@genome-spy/core 0.69.1 → 0.71.0

package/dist/bundle/{index-DbJ0oeYM.js → index-Gt44EOIH.js}

@@ -1,6 +1,6 @@
-import { A as J } from "./AbortablePromiseCache-CcuMrnn7.js";
-import { u as E, Q as U, a as K } from "./unzip-NywezaRR.js";
-import { LocalFile as F, RemoteFile as M } from "./browser-BRemItdO.js";
+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;
@@ -35,8 +35,7 @@ class j {
     })), this.parseP;
   }
   async hasRefSeq(e, t = {}) {
-    var i;
-    return !!((i = (await this.parse(t)).indices[e]) != null && i.binIndex);
+    return !!(await this.parse(t)).indices[e]?.binIndex;
   }
   _parseNameBytes(e) {
     let t = 0, n = 0;
@@ -76,7 +75,7 @@ function X(a, e) {
     (!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 O {
+class E {
   constructor(e, t) {
     this.blockPosition = e, this.dataPosition = t;
   }
@@ -88,7 +87,7 @@ class O {
   }
 }
 function A(a, e = 0) {
-  return new O(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]);
+  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",
@@ -101,7 +100,7 @@ function se(a, e) {
 function W(a, e) {
   return Math.floor(a / 2 ** e);
 }
-class q extends j {
+class V extends j {
   constructor(e) {
     super(e), this.maxBinNumber = 0, this.depth = 0, this.minShift = 0;
   }
@@ -123,19 +122,19 @@ class q extends j {
       ref: n.getInt32(t + 4, !0),
       start: n.getInt32(t + 8, !0),
       end: n.getInt32(t + 12, !0)
-    }, c = n.getInt32(t + 16, !0), m = c ? String.fromCharCode(c) : void 0, f = n.getInt32(t + 20, !0), x = n.getInt32(t + 24, !0), { refIdToName: d, refNameToId: l } = this._parseNameBytes(e.subarray(t + 28, t + 28 + x));
+    }, 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: m,
+      metaChar: u,
       columnNumbers: s,
       format: r,
       coordinateType: o
     };
   }
   async _parse(e = {}) {
-    const t = await E(await this.filehandle.readFile(e)), n = new DataView(t.buffer);
+    const t = await q(await this.filehandle.readFile(e)), n = new DataView(t.buffer);
     let i;
     if (n.getUint32(0, !0) === te)
       i = 1;
@@ -152,27 +151,27 @@ class q extends j {
       coordinateType: "zero-based-half-open",
       format: "generic"
     }, c = n.getInt32(16 + r, !0);
-    let m, f = 16 + r + 4;
-    const x = new Array(c).fill(0).map(() => {
+    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 b = 0; b < d; b += 1) {
-        const k = n.getUint32(f, !0);
-        if (k > this.maxBinNumber)
+      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 w = A(t, f + 4);
-          m = this._findFirstData(m, w);
-          const p = n.getInt32(f + 12, !0);
+          const I = A(t, f + 4);
+          u = this._findFirstData(u, I);
+          const k = n.getInt32(f + 12, !0);
           f += 16;
-          const I = new Array(p);
-          for (let g = 0; g < p; g += 1) {
-            const u = A(t, f), S = A(t, f + 8);
-            f += 16, I[g] = new L(u, S, k);
+          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[k] = I;
+          l[C] = w;
         }
       }
       return { binIndex: l, stats: h };
@@ -182,9 +181,9 @@ class q extends j {
       csi: !0,
       refCount: c,
       maxBlockSize: 65536,
-      firstDataLine: m,
+      firstDataLine: u,
       csiVersion: i,
-      indices: x,
+      indices: m,
       depth: this.depth,
       maxBinNumber: this.maxBinNumber,
       maxRefLength: o
@@ -203,13 +202,13 @@ class q extends j {
     const s = o.indices[r];
     if (!s)
       return [];
-    const c = this.reg2bins(t, n), m = [];
-    for (const [f, x] of c)
-      for (let d = f; d <= x; d++)
+    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])
-            m.push(new L(l.minv, l.maxv, d));
-    return X(m, new O(0, 0));
+            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)
@@ -238,15 +237,14 @@ function ae(a, e) {
     [4681 + (a >> 14), 4681 + (e >> 14)]
   ];
 }
-class R extends j {
+class D extends j {
   async lineCount(e, t = {}) {
-    var r;
     const n = await this.parse(t), i = n.refNameToId[e];
-    return i === void 0 || !n.indices[i] ? -1 : ((r = n.indices[i].stats) == null ? void 0 : r.lineCount) ?? -1;
+    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 E(t), i = new DataView(n.buffer);
+    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 = {
@@ -256,57 +254,57 @@ class R extends j {
     }[s & 15];
     if (!f)
       throw new Error(`invalid Tabix preset format flags ${s}`);
-    const x = {
+    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, b = 2 ** (14 + l * 3), k = d ? String.fromCharCode(d) : void 0, w = i.getInt32(28, !0), p = i.getInt32(32, !0), { refNameToId: I, refIdToName: g } = this._parseNameBytes(n.slice(36, 36 + p));
-    let u = 36 + p, S;
+    }, 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 T = i.getInt32(u, !0);
-        u += 4;
-        const N = {};
-        let _;
-        for (let v = 0; v < T; v += 1) {
-          const y = i.getUint32(u, !0);
-          if (u += 4, y > h + 1)
+        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 (y === h + 1) {
-            const P = i.getInt32(u, !0);
-            u += 4, P === 2 && (_ = this.parsePseudoBin(n, u)), u += 16 * P;
+          if (v === h + 1) {
+            const _ = i.getInt32(x, !0);
+            x += 4, _ === 2 && (M = this.parsePseudoBin(n, x)), x += 16 * _;
           } else {
-            const P = i.getInt32(u, !0);
-            u += 4;
-            const D = new Array(P);
-            for (let V = 0; V < P; V += 1) {
-              const $ = A(n, u), Y = A(n, u + 8);
-              u += 16, S = this._findFirstData(S, $), D[V] = new L($, Y, y);
+            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);
             }
-            N[y] = D;
+            B[v] = O;
           }
         }
-        const z = i.getInt32(u, !0);
-        u += 4;
-        const B = new Array(z);
-        for (let v = 0; v < z; v += 1)
-          B[v] = A(n, u), u += 8, S = this._findFirstData(S, B[v]);
+        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: N,
-          linearIndex: B,
-          stats: _
+          binIndex: B,
+          linearIndex: N,
+          stats: M
         };
       }),
-      metaChar: k,
+      metaChar: C,
       maxBinNumber: h,
-      maxRefLength: b,
-      skipLines: w,
-      firstDataLine: S,
-      columnNumbers: x,
+      maxRefLength: S,
+      skipLines: I,
+      firstDataLine: g,
+      columnNumbers: m,
       coordinateType: c,
       format: f,
-      refIdToName: g,
-      refNameToId: I,
+      refIdToName: b,
+      refNameToId: w,
       maxBlockSize: 65536
     };
   }
@@ -323,19 +321,19 @@ class R extends j {
     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 O(0, 0)) || console.warn("querying outside of possible tabix range");
-    const m = ae(t, n), f = [];
-    for (const [b, k] of m)
-      for (let w = b; w <= k; w++)
-        if (s.binIndex[w])
-          for (const p of s.binIndex[w])
-            f.push(new L(p.minv, p.maxv, w));
-    const x = s.linearIndex.length;
+    (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, x - 1), h = Math.min(n >> 14, x - 1);
-    for (let b = l; b <= h; ++b) {
-      const k = s.linearIndex[b];
-      k && (!d || k.compareTo(d) < 0) && (d = k);
+    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);
   }
@@ -367,7 +365,7 @@ class he {
    * 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: m, renameRefSeqs: f, chunkCacheSize: x = 5 * 2 ** 20 }) {
+  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
     });
@@ -375,52 +373,52 @@ class he {
     if (t)
       this.filehandle = t;
     else if (e)
-      this.filehandle = new F(e);
+      this.filehandle = new R(e);
     else if (n)
-      this.filehandle = new M(n);
+      this.filehandle = new F(n);
     else
       throw new TypeError("must provide either filehandle or path");
     if (r)
-      this.index = new R({
+      this.index = new D({
         filehandle: r,
         renameRefSeqs: d
       });
-    else if (m)
-      this.index = new q({
-        filehandle: m,
+    else if (u)
+      this.index = new V({
+        filehandle: u,
         renameRefSeqs: d
       });
     else if (i)
-      this.index = new R({
-        filehandle: new F(i),
+      this.index = new D({
+        filehandle: new R(i),
         renameRefSeqs: d
       });
     else if (s)
-      this.index = new q({
-        filehandle: new F(s),
+      this.index = new V({
+        filehandle: new R(s),
         renameRefSeqs: d
       });
     else if (e)
-      this.index = new R({
-        filehandle: new F(`${e}.tbi`),
+      this.index = new D({
+        filehandle: new R(`${e}.tbi`),
         renameRefSeqs: d
       });
     else if (c)
-      this.index = new q({
-        filehandle: new M(c)
+      this.index = new V({
+        filehandle: new F(c)
       });
     else if (o)
-      this.index = new R({
-        filehandle: new M(o)
+      this.index = new D({
+        filehandle: new F(o)
       });
     else if (n)
-      this.index = new R({
-        filehandle: new M(`${n}.tbi`)
+      this.index = new D({
+        filehandle: new F(`${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(x / 65536) }),
+      cache: new U({ maxSize: Math.floor(m / 65536) }),
       fill: (l, h) => this.readChunk(l, { signal: h })
     });
   }
@@ -441,55 +439,54 @@ class he {
     return e[n] * 256 + (i - t[n]) + o + 1;
   }
   async getLines(e, t, n, i) {
-    var 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), m = t ?? 0, f = n ?? c.maxRefLength;
-    if (!(m <= f))
+    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 (m === f)
+    if (u === f)
       return;
-    const x = await this.index.blocksForRange(e, m, f, r), d = new TextDecoder("utf8"), l = c.format === "VCF", h = {
+    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
-    }, b = Math.max(h.ref, h.start, h.end), k = (I = c.metaChar) == null ? void 0 : I.charCodeAt(0), w = c.coordinateType === "1-based-closed" ? -1 : 0, p = !this.hasCustomRenameRefSeq;
-    for (const g of x) {
-      const { buffer: u, cpositions: S, dpositions: C } = await this.chunkCache.get(g.toString(), g, o);
-      let T = 0, N = 0;
-      const _ = d.decode(u);
-      if (u.length == _.length)
-        for (; T < _.length; ) {
-          const B = _.indexOf(`
-`, T);
-          if (B === -1)
+    }, 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 v = _.slice(T, B);
-          if (C) {
-            const P = T + g.minv.dataPosition;
-            for (; N < C.length && P >= C[N]; )
-              N++;
+          const N = B.slice(p, P);
+          if (g) {
+            const v = p + w.minv.dataPosition;
+            for (; y < g.length && v >= g[y]; )
+              y++;
           }
-          const y = this.checkLine(e, m, f, v, h.ref, h.start, h.end, b, k, w, l, p);
-          if (y === null)
+          const T = this.checkLine(e, u, f, N, h.ref, h.start, h.end, S, C, I, l, k);
+          if (T === null)
             return;
-          y !== void 0 && s(v, this.calculateFileOffset(S, C, N, T, g.minv.dataPosition), y.start, y.end), T = B + 1;
+          T !== void 0 && s(N, this.calculateFileOffset(x, g, y, p, w.minv.dataPosition), T.start, T.end), p = P + 1;
         }
       else
-        for (; T < u.length; ) {
-          const B = u.indexOf(10, T);
-          if (B === -1)
+        for (; p < b.length; ) {
+          const P = b.indexOf(10, p);
+          if (P === -1)
             break;
-          const v = u.slice(T, B), y = d.decode(v);
-          if (C) {
-            const D = T + g.minv.dataPosition;
-            for (; N < C.length && D >= C[N]; )
-              N++;
+          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 P = this.checkLine(e, m, f, y, h.ref, h.start, h.end, b, k, w, l, p);
-          if (P === null)
+          const v = this.checkLine(e, u, f, T, h.ref, h.start, h.end, S, C, I, l, k);
+          if (v === null)
             return;
-          P !== void 0 && s(y, this.calculateFileOffset(S, C, N, T, g.minv.dataPosition), P.start, P.end), T = B + 1;
+          v !== void 0 && s(T, this.calculateFileOffset(x, g, y, p, w.minv.dataPosition), v.start, v.end), p = P + 1;
         }
     }
   }
@@ -501,15 +498,15 @@ class he {
    * bytes up to the first non-meta line
    */
   async getHeaderBuffer(e = {}) {
-    const { firstDataLine: t, metaChar: n, maxBlockSize: i } = await this.getMetadata(e), o = ((t == null ? void 0 : t.blockPosition) || 0) + i, r = await this.filehandle.read(o, 0, e), s = await E(r);
+    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 m = 10, f = n.charCodeAt(0);
-      for (let x = 0, d = s.length; x < d; x++) {
-        const l = s[x];
-        if (x === c + 1 && l !== f)
+      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 === m && (c = x);
+        l === u && (c = m);
       }
       return s.subarray(0, c + 1);
     }
@@ -557,38 +554,38 @@ class he {
    *
    * @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, m, f, x, d) {
-    if (m !== void 0 && i.charCodeAt(0) === m)
+  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 I = i.split("	"), g = I[o - 1];
-      if (!(d ? g === e : this.renameRefSeq(g) === e))
+      const w = i.split("	"), b = w[o - 1];
+      if (!(d ? b === e : this.renameRefSeq(b) === e))
         return;
-      const S = +I[r - 1] + f;
-      if (S >= n)
+      const g = +w[r - 1] + f;
+      if (g >= n)
         return null;
-      let C;
-      return s === 0 || s === r ? C = S + 1 : x ? C = this._getVcfEnd(S, I[3], I[s - 1]) : C = +I[s - 1], C <= t ? void 0 : { start: S, end: C };
+      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 I = 0; I < c; I++) {
-      const g = i.indexOf("	", l + 1);
-      if (g === -1) {
+    for (let w = 0; w < c; w++) {
+      const b = i.indexOf("	", l + 1);
+      if (b === -1) {
         h.push(i.length);
         break;
       }
-      h.push(g), l = g;
+      h.push(b), l = b;
     }
-    const b = i.slice(h[o - 1] + 1, h[o]);
-    if (!(d ? b === e : this.renameRefSeq(b) === e))
+    const S = i.slice(h[o - 1] + 1, h[o]);
+    if (!(d ? S === e : this.renameRefSeq(S) === e))
       return;
-    const w = +i.slice(h[r - 1] + 1, h[r]) + f;
-    if (w >= n)
+    const I = +i.slice(h[r - 1] + 1, h[r]) + f;
+    if (I >= n)
       return null;
-    let p;
-    if (s === 0 || s === r ? p = w + 1 : x ? p = this._getVcfEnd(w, i.slice(h[3] + 1, h[4]), i.slice(h[s - 1] + 1, h[s])) : p = +i.slice(h[s - 1] + 1, h[s]), !(p <= t))
-      return { start: w, end: p };
+    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;
@@ -625,7 +622,7 @@ class he {
   }
 }
 export {
-  q as CSI,
-  R as TBI,
+  V as CSI,
+  D as TBI,
   he as TabixIndexedFile
 };