@genome-spy/core 0.56.1 → 0.58.0

package/dist/bundle/index-BpoXW6_f.js

@@ -1,1370 +0,0 @@
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-import { b as I } from "./index-B6haPltu.js";
-import { L as A } from "./__vite-browser-external-C--ziKoh.js";
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-import { _ as Y, L as W } from "./index-BhtH2nrr.js";
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-  //  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
-}, F = "=ACMGRSVTWYHKDBN".split(""), C = "MIDNSHP=X???????".split("");
-class me {
-  constructor(e) {
-    this.data = {}, this._tagList = [], this._allTagsParsed = !1;
-    const { bytes: t, fileOffset: n } = e, { byteArray: r, start: s } = t;
-    this.data = {}, this.bytes = t, this._id = n, this._refID = r.readInt32LE(s + 4), this.data.start = r.readInt32LE(s + 8), this.flags = (r.readInt32LE(s + 16) & 4294901760) >> 16;
-  }
-  get(e) {
-    return this[e] ? this.data[e] ? this.data[e] : (this.data[e] = this[e](), this.data[e]) : this._get(e.toLowerCase());
-  }
-  end() {
-    return this.get("start") + this.get("length_on_ref");
-  }
-  seq_id() {
-    return this._refID;
-  }
-  // same as get(), except requires lower-case arguments.  used
-  // internally to save lots of calls to field.toLowerCase()
-  _get(e) {
-    return e in this.data ? this.data[e] : (this.data[e] = this._parseTag(e), this.data[e]);
-  }
-  _tags() {
-    this._parseAllTags();
-    let e = ["seq"];
-    this.isSegmentUnmapped() || e.push("start", "end", "strand", "score", "qual", "MQ", "CIGAR", "length_on_ref", "template_length"), this.isPaired() && e.push("next_segment_position", "pair_orientation"), e = e.concat(this._tagList || []);
-    for (const n of Object.keys(this.data))
-      !n.startsWith("_") && n !== "next_seq_id" && e.push(n);
-    const t = {};
-    return e.filter((n) => {
-      if (n in this.data && this.data[n] === void 0 || n === "CG" || n === "cg")
-        return !1;
-      const r = n.toLowerCase(), s = t[r];
-      return t[r] = !0, !s;
-    });
-  }
-  parent() {
-  }
-  children() {
-    return this.get("subfeatures");
-  }
-  id() {
-    return this._id;
-  }
-  // special parsers
-  /**
-   * Mapping quality score.
-   */
-  mq() {
-    const e = (this.get("_bin_mq_nl") & 65280) >> 8;
-    return e === 255 ? void 0 : e;
-  }
-  score() {
-    return this.get("mq");
-  }
-  qual() {
-    var e;
-    return (e = this.qualRaw()) === null || e === void 0 ? void 0 : e.join(" ");
-  }
-  qualRaw() {
-    if (this.isSegmentUnmapped())
-      return;
-    const { start: e, byteArray: t } = this.bytes, n = e + 36 + this.get("_l_read_name") + this.get("_n_cigar_op") * 4 + this.get("_seq_bytes"), r = this.get("seq_length");
-    return t.subarray(n, n + r);
-  }
-  strand() {
-    return this.isReverseComplemented() ? -1 : 1;
-  }
-  multi_segment_next_segment_strand() {
-    if (!this.isMateUnmapped())
-      return this.isMateReverseComplemented() ? -1 : 1;
-  }
-  name() {
-    return this.get("_read_name");
-  }
-  _read_name() {
-    const e = this.get("_l_read_name"), { byteArray: t, start: n } = this.bytes;
-    return t.toString("ascii", n + 36, n + 36 + e - 1);
-  }
-  /**
-   * Get the value of a tag, parsing the tags as far as necessary.
-   * Only called if we have not already parsed that field.
-   */
-  _parseTag(e) {
-    if (this._allTagsParsed)
-      return;
-    const { byteArray: t, start: n } = this.bytes;
-    let r = this._tagOffset || n + 36 + this.get("_l_read_name") + this.get("_n_cigar_op") * 4 + this.get("_seq_bytes") + this.get("seq_length");
-    const s = this.bytes.end;
-    let a;
-    for (; r < s && a !== e; ) {
-      const h = String.fromCharCode(t[r], t[r + 1]);
-      a = h.toLowerCase();
-      const c = String.fromCharCode(t[r + 2]);
-      r += 3;
-      let i;
-      switch (c) {
-        case "A": {
-          i = String.fromCharCode(t[r]), r += 1;
-          break;
-        }
-        case "i": {
-          i = t.readInt32LE(r), r += 4;
-          break;
-        }
-        case "I": {
-          i = t.readUInt32LE(r), r += 4;
-          break;
-        }
-        case "c": {
-          i = t.readInt8(r), r += 1;
-          break;
-        }
-        case "C": {
-          i = t.readUInt8(r), r += 1;
-          break;
-        }
-        case "s": {
-          i = t.readInt16LE(r), r += 2;
-          break;
-        }
-        case "S": {
-          i = t.readUInt16LE(r), r += 2;
-          break;
-        }
-        case "f": {
-          i = t.readFloatLE(r), r += 4;
-          break;
-        }
-        case "Z":
-        case "H": {
-          for (i = ""; r <= s; ) {
-            const l = t[r++];
-            if (l === 0)
-              break;
-            i += String.fromCharCode(l);
-          }
-          break;
-        }
-        case "B": {
-          i = "";
-          const l = t[r++], u = String.fromCharCode(l), f = t.readInt32LE(r);
-          if (r += 4, u === "i")
-            if (h === "CG")
-              for (let d = 0; d < f; d++) {
-                const _ = t.readInt32LE(r), g = _ >> 4, m = C[_ & 15];
-                i += g + m, r += 4;
-              }
-            else
-              for (let d = 0; d < f; d++)
-                i += t.readInt32LE(r), d + 1 < f && (i += ","), r += 4;
-          if (u === "I")
-            if (h === "CG")
-              for (let d = 0; d < f; d++) {
-                const _ = t.readUInt32LE(r), g = _ >> 4, m = C[_ & 15];
-                i += g + m, r += 4;
-              }
-            else
-              for (let d = 0; d < f; d++)
-                i += t.readUInt32LE(r), d + 1 < f && (i += ","), r += 4;
-          if (u === "s")
-            for (let d = 0; d < f; d++)
-              i += t.readInt16LE(r), d + 1 < f && (i += ","), r += 2;
-          if (u === "S")
-            for (let d = 0; d < f; d++)
-              i += t.readUInt16LE(r), d + 1 < f && (i += ","), r += 2;
-          if (u === "c")
-            for (let d = 0; d < f; d++)
-              i += t.readInt8(r), d + 1 < f && (i += ","), r += 1;
-          if (u === "C")
-            for (let d = 0; d < f; d++)
-              i += t.readUInt8(r), d + 1 < f && (i += ","), r += 1;
-          if (u === "f")
-            for (let d = 0; d < f; d++)
-              i += t.readFloatLE(r), d + 1 < f && (i += ","), r += 4;
-          break;
-        }
-        default:
-          console.warn(`Unknown BAM tag type '${c}', tags may be incomplete`), i = void 0, r = s;
-      }
-      if (this._tagOffset = r, this._tagList.push(h), a === e)
-        return i;
-      this.data[a] = i;
-    }
-    this._allTagsParsed = !0;
-  }
-  _parseAllTags() {
-    this._parseTag("");
-  }
-  _parseCigar(e) {
-    return (
-      //@ts-ignore
-      e.match(/\d+\D/g).map((t) => [t.match(/\D/)[0].toUpperCase(), Number.parseInt(t, 10)])
-    );
-  }
-  /**
-   * @returns {boolean} true if the read is paired, regardless of whether both segments are mapped
-   */
-  isPaired() {
-    return !!(this.flags & b.BAM_FPAIRED);
-  }
-  /** @returns {boolean} true if the read is paired, and both segments are mapped */
-  isProperlyPaired() {
-    return !!(this.flags & b.BAM_FPROPER_PAIR);
-  }
-  /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
-  isSegmentUnmapped() {
-    return !!(this.flags & b.BAM_FUNMAP);
-  }
-  /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
-  isMateUnmapped() {
-    return !!(this.flags & b.BAM_FMUNMAP);
-  }
-  /** @returns {boolean} true if the read is mapped to the reverse strand */
-  isReverseComplemented() {
-    return !!(this.flags & b.BAM_FREVERSE);
-  }
-  /** @returns {boolean} true if the mate is mapped to the reverse strand */
-  isMateReverseComplemented() {
-    return !!(this.flags & b.BAM_FMREVERSE);
-  }
-  /** @returns {boolean} true if this is read number 1 in a pair */
-  isRead1() {
-    return !!(this.flags & b.BAM_FREAD1);
-  }
-  /** @returns {boolean} true if this is read number 2 in a pair */
-  isRead2() {
-    return !!(this.flags & b.BAM_FREAD2);
-  }
-  /** @returns {boolean} true if this is a secondary alignment */
-  isSecondary() {
-    return !!(this.flags & b.BAM_FSECONDARY);
-  }
-  /** @returns {boolean} true if this read has failed QC checks */
-  isFailedQc() {
-    return !!(this.flags & b.BAM_FQCFAIL);
-  }
-  /** @returns {boolean} true if the read is an optical or PCR duplicate */
-  isDuplicate() {
-    return !!(this.flags & b.BAM_FDUP);
-  }
-  /** @returns {boolean} true if this is a supplementary alignment */
-  isSupplementary() {
-    return !!(this.flags & b.BAM_FSUPPLEMENTARY);
-  }
-  cigar() {
-    if (this.isSegmentUnmapped())
-      return;
-    const { byteArray: e, start: t } = this.bytes, n = this.get("_n_cigar_op");
-    let r = t + 36 + this.get("_l_read_name");
-    const s = this.get("seq_length");
-    let a = "", h = 0, c = e.readInt32LE(r), i = c >> 4, l = C[c & 15];
-    if (l === "S" && i === s)
-      return r += 4, c = e.readInt32LE(r), i = c >> 4, l = C[c & 15], l !== "N" && console.warn("CG tag with no N tag"), this.data.length_on_ref = i, this.get("CG");
-    for (let u = 0; u < n; ++u)
-      c = e.readInt32LE(r), i = c >> 4, l = C[c & 15], a += i + l, l !== "H" && l !== "S" && l !== "I" && (h += i), r += 4;
-    return this.data.length_on_ref = h, a;
-  }
-  length_on_ref() {
-    return this.data.length_on_ref ? this.data.length_on_ref : (this.get("cigar"), this.data.length_on_ref);
-  }
-  _n_cigar_op() {
-    return this.get("_flag_nc") & 65535;
-  }
-  _l_read_name() {
-    return this.get("_bin_mq_nl") & 255;
-  }
-  /**
-   * number of bytes in the sequence field
-   */
-  _seq_bytes() {
-    return this.get("seq_length") + 1 >> 1;
-  }
-  getReadBases() {
-    return this.seq();
-  }
-  seq() {
-    const { byteArray: e, start: t } = this.bytes, n = t + 36 + this.get("_l_read_name") + this.get("_n_cigar_op") * 4, r = this.get("_seq_bytes"), s = this.get("seq_length");
-    let a = "", h = 0;
-    for (let c = 0; c < r; ++c) {
-      const i = e[n + c];
-      a += F[(i & 240) >> 4], h++, h < s && (a += F[i & 15], h++);
-    }
-    return a;
-  }
-  // adapted from igv.js
-  getPairOrientation() {
-    if (!this.isSegmentUnmapped() && !this.isMateUnmapped() && this._refID === 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("");
-    }
-    return "";
-  }
-  _bin_mq_nl() {
-    return this.bytes.byteArray.readInt32LE(this.bytes.start + 12);
-  }
-  _flag_nc() {
-    return this.bytes.byteArray.readInt32LE(this.bytes.start + 16);
-  }
-  seq_length() {
-    return this.bytes.byteArray.readInt32LE(this.bytes.start + 20);
-  }
-  _next_refid() {
-    return this.bytes.byteArray.readInt32LE(this.bytes.start + 24);
-  }
-  _next_pos() {
-    return this.bytes.byteArray.readInt32LE(this.bytes.start + 28);
-  }
-  template_length() {
-    return this.bytes.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 G(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((a) => {
-        const h = a.indexOf(":"), c = a.slice(0, h), i = a.slice(h + 1);
-        return { tag: c, value: i };
-      })
-    });
-  }
-  return t;
-}
-const j = 21840194, q = 65536;
-async function ge(o) {
-  let e = [];
-  for await (const t of o)
-    e = e.concat(t);
-  return e;
-}
-class _e {
-  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 pe {
-  constructor({ bamFilehandle: e, bamPath: t, bamUrl: n, baiPath: r, baiFilehandle: s, baiUrl: a, csiPath: h, csiFilehandle: c, csiUrl: i, htsget: l, yieldThreadTime: u = 100, renameRefSeqs: f = (d) => d }) {
-    if (this.htsget = !1, this.featureCache = new Y({
-      cache: new W({
-        maxSize: 50
-      }),
-      fill: async (d, _) => {
-        const { chunk: g, opts: m } = d, { data: p, cpositions: w, dpositions: E } = await this._readChunk({
-          chunk: g,
-          opts: { ...m, signal: _ }
-        });
-        return this.readBamFeatures(p, w, E, g);
-      }
-    }), this.renameRefSeq = f, e)
-      this.bam = e;
-    else if (t)
-      this.bam = new A(t);
-    else if (n)
-      this.bam = new R(n);
-    else if (l)
-      this.htsget = !0, this.bam = new _e();
-    else
-      throw new Error("unable to initialize bam");
-    if (c)
-      this.index = new P({ filehandle: c });
-    else if (h)
-      this.index = new P({ filehandle: new A(h) });
-    else if (i)
-      this.index = new P({ filehandle: new R(i) });
-    else if (s)
-      this.index = new v({ filehandle: s });
-    else if (r)
-      this.index = new v({ filehandle: new A(r) });
-    else if (a)
-      this.index = new v({ filehandle: new R(a) });
-    else if (t)
-      this.index = new v({ filehandle: new A(`${t}.bai`) });
-    else if (n)
-      this.index = new v({ filehandle: new R(`${n}.bai`) });
-    else if (l)
-      this.htsget = !0;
-    else
-      throw new Error("unable to infer index format");
-    this.yieldThreadTime = u;
-  }
-  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 l = r + q, u = await this.bam.read(I.Buffer.alloc(l), 0, l, 0, t);
-      if (!u.bytesRead)
-        throw new Error("Error reading header");
-      s = u.buffer.subarray(0, Math.min(u.bytesRead, r));
-    } else
-      s = await this.bam.readFile(t);
-    const a = await k(s);
-    if (a.readInt32LE(0) !== j)
-      throw new Error("Not a BAM file");
-    const h = a.readInt32LE(4);
-    this.header = a.toString("utf8", 8, 8 + h);
-    const { chrToIndex: c, indexToChr: i } = await this._readRefSeqs(h + 8, 65535, t);
-    return this.chrToIndex = c, this.indexToChr = i, G(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 + q, { bytesRead: s, buffer: a } = await this.bam.read(I.Buffer.alloc(r), 0, t, 0, n);
-    if (!s)
-      throw new Error("Error reading refseqs from header");
-    const h = await k(a.subarray(0, Math.min(s, t))), c = h.readInt32LE(e);
-    let i = e + 4;
-    const l = {}, u = [];
-    for (let f = 0; f < c; f += 1) {
-      const d = h.readInt32LE(i), _ = this.renameRefSeq(h.toString("utf8", i + 4, i + 4 + d - 1)), g = h.readInt32LE(i + d + 4);
-      if (l[_] = f, u.push({ refName: _, length: g }), i = i + 8 + d, i > h.length)
-        return console.warn(`BAM header is very big.  Re-fetching ${t} bytes.`), this._readRefSeqs(e, t * 2, n);
-    }
-    return { chrToIndex: l, indexToChr: u };
-  }
-  async getRecordsForRange(e, t, n, r) {
-    return ge(this.streamRecordsForRange(e, t, n, r));
-  }
-  async *streamRecordsForRange(e, t, n, r) {
-    var s;
-    await this.getHeader(r);
-    const a = (s = this.chrToIndex) === null || s === void 0 ? void 0 : s[e];
-    if (a === void 0 || !this.index)
-      yield [];
-    else {
-      const h = await this.index.blocksForRange(a, t - 1, n, r);
-      yield* this._fetchChunkFeatures(h, a, t, n, r);
-    }
-  }
-  async *_fetchChunkFeatures(e, t, n, r, s = {}) {
-    const { viewAsPairs: a } = s, h = [];
-    let c = !1;
-    for (const i of e) {
-      const l = await this.featureCache.get(i.toString(), { chunk: i, opts: s }, s.signal), u = [];
-      for (const f of l)
-        if (f.seq_id() === t)
-          if (f.get("start") >= r) {
-            c = !0;
-            break;
-          } else f.get("end") >= n && u.push(f);
-      if (h.push(u), yield u, c)
-        break;
-    }
-    K(s.signal), a && (yield this.fetchPairs(t, h, s));
-  }
-  async fetchPairs(e, t, n) {
-    const { pairAcrossChr: r, maxInsertSize: s = 2e5 } = n, a = {}, h = {};
-    t.map((f) => {
-      const d = {};
-      for (const _ of f) {
-        const g = _.name(), m = _.id();
-        d[g] || (d[g] = 0), d[g]++, h[m] = 1;
-      }
-      for (const [_, g] of Object.entries(d))
-        g === 1 && (a[_] = !0);
-    });
-    const c = [];
-    t.map((f) => {
-      for (const d of f) {
-        const _ = d.name(), g = d.get("start"), m = d._next_pos(), p = d._next_refid();
-        this.index && a[_] && (r || p === e && Math.abs(g - m) < s) && c.push(this.index.blocksForRange(p, m, m + 1, n));
-      }
-    });
-    const i = /* @__PURE__ */ new Map(), l = await Promise.all(c);
-    for (const f of l.flat())
-      i.has(f.toString()) || i.set(f.toString(), f);
-    return (await Promise.all([...i.values()].map(async (f) => {
-      const { data: d, cpositions: _, dpositions: g, chunk: m } = await this._readChunk({
-        chunk: f,
-        opts: n
-      }), p = [];
-      for (const w of await this.readBamFeatures(d, _, g, m))
-        a[w.get("name")] && !h[w.id()] && p.push(w);
-      return p;
-    }))).flat();
-  }
-  async _readRegion(e, t, n = {}) {
-    const { bytesRead: r, buffer: s } = await this.bam.read(I.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: a } = await Q(n, e);
-    return { data: r, cpositions: s, dpositions: a, chunk: e };
-  }
-  async readBamFeatures(e, t, n, r) {
-    let s = 0;
-    const a = [];
-    let h = 0, c = +Date.now();
-    for (; s + 4 < e.length; ) {
-      const i = e.readInt32LE(s), l = s + 4 + i - 1;
-      if (n) {
-        for (; s + r.minv.dataPosition >= n[h++]; )
-          ;
-        h--;
-      }
-      if (l < e.length) {
-        const u = new me({
-          bytes: {
-            byteArray: e,
-            start: s,
-            end: l
-          },
-          // 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[h] * 256 + (s - n[h]) + r.minv.dataPosition + 1 : (
-            // must be slice, not subarray for buffer polyfill on web
-            de.signed(e.slice(s, l))
-          )
-        });
-        a.push(u), this.yieldThreadTime && +Date.now() - c > this.yieldThreadTime && (await X(1), c = +Date.now());
-      }
-      s = l + 1;
-    }
-    return a;
-  }
-  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 a = (s = this.chrToIndex) === null || s === void 0 ? void 0 : s[e];
-    return a === void 0 ? [] : this.index.blocksForRange(a, t, n, r);
-  }
-}
-async function N(o, e) {
-  const t = await Promise.all(o.map(async (n) => {
-    const { url: r, headers: s } = n;
-    if (r.startsWith("data:"))
-      return I.Buffer.from(r.split(",")[1], "base64");
-    {
-      const { referer: a, ...h } = s, c = await fetch(r, {
-        ...e,
-        headers: { ...e == null ? void 0 : e.headers, ...h }
-      });
-      if (!c.ok)
-        throw new Error(`HTTP ${c.status} fetching ${r}: ${await c.text()}`);
-      return I.Buffer.from(await c.arrayBuffer());
-    }
-  }));
-  return I.Buffer.concat(await Promise.all(t.map((n) => k(n))));
-}
-class ye extends pe {
-  constructor(e) {
-    super({ htsget: !0 }), this.baseUrl = e.baseUrl, this.trackId = e.trackId;
-  }
-  async *streamRecordsForRange(e, t, n, r) {
-    var s;
-    const h = `${`${this.baseUrl}/${this.trackId}`}?referenceName=${e}&start=${t}&end=${n}&format=BAM`, c = (s = this.chrToIndex) === null || s === void 0 ? void 0 : s[e];
-    if (c === void 0)
-      yield [];
-    else {
-      const i = await fetch(h, { ...r });
-      if (!i.ok)
-        throw new Error(`HTTP ${i.status} fetching ${h}: ${await i.text()}`);
-      const l = await i.json(), u = await N(l.htsget.urls.slice(1), r);
-      yield* this._fetchChunkFeatures([
-        // fake stuff to pretend to be a Chunk
-        {
-          buffer: u,
-          _fetchedSize: void 0,
-          bin: 0,
-          compareTo() {
-            return 0;
-          },
-          toUniqueString() {
-            return `${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}_${n}`;
-          }
-        }
-      ], c, t, n, r);
-    }
-  }
-  async _readChunk({ chunk: e }) {
-    if (!e.buffer)
-      throw new Error("expected chunk.buffer in htsget");
-    return { data: e.buffer, cpositions: [], dpositions: [], chunk: e };
-  }
-  async getHeader(e = {}) {
-    const t = `${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 N(r.htsget.urls, e);
-    if (s.readInt32LE(0) !== j)
-      throw new Error("Not a BAM file");
-    const a = s.readInt32LE(4), h = s.toString("utf8", 8, 8 + a), c = G(h), i = [], l = {}, u = c.filter((f) => f.tag === "SQ");
-    for (const [f, d] of u.entries()) {
-      let _ = "", g = 0;
-      for (const m of d.data)
-        m.tag === "SN" ? _ = m.value : m.tag === "LN" && (g = +m.value);
-      l[_] = f, i[f] = { refName: _, length: g };
-    }
-    return this.chrToIndex = l, this.indexToChr = i, c;
-  }
-}
-export {
-  v as BAI,
-  pe as BamFile,
-  me as BamRecord,
-  P as CSI,
-  ye as HtsgetFile
-};