@genome-spy/app 0.73.0 → 0.75.0

package/dist/index-BYsZN7b0.js

@@ -1,1597 +0,0 @@
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-    const i = this.reg2bins(t, n);
-    if (i.length === 0)
-      return [];
-    const a = [], { binIndex: l } = c;
-    for (const [u, o] of i)
-      for (let f = u; f <= o; f++) {
-        const d = l[f];
-        if (d)
-          for (let b = 0, g = d.length; b < g; b++)
-            a.push(d[b]);
-      }
-    return N(a, new Q(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 c = [];
-    for (; n <= this.depth; s -= 3, r += ue(1, n * 3), n += 1) {
-      const i = r + L(e, s), a = r + L(t, s);
-      if (a - i + c.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`);
-      c.push([i, a]);
-    }
-    return c;
-  }
-  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 = {}) {
-    return !!(await this.parse(t)).indices(e)?.binIndex;
-  }
-};
-class le {
-  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 xe = 3, be = 4, 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
-}, E = "=ACMGRSVTWYHKDBN".split(""), ge = [
-  77,
-  73,
-  68,
-  78,
-  83,
-  72,
-  80,
-  61,
-  88,
-  63,
-  63,
-  63,
-  63,
-  63,
-  63,
-  63
-], O = 461;
-class we {
-  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._cachedFlags === void 0 && (this._cachedFlags = (this._dataView.getInt32(this.bytes.start + 16, !0) & 4294901760) >> 16), this._cachedFlags;
-  }
-  get ref_id() {
-    return this._cachedRefId === void 0 && (this._cachedRefId = this._dataView.getInt32(this.bytes.start + 4, !0)), this._cachedRefId;
-  }
-  get start() {
-    return this._cachedStart === void 0 && (this._cachedStart = this._dataView.getInt32(this.bytes.start + 8, !0)), this._cachedStart;
-  }
-  get end() {
-    return this._cachedEnd === void 0 && (this._cachedEnd = this.start + this.length_on_ref), this._cachedEnd;
-  }
-  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 null;
-    {
-      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 tagsStart() {
-    return this._cachedTagsStart === void 0 && (this._cachedTagsStart = this.b0 + this.read_name_length + this.num_cigar_bytes + this.num_seq_bytes + this.seq_length), this._cachedTagsStart;
-  }
-  // batch fromCharCode: fastest for typical name lengths (see benchmarks/string-building.bench.ts)
-  get name() {
-    const e = this.read_name_length - 1, t = this.b0, n = this.byteArray, r = new Array(e);
-    for (let s = 0; s < e; s++)
-      r[s] = n[t + s];
-    return String.fromCharCode(...r);
-  }
-  get NUMERIC_MD() {
-    if (this._cachedNUMERIC_MD === void 0) {
-      const e = this.getTagRaw("MD");
-      this._cachedNUMERIC_MD = e instanceof Uint8Array ? e : null;
-    }
-    return this._cachedNUMERIC_MD === null ? void 0 : this._cachedNUMERIC_MD;
-  }
-  get tags() {
-    return this._cachedTags === void 0 && (this._cachedTags = this._computeTags()), this._cachedTags;
-  }
-  getTag(e) {
-    return this._cachedTags !== void 0 ? this._cachedTags[e] : this._findTag(e, !1);
-  }
-  getTagRaw(e) {
-    return this._findTag(e, !0);
-  }
-  _findTag(e, t) {
-    const n = e.charCodeAt(0), r = e.charCodeAt(1);
-    let s = this.tagsStart;
-    const c = this.bytes.end, i = this.byteArray;
-    for (; s < c; ) {
-      const a = i[s], l = i[s + 1], u = i[s + 2];
-      s += 3;
-      const o = a === n && l === r;
-      switch (u) {
-        case 65:
-          if (o)
-            return String.fromCharCode(i[s]);
-          s += 1;
-          break;
-        case 105:
-          if (o)
-            return this._dataView.getInt32(s, !0);
-          s += 4;
-          break;
-        case 73:
-          if (o)
-            return this._dataView.getUint32(s, !0);
-          s += 4;
-          break;
-        case 99:
-          if (o)
-            return this._dataView.getInt8(s);
-          s += 1;
-          break;
-        case 67:
-          if (o)
-            return this._dataView.getUint8(s);
-          s += 1;
-          break;
-        case 115:
-          if (o)
-            return this._dataView.getInt16(s, !0);
-          s += 2;
-          break;
-        case 83:
-          if (o)
-            return this._dataView.getUint16(s, !0);
-          s += 2;
-          break;
-        case 102:
-          if (o)
-            return this._dataView.getFloat32(s, !0);
-          s += 4;
-          break;
-        case 90:
-        // 'Z'
-        case 72: {
-          if (o) {
-            const f = s;
-            for (; s < c && i[s] !== 0; )
-              s++;
-            if (t)
-              return i.subarray(f, s);
-            const d = [];
-            for (let b = f; b < s; b++)
-              d.push(String.fromCharCode(i[b]));
-            return d.join("");
-          }
-          for (; s <= c && i[s++] !== 0; )
-            ;
-          break;
-        }
-        case 66: {
-          const f = i[s++], d = this._dataView.getInt32(s, !0);
-          s += 4;
-          const b = i.byteOffset + s;
-          if (o)
-            if (f === 105) {
-              if (b % 4 === 0)
-                return new Int32Array(i.buffer, b, d);
-              const g = new Array(d);
-              for (let x = 0; x < d; x++)
-                g[x] = this._dataView.getInt32(s + x * 4, !0);
-              return g;
-            } else if (f === 73) {
-              if (b % 4 === 0)
-                return new Uint32Array(i.buffer, b, d);
-              const g = new Array(d);
-              for (let x = 0; x < d; x++)
-                g[x] = this._dataView.getUint32(s + x * 4, !0);
-              return g;
-            } else if (f === 115) {
-              if (b % 2 === 0)
-                return new Int16Array(i.buffer, b, d);
-              const g = new Array(d);
-              for (let x = 0; x < d; x++)
-                g[x] = this._dataView.getInt16(s + x * 2, !0);
-              return g;
-            } else if (f === 83) {
-              if (b % 2 === 0)
-                return new Uint16Array(i.buffer, b, d);
-              const g = new Array(d);
-              for (let x = 0; x < d; x++)
-                g[x] = this._dataView.getUint16(s + x * 2, !0);
-              return g;
-            } else {
-              if (f === 99)
-                return new Int8Array(i.buffer, b, d);
-              if (f === 67)
-                return new Uint8Array(i.buffer, b, d);
-              if (f === 102) {
-                if (b % 4 === 0)
-                  return new Float32Array(i.buffer, b, d);
-                const g = new Array(d);
-                for (let x = 0; x < d; x++)
-                  g[x] = this._dataView.getFloat32(s + x * 4, !0);
-                return g;
-              }
-            }
-          f === 105 || f === 73 || f === 102 ? s += d << 2 : f === 115 || f === 83 ? s += d << 1 : (f === 99 || f === 67) && (s += d);
-          break;
-        }
-      }
-    }
-  }
-  _computeTags() {
-    let e = this.tagsStart;
-    const t = this.bytes.end, n = this.byteArray, r = {};
-    for (; e < t; ) {
-      const s = String.fromCharCode(n[e], n[e + 1]), c = n[e + 2];
-      switch (e += 3, c) {
-        case 65:
-          r[s] = String.fromCharCode(n[e]), e += 1;
-          break;
-        case 105:
-          r[s] = this._dataView.getInt32(e, !0), e += 4;
-          break;
-        case 73:
-          r[s] = this._dataView.getUint32(e, !0), e += 4;
-          break;
-        case 99:
-          r[s] = this._dataView.getInt8(e), e += 1;
-          break;
-        case 67:
-          r[s] = this._dataView.getUint8(e), e += 1;
-          break;
-        case 115:
-          r[s] = this._dataView.getInt16(e, !0), e += 2;
-          break;
-        case 83:
-          r[s] = this._dataView.getUint16(e, !0), e += 2;
-          break;
-        case 102:
-          r[s] = this._dataView.getFloat32(e, !0), e += 4;
-          break;
-        case 90:
-        // 'Z'
-        case 72: {
-          const i = [];
-          for (; e <= t; ) {
-            const a = n[e++];
-            if (a !== 0)
-              i.push(String.fromCharCode(a));
-            else
-              break;
-          }
-          r[s] = i.join("");
-          break;
-        }
-        case 66: {
-          const i = n[e++], a = this._dataView.getInt32(e, !0);
-          e += 4;
-          const l = n.byteOffset + e;
-          if (i === 105) {
-            if (l % 4 === 0)
-              r[s] = new Int32Array(n.buffer, l, a);
-            else {
-              const u = new Array(a);
-              for (let o = 0; o < a; o++)
-                u[o] = this._dataView.getInt32(e + o * 4, !0);
-              r[s] = u;
-            }
-            e += a << 2;
-          } else if (i === 73) {
-            if (l % 4 === 0)
-              r[s] = new Uint32Array(n.buffer, l, a);
-            else {
-              const u = new Array(a);
-              for (let o = 0; o < a; o++)
-                u[o] = this._dataView.getUint32(e + o * 4, !0);
-              r[s] = u;
-            }
-            e += a << 2;
-          } else if (i === 115) {
-            if (l % 2 === 0)
-              r[s] = new Int16Array(n.buffer, l, a);
-            else {
-              const u = new Array(a);
-              for (let o = 0; o < a; o++)
-                u[o] = this._dataView.getInt16(e + o * 2, !0);
-              r[s] = u;
-            }
-            e += a << 1;
-          } else if (i === 83) {
-            if (l % 2 === 0)
-              r[s] = new Uint16Array(n.buffer, l, a);
-            else {
-              const u = new Array(a);
-              for (let o = 0; o < a; o++)
-                u[o] = this._dataView.getUint16(e + o * 2, !0);
-              r[s] = u;
-            }
-            e += a << 1;
-          } else if (i === 99)
-            r[s] = new Int8Array(n.buffer, l, a), e += a;
-          else if (i === 67)
-            r[s] = new Uint8Array(n.buffer, l, a), e += a;
-          else if (i === 102) {
-            if (l % 4 === 0)
-              r[s] = new Float32Array(n.buffer, l, a);
-            else {
-              const u = new Array(a);
-              for (let o = 0; o < a; o++)
-                u[o] = this._dataView.getFloat32(e + o * 4, !0);
-              r[s] = u;
-            }
-            e += a << 2;
-          }
-          break;
-        }
-        default:
-          console.error("Unknown BAM tag type", c);
-          break;
-      }
-    }
-    return r;
-  }
-  isPaired() {
-    return !!(this.flags & A.BAM_FPAIRED);
-  }
-  isProperlyPaired() {
-    return !!(this.flags & A.BAM_FPROPER_PAIR);
-  }
-  isSegmentUnmapped() {
-    return !!(this.flags & A.BAM_FUNMAP);
-  }
-  isMateUnmapped() {
-    return !!(this.flags & A.BAM_FMUNMAP);
-  }
-  isReverseComplemented() {
-    return !!(this.flags & A.BAM_FREVERSE);
-  }
-  isMateReverseComplemented() {
-    return !!(this.flags & A.BAM_FMREVERSE);
-  }
-  isRead1() {
-    return !!(this.flags & A.BAM_FREAD1);
-  }
-  isRead2() {
-    return !!(this.flags & A.BAM_FREAD2);
-  }
-  isSecondary() {
-    return !!(this.flags & A.BAM_FSECONDARY);
-  }
-  isFailedQc() {
-    return !!(this.flags & A.BAM_FQCFAIL);
-  }
-  isDuplicate() {
-    return !!(this.flags & A.BAM_FDUP);
-  }
-  isSupplementary() {
-    return !!(this.flags & A.BAM_FSUPPLEMENTARY);
-  }
-  get cigarAndLength() {
-    return this._cachedCigarAndLength === void 0 && (this._cachedCigarAndLength = this._computeCigarAndLength()), this._cachedCigarAndLength;
-  }
-  // Benchmark results for CIGAR parsing strategies (see benchmarks/cigar-lifecycle.bench.ts):
-  //
-  // Aligned data:
-  //   - Plain array is 1.6-1.8x faster than Uint32Array for small CIGARs (≤50 ops)
-  //   - Uint32Array view is 1.3-2.2x faster for large CIGARs (≥200 ops)
-  //   - Crossover point is around 50-100 ops
-  //
-  // Unaligned data (requires slice+copy for Uint32Array):
-  //   - Plain array is 3.7-6.1x faster for typical sizes (50-200 ops)
-  //   - Plain array is 9-10x faster for small CIGARs (1-7 ops)
-  //   - Uint32Array slice+copy only wins at extreme sizes (10000 ops: 1.4x faster)
-  //
-  // Using |0 to force 32-bit integers in plain array path:
-  //   - 1.67x faster for medium CIGARs (50 ops)
-  //   - Neutral for small CIGARs (1-7 ops)
-  //
-  // Strategy: use plain array with |0 for small aligned (≤50 ops) and all unaligned,
-  // Uint32Array view only for large aligned CIGARs.
-  _computeCigarAndLength() {
-    if (this.isSegmentUnmapped())
-      return {
-        length_on_ref: 0,
-        NUMERIC_CIGAR: new Uint32Array(0)
-      };
-    const e = this.num_cigar_ops;
-    let t = this.b0 + this.read_name_length;
-    const n = this._dataView.getInt32(t, !0), r = n >> 4;
-    if ((n & 15) === be && r === this.seq_length) {
-      t += 4;
-      const u = this._dataView.getInt32(t, !0), o = u >> 4;
-      return (u & 15) !== xe && console.warn("CG tag with no N tag"), {
-        NUMERIC_CIGAR: this.tags.CG,
-        length_on_ref: o
-      };
-    }
-    const c = this.byteArray.byteOffset + t;
-    if (c % 4 === 0 && e > 50) {
-      const u = new Uint32Array(this.byteArray.buffer, c, e);
-      let o = 0;
-      for (let f = 0; f < e; ++f) {
-        const d = u[f];
-        o += (d >> 4) * (O >> (d & 15) & 1);
-      }
-      return {
-        NUMERIC_CIGAR: u,
-        length_on_ref: o
-      };
-    }
-    const a = new Array(e);
-    let l = 0;
-    for (let u = 0; u < e; ++u) {
-      const o = this._dataView.getInt32(t + u * 4, !0) | 0;
-      a[u] = o, l += (o >> 4) * (O >> (o & 15) & 1);
-    }
-    return {
-      NUMERIC_CIGAR: a,
-      length_on_ref: l
-    };
-  }
-  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 t = "";
-    for (let n = 0, r = e.length; n < r; n++) {
-      const s = e[n], c = s >> 4, i = ge[s & 15];
-      t += c + String.fromCharCode(i);
-    }
-    return t;
-  }
-  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;
-    return this.byteArray.subarray(e, e + this.num_seq_bytes);
-  }
-  get seq() {
-    const e = this.NUMERIC_SEQ, t = this.seq_length, n = new Array(t);
-    let r = 0;
-    const s = t >> 1;
-    for (let c = 0; c < s; ++c) {
-      const i = e[c];
-      n[r++] = E[(i & 240) >> 4], n[r++] = E[i & 15];
-    }
-    if (r < t) {
-      const c = e[s];
-      n[r] = E[(c & 240) >> 4];
-    }
-    return n.join("");
-  }
-  // adapted from igv.js
-  // uses template literal instead of array+join (6.4x faster, see benchmarks/string-building.bench.ts)
-  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 = " ";
-      return this.isRead1() ? (n = "1", r = "2") : this.isRead2() && (n = "2", r = "1"), this.template_length > 0 ? `${e}${n}${t}${r}` : `${t}${r}${e}${n}`;
-    }
-  }
-  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 t = e >> 1, n = this.byteArray[this.b0 + this.read_name_length + this.num_cigar_bytes + t];
-      return e % 2 === 0 ? E[(n & 240) >> 4] : E[n & 15];
-    } else
-      return;
-  }
-  toJSON() {
-    const e = {};
-    for (const t of Object.keys(this))
-      t.startsWith("_") || t === "bytes" || (e[t] = this[t]);
-    return e;
-  }
-}
-function K(h) {
-  const e = h.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((c) => {
-        const i = c.indexOf(":"), a = c.slice(0, i), l = c.slice(i + 1);
-        return { tag: a, value: l };
-      })
-    });
-  }
-  return t;
-}
-const W = 21840194, _e = 65536;
-class me {
-  constructor({ bamFilehandle: e, bamPath: t, bamUrl: n, baiPath: r, baiFilehandle: s, baiUrl: c, csiPath: i, csiFilehandle: a, csiUrl: l, htsget: u, renameRefSeqs: o = (d) => d, recordClass: f }) {
-    if (this.htsget = !1, this.chunkFeatureCache = new V({
-      maxSize: 100
-    }), this.renameRefSeq = o, this.RecordClass = f ?? we, e)
-      this.bam = e;
-    else if (t)
-      this.bam = new v(t);
-    else if (n)
-      this.bam = new B(n);
-    else if (u)
-      this.htsget = !0, this.bam = new le();
-    else
-      throw new Error("unable to initialize bam");
-    if (a)
-      this.index = new $({ filehandle: a });
-    else if (i)
-      this.index = new $({ filehandle: new v(i) });
-    else if (l)
-      this.index = new $({ filehandle: new B(l) });
-    else if (s)
-      this.index = new F({ filehandle: s });
-    else if (r)
-      this.index = new F({ filehandle: new v(r) });
-    else if (c)
-      this.index = new F({ filehandle: new B(c) });
-    else if (t)
-      this.index = new F({ filehandle: new v(`${t}.bai`) });
-    else if (n)
-      this.index = new F({ filehandle: new B(`${n}.bai`) });
-    else if (u)
-      this.htsget = !0;
-    else
-      throw new Error("unable to infer index format");
-  }
-  async getHeaderPre(e) {
-    const t = Z(e);
-    if (!this.index)
-      return;
-    const n = await this.index.parse(t), r = n.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(n.firstDataLine.blockPosition + _e, 0)
-    ), s = await D(r), c = new DataView(s.buffer);
-    if (c.getInt32(0, !0) !== W)
-      throw new Error("Not a BAM file");
-    const i = c.getInt32(4, !0), a = new TextDecoder("utf8");
-    this.header = a.decode(s.subarray(8, 8 + i));
-    const { chrToIndex: l, indexToChr: u } = this._parseRefSeqs(s, i + 8);
-    return this.chrToIndex = l, this.indexToChr = u, K(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;
-  }
-  _parseRefSeqs(e, t) {
-    const n = new DataView(e.buffer), r = n.getInt32(t, !0);
-    let s = t + 4;
-    const c = {}, i = [], a = new TextDecoder("utf8");
-    for (let l = 0; l < r; l += 1) {
-      if (s + 8 > e.length)
-        throw new Error(`Insufficient data for reference sequences: need more than ${e.length} bytes`);
-      const u = n.getInt32(s, !0), o = this.renameRefSeq(a.decode(e.subarray(s + 4, s + 4 + u - 1))), f = n.getInt32(s + u + 4, !0);
-      c[o] = l, i.push({
-        refName: o,
-        length: f
-      }), s = s + 8 + u;
-    }
-    return { chrToIndex: c, indexToChr: i };
-  }
-  async getRecordsForRange(e, t, n, r) {
-    await this.getHeader(r);
-    const s = this.chrToIndex?.[e];
-    if (s === void 0 || !this.index)
-      return [];
-    const c = await this.index.blocksForRange(s, t - 1, n, r);
-    return this._fetchChunkFeaturesDirect(c, s, t, n, r);
-  }
-  chunkCacheKey(e, t) {
-    const { minv: n, maxv: r } = e;
-    return `${n.blockPosition}:${n.dataPosition}-${r.blockPosition}:${r.dataPosition}${re(t)}`;
-  }
-  blocksOverlap(e, t, n, r) {
-    return e <= r && t >= n;
-  }
-  // Evict any cached chunks that overlap with the given block range
-  evictOverlappingChunks(e, t) {
-    for (const [n, r] of this.chunkFeatureCache)
-      this.blocksOverlap(e, t, r.minBlock, r.maxBlock) && this.chunkFeatureCache.delete(n);
-  }
-  async _fetchChunkFeaturesDirect(e, t, n, r, s = {}) {
-    const { viewAsPairs: c, filterBy: i } = s, { flagInclude: a = 0, flagExclude: l = 0, tagFilter: u } = i || {}, o = [];
-    for (let f = 0, d = e.length; f < d; f++) {
-      const b = e[f], g = this.chunkCacheKey(b, i), x = b.minv.blockPosition, w = b.maxv.blockPosition;
-      let _;
-      const m = this.chunkFeatureCache.get(g);
-      if (m)
-        _ = m.features;
-      else {
-        this.evictOverlappingChunks(x, w);
-        const { data: p, cpositions: C, dpositions: I } = await this._readChunk({
-          chunk: b,
-          opts: s
-        }), k = await this.readBamFeatures(p, C, I, b);
-        if (i) {
-          _ = [];
-          for (let R = 0, T = k.length; R < T; R++) {
-            const P = k[R];
-            ne(P.flags, a, l) || u && se(P.tags[u.tag], u.value) || _.push(P);
-          }
-        } else
-          _ = k;
-        this.chunkFeatureCache.set(g, {
-          minBlock: x,
-          maxBlock: w,
-          features: _
-        });
-      }
-      let y = !1;
-      for (let p = 0, C = _.length; p < C; p++) {
-        const I = _[p];
-        if (I.ref_id === t)
-          if (I.start >= r) {
-            y = !0;
-            break;
-          } else I.end >= n && o.push(I);
-      }
-      if (y)
-        break;
-    }
-    if (c) {
-      const f = await this.fetchPairs(t, o, s);
-      for (let d = 0, b = f.length; d < b; d++)
-        o.push(f[d]);
-    }
-    return o;
-  }
-  async fetchPairs(e, t, n) {
-    const { pairAcrossChr: r, maxInsertSize: s = 2e5 } = n, c = {}, i = {};
-    for (let f = 0, d = t.length; f < d; f++) {
-      const b = t[f], g = b.name;
-      c[g] = (c[g] || 0) + 1, i[b.fileOffset] = 1;
-    }
-    const a = [];
-    for (let f = 0, d = t.length; f < d; f++) {
-      const b = t[f], g = b.name;
-      this.index && c[g] === 1 && (r || b.next_refid === e && Math.abs(b.start - b.next_pos) < s) && a.push(this.index.blocksForRange(b.next_refid, b.next_pos, b.next_pos + 1, n));
-    }
-    const l = /* @__PURE__ */ new Map(), u = await Promise.all(a);
-    for (let f = 0, d = u.length; f < d; f++) {
-      const b = u[f];
-      for (let g = 0, x = b.length; g < x; g++) {
-        const w = b[g], _ = w.toString();
-        l.has(_) || l.set(_, w);
-      }
-    }
-    return (await Promise.all([...l.values()].map(async (f) => {
-      const { data: d, cpositions: b, dpositions: g, chunk: x } = await this._readChunk({
-        chunk: f,
-        opts: n
-      }), w = [], _ = await this.readBamFeatures(d, b, g, x);
-      for (let m = 0, y = _.length; m < y; m++) {
-        const p = _[m];
-        c[p.name] === 1 && !i[p.fileOffset] && w.push(p);
-      }
-      return w;
-    }))).flat();
-  }
-  async _readChunk({ chunk: e, opts: t }) {
-    const n = await this.bam.read(e.fetchedSize(), e.minv.blockPosition, t), { buffer: r, cpositions: s, dpositions: c } = await Y(n, e);
-    return { data: r, cpositions: s, dpositions: c, chunk: e };
-  }
-  async readBamFeatures(e, t, n, r) {
-    let s = 0;
-    const c = [];
-    let i = 0;
-    const a = new DataView(e.buffer), l = n.length > 0, u = t.length > 0;
-    for (; s + 4 < e.length; ) {
-      const o = a.getInt32(s, !0), f = s + 4 + o - 1;
-      if (l) {
-        for (; s + r.minv.dataPosition >= n[i++]; )
-          ;
-        i--;
-      }
-      if (f < e.length) {
-        const d = new this.RecordClass({
-          bytes: {
-            byteArray: e,
-            start: s,
-            end: f
-          },
-          fileOffset: u ? t[i] * 256 + (s - n[i]) + r.minv.dataPosition + 1 : de(e.subarray(s, f)) >>> 0
-        });
-        c.push(d);
-      }
-      s = f + 1;
-    }
-    return c;
-  }
-  async hasRefSeq(e) {
-    const t = this.chrToIndex?.[e];
-    return t === void 0 ? !1 : this.index?.hasRefSeq(t);
-  }
-  async lineCount(e) {
-    const t = this.chrToIndex?.[e];
-    return t === void 0 || !this.index ? 0 : this.index.lineCount(t);
-  }
-  async indexCov(e, t, n) {
-    if (!this.index)
-      return [];
-    await this.index.parse();
-    const r = this.chrToIndex?.[e];
-    return r === void 0 ? [] : this.index.indexCov(r, t, n);
-  }
-  async blocksForRange(e, t, n, r) {
-    if (!this.index)
-      return [];
-    await this.index.parse();
-    const s = this.chrToIndex?.[e];
-    return s === void 0 ? [] : this.index.blocksForRange(s, t, n, r);
-  }
-  clearFeatureCache() {
-    this.chunkFeatureCache.clear();
-  }
-  async estimatedBytesForRegions(e, t) {
-    if (!this.index)
-      return 0;
-    if (await this.getHeader(t), !this.chrToIndex)
-      throw new Error("Header not yet parsed");
-    return this.index.estimatedBytesForRegions(e.map((n) => {
-      const r = this.chrToIndex[n.refName];
-      if (r === void 0)
-        throw new Error(`Unknown reference name: ${n.refName}`);
-      return {
-        refId: r,
-        start: n.start,
-        end: n.end
-      };
-    }), t);
-  }
-}
-async function z(h, e) {
-  const t = await Promise.all(h.map(async (n) => {
-    const { url: r, headers: s } = n;
-    if (r.startsWith("data:")) {
-      const c = await fetch(r);
-      if (!c.ok)
-        throw new Error("failed to decode base64");
-      const i = await c.arrayBuffer();
-      return new Uint8Array(i);
-    } else {
-      const { referer: c, ...i } = s, a = await fetch(r, {
-        ...e,
-        headers: { ...e?.headers, ...i }
-      });
-      if (!a.ok)
-        throw new Error(`HTTP ${a.status} fetching ${r}: ${await a.text()}`);
-      return new Uint8Array(await a.arrayBuffer());
-    }
-  }));
-  return te(await Promise.all(t.map((n) => D(n))));
-}
-class Re extends me {
-  constructor(e) {
-    super({ htsget: !0, recordClass: e.recordClass }), this.baseUrl = e.baseUrl, this.trackId = e.trackId;
-  }
-  async getRecordsForRange(e, t, n, r) {
-    const c = `${`${this.baseUrl}/${this.trackId}`}?referenceName=${e}&start=${t}&end=${n}&format=BAM`, i = this.chrToIndex?.[e];
-    if (i === void 0)
-      return [];
-    const a = await fetch(c, { ...r });
-    if (!a.ok)
-      throw new Error(`HTTP ${a.status} fetching ${c}: ${await a.text()}`);
-    const l = await a.json(), u = await z(l.htsget.urls.slice(1), r), o = await this.readBamFeatures(u, [], [], {
-      minv: { dataPosition: 0, blockPosition: 0 },
-      maxv: { dataPosition: 0, blockPosition: 0 }
-    }), f = [];
-    for (let d = 0, b = o.length; d < b; d++) {
-      const g = o[d];
-      if (g.ref_id === i) {
-        if (g.start >= n)
-          break;
-        g.end >= t && f.push(g);
-      }
-    }
-    return f;
-  }
-  async getHeader(e = {}) {
-    const t = `${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 z(r.htsget.urls, e), c = new DataView(s.buffer);
-    if (c.getInt32(0, !0) !== W)
-      throw new Error("Not a BAM file");
-    const i = c.getInt32(4, !0), l = new TextDecoder("utf8").decode(s.subarray(8, 8 + i)), u = K(l), o = [], f = {}, d = u.filter((b) => b.tag === "SQ");
-    for (const [b, g] of d.entries()) {
-      let x = "", w = 0;
-      for (const _ of g.data)
-        _.tag === "SN" ? x = _.value : _.tag === "LN" && (w = +_.value);
-      f[x] = b, o[b] = { refName: x, length: w };
-    }
-    return this.chrToIndex = f, this.indexToChr = o, u;
-  }
-}
-export {
-  F as BAI,
-  me as BamFile,
-  we as BamRecord,
-  $ as CSI,
-  Re as HtsgetFile
-};