@genome-spy/app 0.73.0 → 0.75.0

package/dist/index-BUsSzlHg.js

@@ -1,1771 +0,0 @@
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-      H(s), await Promise.all(a.map(async (c) => {
-        H(s);
-        const { length: h, offset: d } = c, b = await this.featureCache.get(`${h}_${d}`, c, s);
-        for (const f of c.blocks) {
-          H(s);
-          let m = b.subarray(f.offset - c.offset);
-          switch (o && (m = _t(m)), H(s), i) {
-            case "summary": {
-              r.next(this.parseSummaryBlock(m, 0, u));
-              break;
-            }
-            case "bigwig": {
-              r.next(this.parseBigWigBlock(m, 0, u));
-              break;
-            }
-            case "bigbed": {
-              r.next(this.parseBigBedBlock(m, 0, f.offset * 256, u));
-              break;
-            }
-            default:
-              console.warn(`Don't know what to do with ${i}`);
-          }
-        }
-      })), r.complete();
-    } catch (i) {
-      r.error(i);
-    }
-  }
-}
-const At = -2003829722, ae = -2021002517;
-function A(t) {
-  return new DataView(t.buffer, t.byteOffset, t.length);
-}
-class Fe {
-  bbi;
-  headerP;
-  renameRefSeqs;
-  getHeader(r) {
-    return this.headerP || (this.headerP = this._getHeader(r).catch((e) => {
-      throw this.headerP = void 0, e;
-    })), this.headerP;
-  }
-  /*
-   * @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(r) {
-    const { filehandle: e, renameRefSeqs: n = (s) => s, path: i, url: o } = r;
-    if (this.renameRefSeqs = n, e)
-      this.bbi = e;
-    else if (o)
-      this.bbi = new Re(o);
-    else if (i)
-      this.bbi = new De(i);
-    else
-      throw new Error("no file given");
-  }
-  async _getHeader(r) {
-    const e = await this._getMainHeader(r), n = await this._readChromTree(e, r);
-    return {
-      ...e,
-      ...n
-    };
-  }
-  async _getMainHeader(r, e = 2e3) {
-    const n = await this.bbi.read(e, 0, r), i = A(n), o = i.getInt32(0, !0);
-    if (o !== At && o !== ae)
-      throw new Error("not a BigWig/BigBed file");
-    let s = 0;
-    const u = i.getInt32(s, !0);
-    s += 4;
-    const a = i.getUint16(s, !0);
-    s += 2;
-    const c = i.getUint16(s, !0);
-    s += 2;
-    const h = Number(i.getBigUint64(s, !0));
-    s += 8;
-    const d = Number(i.getBigUint64(s, !0));
-    s += 8;
-    const b = Number(i.getBigUint64(s, !0));
-    s += 8;
-    const f = i.getUint16(s, !0);
-    s += 2;
-    const m = i.getUint16(s, !0);
-    s += 2;
-    const l = Number(i.getBigUint64(s, !0));
-    s += 8;
-    const B = Number(i.getBigUint64(s, !0));
-    s += 8;
-    const w = i.getUint32(s, !0);
-    s += 4;
-    const S = Number(i.getBigUint64(s, !0));
-    s += 8;
-    const x = [];
-    for (let y = 0; y < c; y++) {
-      const U = i.getUint32(s, !0);
-      s += 4;
-      const T = i.getUint32(s, !0);
-      s += 4;
-      const k = Number(i.getBigUint64(s, !0));
-      s += 8;
-      const I = Number(i.getBigUint64(s, !0));
-      s += 8, x.push({
-        reductionLevel: U,
-        reserved: T,
-        dataOffset: k,
-        indexOffset: I
-      });
-    }
-    const v = u === ae ? "bigbed" : "bigwig";
-    if (l > e || B > e - 40)
-      return this._getMainHeader(r, e * 2);
-    let p;
-    if (B) {
-      const y = n.subarray(B);
-      let U = 0;
-      const T = A(y), k = Number(T.getBigUint64(U, !0));
-      U += 8;
-      const I = T.getFloat64(U, !0);
-      U += 8;
-      const E = T.getFloat64(U, !0);
-      U += 8;
-      const C = T.getFloat64(U, !0);
-      U += 8;
-      const P = T.getFloat64(U, !0);
-      U += 8, p = {
-        scoreMin: I,
-        scoreMax: E,
-        scoreSum: C,
-        scoreSumSquares: P,
-        basesCovered: k
-      };
-    } else
-      throw new Error("no stats");
-    const g = new TextDecoder("utf8");
-    return {
-      zoomLevels: x,
-      magic: u,
-      extHeaderOffset: S,
-      numZoomLevels: c,
-      fieldCount: f,
-      totalSummary: p,
-      definedFieldCount: m,
-      uncompressBufSize: w,
-      asOffset: l,
-      chromTreeOffset: h,
-      totalSummaryOffset: B,
-      unzoomedDataOffset: d,
-      unzoomedIndexOffset: b,
-      fileType: v,
-      version: a,
-      autoSql: l ? g.decode(n.subarray(l, n.indexOf(0, l))) : ""
-    };
-  }
-  async _readChromTree(r, e) {
-    const n = [], i = {}, o = r.chromTreeOffset, s = A(await this.bbi.read(32, o, e));
-    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 h = new TextDecoder("utf8"), d = async (b) => {
-      const f = await this.bbi.read(4, b), m = A(f);
-      let l = 0;
-      const B = m.getUint8(l);
-      l += 1, l += 1;
-      const w = m.getUint16(l, !0);
-      if (l += 2, B) {
-        const S = await this.bbi.read(w * (a + c), b + l), x = A(S);
-        l = 0;
-        for (let v = 0; v < w; v++) {
-          const p = h.decode(S.subarray(l, l + a)).replaceAll("\0", "");
-          l += a;
-          const g = x.getUint32(l, !0);
-          l += 4;
-          const y = x.getUint32(l, !0);
-          l += 4, i[this.renameRefSeqs(p)] = g, n[g] = {
-            name: p,
-            id: g,
-            length: y
-          };
-        }
-      } else {
-        const S = [], x = A(await this.bbi.read(w * (a + 8), b + l));
-        l = 0;
-        for (let v = 0; v < w; v++) {
-          l += a;
-          const p = Number(x.getBigUint64(l, !0));
-          l += 8, S.push(d(p));
-        }
-        await Promise.all(S);
-      }
-    };
-    return await d(o + 32), {
-      refsByName: i,
-      refsByNumber: n
-    };
-  }
-  /*
-   * 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(r) {
-    const { unzoomedIndexOffset: e, refsByName: n, uncompressBufSize: i, fileType: o } = await this.getHeader(r);
-    return new ze(this.bbi, n, e, i > 0, o);
-  }
-  /**
-   * 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(r, e, n, i) {
-    await this.getHeader(i);
-    const o = this.renameRefSeqs(r);
-    let s;
-    const { basesPerSpan: u, scale: a } = i || {};
-    return u ? s = await this.getView(1 / u, i) : a ? s = await this.getView(a, i) : s = await this.getView(1, i), new _((c) => {
-      s.readWigData(o, e, n, c, i).catch((h) => {
-        c.error(h);
-      });
-    });
-  }
-  async getFeatures(r, e, n, i) {
-    const o = await this.getFeatureStream(r, e, n, i);
-    return (await _e(o.pipe(kt()))).flat();
-  }
-}
-class Nt extends Fe {
-  /**
-   * 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(r, e) {
-    const { zoomLevels: n, refsByName: i, uncompressBufSize: o } = await this.getHeader(e), s = 1 / r, u = n.length - 1;
-    for (let a = u; a >= 0; a -= 1) {
-      const c = n[a];
-      if (c && c.reductionLevel <= 2 * s)
-        return new ze(this.bbi, i, c.indexOffset, o > 0, "summary");
-    }
-    return this.getUnzoomedView(e);
-  }
-}
-function zt(t) {
-  return t.filter((r) => !!r);
-}
-class Lt extends Fe {
-  readIndicesCache = new ue({
-    cache: new Ae({ maxSize: 1 }),
-    fill: (r, e) => this._readIndices({ ...r, signal: e })
-  });
-  readIndices(r = {}) {
-    const { signal: e, ...n } = r;
-    return this.readIndicesCache.get(JSON.stringify(n), r, e);
-  }
-  /*
-   * retrieve unzoomed view for any scale
-   */
-  async getView(r, e) {
-    return this.getUnzoomedView(e);
-  }
-  /*
-   * 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(r) {
-    const { extHeaderOffset: e } = await this.getHeader(r), n = await this.bbi.read(64, e), i = new DataView(n.buffer, n.byteOffset, n.length);
-    let o = 0;
-    o += 2;
-    const s = i.getUint16(o, !0);
-    o += 2;
-    const u = Number(i.getBigUint64(o, !0));
-    if (o += 8, s === 0)
-      return [];
-    const a = 20, c = a * s, h = await this.bbi.read(c, u), d = [];
-    for (let b = 0; b < s; b += 1) {
-      const f = h.subarray(b * a), m = new DataView(f.buffer, f.byteOffset, f.length);
-      let l = 0;
-      const B = m.getInt16(l, !0);
-      l += 2;
-      const w = m.getInt16(l, !0);
-      l += 2;
-      const S = Number(m.getBigUint64(l, !0));
-      l += 12;
-      const x = m.getInt16(l, !0);
-      d.push({
-        type: B,
-        fieldcount: w,
-        offset: S,
-        field: x
-      });
-    }
-    return d;
-  }
-  /*
-   * 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(r, e = {}) {
-    const n = await this.readIndices(e);
-    if (n.length === 0)
-      return [];
-    const i = new TextDecoder("utf8"), o = n.map(async (s) => {
-      const { offset: u, field: a } = s, c = await this.bbi.read(32, u, e), h = new DataView(c.buffer, c.byteOffset, c.length);
-      let d = 0;
-      d += 4;
-      const b = h.getInt32(d, !0);
-      d += 4;
-      const f = h.getInt32(d, !0);
-      d += 4;
-      const m = h.getInt32(d, !0);
-      d += 4, d += 8;
-      const l = async (B) => {
-        const w = B, S = 4 + b * (f + m), v = await this.bbi.read(S, w, e), p = new DataView(v.buffer, v.byteOffset, v.length);
-        let g = 0;
-        const y = p.getInt8(g);
-        g += 2;
-        const U = p.getInt16(g, !0);
-        g += 2;
-        const T = [];
-        if (y === 0) {
-          const k = [];
-          for (let E = 0; E < U; E++) {
-            const C = i.decode(v.subarray(g, g + f)).replaceAll("\0", "");
-            g += f;
-            const P = Number(p.getBigUint64(g, !0));
-            g += 8, k.push({
-              key: C,
-              offset: P
-            });
-          }
-          let I = 0;
-          for (const { key: E, offset: C } of k) {
-            if (r.localeCompare(E) < 0 && I)
-              return l(I);
-            I = C;
-          }
-          return l(I);
-        } else if (y === 1) {
-          for (let k = 0; k < U; k++) {
-            const I = i.decode(v.subarray(g, g + f)).replaceAll("\0", "");
-            g += f;
-            const E = Number(p.getBigUint64(g, !0));
-            g += 8;
-            const C = p.getUint32(g, !0);
-            g += 4;
-            const P = p.getUint32(g, !0);
-            g += 4, T.push({
-              key: I,
-              offset: E,
-              length: C,
-              reserved: P
-            });
-          }
-          for (const k of T)
-            if (k.key === r)
-              return {
-                ...k,
-                field: a
-              };
-          return;
-        }
-      };
-      return l(u + 32);
-    });
-    return zt(await Promise.all(o));
-  }
-  /*
-   * 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(r, e = {}) {
-    const n = await this.searchExtraIndexBlocks(r, e);
-    if (n.length === 0)
-      return [];
-    const i = await this.getUnzoomedView(e), o = n.map((u) => new _((a) => {
-      i.readFeatures(a, [u], e).catch((c) => {
-        a.error(c);
-      });
-    }).pipe(Ve((a, c) => a.concat(c)), Ce((a) => {
-      for (const c of a)
-        c.field = u.field;
-      return a;
-    })));
-    return (await _e(Bt(...o))).filter((u) => u.rest?.split("	")[(u.field || 0) - 3] === r);
-  }
-}
-export {
-  Lt as BigBed,
-  Nt as BigWig
-};