@genome-spy/core 0.69.1 → 0.71.0

package/dist/bundle/{index-D-w7Mmt9.js → index-C7wOh6y1.js}

@@ -1,78 +1,78 @@
-function R(d, t, e) {
-  const r = /* @__PURE__ */ Object.create(null), i = e.length, a = t.length, l = 9, s = 58;
+function S(m, t, e) {
+  const r = /* @__PURE__ */ Object.create(null), o = e.length, s = t.length, c = 9, i = 58;
   let n = 0;
-  if (d === "GT") {
-    for (let o = 0; o < i; o++) {
-      const p = n;
-      for (; n < a && t.charCodeAt(n) !== l; )
+  if (m === "GT") {
+    for (let l = 0; l < o; l++) {
+      const d = n;
+      for (; n < s && t.charCodeAt(n) !== c; )
         n++;
-      r[e[o]] = t.slice(p, n), n++;
+      r[e[l]] = t.slice(d, n), n++;
     }
     return r;
   }
-  const c = d.indexOf("GT");
-  if (c === -1)
+  const a = m.indexOf("GT");
+  if (a === -1)
     return r;
-  if (c === 0) {
-    for (let o = 0; o < i; o++) {
-      const p = n;
-      for (; n < a && t.charCodeAt(n) !== s && t.charCodeAt(n) !== l; )
+  if (a === 0) {
+    for (let l = 0; l < o; l++) {
+      const d = n;
+      for (; n < s && t.charCodeAt(n) !== i && t.charCodeAt(n) !== c; )
         n++;
-      for (r[e[o]] = t.slice(p, n); n < a && t.charCodeAt(n) !== l; )
+      for (r[e[l]] = t.slice(d, n); n < s && t.charCodeAt(n) !== c; )
         n++;
       n++;
     }
     return r;
   }
-  let b = 0;
-  for (let o = 0; o < c; o++)
-    d.charCodeAt(o) === s && b++;
-  for (let o = 0; o < i; o++) {
-    const p = n;
-    let u = n;
-    for (; u < a && t.charCodeAt(u) !== l; )
-      u++;
-    let g = 0, N = p;
-    for (let h = p; h <= u; h++)
-      if (h === u || t.charCodeAt(h) === s) {
-        if (g === b) {
-          r[e[o]] = t.slice(N, h);
+  let u = 0;
+  for (let l = 0; l < a; l++)
+    m.charCodeAt(l) === i && u++;
+  for (let l = 0; l < o; l++) {
+    const d = n;
+    let f = n;
+    for (; f < s && t.charCodeAt(f) !== c; )
+      f++;
+    let y = 0, b = d;
+    for (let p = d; p <= f; p++)
+      if (p === f || t.charCodeAt(p) === i) {
+        if (y === u) {
+          r[e[l]] = t.slice(b, p);
           break;
         }
-        g++, N = h + 1;
+        y++, b = p + 1;
       }
-    n = u + 1;
+    n = f + 1;
   }
   return r;
 }
-function E(d) {
+function R(m) {
   const t = [], e = [];
-  let r = !1, i = !1;
-  const a = d.length;
-  for (let l = 0; l < a; l++) {
-    const s = d[l];
-    s === '"' ? (r = !r, e.push(s)) : s === "[" ? (i = !0, e.push(s)) : s === "]" ? (i = !1, e.push(s)) : s === "," && !r && !i ? (t.push(e.join("").trim()), e.length = 0) : e.push(s);
+  let r = !1, o = !1;
+  const s = m.length;
+  for (let c = 0; c < s; c++) {
+    const i = m[c];
+    i === '"' ? (r = !r, e.push(i)) : i === "[" ? (o = !0, e.push(i)) : i === "]" ? (o = !1, e.push(i)) : i === "," && !r && !o ? (t.push(e.join("").trim()), e.length = 0) : e.push(i);
   }
   return e.length > 0 && t.push(e.join("").trim()), t;
 }
-function F(d, t) {
-  const e = d.indexOf(t);
-  return [d.slice(0, e), d.slice(e + 1)];
+function E(m, t) {
+  const e = m.indexOf(t);
+  return [m.slice(0, e), m.slice(e + 1)];
 }
-function C(d) {
-  const t = d.slice(1, -1), e = E(t), r = [];
-  for (let i = 0; i < e.length; i++) {
-    const a = e[i], [l, s] = F(a, "=");
-    if (s && s.startsWith("[") && s.endsWith("]")) {
-      const n = s.slice(1, -1).split(",");
-      for (let c = 0; c < n.length; c++)
-        n[c] = n[c].trim();
-      r.push([l, n]);
-    } else s && s.startsWith('"') && s.endsWith('"') ? r.push([l, s.slice(1, -1)]) : r.push([l, s]);
+function F(m) {
+  const t = m.slice(1, -1), e = R(t), r = [];
+  for (let o = 0; o < e.length; o++) {
+    const s = e[o], [c, i] = E(s, "=");
+    if (i && i.startsWith("[") && i.endsWith("]")) {
+      const n = i.slice(1, -1).split(",");
+      for (let a = 0; a < n.length; a++)
+        n[a] = n[a].trim();
+      r.push([c, n]);
+    } else i && i.startsWith('"') && i.endsWith('"') ? r.push([c, i.slice(1, -1)]) : r.push([c, i]);
   }
   return Object.fromEntries(r);
 }
-const S = {
+const A = {
   // INFO fields
   InfoFields: {
     // from the VCF4.3 spec, https://samtools.github.io/hts-specs/VCFv4.3.pdf
@@ -417,14 +417,14 @@ const S = {
     }
   }
 };
-function L(d) {
+function C(m) {
   try {
-    return decodeURIComponent(d);
+    return decodeURIComponent(m);
   } catch {
-    return d;
+    return m;
   }
 }
-class M {
+class L {
   constructor({ header: t = "", strict: e = !0 }) {
     if (!t.length)
       throw new Error("empty header received");
@@ -432,22 +432,22 @@ class M {
     if (!r.length)
       throw new Error("no non-empty header lines specified");
     this.strict = e, this.metadata = {
-      INFO: { ...S.InfoFields },
-      FORMAT: { ...S.GenotypeFields },
-      ALT: { ...S.AltTypes },
-      FILTER: { ...S.FilterTypes }
+      INFO: { ...A.InfoFields },
+      FORMAT: { ...A.GenotypeFields },
+      ALT: { ...A.AltTypes },
+      FILTER: { ...A.FilterTypes }
     };
-    let i;
+    let o;
     for (let n = 0; n < r.length; n++) {
-      const c = r[n];
-      if (c.startsWith("#"))
-        c.startsWith("##") ? this.parseMetadata(c) : i = c;
+      const a = r[n];
+      if (a.startsWith("#"))
+        a.startsWith("##") ? this.parseMetadata(a) : o = a;
       else throw new Error(`Bad line in header:
-${c}`);
+${a}`);
     }
-    if (!i)
+    if (!o)
       throw new Error("No format line found in header");
-    const a = i.trim().split("	"), l = a.slice(0, 8), s = [
+    const s = o.trim().split("	"), c = s.slice(0, 8), i = [
       "#CHROM",
       "POS",
       "ID",
@@ -457,85 +457,83 @@ ${c}`);
       "FILTER",
       "INFO"
     ];
-    if (a.length < 8)
+    if (s.length < 8)
       throw new Error(`VCF header missing columns:
-${i}`);
-    if (l.length !== s.length || !l.every((n, c) => n === s[c]))
+${o}`);
+    if (c.length !== i.length || !c.every((n, a) => n === i[a]))
       throw new Error(`VCF column headers not correct:
-${i}`);
-    this.samples = a.slice(9);
+${o}`);
+    this.samples = s.slice(9);
   }
   parseInfo(t) {
-    var s;
-    const e = {}, r = t.includes("%"), i = t.split(";"), a = this.metadata.INFO, l = i.length;
-    for (let n = 0; n < l; n++) {
-      const c = i[n], b = c.indexOf("="), o = b === -1 ? c : c.slice(0, b), p = b === -1 ? void 0 : c.slice(b + 1), u = (s = a[o]) == null ? void 0 : s.Type;
-      if (u === "Flag")
-        e[o] = !0;
-      else if (!p)
-        e[o] = !0;
+    const e = {}, r = t.includes("%"), o = t.split(";"), s = this.metadata.INFO, c = o.length;
+    for (let i = 0; i < c; i++) {
+      const n = o[i], a = n.indexOf("="), u = a === -1 ? n : n.slice(0, a), l = a === -1 ? void 0 : n.slice(a + 1), d = s[u]?.Type;
+      if (d === "Flag")
+        e[u] = !0;
+      else if (!l)
+        e[u] = !0;
       else {
-        const g = u === "Integer" || u === "Float", N = p.split(","), h = N.length;
+        const f = d === "Integer" || d === "Float", y = l.split(","), b = y.length;
         if (r) {
-          const f = [];
-          for (let m = 0; m < h; m++) {
-            const y = N[m];
-            if (y === ".")
-              f.push(void 0);
+          const p = [];
+          for (let h = 0; h < b; h++) {
+            const D = y[h];
+            if (D === ".")
+              p.push(void 0);
             else {
-              const D = L(y);
-              f.push(g ? Number(D) : D);
+              const g = C(D);
+              p.push(f ? Number(g) : g);
             }
           }
-          e[o] = f;
+          e[u] = p;
         } else {
-          const f = [];
-          for (let m = 0; m < h; m++) {
-            const y = N[m];
-            y === "." ? f.push(void 0) : f.push(g ? Number(y) : y);
+          const p = [];
+          for (let h = 0; h < b; h++) {
+            const D = y[h];
+            D === "." ? p.push(void 0) : p.push(f ? Number(D) : D);
           }
-          e[o] = f;
+          e[u] = p;
         }
       }
     }
     return e;
   }
   parseSamples(t, e) {
-    var i;
     const r = {};
     if (t) {
-      const a = e.split("	"), l = t.split(":"), s = this.metadata.FORMAT, n = [];
-      for (let o = 0; o < l.length; o++) {
-        const p = (i = s[l[o]]) == null ? void 0 : i.Type;
-        n.push(p === "Integer" || p === "Float");
+      const o = e.split("	"), s = t.split(":"), c = this.metadata.FORMAT, i = [];
+      for (let u = 0; u < s.length; u++) {
+        const l = c[s[u]]?.Type;
+        i.push(l === "Integer" || l === "Float");
       }
-      const c = l.length, b = this.samples.length;
-      for (let o = 0; o < b; o++) {
-        const p = this.samples[o], u = {}, g = a[o], N = g.length;
-        let h = 0, f = 0;
-        for (let m = 0; m <= N; m++)
-          if (m === N || g[m] === ":") {
-            const y = g.slice(h, m);
-            if (y === "" || y === ".")
-              u[l[f]] = void 0;
+      const n = s.length, a = this.samples.length;
+      for (let u = 0; u < a; u++) {
+        const l = this.samples[u], d = {}, f = o[u], y = f.length;
+        let b = 0, p = 0;
+        for (let h = 0; h <= y; h++)
+          if (h === y || f[h] === ":") {
+            const D = f.slice(b, h);
+            if (D === "" || D === ".")
+              d[s[p]] = void 0;
             else {
-              const D = y.split(","), I = [];
-              if (n[f])
-                for (let T = 0; T < D.length; T++) {
-                  const A = D[T];
-                  I.push(A === "." ? void 0 : +A);
+              const g = D.split(","), T = [];
+              if (i[p])
+                for (let N = 0; N < g.length; N++) {
+                  const I = g[N];
+                  T.push(I === "." ? void 0 : +I);
                 }
               else
-                for (let T = 0; T < D.length; T++) {
-                  const A = D[T];
-                  I.push(A === "." ? void 0 : A);
+                for (let N = 0; N < g.length; N++) {
+                  const I = g[N];
+                  T.push(I === "." ? void 0 : I);
                 }
-              u[l[f]] = I;
+              d[s[p]] = T;
             }
-            if (h = m + 1, f += 1, f >= c)
+            if (b = h + 1, p += 1, p >= n)
               break;
           }
-        r[p] = u;
+        r[l] = d;
       }
     }
     return r;
@@ -551,13 +549,13 @@ ${i}`);
     const e = /^##(.+?)=(.*)/.exec(t.trim());
     if (!e)
       throw new Error(`Line is not a valid metadata line: ${t}`);
-    const [r, i] = e.slice(1, 3), a = r;
-    if (i != null && i.startsWith("<")) {
-      a in this.metadata || (this.metadata[a] = {});
-      const [l, s] = this.parseStructuredMetaVal(i);
-      l ? this.metadata[a][l] = s : this.metadata[a] = s;
+    const [r, o] = e.slice(1, 3), s = r;
+    if (o?.startsWith("<")) {
+      s in this.metadata || (this.metadata[s] = {});
+      const [c, i] = this.parseStructuredMetaVal(o);
+      c ? this.metadata[s][c] = i : this.metadata[s] = i;
     } else
-      this.metadata[a] = i;
+      this.metadata[s] = o;
   }
   /**
    * Parse a VCF header structured meta string (i.e. a meta value that starts
@@ -569,7 +567,7 @@ ${i}`);
    * and 2) an object with the other key-value pairs in the metadata
    */
   parseStructuredMetaVal(t) {
-    const e = C(t), r = e.ID;
+    const e = F(t), r = e.ID;
     return delete e.ID, "Number" in e && (Number.isNaN(Number(e.Number)) || (e.Number = Number(e.Number))), [r, e];
   }
   /**
@@ -584,8 +582,8 @@ ${i}`);
   getMetadata(...t) {
     let e = this.metadata;
     const r = t.length;
-    for (let i = 0; i < r; i++)
-      if (e = e[t[i]], !e)
+    for (let o = 0; o < r; o++)
+      if (e = e[t[o]], !e)
         return e;
     return e;
   }
@@ -635,25 +633,25 @@ ${i}`);
     let e = 0, r = 0;
     for (; e < t.length && r < 9; )
       t[e] === "	" && (r += 1), e += 1;
-    const i = r === 9 ? e - 1 : e, a = t.slice(0, i).split("	"), l = t.slice(i + 1), [s, n, c, b, o, p, u] = a, g = s, N = +n, h = c === "." ? void 0 : c.split(";"), f = b, m = o === "." ? void 0 : o.split(","), y = p === "." ? void 0 : +p, D = u === "." ? void 0 : u.split(";"), I = a[8];
-    if (this.strict && !a[7])
+    const o = r === 9 ? e - 1 : e, s = t.slice(0, o).split("	"), c = t.slice(o + 1), [i, n, a, u, l, d, f] = s, y = i, b = +n, p = a === "." ? void 0 : a.split(";"), h = u, D = l === "." ? void 0 : l.split(","), g = d === "." ? void 0 : +d, T = f === "." ? void 0 : f.split(";"), N = s[8];
+    if (this.strict && !s[7])
       throw new Error("no INFO field specified, must contain at least a '.' (turn off strict mode to allow)");
-    const T = a[7] === void 0 || a[7] === "." ? {} : this.parseInfo(a[7]);
+    const I = s[7] === void 0 || s[7] === "." ? {} : this.parseInfo(s[7]);
     return {
-      CHROM: g,
-      POS: N,
-      ALT: m,
-      INFO: T,
-      REF: f,
-      FILTER: (D == null ? void 0 : D.length) === 1 && D[0] === "PASS" ? "PASS" : D,
-      ID: h,
-      QUAL: y,
-      FORMAT: I,
-      SAMPLES: () => this.parseSamples(a[8] ?? "", l),
-      GENOTYPES: () => R(a[8] ?? "", l, this.samples)
+      CHROM: y,
+      POS: b,
+      ALT: D,
+      INFO: I,
+      REF: h,
+      FILTER: T?.length === 1 && T[0] === "PASS" ? "PASS" : T,
+      ID: p,
+      QUAL: g,
+      FORMAT: N,
+      SAMPLES: () => this.parseSamples(s[8] ?? "", c),
+      GENOTYPES: () => S(s[8] ?? "", c, this.samples)
     };
   }
 }
 export {
-  M as default
+  L as default
 };