@genome-spy/app 0.73.0 → 0.74.0

package/dist/index-C7wOh6y1.js

@@ -1,657 +0,0 @@
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-  const t = [], e = [];
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-}
-function E(m, t) {
-  const e = m.indexOf(t);
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-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, "=");
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-  }
-  return Object.fromEntries(r);
-}
-const A = {
-  // INFO fields
-  InfoFields: {
-    // from the VCF4.3 spec, https://samtools.github.io/hts-specs/VCFv4.3.pdf
-    AA: { Number: 1, Type: "String", Description: "Ancestral allele" },
-    AC: {
-      Number: "A",
-      Type: "Integer",
-      Description: "Allele count in genotypes, for each ALT allele, in the same order as listed"
-    },
-    AD: {
-      Number: "R",
-      Type: "Integer",
-      Description: "Total read depth for each allele"
-    },
-    ADF: {
-      Number: "R",
-      Type: "Integer",
-      Description: "Read depth for each allele on the forward strand"
-    },
-    ADR: {
-      Number: "R",
-      Type: "Integer",
-      Description: "Read depth for each allele on the reverse strand"
-    },
-    AF: {
-      Number: "A",
-      Type: "Float",
-      Description: "Allele frequency for each ALT allele in the same order as listed (estimated from primary data, not called genotypes)"
-    },
-    AN: {
-      Number: 1,
-      Type: "Integer",
-      Description: "Total number of alleles in called genotypes"
-    },
-    BQ: {
-      Number: 1,
-      Type: "Float",
-      Description: "RMS base quality"
-    },
-    CIGAR: {
-      Number: 1,
-      Type: "Float",
-      Description: "Cigar string describing how to align an alternate allele to the reference allele"
-    },
-    DB: {
-      Number: 0,
-      Type: "Flag",
-      Description: "dbSNP membership"
-    },
-    DP: {
-      Number: 1,
-      Type: "Integer",
-      Description: "combined depth across samples"
-    },
-    END: {
-      Number: 1,
-      Type: "Integer",
-      Description: "End position (for use with symbolic alleles)"
-    },
-    H2: {
-      Number: 0,
-      Type: "Flag",
-      Description: "HapMap2 membership"
-    },
-    H3: {
-      Number: 0,
-      Type: "Flag",
-      Description: "HapMap3 membership"
-    },
-    MQ: {
-      Number: 1,
-      Type: null,
-      Description: "RMS mapping quality"
-    },
-    MQ0: {
-      Number: 1,
-      Type: "Integer",
-      Description: "Number of MAPQ == 0 reads"
-    },
-    NS: {
-      Number: 1,
-      Type: "Integer",
-      Description: "Number of samples with data"
-    },
-    SB: {
-      Number: 4,
-      Type: "Integer",
-      Description: "Strand bias"
-    },
-    SOMATIC: {
-      Number: 0,
-      Type: "Flag",
-      Description: "Somatic mutation (for cancer genomics)"
-    },
-    VALIDATED: {
-      Number: 0,
-      Type: "Flag",
-      Description: "Validated by follow-up experiment"
-    },
-    "1000G": {
-      Number: 0,
-      Type: "Flag",
-      Description: "1000 Genomes membership"
-    },
-    // specifically for structural variants
-    IMPRECISE: {
-      Number: 0,
-      Type: "Flag",
-      Description: "Imprecise structural variation"
-    },
-    NOVEL: {
-      Number: 0,
-      Type: "Flag",
-      Description: "Indicates a novel structural variation"
-    },
-    // For precise variants, END is POS + length of REF allele - 1,
-    // and the for imprecise variants the corresponding best estimate.
-    SVTYPE: {
-      Number: 1,
-      Type: "String",
-      Description: "Type of structural variant"
-    },
-    // Value should be one of DEL, INS, DUP, INV, CNV, BND. This key can
-    // be derived from the REF/ALT fields but is useful for filtering.
-    SVLEN: {
-      Number: null,
-      Type: "Integer",
-      Description: "Difference in length between REF and ALT alleles"
-    },
-    // One value for each ALT allele. Longer ALT alleles (e.g. insertions)
-    // have positive values, shorter ALT alleles (e.g. deletions)
-    // have negative values.
-    CIPOS: {
-      Number: 2,
-      Type: "Integer",
-      Description: "Confidence interval around POS for imprecise variants"
-    },
-    CIEND: {
-      Number: 2,
-      Type: "Integer",
-      Description: "Confidence interval around END for imprecise variants"
-    },
-    HOMLEN: {
-      Type: "Integer",
-      Description: "Length of base pair identical micro-homology at event breakpoints"
-    },
-    HOMSEQ: {
-      Type: "String",
-      Description: "Sequence of base pair identical micro-homology at event breakpoints"
-    },
-    BKPTID: {
-      Type: "String",
-      Description: "ID of the assembled alternate allele in the assembly file"
-    },
-    // For precise variants, the consensus sequence the alternate allele assembly
-    // is derivable from the REF and ALT fields. However, the alternate allele
-    // assembly file may contain additional information about the characteristics
-    // of the alt allele contigs.
-    MEINFO: {
-      Number: 4,
-      Type: "String",
-      Description: "Mobile element info of the form NAME,START,END,POLARITY"
-    },
-    METRANS: {
-      Number: 4,
-      Type: "String",
-      Description: "Mobile element transduction info of the form CHR,START,END,POLARITY"
-    },
-    DGVID: {
-      Number: 1,
-      Type: "String",
-      Description: "ID of this element in Database of Genomic Variation"
-    },
-    DBVARID: {
-      Number: 1,
-      Type: "String",
-      Description: "ID of this element in DBVAR"
-    },
-    DBRIPID: {
-      Number: 1,
-      Type: "String",
-      Description: "ID of this element in DBRIP"
-    },
-    MATEID: {
-      Number: null,
-      Type: "String",
-      Description: "ID of mate breakends"
-    },
-    PARID: {
-      Number: 1,
-      Type: "String",
-      Description: "ID of partner breakend"
-    },
-    EVENT: {
-      Number: 1,
-      Type: "String",
-      Description: "ID of event associated to breakend"
-    },
-    CILEN: {
-      Number: 2,
-      Type: "Integer",
-      Description: "Confidence interval around the inserted material between breakend"
-    },
-    DPADJ: { Type: "Integer", Description: "Read Depth of adjacency" },
-    CN: {
-      Number: 1,
-      Type: "Integer",
-      Description: "Copy number of segment containing breakend"
-    },
-    CNADJ: {
-      Number: null,
-      Type: "Integer",
-      Description: "Copy number of adjacency"
-    },
-    CICN: {
-      Number: 2,
-      Type: "Integer",
-      Description: "Confidence interval around copy number for the segment"
-    },
-    CICNADJ: {
-      Number: null,
-      Type: "Integer",
-      Description: "Confidence interval around copy number for the adjacency"
-    }
-  },
-  // FORMAT fields
-  GenotypeFields: {
-    // from the VCF4.3 spec, https://samtools.github.io/hts-specs/VCFv4.3.pdf
-    AD: {
-      Number: "R",
-      Type: "Integer",
-      Description: "Read depth for each allele"
-    },
-    ADF: {
-      Number: "R",
-      Type: "Integer",
-      Description: "Read depth for each allele on the forward strand"
-    },
-    ADR: {
-      Number: "R",
-      Type: "Integer",
-      Description: "Read depth for each allele on the reverse strand"
-    },
-    DP: {
-      Number: 1,
-      Type: "Integer",
-      Description: "Read depth"
-    },
-    EC: {
-      Number: "A",
-      Type: "Integer",
-      Description: "Expected alternate allele counts"
-    },
-    FT: {
-      Number: 1,
-      Type: "String",
-      Description: 'Filter indicating if this genotype was "called"'
-    },
-    GL: {
-      Number: "G",
-      Type: "Float",
-      Description: "Genotype likelihoods"
-    },
-    GP: {
-      Number: "G",
-      Type: "Float",
-      Description: "Genotype posterior probabilities"
-    },
-    GQ: {
-      Number: 1,
-      Type: "Integer",
-      Description: "Conditional genotype quality"
-    },
-    GT: {
-      Number: 1,
-      Type: "String",
-      Description: "Genotype"
-    },
-    HQ: {
-      Number: 2,
-      Type: "Integer",
-      Description: "Haplotype quality"
-    },
-    MQ: {
-      Number: 1,
-      Type: "Integer",
-      Description: "RMS mapping quality"
-    },
-    PL: {
-      Number: "G",
-      Type: "Integer",
-      Description: "Phred-scaled genotype likelihoods rounded to the closest integer"
-    },
-    PQ: {
-      Number: 1,
-      Type: "Integer",
-      Description: "Phasing quality"
-    },
-    PS: {
-      Number: 1,
-      Type: "Integer",
-      Description: "Phase set"
-    }
-  },
-  // ALT fields
-  AltTypes: {
-    DEL: {
-      Description: "Deletion relative to the reference"
-    },
-    INS: {
-      Description: "Insertion of novel sequence relative to the reference"
-    },
-    DUP: {
-      Description: "Region of elevated copy number relative to the reference"
-    },
-    INV: {
-      Description: "Inversion of reference sequence"
-    },
-    CNV: {
-      Description: "Copy number variable region (may be both deletion and duplication)"
-    },
-    "DUP:TANDEM": {
-      Description: "Tandem duplication"
-    },
-    "DEL:ME": {
-      Description: "Deletion of mobile element relative to the reference"
-    },
-    "INS:ME": {
-      Description: "Insertion of a mobile element relative to the reference"
-    },
-    NON_REF: {
-      Description: "Represents any possible alternative allele at this location"
-    },
-    "*": {
-      Description: "Represents any possible alternative allele at this location"
-    }
-  },
-  // FILTER fields
-  FilterTypes: {
-    PASS: {
-      Description: "Passed all filters"
-    }
-  }
-};
-function C(m) {
-  try {
-    return decodeURIComponent(m);
-  } catch {
-    return m;
-  }
-}
-class L {
-  constructor({ header: t = "", strict: e = !0 }) {
-    if (!t.length)
-      throw new Error("empty header received");
-    const r = t.split(/[\r\n]+/).filter(Boolean);
-    if (!r.length)
-      throw new Error("no non-empty header lines specified");
-    this.strict = e, this.metadata = {
-      INFO: { ...A.InfoFields },
-      FORMAT: { ...A.GenotypeFields },
-      ALT: { ...A.AltTypes },
-      FILTER: { ...A.FilterTypes }
-    };
-    let o;
-    for (let n = 0; n < r.length; n++) {
-      const a = r[n];
-      if (a.startsWith("#"))
-        a.startsWith("##") ? this.parseMetadata(a) : o = a;
-      else throw new Error(`Bad line in header:
-${a}`);
-    }
-    if (!o)
-      throw new Error("No format line found in header");
-    const s = o.trim().split("	"), c = s.slice(0, 8), i = [
-      "#CHROM",
-      "POS",
-      "ID",
-      "REF",
-      "ALT",
-      "QUAL",
-      "FILTER",
-      "INFO"
-    ];
-    if (s.length < 8)
-      throw new Error(`VCF header missing columns:
-${o}`);
-    if (c.length !== i.length || !c.every((n, a) => n === i[a]))
-      throw new Error(`VCF column headers not correct:
-${o}`);
-    this.samples = s.slice(9);
-  }
-  parseInfo(t) {
-    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 f = d === "Integer" || d === "Float", y = l.split(","), b = y.length;
-        if (r) {
-          const p = [];
-          for (let h = 0; h < b; h++) {
-            const D = y[h];
-            if (D === ".")
-              p.push(void 0);
-            else {
-              const g = C(D);
-              p.push(f ? Number(g) : g);
-            }
-          }
-          e[u] = p;
-        } else {
-          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[u] = p;
-        }
-      }
-    }
-    return e;
-  }
-  parseSamples(t, e) {
-    const r = {};
-    if (t) {
-      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 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 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 N = 0; N < g.length; N++) {
-                  const I = g[N];
-                  T.push(I === "." ? void 0 : I);
-                }
-              d[s[p]] = T;
-            }
-            if (b = h + 1, p += 1, p >= n)
-              break;
-          }
-        r[l] = d;
-      }
-    }
-    return r;
-  }
-  /**
-   * Parse a VCF metadata line (i.e. a line that starts with "##") and add its
-   * properties to the object.
-   *
-   * @param {string} line - A line from the VCF. Supports both LF and CRLF
-   * newlines.
-   */
-  parseMetadata(t) {
-    const e = /^##(.+?)=(.*)/.exec(t.trim());
-    if (!e)
-      throw new Error(`Line is not a valid metadata line: ${t}`);
-    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[s] = o;
-  }
-  /**
-   * Parse a VCF header structured meta string (i.e. a meta value that starts
-   * with "<ID=...")
-   *
-   * @param {string} metaVal - The VCF metadata value
-   *
-   * @returns {Array} - Array with two entries, 1) a string of the metadata ID
-   * and 2) an object with the other key-value pairs in the metadata
-   */
-  parseStructuredMetaVal(t) {
-    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];
-  }
-  /**
-   * Get metadata filtered by the elements in args. For example, can pass
-   * ('INFO', 'DP') to only get info on an metadata tag that was like
-   * "##INFO=<ID=DP,...>"
-   *
-   * @param  {...string} args - List of metadata filter strings.
-   *
-   * @returns {any} An object, string, or number, depending on the filtering
-   */
-  getMetadata(...t) {
-    let e = this.metadata;
-    const r = t.length;
-    for (let o = 0; o < r; o++)
-      if (e = e[t[o]], !e)
-        return e;
-    return e;
-  }
-  /**
-   * Parse a VCF line into an object like
-   *
-   * ```typescript
-   * {
-   *   CHROM: 'contigA',
-   *   POS: 3000,
-   *   ID: ['rs17883296'],
-   *   REF: 'G',
-   *   ALT: ['T', 'A'],
-   *   QUAL: 100,
-   *   FILTER: 'PASS',
-   *   INFO: {
-   *     NS: [3],
-   *     DP: [14],
-   *     AF: [0.5],
-   *     DB: true,
-   *     XYZ: ['5'],
-   *   },
-   *   SAMPLES: () => ({
-   *     HG00096: {
-   *       GT: ['0|0'],
-   *       AP: ['0.000', '0.000'],
-   *     }
-   *   }),
-   *   GENOTYPES: () => ({
-   *     HG00096: '0|0'
-   *   })
-   * }
-   * ```
-   *
-   * SAMPLES and GENOTYPES methods are functions instead of static data fields
-   * because it avoids parsing the potentially long list of samples from e.g.
-   * 1000 genotypes data unless requested.
-   *
-   * The SAMPLES function gives all info about the samples
-   *
-   * The GENOTYPES function only extracts the raw GT string if it exists, for
-   * potentially optimized parsing by programs that need it
-   *
-   * @param {string} line - A string of a line from a VCF
-   */
-  parseLine(t) {
-    let e = 0, r = 0;
-    for (; e < t.length && r < 9; )
-      t[e] === "	" && (r += 1), e += 1;
-    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 I = s[7] === void 0 || s[7] === "." ? {} : this.parseInfo(s[7]);
-    return {
-      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 {
-  L as default
-};