@genome-spy/core 0.56.1 → 0.58.0

package/dist/bundle/index-DwLfOHEk.js

@@ -0,0 +1,1319 @@
+import { L as Y, u as P, a as Q } from "./long-BviWyoZx.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);
+  }
+}
+let B = [
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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
+};