@genome-spy/app 0.73.0 → 0.74.0

package/dist/index-Gt44EOIH.js

@@ -1,628 +0,0 @@
-import { A as J } from "./AbortablePromiseCache-Dj0vzLnp.js";
-import { u as q, Q as U, a as K } from "./unzip-Bac01w6X.js";
-import { LocalFile as R, RemoteFile as F } from "./browser-0iNU5Wit.js";
-class L {
-  constructor(e, t, n, i) {
-    this.minv = e, this.maxv = t, this.bin = n, this._fetchedSize = i;
-  }
-  toUniqueString() {
-    return `${this.minv}..${this.maxv} (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;
-  }
-}
-class j {
-  constructor({ filehandle: e, renameRefSeqs: t = (n) => n }) {
-    this.filehandle = e, this.renameRefSeq = t;
-  }
-  async getMetadata(e = {}) {
-    const { indices: t, ...n } = await this.parse(e);
-    return n;
-  }
-  _findFirstData(e, t) {
-    return e ? e.compareTo(t) > 0 ? t : e : t;
-  }
-  async parse(e = {}) {
-    return this.parseP || (this.parseP = this._parse(e).catch((t) => {
-      throw this.parseP = void 0, t;
-    })), this.parseP;
-  }
-  async hasRefSeq(e, t = {}) {
-    return !!(await this.parse(t)).indices[e]?.binIndex;
-  }
-  _parseNameBytes(e) {
-    let t = 0, n = 0;
-    const i = [], o = {}, r = new TextDecoder("utf8");
-    for (let s = 0; s < e.length; s += 1)
-      if (!e[s]) {
-        if (n < s) {
-          const c = this.renameRefSeq(r.decode(e.subarray(n, s)));
-          i[t] = c, o[c] = t;
-        }
-        n = s + 1, t += 1;
-      }
-    return {
-      refNameToId: o,
-      refIdToName: i
-    };
-  }
-}
-const H = 65536, Z = H * H;
-function Q(a, e = 0) {
-  const t = a[e] | a[e + 1] << 8 | a[e + 2] << 16 | a[e + 3] << 24;
-  return ((a[e + 4] | a[e + 5] << 8 | a[e + 6] << 16 | a[e + 7] << 24) >>> 0) * Z + (t >>> 0);
-}
-function ee(a, e) {
-  return e.minv.blockPosition - a.maxv.blockPosition < 65e3 && e.maxv.blockPosition - a.minv.blockPosition < 5e6;
-}
-function X(a, e) {
-  const t = [];
-  let n;
-  if (a.length === 0)
-    return a;
-  a.sort(function(i, o) {
-    const r = i.minv.blockPosition - o.minv.blockPosition;
-    return r === 0 ? i.minv.dataPosition - o.minv.dataPosition : r;
-  });
-  for (const i of a)
-    (!e || i.maxv.compareTo(e) > 0) && (n === void 0 ? (t.push(i), n = i) : ee(n, i) ? i.maxv.compareTo(n.maxv) > 0 && (n.maxv = i.maxv) : (t.push(i), n = i));
-  return t;
-}
-class E {
-  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;
-  }
-}
-function A(a, e = 0) {
-  return new E(a[e + 7] * 1099511627776 + a[e + 6] * 4294967296 + a[e + 5] * 16777216 + a[e + 4] * 65536 + a[e + 3] * 256 + a[e + 2], a[e + 1] << 8 | a[e]);
-}
-const te = 21582659, ne = 38359875, ie = {
-  0: "generic",
-  1: "SAM",
-  2: "VCF"
-};
-function se(a, e) {
-  return a * 2 ** e;
-}
-function W(a, e) {
-  return Math.floor(a / 2 ** e);
-}
-class V extends j {
-  constructor(e) {
-    super(e), this.maxBinNumber = 0, this.depth = 0, this.minShift = 0;
-  }
-  async lineCount(e, t = {}) {
-    const n = await this.parse(t), i = n.refNameToId[e];
-    if (i === void 0 || !n.indices[i])
-      return -1;
-    const { stats: r } = n.indices[i];
-    return r ? r.lineCount : -1;
-  }
-  indexCov() {
-    throw new Error("CSI indexes do not support indexcov");
-  }
-  parseAuxData(e, t) {
-    const n = new DataView(e.buffer), i = n.getInt32(t, !0), o = i & 65536 ? "zero-based-half-open" : "1-based-closed", r = ie[i & 15];
-    if (!r)
-      throw new Error(`invalid Tabix preset format flags ${i}`);
-    const s = {
-      ref: n.getInt32(t + 4, !0),
-      start: n.getInt32(t + 8, !0),
-      end: n.getInt32(t + 12, !0)
-    }, c = n.getInt32(t + 16, !0), u = c ? String.fromCharCode(c) : void 0, f = n.getInt32(t + 20, !0), m = n.getInt32(t + 24, !0), { refIdToName: d, refNameToId: l } = this._parseNameBytes(e.subarray(t + 28, t + 28 + m));
-    return {
-      refIdToName: d,
-      refNameToId: l,
-      skipLines: f,
-      metaChar: u,
-      columnNumbers: s,
-      format: r,
-      coordinateType: o
-    };
-  }
-  async _parse(e = {}) {
-    const t = await q(await this.filehandle.readFile(e)), n = new DataView(t.buffer);
-    let i;
-    if (n.getUint32(0, !0) === te)
-      i = 1;
-    else if (n.getUint32(0, !0) === ne)
-      i = 2;
-    else
-      throw new Error("Not a CSI file");
-    this.minShift = n.getInt32(4, !0), this.depth = n.getInt32(8, !0), this.maxBinNumber = ((1 << (this.depth + 1) * 3) - 1) / 7;
-    const o = 2 ** (this.minShift + this.depth * 3), r = n.getInt32(12, !0), s = r && r >= 30 ? this.parseAuxData(t, 16) : {
-      refIdToName: [],
-      refNameToId: {},
-      metaChar: void 0,
-      columnNumbers: { ref: 0, start: 1, end: 2 },
-      coordinateType: "zero-based-half-open",
-      format: "generic"
-    }, c = n.getInt32(16 + r, !0);
-    let u, f = 16 + r + 4;
-    const m = new Array(c).fill(0).map(() => {
-      const d = n.getInt32(f, !0);
-      f += 4;
-      const l = {};
-      let h;
-      for (let S = 0; S < d; S += 1) {
-        const C = n.getUint32(f, !0);
-        if (C > this.maxBinNumber)
-          h = this.parsePseudoBin(t, f + 4), f += 48;
-        else {
-          const I = A(t, f + 4);
-          u = this._findFirstData(u, I);
-          const k = n.getInt32(f + 12, !0);
-          f += 16;
-          const w = new Array(k);
-          for (let b = 0; b < k; b += 1) {
-            const x = A(t, f), g = A(t, f + 8);
-            f += 16, w[b] = new L(x, g, C);
-          }
-          l[C] = w;
-        }
-      }
-      return { binIndex: l, stats: h };
-    });
-    return {
-      ...s,
-      csi: !0,
-      refCount: c,
-      maxBlockSize: 65536,
-      firstDataLine: u,
-      csiVersion: i,
-      indices: m,
-      depth: this.depth,
-      maxBinNumber: this.maxBinNumber,
-      maxRefLength: o
-    };
-  }
-  parsePseudoBin(e, t) {
-    return {
-      lineCount: Q(e, t + 28)
-    };
-  }
-  async blocksForRange(e, t, n, i = {}) {
-    t < 0 && (t = 0);
-    const o = await this.parse(i), r = o.refNameToId[e];
-    if (r === void 0)
-      return [];
-    const s = o.indices[r];
-    if (!s)
-      return [];
-    const c = this.reg2bins(t, n), u = [];
-    for (const [f, m] of c)
-      for (let d = f; d <= m; d++)
-        if (s.binIndex[d])
-          for (const l of s.binIndex[d])
-            u.push(new L(l.minv, l.maxv, d));
-    return X(u, new E(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, i = 0, o = this.minShift + this.depth * 3;
-    const r = [];
-    for (; n <= this.depth; o -= 3, i += se(1, n * 3), n += 1) {
-      const s = i + W(e, o), c = i + W(t, o);
-      if (c - s + r.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`);
-      r.push([s, c]);
-    }
-    return r;
-  }
-}
-const re = 21578324, G = 14;
-function ae(a, e) {
-  return a += 1, e -= 1, [
-    [0, 0],
-    [1 + (a >> 26), 1 + (e >> 26)],
-    [9 + (a >> 23), 9 + (e >> 23)],
-    [73 + (a >> 20), 73 + (e >> 20)],
-    [585 + (a >> 17), 585 + (e >> 17)],
-    [4681 + (a >> 14), 4681 + (e >> 14)]
-  ];
-}
-class D extends j {
-  async lineCount(e, t = {}) {
-    const n = await this.parse(t), i = n.refNameToId[e];
-    return i === void 0 || !n.indices[i] ? -1 : n.indices[i].stats?.lineCount ?? -1;
-  }
-  // fetch and parse the index
-  async _parse(e = {}) {
-    const t = await this.filehandle.readFile(e), n = await q(t), i = new DataView(n.buffer);
-    if (i.getUint32(0, !0) !== re)
-      throw new Error("Not a TBI file");
-    const r = i.getUint32(4, !0), s = i.getUint32(8, !0), c = s & 65536 ? "zero-based-half-open" : "1-based-closed", f = {
-      0: "generic",
-      1: "SAM",
-      2: "VCF"
-    }[s & 15];
-    if (!f)
-      throw new Error(`invalid Tabix preset format flags ${s}`);
-    const m = {
-      ref: i.getInt32(12, !0),
-      start: i.getInt32(16, !0),
-      end: i.getInt32(20, !0)
-    }, d = i.getInt32(24, !0), l = 5, h = ((1 << (l + 1) * 3) - 1) / 7, S = 2 ** (14 + l * 3), C = d ? String.fromCharCode(d) : void 0, I = i.getInt32(28, !0), k = i.getInt32(32, !0), { refNameToId: w, refIdToName: b } = this._parseNameBytes(n.slice(36, 36 + k));
-    let x = 36 + k, g;
-    return {
-      indices: new Array(r).fill(0).map(() => {
-        const y = i.getInt32(x, !0);
-        x += 4;
-        const B = {};
-        let M;
-        for (let T = 0; T < y; T += 1) {
-          const v = i.getUint32(x, !0);
-          if (x += 4, v > h + 1)
-            throw new Error("tabix index contains too many bins, please use a CSI index");
-          if (v === h + 1) {
-            const _ = i.getInt32(x, !0);
-            x += 4, _ === 2 && (M = this.parsePseudoBin(n, x)), x += 16 * _;
-          } else {
-            const _ = i.getInt32(x, !0);
-            x += 4;
-            const O = new Array(_);
-            for (let z = 0; z < _; z += 1) {
-              const $ = A(n, x), Y = A(n, x + 8);
-              x += 16, g = this._findFirstData(g, $), O[z] = new L($, Y, v);
-            }
-            B[v] = O;
-          }
-        }
-        const P = i.getInt32(x, !0);
-        x += 4;
-        const N = new Array(P);
-        for (let T = 0; T < P; T += 1)
-          N[T] = A(n, x), x += 8, g = this._findFirstData(g, N[T]);
-        return {
-          binIndex: B,
-          linearIndex: N,
-          stats: M
-        };
-      }),
-      metaChar: C,
-      maxBinNumber: h,
-      maxRefLength: S,
-      skipLines: I,
-      firstDataLine: g,
-      columnNumbers: m,
-      coordinateType: c,
-      format: f,
-      refIdToName: b,
-      refNameToId: w,
-      maxBlockSize: 65536
-    };
-  }
-  parsePseudoBin(e, t) {
-    return {
-      lineCount: Q(e, t + 16)
-    };
-  }
-  async blocksForRange(e, t, n, i = {}) {
-    t < 0 && (t = 0);
-    const o = await this.parse(i), r = o.refNameToId[e];
-    if (r === void 0)
-      return [];
-    const s = o.indices[r];
-    if (!s)
-      return [];
-    (s.linearIndex.length > 0 ? s.linearIndex[t >> G >= s.linearIndex.length ? s.linearIndex.length - 1 : t >> G] : new E(0, 0)) || console.warn("querying outside of possible tabix range");
-    const u = ae(t, n), f = [];
-    for (const [S, C] of u)
-      for (let I = S; I <= C; I++)
-        if (s.binIndex[I])
-          for (const k of s.binIndex[I])
-            f.push(new L(k.minv, k.maxv, I));
-    const m = s.linearIndex.length;
-    let d;
-    const l = Math.min(t >> 14, m - 1), h = Math.min(n >> 14, m - 1);
-    for (let S = l; S <= h; ++S) {
-      const C = s.linearIndex[S];
-      C && (!d || C.compareTo(d) < 0) && (d = C);
-    }
-    return X(f, d);
-  }
-}
-class he {
-  /**
-   * @param {object} args
-   *
-   * @param {string} [args.path]
-   *
-   * @param {filehandle} [args.filehandle]
-   *
-   * @param {string} [args.tbiPath]
-   *
-   * @param {filehandle} [args.tbiFilehandle]
-   *
-   * @param {string} [args.csiPath]
-   *
-   * @param {filehandle} [args.csiFilehandle]
-   *
-   * @param {url} [args.url]
-   *
-   * @param {csiUrl} [args.csiUrl]
-   *
-   * @param {tbiUrl} [args.tbiUrl]
-   *
-   * @param {function} [args.renameRefSeqs] optional function with sig `string
-   * => string` to transform reference sequence names for the purpose of
-   * indexing and querying. note that the data that is returned is not altered,
-   * just the names of the reference sequences that are used for querying.
-   */
-  constructor({ path: e, filehandle: t, url: n, tbiPath: i, tbiUrl: o, tbiFilehandle: r, csiPath: s, csiUrl: c, csiFilehandle: u, renameRefSeqs: f, chunkCacheSize: m = 5 * 2 ** 20 }) {
-    this.cache = new U({
-      maxSize: 1e3
-    });
-    const d = f ?? ((l) => l);
-    if (t)
-      this.filehandle = t;
-    else if (e)
-      this.filehandle = new R(e);
-    else if (n)
-      this.filehandle = new F(n);
-    else
-      throw new TypeError("must provide either filehandle or path");
-    if (r)
-      this.index = new D({
-        filehandle: r,
-        renameRefSeqs: d
-      });
-    else if (u)
-      this.index = new V({
-        filehandle: u,
-        renameRefSeqs: d
-      });
-    else if (i)
-      this.index = new D({
-        filehandle: new R(i),
-        renameRefSeqs: d
-      });
-    else if (s)
-      this.index = new V({
-        filehandle: new R(s),
-        renameRefSeqs: d
-      });
-    else if (e)
-      this.index = new D({
-        filehandle: new R(`${e}.tbi`),
-        renameRefSeqs: d
-      });
-    else if (c)
-      this.index = new V({
-        filehandle: new F(c)
-      });
-    else if (o)
-      this.index = new D({
-        filehandle: new F(o)
-      });
-    else if (n)
-      this.index = new D({
-        filehandle: new F(`${n}.tbi`)
-      });
-    else
-      throw new TypeError("must provide one of tbiFilehandle, tbiPath, csiFilehandle, csiPath, tbiUrl, csiUrl");
-    this.renameRefSeq = d, this.hasCustomRenameRefSeq = f !== void 0, this.chunkCache = new J({
-      cache: new U({ maxSize: Math.floor(m / 65536) }),
-      fill: (l, h) => this.readChunk(l, { signal: h })
-    });
-  }
-  /**
-   * @param refName name of the reference sequence
-   *
-   * @param start start of the region (in 0-based half-open coordinates)
-   *
-   * @param end end of the region (in 0-based half-open coordinates)
-   *
-   * @param opts callback called for each line in the region. can also pass a
-   * object param containing obj.lineCallback, obj.signal, etc
-   *
-   * @returns promise that is resolved when the whole read is finished,
-   * rejected on error
-   */
-  calculateFileOffset(e, t, n, i, o) {
-    return e[n] * 256 + (i - t[n]) + o + 1;
-  }
-  async getLines(e, t, n, i) {
-    let o, r = {}, s;
-    typeof i == "function" ? s = i : (r = i, s = i.lineCallback, o = i.signal);
-    const c = await this.index.getMetadata(r), u = t ?? 0, f = n ?? c.maxRefLength;
-    if (!(u <= f))
-      throw new TypeError("invalid start and end coordinates. start must be less than or equal to end");
-    if (u === f)
-      return;
-    const m = await this.index.blocksForRange(e, u, f, r), d = new TextDecoder("utf8"), l = c.format === "VCF", h = {
-      ref: c.columnNumbers.ref || 0,
-      start: c.columnNumbers.start || 0,
-      end: l ? 8 : c.columnNumbers.end || 0
-    }, S = Math.max(h.ref, h.start, h.end), C = c.metaChar?.charCodeAt(0), I = c.coordinateType === "1-based-closed" ? -1 : 0, k = !this.hasCustomRenameRefSeq;
-    for (const w of m) {
-      const { buffer: b, cpositions: x, dpositions: g } = await this.chunkCache.get(w.toString(), w, o);
-      let p = 0, y = 0;
-      const B = d.decode(b);
-      if (b.length == B.length)
-        for (; p < B.length; ) {
-          const P = B.indexOf(`
-`, p);
-          if (P === -1)
-            break;
-          const N = B.slice(p, P);
-          if (g) {
-            const v = p + w.minv.dataPosition;
-            for (; y < g.length && v >= g[y]; )
-              y++;
-          }
-          const T = this.checkLine(e, u, f, N, h.ref, h.start, h.end, S, C, I, l, k);
-          if (T === null)
-            return;
-          T !== void 0 && s(N, this.calculateFileOffset(x, g, y, p, w.minv.dataPosition), T.start, T.end), p = P + 1;
-        }
-      else
-        for (; p < b.length; ) {
-          const P = b.indexOf(10, p);
-          if (P === -1)
-            break;
-          const N = b.slice(p, P), T = d.decode(N);
-          if (g) {
-            const _ = p + w.minv.dataPosition;
-            for (; y < g.length && _ >= g[y]; )
-              y++;
-          }
-          const v = this.checkLine(e, u, f, T, h.ref, h.start, h.end, S, C, I, l, k);
-          if (v === null)
-            return;
-          v !== void 0 && s(T, this.calculateFileOffset(x, g, y, p, w.minv.dataPosition), v.start, v.end), p = P + 1;
-        }
-    }
-  }
-  async getMetadata(e = {}) {
-    return this.index.getMetadata(e);
-  }
-  /**
-   * get a buffer containing the "header" region of the file, which are the
-   * bytes up to the first non-meta line
-   */
-  async getHeaderBuffer(e = {}) {
-    const { firstDataLine: t, metaChar: n, maxBlockSize: i } = await this.getMetadata(e), o = (t?.blockPosition || 0) + i, r = await this.filehandle.read(o, 0, e), s = await q(r);
-    if (n) {
-      let c = -1;
-      const u = 10, f = n.charCodeAt(0);
-      for (let m = 0, d = s.length; m < d; m++) {
-        const l = s[m];
-        if (m === c + 1 && l !== f)
-          break;
-        l === u && (c = m);
-      }
-      return s.subarray(0, c + 1);
-    }
-    return s;
-  }
-  /**
-   * get a string containing the "header" region of the file, is the portion up
-   * to the first non-meta line
-   */
-  async getHeader(e = {}) {
-    const t = new TextDecoder("utf8"), n = await this.getHeaderBuffer(e);
-    return t.decode(n);
-  }
-  /**
-   * get an array of reference sequence names, in the order in which they occur
-   * in the file. reference sequence renaming is not applied to these names.
-   */
-  async getReferenceSequenceNames(e = {}) {
-    return (await this.getMetadata(e)).refIdToName;
-  }
-  /**
-   * @param {string} regionRefName
-   *
-   * @param {number} regionStart region start coordinate (0-based-half-open)
-   *
-   * @param {number} regionEnd region end coordinate (0-based-half-open)
-   *
-   * @param {string} line
-   *
-   * @param {number} refColumn column number for ref
-   *
-   * @param {number} startColumn column number for start
-   *
-   * @param {number} endColumn column number for end
-   *
-   * @param {number} maxColumn pre-calculated max column
-   *
-   * @param {number} metaCharCode pre-calculated metaChar code
-   *
-   * @param {number} coordinateOffset 0 or -1 for coordinate adjustment
-   *
-   * @param {boolean} isVCF whether this is VCF format
-   *
-   * @param {boolean} isIdentityRename whether renameRefSeq is the identity function
-   *
-   * @returns {{ start: number, end: number } | null | undefined} coordinates if overlapping, null if should stop processing, undefined otherwise
-   */
-  checkLine(e, t, n, i, o, r, s, c, u, f, m, d) {
-    if (u !== void 0 && i.charCodeAt(0) === u)
-      return;
-    if (i.length < 500) {
-      const w = i.split("	"), b = w[o - 1];
-      if (!(d ? b === e : this.renameRefSeq(b) === e))
-        return;
-      const g = +w[r - 1] + f;
-      if (g >= n)
-        return null;
-      let p;
-      return s === 0 || s === r ? p = g + 1 : m ? p = this._getVcfEnd(g, w[3], w[s - 1]) : p = +w[s - 1], p <= t ? void 0 : { start: g, end: p };
-    }
-    let l = -1;
-    const h = [-1];
-    for (let w = 0; w < c; w++) {
-      const b = i.indexOf("	", l + 1);
-      if (b === -1) {
-        h.push(i.length);
-        break;
-      }
-      h.push(b), l = b;
-    }
-    const S = i.slice(h[o - 1] + 1, h[o]);
-    if (!(d ? S === e : this.renameRefSeq(S) === e))
-      return;
-    const I = +i.slice(h[r - 1] + 1, h[r]) + f;
-    if (I >= n)
-      return null;
-    let k;
-    if (s === 0 || s === r ? k = I + 1 : m ? k = this._getVcfEnd(I, i.slice(h[3] + 1, h[4]), i.slice(h[s - 1] + 1, h[s])) : k = +i.slice(h[s - 1] + 1, h[s]), !(k <= t))
-      return { start: I, end: k };
-  }
-  _getVcfEnd(e, t, n) {
-    let i = e + t.length;
-    if (n.includes("SVTYPE=TRA"))
-      return e + 1;
-    if (n[0] !== ".") {
-      const r = n.indexOf("END=");
-      if (r !== -1 && (r === 0 || n[r - 1] === ";")) {
-        const s = r + 4;
-        let c = n.indexOf(";", s);
-        c === -1 && (c = n.length), i = Number.parseInt(n.slice(s, c), 10);
-      }
-    }
-    return i;
-  }
-  /**
-   * return the approximate number of data lines in the given reference
-   * sequence
-   *
-   * @param refSeq reference sequence name
-   *
-   * @returns number of data lines present on that reference sequence
-   */
-  async lineCount(e, t = {}) {
-    return this.index.lineCount(e, t);
-  }
-  /**
-   * read and uncompress the data in a chunk (composed of one or more
-   * contiguous bgzip blocks) of the file
-   */
-  async readChunk(e, t = {}) {
-    const n = await this.filehandle.read(e.fetchedSize(), e.minv.blockPosition, t);
-    return K(n, e, this.cache);
-  }
-}
-export {
-  V as CSI,
-  D as TBI,
-  he as TabixIndexedFile
-};