@genome-spy/core 0.65.0 → 0.67.0

package/dist/bundle/index-BQpbYrv4.js

@@ -1,1712 +0,0 @@
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-  contains(e) {
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-  union(e) {
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-      offset: o.offset
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-function j(t) {
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-  }
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-      let y = [], g = 0;
-      const f = (b, x, B) => {
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-          h += 2;
-          const E = w.getUint16(h, !0);
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-              h += 4;
-              const V = w.getUint32(h, !0);
-              h += 4;
-              const _ = w.getUint32(h, !0);
-              h += 4;
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-              h += 4;
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-              h += 8;
-              const Y = Number(w.getBigUint64(h, !0));
-              h += 8, P.push({
-                startChrom: O,
-                startBase: V,
-                endBase: F,
-                endChrom: _,
-                blockOffset: W,
-                blockSize: Y,
-                offset: h
-              });
-            }
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-              offset: I.blockOffset,
-              length: I.blockSize
-            })));
-          } else if (U === 0) {
-            const P = [];
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-              h += 4;
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-              h += 4;
-              const F = w.getUint32(h, !0);
-              h += 4;
-              const W = w.getUint32(h, !0);
-              h += 4;
-              const Y = Number(w.getBigUint64(h, !0));
-              h += 8, P.push({
-                startChrom: V,
-                startBase: _,
-                endChrom: F,
-                endBase: W,
-                blockOffset: Y,
-                offset: h
-              });
-            }
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-      }, m = (b) => {
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-      }, l = async (b, x, B) => {
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-              o.error(U);
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-          o.error(S);
-        }
-      }, v = (b, x) => {
-        try {
-          g += b.length;
-          const B = 4 + d * 32;
-          let S = new N([
-            {
-              min: b[0],
-              max: b[0] + B
-            }
-          ]);
-          for (let p = 1; p < b.length; p += 1) {
-            const w = new N([
-              {
-                min: b[p],
-                max: b[p] + B
-              }
-            ]);
-            S = S.union(w);
-          }
-          S.getRanges().map((p) => l(b, p, x));
-        } catch (B) {
-          o.error(B);
-        }
-      };
-      v([this.cirTreeOffset + 48], 1);
-      return;
-    } catch (s) {
-      o.error(s);
-    }
-  }
-  parseSummaryBlock(e, n, r) {
-    const o = [];
-    let i = n;
-    const s = new DataView(e.buffer, e.byteOffset, e.length);
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-      const u = s.getUint32(i, !0);
-      i += 4;
-      const a = s.getUint32(i, !0);
-      i += 4;
-      const c = s.getUint32(i, !0);
-      i += 4;
-      const d = s.getUint32(i, !0);
-      i += 4;
-      const y = s.getFloat32(i, !0);
-      i += 4;
-      const g = s.getFloat32(i, !0);
-      i += 4;
-      const f = s.getFloat32(i, !0);
-      i += 4, i += 4, (!r || u === r.chrId && Z(a, c, r.start, r.end)) && o.push({
-        start: a,
-        end: c,
-        maxScore: g,
-        minScore: y,
-        summary: !0,
-        score: f / (d || 1)
-      });
-    }
-    return o;
-  }
-  parseBigBedBlock(e, n, r, o) {
-    const i = [];
-    let s = n;
-    const u = e, a = new DataView(u.buffer, u.byteOffset, u.length);
-    for (; s < e.byteLength; ) {
-      const c = s, d = a.getUint32(s, !0);
-      s += 4;
-      const y = a.getInt32(s, !0);
-      s += 4;
-      const g = a.getInt32(s, !0);
-      s += 4;
-      let f = s;
-      for (; f < e.length && e[f] !== 0; f++)
-        ;
-      const m = e.subarray(s, f), l = (J == null ? void 0 : J.decode(m)) ?? m.toString();
-      s = f + 1, i.push({
-        chromId: d,
-        start: y,
-        end: g,
-        rest: l,
-        uniqueId: `bb-${r + c}`
-      });
-    }
-    return o ? i.filter((c) => Z(c.start, c.end, o.start, o.end)) : i;
-  }
-  parseBigWigBlock(e, n, r) {
-    const o = e.subarray(n), i = new DataView(o.buffer, o.byteOffset, o.length);
-    let s = 0;
-    s += 4;
-    const u = i.getInt32(s, !0);
-    s += 8;
-    const a = i.getUint32(s, !0);
-    s += 4;
-    const c = i.getUint32(s, !0);
-    s += 4;
-    const d = i.getUint8(s);
-    s += 2;
-    const y = i.getUint16(s, !0);
-    s += 2;
-    const g = new Array(y);
-    switch (d) {
-      case 1: {
-        for (let f = 0; f < y; f++) {
-          const m = i.getInt32(s, !0);
-          s += 4;
-          const l = i.getInt32(s, !0);
-          s += 4;
-          const v = i.getFloat32(s, !0);
-          s += 4, g[f] = {
-            start: m,
-            end: l,
-            score: v
-          };
-        }
-        break;
-      }
-      case 2: {
-        for (let f = 0; f < y; f++) {
-          const m = i.getInt32(s, !0);
-          s += 4;
-          const l = i.getFloat32(s, !0);
-          s += 4, g[f] = {
-            score: l,
-            start: m,
-            end: m + c
-          };
-        }
-        break;
-      }
-      case 3: {
-        for (let f = 0; f < y; f++) {
-          const m = i.getFloat32(s, !0);
-          s += 4;
-          const l = u + f * a;
-          g[f] = {
-            score: m,
-            start: l,
-            end: l + c
-          };
-        }
-        break;
-      }
-    }
-    return r ? g.filter((f) => Z(f.start, f.end, r.start, r.end)) : g;
-  }
-  async readFeatures(e, n, r = {}) {
-    try {
-      const { blockType: o, isCompressed: i } = this, { signal: s, request: u } = r, a = Ve(n);
-      j(s), await Promise.all(a.map(async (c) => {
-        j(s);
-        const { length: d, offset: y } = c, g = await this.featureCache.get(`${d}_${y}`, c, s);
-        for (const f of c.blocks) {
-          j(s);
-          let m = g.subarray(f.offset - c.offset);
-          switch (i && (m = Ee(m)), j(s), o) {
-            case "summary": {
-              e.next(this.parseSummaryBlock(m, 0, u));
-              break;
-            }
-            case "bigwig": {
-              e.next(this.parseBigWigBlock(m, 0, u));
-              break;
-            }
-            case "bigbed": {
-              e.next(this.parseBigBedBlock(m, 0, f.offset * 256, u));
-              break;
-            }
-            default:
-              console.warn(`Don't know what to do with ${o}`);
-          }
-        }
-      })), e.complete();
-    } catch (o) {
-      e.error(o);
-    }
-  }
-}
-const Ae = -2003829722, at = -2021002517;
-function R(t) {
-  return new DataView(t.buffer, t.byteOffset, t.length);
-}
-class Rt {
-  /*
-   * @param filehandle - a filehandle from generic-filehandle2
-   *
-   * @param path - a Local file path as a string
-   *
-   * @param url - a URL string
-   *
-   * @param renameRefSeqs - an optional method to rename the internal reference
-   * sequences using a mapping function
-   */
-  constructor(e) {
-    T(this, "bbi");
-    T(this, "headerP");
-    T(this, "renameRefSeqs");
-    const { filehandle: n, renameRefSeqs: r = (s) => s, path: o, url: i } = e;
-    if (this.renameRefSeqs = r, n)
-      this.bbi = n;
-    else if (i)
-      this.bbi = new zt(i);
-    else if (o)
-      this.bbi = new Lt(o);
-    else
-      throw new Error("no file given");
-  }
-  getHeader(e) {
-    return this.headerP || (this.headerP = this._getHeader(e).catch((n) => {
-      throw this.headerP = void 0, n;
-    })), this.headerP;
-  }
-  async _getHeader(e) {
-    const n = await this._getMainHeader(e), r = await this._readChromTree(n, e);
-    return {
-      ...n,
-      ...r
-    };
-  }
-  async _getMainHeader(e, n = 2e3) {
-    const r = await this.bbi.read(n, 0, e), o = R(r), i = o.getInt32(0, !0);
-    if (i !== Ae && i !== at)
-      throw new Error("not a BigWig/BigBed file");
-    let s = 0;
-    const u = o.getInt32(s, !0);
-    s += 4;
-    const a = o.getUint16(s, !0);
-    s += 2;
-    const c = o.getUint16(s, !0);
-    s += 2;
-    const d = Number(o.getBigUint64(s, !0));
-    s += 8;
-    const y = Number(o.getBigUint64(s, !0));
-    s += 8;
-    const g = Number(o.getBigUint64(s, !0));
-    s += 8;
-    const f = o.getUint16(s, !0);
-    s += 2;
-    const m = o.getUint16(s, !0);
-    s += 2;
-    const l = Number(o.getBigUint64(s, !0));
-    s += 8;
-    const v = Number(o.getBigUint64(s, !0));
-    s += 8;
-    const b = o.getUint32(s, !0);
-    s += 4;
-    const x = Number(o.getBigUint64(s, !0));
-    s += 8;
-    const B = [];
-    for (let h = 0; h < c; h++) {
-      const U = o.getUint32(s, !0);
-      s += 4;
-      const E = o.getUint32(s, !0);
-      s += 4;
-      const P = Number(o.getBigUint64(s, !0));
-      s += 8;
-      const I = Number(o.getBigUint64(s, !0));
-      s += 8, B.push({
-        reductionLevel: U,
-        reserved: E,
-        dataOffset: P,
-        indexOffset: I
-      });
-    }
-    const S = u === at ? "bigbed" : "bigwig";
-    if (l > n || v > n - 8 * 5)
-      return this._getMainHeader(e, n * 2);
-    let p;
-    if (v) {
-      const h = r.subarray(v);
-      let U = 0;
-      const E = R(h), P = Number(E.getBigUint64(U, !0));
-      U += 8;
-      const I = E.getFloat64(U, !0);
-      U += 8;
-      const O = E.getFloat64(U, !0);
-      U += 8;
-      const V = E.getFloat64(U, !0);
-      U += 8;
-      const _ = E.getFloat64(U, !0);
-      U += 8, p = {
-        scoreMin: I,
-        scoreMax: O,
-        scoreSum: V,
-        scoreSumSquares: _,
-        basesCovered: P
-      };
-    } else
-      throw new Error("no stats");
-    const w = new TextDecoder("utf8");
-    return {
-      zoomLevels: B,
-      magic: u,
-      extHeaderOffset: x,
-      numZoomLevels: c,
-      fieldCount: f,
-      totalSummary: p,
-      definedFieldCount: m,
-      uncompressBufSize: b,
-      asOffset: l,
-      chromTreeOffset: d,
-      totalSummaryOffset: v,
-      unzoomedDataOffset: y,
-      unzoomedIndexOffset: g,
-      fileType: S,
-      version: a,
-      autoSql: l ? w.decode(r.subarray(l, r.indexOf(0, l))) : ""
-    };
-  }
-  async _readChromTree(e, n) {
-    const r = [], o = {}, i = e.chromTreeOffset, s = R(await this.bbi.read(32, i, n));
-    let u = 0;
-    u += 4, u += 4;
-    const a = s.getUint32(u, !0);
-    u += 4;
-    const c = s.getUint32(u, !0);
-    u += 4, u += 8;
-    const d = new TextDecoder("utf8"), y = async (g) => {
-      const f = await this.bbi.read(4, g), m = R(f);
-      let l = 0;
-      const v = m.getUint8(l);
-      l += 1, l += 1;
-      const b = m.getUint16(l, !0);
-      if (l += 2, v) {
-        const x = await this.bbi.read(b * (a + c), g + l), B = R(x);
-        l = 0;
-        for (let S = 0; S < b; S++) {
-          const p = d.decode(x.subarray(l, l + a)).replaceAll("\0", "");
-          l += a;
-          const w = B.getUint32(l, !0);
-          l += 4;
-          const h = B.getUint32(l, !0);
-          l += 4, o[this.renameRefSeqs(p)] = w, r[w] = {
-            name: p,
-            id: w,
-            length: h
-          };
-        }
-      } else {
-        const x = [], B = R(await this.bbi.read(b * (a + 8), g + l));
-        l = 0;
-        for (let S = 0; S < b; S++) {
-          l += a;
-          const p = Number(B.getBigUint64(l, !0));
-          l += 8, x.push(y(p));
-        }
-        await Promise.all(x);
-      }
-    };
-    return await y(i + 32), {
-      refsByName: o,
-      refsByNumber: r
-    };
-  }
-  /*
-   * fetches the "unzoomed" view of the bigwig data. this is the default for bigbed
-   * @param abortSignal - a signal to optionally abort this operation
-   */
-  async getUnzoomedView(e) {
-    const { unzoomedIndexOffset: n, refsByName: r, uncompressBufSize: o, fileType: i } = await this.getHeader(e);
-    return new Dt(this.bbi, r, n, o > 0, i);
-  }
-  /**
-   * Gets features from a BigWig file
-   *
-   * @param refName - The chromosome name
-   *
-   * @param start - The start of a region
-   *
-   * @param end - The end of a region
-   *
-   * @param opts - An object containing basesPerSpan (e.g. pixels per basepair)
-   * or scale used to infer the zoomLevel to use
-   */
-  async getFeatureStream(e, n, r, o) {
-    await this.getHeader(o);
-    const i = this.renameRefSeqs(e);
-    let s;
-    const { basesPerSpan: u, scale: a } = o || {};
-    return u ? s = await this.getView(1 / u, o) : a ? s = await this.getView(a, o) : s = await this.getView(1, o), new A((c) => {
-      s.readWigData(i, n, r, c, o).catch((d) => {
-        c.error(d);
-      });
-    });
-  }
-  async getFeatures(e, n, r, o) {
-    const i = await this.getFeatureStream(e, n, r, o);
-    return (await Vt(i.pipe(Te()))).flat();
-  }
-}
-class ze extends Rt {
-  /**
-   * Retrieves a BlockView of a specific zoomLevel
-   *
-   * @param scale - number
-   *
-   * @param opts - An object containing basesPerSpan (e.g. pixels per basepair)
-   * or scale used to infer the zoomLevel to use
-   */
-  async getView(e, n) {
-    const { zoomLevels: r, refsByName: o, uncompressBufSize: i } = await this.getHeader(n), s = 1 / e, u = r.length - 1;
-    for (let a = u; a >= 0; a -= 1) {
-      const c = r[a];
-      if (c && c.reductionLevel <= 2 * s)
-        return new Dt(this.bbi, o, c.indexOffset, i > 0, "summary");
-    }
-    return this.getUnzoomedView(n);
-  }
-}
-function _e(t) {
-  return t.filter((e) => !!e);
-}
-class Le extends Rt {
-  constructor() {
-    super(...arguments);
-    T(this, "readIndicesCache", new ut({
-      cache: new ft({ maxSize: 1 }),
-      fill: (n, r) => this._readIndices({ ...n, signal: r })
-    }));
-  }
-  readIndices(n = {}) {
-    const { signal: r, ...o } = n;
-    return this.readIndicesCache.get(JSON.stringify(o), n, r);
-  }
-  /*
-   * retrieve unzoomed view for any scale
-   */
-  async getView(n, r) {
-    return this.getUnzoomedView(r);
-  }
-  /*
-   * parse the bigbed extraIndex fields
-   *
-   *
-   * @return a Promise for an array of Index data structure since there can be
-   * multiple extraIndexes in a bigbed, see bedToBigBed documentation
-   */
-  async _readIndices(n) {
-    const { extHeaderOffset: r } = await this.getHeader(n), o = await this.bbi.read(64, r), i = new DataView(o.buffer, o.byteOffset, o.length);
-    let s = 0;
-    s += 2;
-    const u = i.getUint16(s, !0);
-    s += 2;
-    const a = Number(i.getBigUint64(s, !0));
-    if (s += 8, u === 0)
-      return [];
-    const c = 20, d = c * u, y = await this.bbi.read(d, a), g = [];
-    for (let f = 0; f < u; f += 1) {
-      const m = y.subarray(f * c), l = new DataView(m.buffer, m.byteOffset, m.length);
-      let v = 0;
-      const b = l.getInt16(v, !0);
-      v += 2;
-      const x = l.getInt16(v, !0);
-      v += 2;
-      const B = Number(l.getBigUint64(v, !0));
-      v += 12;
-      const S = l.getInt16(v, !0);
-      g.push({
-        type: b,
-        fieldcount: x,
-        offset: B,
-        field: S
-      });
-    }
-    return g;
-  }
-  /*
-   * perform a search in the bigbed extraIndex to find which blocks in the
-   * bigbed data to look for the actual feature data
-   *
-   * @param name - the name to search for
-   *
-   * @param opts - a SearchOptions argument with optional signal
-   *
-   * @return a Promise for an array of bigbed block Loc entries
-   */
-  async searchExtraIndexBlocks(n, r = {}) {
-    const o = await this.readIndices(r);
-    if (o.length === 0)
-      return [];
-    const i = new TextDecoder("utf8"), s = o.map(async (u) => {
-      const { offset: a, field: c } = u, d = await this.bbi.read(32, a, r), y = new DataView(d.buffer, d.byteOffset, d.length);
-      let g = 0;
-      g += 4;
-      const f = y.getInt32(g, !0);
-      g += 4;
-      const m = y.getInt32(g, !0);
-      g += 4;
-      const l = y.getInt32(g, !0);
-      g += 4, g += 8;
-      const v = async (b) => {
-        const x = b, B = 4 + f * (m + l), p = await this.bbi.read(B, x, r), w = new DataView(p.buffer, p.byteOffset, p.length);
-        let h = 0;
-        const U = w.getInt8(h);
-        h += 2;
-        const E = w.getInt16(h, !0);
-        h += 2;
-        const P = [];
-        if (U === 0) {
-          const I = [];
-          for (let V = 0; V < E; V++) {
-            const _ = i.decode(p.subarray(h, h + m)).replaceAll("\0", "");
-            h += m;
-            const F = Number(w.getBigUint64(h, !0));
-            h += 8, I.push({
-              key: _,
-              offset: F
-            });
-          }
-          let O = 0;
-          for (const { key: V, offset: _ } of I) {
-            if (n.localeCompare(V) < 0 && O)
-              return v(O);
-            O = _;
-          }
-          return v(O);
-        } else if (U === 1) {
-          for (let I = 0; I < E; I++) {
-            const O = i.decode(p.subarray(h, h + m)).replaceAll("\0", "");
-            h += m;
-            const V = Number(w.getBigUint64(h, !0));
-            h += 8;
-            const _ = w.getUint32(h, !0);
-            h += 4;
-            const F = w.getUint32(h, !0);
-            h += 4, P.push({
-              key: O,
-              offset: V,
-              length: _,
-              reserved: F
-            });
-          }
-          for (const I of P)
-            if (I.key === n)
-              return {
-                ...I,
-                field: c
-              };
-          return;
-        }
-      };
-      return v(a + 32);
-    });
-    return _e(await Promise.all(s));
-  }
-  /*
-   * retrieve the features from the bigbed data that were found through the
-   * lookup of the extraIndex note that there can be multiple extraIndex, see
-   * the BigBed specification and the -extraIndex argument to bedToBigBed
-   *
-   * @param name - the name to search for
-   *
-   * @param opts - options object with optional AboutSignal
-   *
-   * @return array of Feature
-   */
-  async searchExtraIndex(n, r = {}) {
-    const o = await this.searchExtraIndexBlocks(n, r);
-    if (o.length === 0)
-      return [];
-    const i = await this.getUnzoomedView(r), s = o.map((a) => new A((c) => {
-      i.readFeatures(c, [a], r).catch((d) => {
-        c.error(d);
-      });
-    }).pipe(Ft((c, d) => c.concat(d)), At((c) => {
-      for (const d of c)
-        d.field = a.field;
-      return c;
-    })));
-    return (await Vt(Ue(...s))).filter((a) => {
-      var c;
-      return ((c = a.rest) == null ? void 0 : c.split("	")[(a.field || 0) - 3]) === n;
-    });
-  }
-}
-export {
-  Le as BigBed,
-  ze as BigWig
-};