@genome-spy/app 0.56.1 → 0.58.0

package/dist/_commonjsHelpers-DjF3Plf2.js

@@ -0,0 +1,26 @@
+function n(e) {
+  return e && e.__esModule && Object.prototype.hasOwnProperty.call(e, "default") ? e.default : e;
+}
+function c(e) {
+  if (e.__esModule) return e;
+  var o = e.default;
+  if (typeof o == "function") {
+    var t = function r() {
+      return this instanceof r ? Reflect.construct(o, arguments, this.constructor) : o.apply(this, arguments);
+    };
+    t.prototype = o.prototype;
+  } else t = {};
+  return Object.defineProperty(t, "__esModule", { value: !0 }), Object.keys(e).forEach(function(r) {
+    var u = Object.getOwnPropertyDescriptor(e, r);
+    Object.defineProperty(t, r, u.get ? u : {
+      enumerable: !0,
+      get: function() {
+        return e[r];
+      }
+    });
+  }), t;
+}
+export {
+  c as a,
+  n as g
+};

package/dist/app.css

@@ -0,0 +1 @@
+.gs-modal{z-index:101;font-family:system-ui,Segoe UI,Roboto,Helvetica,Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji",Segoe UI Symbol;font-size:14px;position:fixed;top:0;right:0;bottom:0;left:0;display:grid;justify-content:center;align-content:center}.gs-modal .backdrop{position:absolute;top:0;right:0;bottom:0;left:0;background-color:#4b4b4b;opacity:0;transition:opacity .3s ease-in-out}.gs-modal .content{z-index:1;box-shadow:0 3px 15px #00000036;background:#fff;border-radius:3px;min-width:300px;opacity:0;transform:translateY(-15px);transition:opacity .2s ease-in-out,transform .2s ease-in-out}.gs-modal.visible .backdrop{opacity:.4}.gs-modal.visible .content{transform:translate(0);opacity:1}.gs-modal .modal-body,.gs-modal .modal-title,.gs-modal .modal-buttons{padding:10px}.gs-modal .modal-title{font-weight:700;padding-bottom:0}.gs-modal .modal-body>:first-child{margin-top:0}.gs-modal .modal-body>:last-child{margin-bottom:0}.gs-modal .modal-buttons{display:flex;justify-content:flex-end;gap:10px;border-top:1px solid #d0d0d0}.gs-modal .btn{display:inline-block;padding:4px 12px;margin:0;font-size:1em;line-height:20px;color:#333;text-align:center;text-shadow:0 1px 1px rgba(255,255,255,.75);vertical-align:middle;background-image:linear-gradient(to bottom,#fff,#e6e6e6);border:1px solid #cccccc;border-color:rgba(0,0,0,.1) rgba(0,0,0,.1) rgba(0,0,0,.25);border-bottom-color:#b3b3b3;border-radius:4px;box-shadow:inset 0 1px #fff3,0 1px 2px #0000000d;transition:color .15s}.gs-modal .btn:hover:not(:disabled){background-image:linear-gradient(to bottom,#f8f8f8,#d8d8d8)}.gs-modal .btn:active{border-color:rgba(0,0,0,.2) rgba(0,0,0,.2) rgba(0,0,0,.5)}.gs-modal .btn:disabled{color:#a0a0a0}.gs-modal .btn:not(:disabled){cursor:pointer}.gs-modal .btn svg:first-child:not(:last-child){font-size:85%;margin-right:.3em}.gs-modal .btn svg:last-child:not(:first-child){font-size:85%;margin-left:.3em}.gs-modal 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button{border-color:transparent;border-bottom-color:#d0d0d0}.gs-tabs .panes>:not(.active-tab){display:none}.gs-alert{display:flex;align-items:center;position:relative;padding:.8em;margin-bottom:1em;border:1px solid transparent;border-radius:.25rem}.gs-alert>svg:first-child{width:2em;height:2em;margin-right:.8em}.gs-alert.warning{color:#664d03;background-color:#fff3cd;border-color:#ffecb5}.gs-alert.info{color:#055160;background-color:#cff4fc;border-color:#b6effb}.gs-form-group>p:first-child{margin-top:0}.gs-form-group:not(:first-child){margin-top:.5em}.gs-form-group label{display:inline-block;margin-bottom:.5em}.gs-form-group input[type=text],.gs-form-group input[type=number],.gs-form-group select,.gs-form-group textarea{display:block;width:100%;padding:.375em .75em;font-size:1em;font-family:system-ui,Segoe UI,Roboto,Helvetica,Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji",Segoe UI Symbol;line-height:1.5;color:#212529;background-color:#fff;background-clip:padding-box;border:1px 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package/dist/index-BftNdA0O.js

@@ -0,0 +1,27 @@
+import { g as i } from "./_commonjsHelpers-DjF3Plf2.js";
+import { r as s } from "./index-DnIkxb0L.js";
+function u(t, n) {
+  for (var o = 0; o < n.length; o++) {
+    const e = n[o];
+    if (typeof e != "string" && !Array.isArray(e)) {
+      for (const r in e)
+        if (r !== "default" && !(r in t)) {
+          const f = Object.getOwnPropertyDescriptor(e, r);
+          f && Object.defineProperty(t, r, f.get ? f : {
+            enumerable: !0,
+            get: () => e[r]
+          });
+        }
+    }
+  }
+  return Object.freeze(Object.defineProperty(t, Symbol.toStringTag, { value: "Module" }));
+}
+var a = s();
+const c = /* @__PURE__ */ i(a), l = /* @__PURE__ */ u({
+  __proto__: null,
+  default: c
+}, [a]);
+export {
+  a as b,
+  l as i
+};

package/dist/index-C08YCM2T.js

@@ -0,0 +1,539 @@
+const h = {
+  // 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 v(b) {
+  try {
+    return decodeURIComponent(b);
+  } catch {
+    return b;
+  }
+}
+class M {
+  constructor({ header: a = "", strict: r = !0 }) {
+    if (!a.length)
+      throw new Error("empty header received");
+    const n = a.split(/[\r\n]+/).filter((o) => o);
+    if (!n.length)
+      throw new Error("no non-empty header lines specified");
+    this.strict = r, this.metadata = JSON.parse(JSON.stringify({
+      INFO: h.InfoFields,
+      FORMAT: h.GenotypeFields,
+      ALT: h.AltTypes,
+      FILTER: h.FilterTypes
+    }));
+    let e;
+    if (n.forEach((o) => {
+      if (o.startsWith("#"))
+        o.startsWith("##") ? this.parseMetadata(o) : e = o;
+      else throw new Error(`Bad line in header:
+${o}`);
+    }), !e)
+      throw new Error("No format line found in header");
+    const t = e.trim().split("	"), s = t.slice(0, 8), i = [
+      "#CHROM",
+      "POS",
+      "ID",
+      "REF",
+      "ALT",
+      "QUAL",
+      "FILTER",
+      "INFO"
+    ];
+    if (t.length < 8)
+      throw new Error(`VCF header missing columns:
+${e}`);
+    if (s.length !== i.length || !s.every((o, p) => o === i[p]))
+      throw new Error(`VCF column headers not correct:
+${e}`);
+    this.samples = t.slice(9);
+  }
+  parseSamples(a, r) {
+    const n = {};
+    if (a) {
+      const e = r.split("	"), t = a.split(":"), s = t.map((i) => {
+        const o = this.getMetadata("FORMAT", i, "Type");
+        return o === "Integer" || o === "Float";
+      });
+      for (let i = 0; i < this.samples.length; i++) {
+        const o = this.samples[i];
+        n[o] = {};
+        const p = e[i].split(":");
+        for (let c = 0; c < p.length; c++) {
+          const m = p[c];
+          n[o][t[c]] = m === "" || m === "." ? void 0 : m.split(",").map((u) => u === "." ? void 0 : s[c] ? +u : u);
+        }
+      }
+    }
+    return n;
+  }
+  parseGenotypesOnly(a, r) {
+    const n = r.split("	"), e = {};
+    let t = 0;
+    const s = a.split(":");
+    if (s.length === 1)
+      for (const i of this.samples)
+        e[i] = n[t++];
+    else {
+      const i = s.findIndex((o) => o === "GT");
+      if (i === 0)
+        for (const o of this.samples) {
+          const p = n[t++], c = p.indexOf(":");
+          c !== -1 ? e[o] = p.slice(0, c) : console.warn("unknown");
+        }
+      else
+        for (const o of this.samples) {
+          const p = n[t++].split(":");
+          e[o] = p[i];
+        }
+    }
+    return e;
+  }
+  /**
+   * 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(a) {
+    const r = /^##(.+?)=(.*)/.exec(a.trim());
+    if (!r)
+      throw new Error(`Line is not a valid metadata line: ${a}`);
+    const [n, e] = r.slice(1, 3), t = n;
+    if (e != null && e.startsWith("<")) {
+      t in this.metadata || (this.metadata[t] = {});
+      const [s, i] = this.parseStructuredMetaVal(e);
+      this.metadata[t][s] = i;
+    } else
+      this.metadata[t] = e;
+  }
+  /**
+   * Parse a VCF header structured meta string (i.e. a meta value that starts
+   * with "<ID=...")
+   *
+   * @param {string} metaVal - The VCF metadata value
+   *
+   * @returns {Array} - Array with two entries, 1) a string of the metadata ID
+   * and 2) an object with the other key-value pairs in the metadata
+   */
+  parseStructuredMetaVal(a) {
+    const r = this.parseKeyValue(a.replace(/^<|>$/g, ""), ","), n = r.ID;
+    return delete r.ID, "Number" in r && (Number.isNaN(Number(r.Number)) || (r.Number = Number(r.Number))), [n, r];
+  }
+  /**
+   * 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(...a) {
+    let r = this.metadata;
+    for (const n of a)
+      if (r = r[n], !r)
+        return r;
+    return r;
+  }
+  /**
+   * Sometimes VCFs have key-value strings that allow the separator within the
+   * value if it's in quotes, like:
+   * 'ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129"'
+   *
+   * Parse this at a low level since we can't just split at "," (or whatever
+   * separator). Above line would be parsed to: {ID: 'DB', Number: '0', Type:
+   * 'Flag', Description: 'dbSNP membership, build 129'}
+   */
+  parseKeyValue(a, r = ";") {
+    const n = {};
+    let e = "", t = "", s = 1;
+    for (const i of a)
+      s === 1 ? i === "=" ? s = 2 : i !== r ? e += i : t === "" && (n[e] = void 0, e = "") : s === 2 ? i === r ? (n[e] = t, e = "", t = "", s = 1) : i === '"' ? s = 3 : t += i : s === 3 && (i !== '"' ? t += i : s = 2);
+    return s === 2 || s === 3 ? n[e] = t : s === 1 && (n[e] = void 0), n;
+  }
+  /**
+   * Parse a VCF line into an object like { CHROM POS ID REF ALT QUAL FILTER
+   * INFO } with SAMPLES optionally included if present in the VCF
+   *
+   * @param {string} line - A string of a line from a VCF. Supports both LF and
+   * CRLF newlines.
+   */
+  parseLine(a) {
+    var r, n;
+    let e = 0;
+    for (let l = 0; e < a.length && (a[e] === "	" && (l += 1), l !== 9); e += 1)
+      ;
+    const t = a.slice(0, e).split("	"), s = a.slice(e + 1), [i, o, p, c, m, u, T] = t, g = i, I = +o, A = p === "." ? void 0 : p.split(";"), S = c, R = m === "." ? void 0 : m.split(","), E = u === "." ? void 0 : +u, y = T === "." ? void 0 : T.split(";");
+    if (this.strict && !t[7])
+      throw new Error("no INFO field specified, must contain at least a '.' (turn off strict mode to allow)");
+    const F = (r = t[7]) === null || r === void 0 ? void 0 : r.includes("%"), f = t[7] === void 0 || t[7] === "." ? {} : this.parseKeyValue(t[7]);
+    for (const l of Object.keys(f)) {
+      const D = (n = f[l]) === null || n === void 0 ? void 0 : n.split(",").map((d) => d === "." ? void 0 : d).map((d) => d && F ? v(d) : d), N = this.getMetadata("INFO", l, "Type");
+      N === "Integer" || N === "Float" ? f[l] = D == null ? void 0 : D.map((d) => d === void 0 ? void 0 : Number(d)) : N === "Flag" ? f[l] = !0 : f[l] = D;
+    }
+    return {
+      CHROM: g,
+      POS: I,
+      ALT: R,
+      INFO: f,
+      REF: S,
+      FILTER: y && y.length === 1 && y[0] === "PASS" ? "PASS" : y,
+      ID: A,
+      QUAL: E,
+      SAMPLES: () => {
+        var l;
+        return this.parseSamples((l = t[8]) !== null && l !== void 0 ? l : "", s);
+      },
+      GENOTYPES: () => {
+        var l;
+        return this.parseGenotypesOnly((l = t[8]) !== null && l !== void 0 ? l : "", s);
+      }
+    };
+  }
+}
+export {
+  M as default
+};