          //
-          // 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
-          //
-          // this has an extra chunk.minv.dataPosition added on because it
-          // blockStart starts at 0 instead of chunk.minv.dataPosition
-          //
-          // the +1 is just to avoid any possible uniqueId 0 but this does not
-          // realistically happen
-          fileOffset: t.length > 0 ? t[c] * 256 + (s - n[c]) + r.minv.dataPosition + 1 : (
-            // must be slice, not subarray for buffer polyfill on web
-            // eslint-disable-next-line @typescript-eslint/no-deprecated
-            ce.signed(e.slice(s, f))
-          )
-        });
-        i.push(h), this.yieldThreadTime && +Date.now() - a > this.yieldThreadTime && (await J(1), a = +Date.now());
-      }
-      s = f + 1;
-    }
-    return i;
-  }
-  async hasRefSeq(e) {
-    var t, n;
-    const r = (t = this.chrToIndex) === null || t === void 0 ? void 0 : t[e];
-    return r === void 0 ? !1 : (n = this.index) === null || n === void 0 ? void 0 : n.hasRefSeq(r);
-  }
-  async lineCount(e) {
-    var t;
-    const n = (t = this.chrToIndex) === null || t === void 0 ? void 0 : t[e];
-    return n === void 0 || !this.index ? 0 : this.index.lineCount(n);
-  }
-  async indexCov(e, t, n) {
-    var r;
-    if (!this.index)
-      return [];
-    await this.index.parse();
-    const s = (r = this.chrToIndex) === null || r === void 0 ? void 0 : r[e];
-    return s === void 0 ? [] : this.index.indexCov(s, t, n);
-  }
-  async blocksForRange(e, t, n, r) {
-    var s;
-    if (!this.index)
-      return [];
-    await this.index.parse();
-    const i = (s = this.chrToIndex) === null || s === void 0 ? void 0 : s[e];
-    return i === void 0 ? [] : this.index.blocksForRange(i, t, n, r);
-  }
-}
-async function U(o, e) {
-  const t = await Promise.all(o.map(async (n) => {
-    const { url: r, headers: s } = n;
-    if (r.startsWith("data:"))
-      return y.Buffer.from(r.split(",")[1], "base64");
-    {
-      const { referer: i, ...c } = s, a = await fetch(r, {
-        ...e,
-        headers: { ...e == null ? void 0 : e.headers, ...c }
-      });
-      if (!a.ok)
-        throw new Error(`HTTP ${a.status} fetching ${r}: ${await a.text()}`);
-      return y.Buffer.from(await a.arrayBuffer());
-    }
-  }));
-  return y.Buffer.concat(await Promise.all(t.map((n) => P(n))));
-}
-class _e extends ue {
-  constructor(e) {
-    super({ htsget: !0 }), this.baseUrl = e.baseUrl, this.trackId = e.trackId;
-  }
-  async *streamRecordsForRange(e, t, n, r) {
-    var s;
-    const c = `${`${this.baseUrl}/${this.trackId}`}?referenceName=${e}&start=${t}&end=${n}&format=BAM`, a = (s = this.chrToIndex) === null || s === void 0 ? void 0 : s[e];
-    if (a === void 0)
-      yield [];
-    else {
-      const d = await fetch(c, { ...r });
-      if (!d.ok)
-        throw new Error(`HTTP ${d.status} fetching ${c}: ${await d.text()}`);
-      const f = await d.json(), h = await U(f.htsget.urls.slice(1), r);
-      yield* this._fetchChunkFeatures([
-        // fake stuff to pretend to be a Chunk
-        {
-          buffer: h,
-          _fetchedSize: void 0,
-          bin: 0,
-          compareTo() {
-            return 0;
-          },
-          toUniqueString() {
-            return `${e}_${t}_${n}`;
-          },
-          fetchedSize() {
-            return 0;
-          },
-          minv: {
-            dataPosition: 0,
-            blockPosition: 0,
-            compareTo: () => 0
-          },
-          maxv: {
-            dataPosition: Number.MAX_SAFE_INTEGER,
-            blockPosition: 0,
-            compareTo: () => 0
-          },
-          toString() {
-            return `${e}_${t}_${n}`;
-          }
-        }
-      ], a, t, n, r);
-    }
-  }
-  async _readChunk({ chunk: e }) {
-    if (!e.buffer)
-      throw new Error("expected chunk.buffer in htsget");
-    return { data: e.buffer, cpositions: [], dpositions: [], chunk: e };
-  }
-  async getHeader(e = {}) {
-    const t = `${this.baseUrl}/${this.trackId}?referenceName=na&class=header`, n = await fetch(t, e);
-    if (!n.ok)
-      throw new Error(`HTTP ${n.status} fetching ${t}: ${await n.text()}`);
-    const r = await n.json(), s = await U(r.htsget.urls, e);
-    if (s.readInt32LE(0) !== V)
-      throw new Error("Not a BAM file");
-    const i = s.readInt32LE(4), c = s.toString("utf8", 8, 8 + i), a = j(c), d = [], f = {}, h = a.filter((l) => l.tag === "SQ");
-    for (const [l, x] of h.entries()) {
-      let m = "", b = 0;
-      for (const u of x.data)
-        u.tag === "SN" ? m = u.value : u.tag === "LN" && (b = +u.value);
-      f[m] = l, d[l] = { refName: m, length: b };
-    }
-    return this.chrToIndex = f, this.indexToChr = d, a;
-  }
-}
-export {
-  v as BAI,
-  ue as BamFile,
-  R as BamRecord,
-  T as CSI,
-  _e as HtsgetFile
-};