@sjcrh/proteinpaint-client 2.184.0 → 2.185.0

package/dist/chunk-RCYTUKAJ.js

@@ -1,1745 +0,0 @@
-import {
-  deepFreeze,
-  sleep
-} from "./chunk-MVTCBVSX.js";
-import {
-  ISOFORM_EXPRESSION,
-  SINGLECELL_CELLTYPE,
-  SINGLECELL_GENE_EXPRESSION,
-  TermTypes,
-  isNumericTerm
-} from "./chunk-SOED2SLH.js";
-import {
-  dtcnv,
-  dtfusionrna,
-  dtsnvindel as dtsnvindel2,
-  dtsv,
-  mclass,
-  mclassdeletion,
-  mclassinsertion,
-  mclassmnv,
-  mclassnonstandard as mclassnonstandard2,
-  mclasssnv,
-  morigingermline,
-  morigingermlinenonpathogenic,
-  morigingermlinepathogenic,
-  moriginrelapse,
-  moriginsomatic,
-  vepinfo
-} from "./chunk-XRVBHNCW.js";
-import {
-  isNumeric
-} from "./chunk-BEWDIM6H.js";
-import {
-  select_default
-} from "./chunk-NDWTN4U5.js";
-
-// ../shared/utils/src/bulk.js
-function init_bulk_flag(genome) {
-  if (!genome) {
-    return null;
-  }
-  const mclasslabel2key2 = {};
-  for (const n in mclass) {
-    mclasslabel2key2[mclass[n].label.toUpperCase()] = n;
-  }
-  return {
-    genome,
-    mclasslabel2key: mclasslabel2key2,
-    data: {},
-    sample2disease: {},
-    // (proof) k: sample, v: disease
-    // will only record this when origin is used
-    patient2st: {},
-    // k: patient, v: { k: sampletype, v: sample }
-    // new sample names always override old
-    good: 0,
-    geneToUpper: true,
-    // option to not force uppercase on gene names
-    snv: {
-      loaded: false,
-      header: null,
-      badlines: [],
-      // jinghui: based on missense/silent ratio of entire dataset to decide whether to include silent when importing...
-      // hard-coded class codes
-      missense: 0,
-      silent: 0
-    },
-    svjson: {
-      loaded: false,
-      header: null,
-      badlines: []
-    },
-    fusion: {
-      loaded: false,
-      header: null,
-      badlines: [],
-      original: []
-    },
-    sv: {
-      loaded: false,
-      header: null,
-      badlines: [],
-      original: []
-    },
-    cnv: {
-      loaded: false,
-      header: null,
-      badlines: []
-    },
-    itd: {
-      loaded: false,
-      header: null,
-      badlines: []
-    },
-    del: {
-      loaded: false,
-      header: null,
-      badlines: []
-    },
-    truncation: {
-      loaded: false,
-      header: null,
-      badlines: []
-    }
-  };
-}
-function parsesample(m, flag, i2, lst, badline) {
-  let variantorigin = moriginsomatic;
-  if (m.sampletype) {
-    const s = m.sampletype.toLowerCase();
-    switch (s) {
-      case "relapse":
-        variantorigin = moriginrelapse;
-        break;
-      case "germline":
-        variantorigin = morigingermline;
-        break;
-      case "somatic":
-      case "diagnosis":
-        break;
-    }
-    if (m.sample) {
-      if (m.patient) {
-      } else {
-        m.patient = m.sample + " " + m.sampletype;
-      }
-    } else {
-      if (m.patient) {
-        m.sample = m.patient + " " + m.sampletype;
-      } else {
-      }
-    }
-  } else {
-    if (m.patient) {
-      if (m.sample) {
-        m.sampletype = m.sample;
-      } else {
-        m.sample = m.sampletype = m.patient;
-      }
-    } else {
-      if (m.sample) {
-        m.sampletype = m.sample;
-      } else {
-      }
-    }
-  }
-  if (m.origin) {
-    const s = m.origin.toLowerCase();
-    switch (s) {
-      case "r":
-      case "relapse":
-        variantorigin = moriginrelapse;
-        m.isrim2 = true;
-        break;
-      case "g":
-      case "germline":
-        variantorigin = morigingermline;
-        m.isrim1 = true;
-        break;
-      case "gp":
-      case "germline pathogenic":
-        variantorigin = morigingermlinepathogenic;
-        m.isrim1 = true;
-        break;
-      case "gnp":
-      case "germline nonpathogenic":
-      case "germline non-pathogenic":
-        variantorigin = morigingermlinenonpathogenic;
-        m.isrim1 = true;
-        break;
-      case "s":
-      case "somatic":
-      case "diagnosis":
-        variantorigin = moriginsomatic;
-        break;
-    }
-  }
-  m.origin = variantorigin;
-  if (!m.sample && !m.patient) {
-    return;
-  }
-  const nopatientname = "no patient/individual name";
-  let p;
-  if (m.patient) {
-    if (!flag.patient2st[m.patient]) {
-      flag.patient2st[m.patient] = {};
-    }
-    flag.patient2st[m.patient][m.sampletype] = m.sample;
-  } else {
-    if (!flag.patient2st[nopatientname]) {
-      flag.patient2st[nopatientname] = {};
-    }
-    flag.patient2st[nopatientname][m.sampletype] = m.sample;
-  }
-  if (m.sample) {
-    if (m.disease) {
-      if (m.sample in flag.sample2disease) {
-        if (m.disease != flag.sample2disease[m.sample]) {
-          flag.snv.badlines.push([
-            i2,
-            'conflict of disease types for sample "' + m.sample + '": ' + m.disease + ", " + flag.sample2disease[m.sample],
-            lst
-          ]);
-          return true;
-        }
-      } else {
-        flag.sample2disease[m.sample] = m.disease;
-      }
-    }
-  }
-  return false;
-}
-
-// ../shared/utils/src/clustering.js
-var clusterMethodLst = [
-  {
-    label: "Average",
-    value: "average",
-    title: `Cluster by average value`
-  },
-  {
-    label: `Complete`,
-    value: "complete",
-    title: `Use the complete clustering method`
-  },
-  {
-    label: `Single`,
-    value: "single",
-    title: `Use the single clustering method`
-  },
-  {
-    label: `Ward.D`,
-    value: "ward.D",
-    title: `Use the ward.D clustering method`
-  },
-  {
-    label: `Ward.D2`,
-    value: "ward.D2",
-    title: `Use the ward.D2 clustering method`
-  },
-  {
-    label: `Mcquitty`,
-    value: "mcquitty",
-    title: `Use the Mcquity clustering method`
-  }
-  /* These methods are currently disabled because the dendrogram lines tend to cross one another.
-  {
-  	label: `Centroid`,
-  	value: 'centroid',
-  	title: `Use the centroid clustering method`
-  },
-     	{
-  	label: `Median`,
-  	value: 'median',
-  	title: `Use the median clustering method`
-  }
-         */
-];
-var distanceMethodLst = [
-  {
-    label: "Euclidean",
-    value: "euclidean",
-    title: `Calculate distance using euclidean method`
-  },
-  {
-    label: "Maximum",
-    value: "maximum",
-    title: `Maximum distance between two components of x and y`
-  },
-  {
-    label: "Manhattan",
-    value: "manhattan",
-    title: `Calculate distance using the absolute distance between the two vectors`
-  },
-  {
-    label: "Canberra",
-    value: "canberra",
-    title: `Calculate distance using Canberra method`
-  }
-];
-
-// ../shared/utils/src/fileSize.js
-function fileSize(v) {
-  if (v > 1e9) return (v / 1e9).toFixed(2) + " GB";
-  if (v > 1e6) return (v / 1e6).toFixed(2) + " MB";
-  if (v > 1e3) return (v / 1e3).toFixed(2) + " KB";
-  return v + " Bytes";
-}
-
-// ../shared/utils/src/mds3tk.js
-var ssmIdFieldsSeparator = "__";
-function summarize_mclass(mlst) {
-  const m2c = /* @__PURE__ */ new Map();
-  const cnvs = [];
-  for (const m of mlst) {
-    if (m.dt == dtcnv) {
-      cnvs.push(m);
-      continue;
-    }
-    const key = m.class || m.dt;
-    m2c.set(key, 1 + (m2c.get(key) || 0));
-  }
-  if (cnvs.length) {
-    if (Number.isFinite(cnvs[0].value)) {
-      m2c.set(dtcnv, cnvs.length);
-    } else {
-      for (const c of cnvs) {
-        if (!c.class) continue;
-        m2c.set(c.class, 1 + (m2c.get(c.class) || 0));
-      }
-    }
-  }
-  return [...m2c].sort((i2, j) => j[1] - i2[1]);
-}
-function guessSsmid(ssmid) {
-  const l = ssmid.split(ssmIdFieldsSeparator);
-  if (l.length == 4) {
-    const [chr, tmp, ref, alt] = l;
-    const pos = Number(tmp);
-    if (Number.isNaN(pos)) throw "ssmid snvindel pos not integer";
-    return { dt: dtsnvindel2, l: [chr, pos, ref, alt] };
-  }
-  if (l.length == 5) {
-    const [chr, _start, _stop, _class, _value] = l;
-    const start = Number(_start), stop = Number(_stop), value = _value == "" ? null : Number(_value);
-    if (Number.isNaN(start) || Number.isNaN(stop)) throw "ssmid cnv start/stop not integer";
-    return { dt: dtcnv, l: [chr, start, stop, _class, value] };
-  }
-  if (l.length == 6) {
-    if (l[3] == "+" || l[3] == "-") {
-      const [_dt, chr2, _pos, strand, _pi, _mname] = l;
-      const mname = decodeURIComponent(_mname);
-      const dt = Number(_dt);
-      if (dt != dtsv && dt != dtfusionrna) throw "ssmid dt not sv/fusion";
-      const pos = Number(_pos);
-      if (Number.isNaN(pos)) throw "ssmid svfusion position not integer";
-      const pairlstIdx = Number(_pi);
-      if (Number.isNaN(pairlstIdx)) throw "ssmid pairlstIdx not integer";
-      return { dt, l: [dt, chr2, pos, strand, pairlstIdx, mname] };
-    }
-    const [chr, _start, _stop, _class, _value, sample] = l;
-    const start = Number(_start), stop = Number(_stop), value = _value == "" ? null : Number(_value);
-    if (Number.isNaN(start) || Number.isNaN(stop)) throw "ssmid cnv start/stop not integer";
-    return { dt: dtcnv, l: [chr, start, stop, _class, value, sample] };
-  }
-  throw "unknown ssmid";
-}
-
-// ../shared/utils/src/termdb.initbinconfig.js
-function initBinConfig(data, opts = {}) {
-  if (!data.length)
-    return { mode: "discrete", type: "regular-bin", startinclusive: true, bin_size: null, first_bin: { stop: null } };
-  if (data.find((d) => !Number.isFinite(d))) throw new Error("non-numeric values found");
-  let binConfig;
-  const s = new Set(data);
-  if (s.size === 1) {
-    const value = [...s][0];
-    binConfig = {
-      type: "custom-bin",
-      lst: [
-        { stop: value, stopinclusive: false, startunbounded: true, label: "<" + value },
-        { start: value, stop: value, startinclusive: true, stopinclusive: true, label: "=" + value },
-        { start: value, startinclusive: false, stopunbounded: true, label: ">" + value }
-      ]
-    };
-  } else {
-    data.sort((a, b) => a - b);
-    const l = data.length;
-    const min = data[0];
-    const max = data[l - 1];
-    const p5idx = Math.ceil(l * 0.05) - 1;
-    const p98idx = Math.ceil(l * 0.98) - 1;
-    const p5 = data[p5idx];
-    const p98 = data[p98idx];
-    const binSize = p98 != p5 ? (p98 - p5) / 8 : (max - min) / 8;
-    const firstBinStop = Math.max(min + binSize, p5);
-    let [binSize_rnd, firstBinStop_rnd, lastBinStart_rnd, rounding] = roundBinVals(binSize, firstBinStop, max, min);
-    binConfig = {
-      type: "regular-bin",
-      startinclusive: true,
-      bin_size: binSize_rnd,
-      first_bin: { stop: firstBinStop_rnd }
-    };
-    if (lastBinStart_rnd) binConfig.last_bin = { start: lastBinStart_rnd };
-    if (rounding) binConfig.rounding = rounding;
-  }
-  if ("format" in opts) {
-    if (opts.format === "string") {
-      return JSON.stringify(binConfig);
-    } else {
-      throw "options are not in the correct format";
-    }
-  } else {
-    return binConfig;
-  }
-}
-function roundBinVals(binSize, firstBinStop, max, min) {
-  let binSize_rnd, firstBinStop_rnd, lastBinStart_rnd, rounding;
-  const log = Math.floor(Math.log10(binSize));
-  if (binSize >= 0.1 && binSize <= 2) {
-    binSize_rnd = Math.round(binSize / (1 * 10 ** log)) * (1 * 10 ** log);
-    firstBinStop_rnd = Math.round(firstBinStop / (1 * 10 ** log)) * (1 * 10 ** log);
-  } else {
-    binSize_rnd = Math.round(binSize / (5 * 10 ** log)) * (5 * 10 ** log);
-    firstBinStop_rnd = Math.round(firstBinStop / (5 * 10 ** log)) * (5 * 10 ** log);
-    if (binSize_rnd === 0) binSize_rnd = 1 * 10 ** log;
-    if (firstBinStop_rnd === 0) firstBinStop_rnd = 1 * 10 ** log;
-    if (binSize_rnd === 5 * 10 ** log && firstBinStop_rnd === 1 * 10 ** log) firstBinStop_rnd = 5 * 10 ** log;
-  }
-  if (firstBinStop_rnd < min) firstBinStop_rnd = firstBinStop_rnd * 2;
-  const eighthBinStop_rnd = firstBinStop_rnd + binSize_rnd * 7;
-  if (max > eighthBinStop_rnd) {
-    lastBinStart_rnd = firstBinStop_rnd + binSize_rnd * 6;
-  }
-  if (binSize < 1) {
-    const digits = Math.abs(log);
-    binSize_rnd = Number(binSize_rnd.toFixed(digits));
-    firstBinStop_rnd = Number(firstBinStop_rnd.toFixed(digits));
-    if (lastBinStart_rnd) lastBinStart_rnd = Number(lastBinStart_rnd.toFixed(digits));
-    rounding = "." + digits + "f";
-  }
-  if (Object.is(firstBinStop_rnd, -0)) firstBinStop_rnd = 0;
-  return [binSize_rnd, firstBinStop_rnd, lastBinStart_rnd, rounding];
-}
-
-// ../shared/utils/src/vcf.info.js
-function dissect_INFO(str) {
-  let findsemicolon = false;
-  let findequalorsemicolon = true;
-  let i2 = 0;
-  let idx = 0;
-  const k2v = {};
-  let lastkey;
-  while (i2 < str.length) {
-    const c = str[i2];
-    if (findequalorsemicolon) {
-      if (c == "=") {
-        findsemicolon = true;
-        findequalorsemicolon = false;
-        lastkey = str.substring(idx, i2);
-        idx = i2 + 1;
-      } else if (c == ";") {
-        k2v[str.substring(idx, i2)] = 1;
-        idx = i2 + 1;
-      }
-    } else if (findsemicolon && c == ";") {
-      findequalorsemicolon = true;
-      findsemicolon = false;
-      k2v[lastkey] = str.substring(idx, i2);
-      lastkey = null;
-      idx = i2 + 1;
-    }
-    i2++;
-  }
-  const remainstr = str.substr(idx, i2);
-  if (lastkey) {
-    k2v[lastkey] = remainstr;
-  } else {
-    k2v[remainstr] = 1;
-  }
-  return k2v;
-}
-
-// ../shared/utils/src/vcf.csq.js
-function parse_CSQ(str, header, m) {
-  if (!header) {
-    return null;
-  }
-  for (const thisannotation of str.split(",")) {
-    const lst = thisannotation.replace(/&/g, ",").split("|");
-    const o = {};
-    for (let i2 = 0; i2 < header.length; i2++) {
-      if (lst[i2]) {
-        o[header[i2].name] = lst[i2];
-      }
-    }
-    if (!o.Allele) {
-      continue;
-    }
-    let allele = null;
-    for (const a of m.mlst || m.alleles) {
-      if (a.allele_original == o.Allele) {
-        allele = a;
-        break;
-      }
-    }
-    if (!allele) {
-      if (o.Allele == "-") {
-        if (m.mlst) {
-          if (m.mlst.length == 1) {
-            allele = m.mlst[0];
-          }
-        } else if (m.alleles) {
-          if (m.alleles.length == 1) {
-            allele = m.alleles[0];
-          }
-        }
-      } else {
-        for (const a of m.mlst || m.alleles) {
-          if (a.allele_original.substr(1) == o.Allele) {
-            allele = a;
-            break;
-          }
-        }
-      }
-      if (!allele) {
-        continue;
-      }
-    }
-    if (!allele.csq) {
-      allele.csq = [];
-    }
-    allele.csq.push(o);
-    o._gene = o.SYMBOL || o.Gene;
-    if (o.Feature_type && o.Feature_type == "Transcript") {
-      o._isoform = o.Feature.split(".")[0];
-    } else {
-      o._isoform = o._gene;
-    }
-    if (o.Consequence) {
-      const [dt, cls, rank] = vepinfo(o.Consequence);
-      o._dt = dt;
-      o._class = cls;
-      o._csqrank = rank;
-    } else {
-      o._dt = dtsnvindel;
-      o._class = mclassnonstandard;
-    }
-    if (o.HGVSp) {
-      o._mname = decodeURIComponent(o.HGVSp.substr(o.HGVSp.indexOf(":") + 1));
-    } else if (o.Protein_position && o.Amino_acids) {
-      o._mname = decodeURIComponent(o.Protein_position + o.Amino_acids);
-    } else if (o.HGVSc) {
-      o._mname = o.HGVSc.substr(o.HGVSc.indexOf(":") + 1);
-    } else if (o.Existing_variation) {
-      o._name = o.Existing_variation;
-    } else {
-    }
-  }
-  return true;
-}
-
-// ../shared/utils/src/vcf.ann.js
-function parse_ANN(str, header, m) {
-  if (!header) {
-    return null;
-  }
-  for (const thisannotation of str.split(",")) {
-    const lst = thisannotation.replace(/&/g, ",").split("|");
-    const o = {};
-    for (let i2 = 0; i2 < header.length; i2++) {
-      if (lst[i2]) {
-        o[header[i2].name] = lst[i2];
-      }
-    }
-    if (!o.Allele) {
-      continue;
-    }
-    let allele = null;
-    for (const a of m.alleles) {
-      if (a.allele == o.Allele) {
-        allele = a;
-        break;
-      }
-    }
-    if (!allele) {
-      continue;
-    }
-    if (!allele.ann) {
-      allele.ann = [];
-    }
-    allele.ann.push(o);
-    o._gene = o.Gene_Name;
-    if (o.Feature_Type && o.Feature_Type == "transcript" && o.Feature_ID) {
-      o._isoform = o.Feature_ID.split(".")[0];
-    }
-    if (o.Annotation) {
-      const [dt, cls, rank] = vepinfo(o.Annotation);
-      o._dt = dt;
-      o._class = cls;
-      o._csqrank = rank;
-    } else {
-      o._dt = dtsnvindel;
-      o._class = mclassnonstandard;
-    }
-    if (o["HGVS.p"]) {
-      o._mname = o["HGVS.p"];
-    } else if (o["HGVS.c"]) {
-      o._mname = o["HGVS.c"];
-    } else {
-    }
-  }
-  return true;
-}
-
-// ../shared/utils/src/vcf.type.js
-function getVariantType(ref, alt) {
-  if (ref.length == 1 && alt.length == 1) {
-    if (alt == ".") {
-      return mclassdeletion;
-    }
-    return mclasssnv;
-  }
-  if (ref.length == alt.length) return mclassmnv;
-  if (ref.length < alt.length) return mclassinsertion;
-  if (ref.length > alt.length) return mclassdeletion;
-  return mclassnonstandard2;
-}
-
-// ../shared/utils/src/vcf.js
-var getallelename = new RegExp(/<(.+)>/);
-var mclasslabel2key = {};
-for (const k in mclass) {
-  mclasslabel2key[mclass[k].label.toUpperCase()] = k;
-}
-function vcfparsemeta(lines) {
-  let sample = [], errlst = [], info = {}, hasinfo = false, format = {}, hasformat = false;
-  for (const line of lines) {
-    if (!line.startsWith("#")) {
-      continue;
-    }
-    if (line.startsWith("#C")) {
-      sample = line.split("	").slice(9);
-      continue;
-    }
-    if (line.startsWith("##INFO")) {
-      const e = tohash(line.substring(8, line.length - 1), info);
-      if (e) {
-        errlst.push("INFO error: " + e);
-      } else {
-        hasinfo = true;
-      }
-      continue;
-    }
-    if (line.startsWith("##FORMAT")) {
-      const e = tohash(line.substring(10, line.length - 1), format);
-      if (e) {
-        errlst.push("FORMAT error: " + e);
-      } else {
-        hasformat = true;
-      }
-    }
-  }
-  const sampleobjlst = [];
-  for (const samplename of sample) {
-    const a = { name: samplename };
-    sampleobjlst.push(a);
-  }
-  if (info.CSQ) {
-    const lst = info.CSQ.Description.split(" Format: ");
-    if (lst[1]) {
-      const lst2 = lst[1].split("|");
-      if (lst2.length > 1) {
-        info.CSQ.csqheader = [];
-        for (const str of lst2) {
-          const attr = { name: str };
-          info.CSQ.csqheader.push(attr);
-        }
-      } else {
-        errlst.push("unknown format for CSQ header: " + info.CSQ.Description);
-      }
-    } else {
-      errlst.push("unknown format for CSQ header: " + info.CSQ.Description);
-    }
-  }
-  if (info.ANN) {
-    const lst = info.ANN.Description.split("'");
-    if (lst[1]) {
-      const lst2 = lst[1].split(" | ");
-      if (lst2.length) {
-        info.ANN.annheader = [];
-        for (const s of lst2) {
-          const attr = { name: s };
-          info.ANN.annheader.push(attr);
-        }
-      } else {
-        errlst.push('no " | " joined annotation fields for ANN (snpEff annotation): ' + info.ANN.Description);
-      }
-    } else {
-      errlst.push("no single-quote enclosed annotation fields for ANN (snpEff annotation): " + info.ANN.Description);
-    }
-  }
-  return [hasinfo ? info : null, hasformat ? format : null, sampleobjlst, errlst.length ? errlst : null];
-}
-function vcfparseline(line, vcf) {
-  const lst = line.split("	");
-  if (lst.length < 8) {
-    return ["line has less than 8 fields", null, null];
-  }
-  const rawpos = Number.parseInt(lst[2 - 1]);
-  if (!Number.isInteger(rawpos)) {
-    return ["invalid value for genomic position", null, null];
-  }
-  const refallele = lst[4 - 1];
-  const m = {
-    vcf_ID: lst[3 - 1],
-    chr: (vcf.nochr ? "chr" : "") + lst[1 - 1],
-    pos: rawpos - 1,
-    ref: refallele,
-    //refstr:refallele, // e.g. GA>GCC, ref:A, refstr:GA, "refstr" is required for matching in FORMAT
-    altstr: lst[5 - 1],
-    alleles: [
-      {
-        /*
-        ref allele only a placeholder, to be removed, this array only contains alt alleles
-        this is a must
-        also allows GT allele index to work
-        */
-        allele: refallele,
-        sampledata: []
-      }
-    ],
-    info: {},
-    // locus info, do not contain allele info
-    name: lst[3 - 1] == "." ? null : lst[3 - 1]
-  };
-  const altinvalid = [];
-  for (const alt of lst[5 - 1].split(",")) {
-    const a = {
-      ref: m.ref,
-      // may be corrected just below!
-      allele: alt,
-      // 5078356.TATCAGAGAA.GGGAGGA keep original allele for matching with csq which hardcodes original allele
-      allele_original: alt,
-      sampledata: [],
-      _m: m,
-      info: {}
-      // allele info, do not contain locus info
-    };
-    m.alleles.push(a);
-    if (alt[0] == "<") {
-      const tmp2 = alt.match(getallelename);
-      if (!tmp2) {
-        altinvalid.push(alt);
-        continue;
-      }
-      a.type = tmp2[1];
-      a.allele = tmp2[1];
-      a.issymbolicallele = true;
-    } else {
-      const [p, ref, alt2] = correctRefAlt(m.pos, m.ref, a.allele);
-      a.pos = p;
-      a.ref = ref;
-      a.allele = alt2;
-    }
-  }
-  if (lst[9 - 1] && lst[10 - 1]) {
-    parse_FORMAT2(lst, m, vcf);
-  }
-  m.alleles.shift();
-  const tmp = lst[8 - 1] == "." ? [] : dissect_INFO(lst[8 - 1]);
-  let badinfokeys = [];
-  if (vcf.info) {
-    badinfokeys = parse_INFO(tmp, m, vcf);
-  } else {
-    m.info = tmp;
-  }
-  const mlst = [];
-  for (const a of m.alleles) {
-    const m2 = {};
-    for (const k in m) {
-      if (k != "alleles") {
-        m2[k] = m[k];
-      }
-    }
-    for (const k in a) {
-      if (k == "allele") {
-        m2.alt = a[k];
-      } else if (k == "info") {
-        m2.altinfo = a[k];
-      } else {
-        m2[k] = a[k];
-      }
-    }
-    if (!m2.issymbolicallele && m2.alt != "NON_REF") {
-      m2.type = getVariantType(m2.ref, m2.alt);
-    }
-    mlst.push(m2);
-  }
-  return [
-    badinfokeys.length ? "unknown info keys: " + badinfokeys.join(",") : null,
-    mlst,
-    altinvalid.length > 0 ? altinvalid : null
-  ];
-}
-function correctRefAlt(p, ref, alt) {
-  while (ref.length > 1 && alt.length > 1 && ref[ref.length - 1] == alt[alt.length - 1]) {
-    ref = ref.substr(0, ref.length - 1);
-    alt = alt.substr(0, alt.length - 1);
-  }
-  while (ref.length > 1 && alt.length > 1 && ref[0] == alt[0]) {
-    ref = ref.substr(1);
-    alt = alt.substr(1);
-    p++;
-  }
-  return [p, ref, alt];
-}
-function parse_FORMAT2(lst, m, vcf) {
-  const formatfields = lst[9 - 1].split(":");
-  for (let _sampleidx = 9; _sampleidx < lst.length; _sampleidx++) {
-    const valuelst = lst[_sampleidx].split(":");
-    {
-      let none = true;
-      for (const v of valuelst) {
-        if (v != ".") {
-          none = false;
-          break;
-        }
-      }
-      if (none) {
-        continue;
-      }
-    }
-    const sampleidx = _sampleidx - 9;
-    for (let i2 = 1; i2 < m.alleles.length; i2++) {
-      const sobj = {};
-      if (vcf.samples && vcf.samples[sampleidx]) {
-        for (const k in vcf.samples[sampleidx]) {
-          sobj[k] = vcf.samples[sampleidx][k];
-        }
-      } else {
-        sobj.name = "missing_samplename_from_vcf_header";
-      }
-      m.alleles[i2].sampledata.push({
-        sampleobj: sobj
-      });
-    }
-    for (let fi = 0; fi < formatfields.length; fi++) {
-      const field = formatfields[fi];
-      const value = valuelst[fi];
-      if (value == ".") {
-        continue;
-      }
-      if (field == "GT") {
-        const splitter = value.indexOf("/") != -1 ? "/" : "|";
-        let gtsum = 0;
-        let unknowngt = false;
-        const gtalleles = [];
-        for (const i2 of value.split(splitter)) {
-          if (i2 == ".") {
-            unknowngt = true;
-            continue;
-          }
-          const j = Number.parseInt(i2);
-          if (Number.isNaN(j)) {
-            unknowngt = true;
-            continue;
-          }
-          gtsum += j;
-          const ale = m.alleles[j];
-          if (ale) {
-            gtalleles.push(ale.allele);
-          }
-        }
-        let gtallref = false;
-        if (!unknowngt) {
-          gtallref = gtsum == 0;
-        }
-        const genotype = gtalleles.join(splitter);
-        for (let i2 = 1; i2 < m.alleles.length; i2++) {
-          const ms = m.alleles[i2].sampledata[m.alleles[i2].sampledata.length - 1];
-          ms.GT = value;
-          ms.genotype = genotype;
-          if (gtallref) {
-            ms.gtallref = true;
-          }
-          ms.__gtalleles = gtalleles;
-        }
-        continue;
-      }
-      const formatdesc = vcf.format ? vcf.format[field] : null;
-      if (!formatdesc) {
-        for (let i2 = 1; i2 < m.alleles.length; i2++) {
-          m.alleles[i2].sampledata[m.alleles[i2].sampledata.length - 1][field] = value;
-        }
-        continue;
-      }
-      const isinteger = formatdesc.Type == "Integer";
-      const isfloat = formatdesc.Type == "Float";
-      if (formatdesc.Number && formatdesc.Number == "R" || field == "AD") {
-        const fvlst = value.split(",").map((i2) => {
-          if (isinteger) return Number.parseInt(i2);
-          if (isfloat) return Number.parseFloat(i2);
-          return i2;
-        });
-        for (let i2 = 1; i2 < m.alleles.length; i2++) {
-          if (fvlst[i2] != void 0) {
-            const m2 = m.alleles[i2];
-            const m2s = m2.sampledata[m2.sampledata.length - 1];
-            m2s[field] = {};
-            m2s[field][m2.ref] = fvlst[0];
-            m2s[field][m2.allele] = fvlst[i2];
-          }
-        }
-        continue;
-      }
-      if (formatdesc.Number && formatdesc.Number == "A") {
-        const fvlst = value.split(",").map((i2) => {
-          if (isinteger) return Number.parseInt(i2);
-          if (isfloat) return Number.parseFloat(i2);
-          return i2;
-        });
-        for (let i2 = 1; i2 < m.alleles.length; i2++) {
-          if (fvlst[i2 - 1] != void 0) {
-            const m2 = m.alleles[i2];
-            const m2s = m2.sampledata[m2.sampledata.length - 1];
-            m2s[field] = {};
-            m2s[field][m2.allele] = fvlst[i2 - 1];
-          }
-        }
-        continue;
-      }
-      for (let i2 = 1; i2 < m.alleles.length; i2++) {
-        m.alleles[i2].sampledata[m.alleles[i2].sampledata.length - 1][field] = value;
-      }
-    }
-  }
-  for (const a of m.alleles) {
-    for (const s of a.sampledata) {
-      if (s.AD) {
-        s.allele2readcount = {};
-        for (const k in s.AD) {
-          s.allele2readcount[k] = s.AD[k];
-        }
-      }
-    }
-  }
-}
-function tohash(s, hash2) {
-  const h = {}, err = [];
-  let prev = 0, prevdoublequote = false, k = null;
-  for (let i2 = 0; i2 < s.length; i2++) {
-    if (s[i2] == '"') {
-      i2++;
-      const thisstart = i2;
-      while (s[i2] != '"') {
-        i2++;
-      }
-      if (k) {
-        h[k] = s.substring(thisstart, i2);
-        k = null;
-      } else {
-        err.push("k undefined before double quotes");
-      }
-      prevdoublequote = true;
-      continue;
-    }
-    if (s[i2] == "=") {
-      k = s.substring(prev, i2);
-      prev = i2 + 1;
-      continue;
-    }
-    if (s[i2] == ",") {
-      if (prevdoublequote) {
-        prevdoublequote = false;
-      } else {
-        if (k) {
-          h[k] = s.substring(prev, i2);
-          k = null;
-        } else {
-          err.push("k undefined");
-        }
-      }
-      prev = i2 + 1;
-      continue;
-    }
-  }
-  if (k) {
-    h[k] = s.substring(prev, i);
-  }
-  if (h.ID) {
-    hash2[h.ID] = h;
-  } else {
-    return "no ID";
-  }
-  if (err.length) return err.join("\n");
-}
-function parse_INFO(tmp, m, vcf) {
-  const badinfokeys = [];
-  for (const key in tmp) {
-    if (vcf.info[key] == void 0) {
-      badinfokeys.push(key);
-      continue;
-    }
-    const value = tmp[key];
-    if (key == "CSQ") {
-      const okay = parse_CSQ(value, vcf.info.CSQ.csqheader, m);
-      if (!okay) {
-        m.info[key] = value;
-      }
-      continue;
-    }
-    if (key == "ANN") {
-      const okay = parse_ANN(value, vcf.info.ANN.annheader, m);
-      if (!okay) {
-        m.info[key] = value;
-      }
-      continue;
-    }
-    if (vcf.info[key].Type == "Flag") {
-      m.info[key] = key;
-      continue;
-    }
-    const __number = vcf.info[key].Number;
-    const isinteger = vcf.info[key].Type == "Integer";
-    const isfloat = vcf.info[key].Type == "Float";
-    if (__number == "0") {
-      m.info[key] = key;
-      continue;
-    }
-    if (__number == "A") {
-      const tt = value.split(",");
-      for (let j = 0; j < tt.length; j++) {
-        if (m.alleles[j]) {
-          m.alleles[j].info[key] = isinteger ? Number.parseInt(tt[j]) : isfloat ? Number.parseFloat(tt[j]) : tt[j];
-        }
-      }
-      continue;
-    }
-    if (__number == "R") {
-    }
-    if (__number == "1") {
-      m.info[key] = isinteger ? Number.parseInt(value) : isfloat ? Number.parseFloat(value) : value;
-      continue;
-    }
-    if (!value.split) {
-      continue;
-    }
-    const lst = value.split(",");
-    if (isinteger) {
-      m.info[key] = lst.map(Number.parseInt);
-    } else if (isfloat) {
-      m.info[key] = lst.map(Number.parseFloat);
-    } else {
-      m.info[key] = lst;
-    }
-  }
-  return badinfokeys;
-}
-
-// ../shared/utils/src/compute.percentile.js
-function computePercentile(values, percentile, sorted = false) {
-  if (!sorted) values.sort((a, b) => a - b);
-  const index = Math.abs(percentile / 100 * values.length - 1);
-  const value = Number.isInteger(index) ? (values[index] + values[index + 1]) / 2 : values[Math.ceil(index)];
-  return value;
-}
-
-// ../shared/utils/src/hash.js
-var encoder = new TextEncoder();
-async function hash(message) {
-  const msgUint8 = encoder.encode(message);
-  const hashBuffer = await crypto.subtle.digest("SHA-1", msgUint8);
-  const hashArray = Array.from(new Uint8Array(hashBuffer));
-  const hashHex = hashArray.map((b) => b.toString(16).padStart(2, "0")).join("");
-  return hexToBase64(hashHex).replace("=", "-");
-}
-function hexToBase64(hexStr) {
-  return btoa(
-    [...hexStr].reduce(
-      (acc, _, i2) => acc += !(i2 - 1 & 1) ? String.fromCharCode(parseInt(hexStr.substring(i2 - 1, i2 + 1), 16)) : "",
-      ""
-    )
-  );
-}
-
-// ../shared/utils/src/urljson.js
-var reserved = ["false", "true", "null", "undefined"];
-var delimiters = ['"', "{", "["];
-function encode(rawObject) {
-  const params = [];
-  for (const [key, value] of Object.entries(rawObject)) {
-    if (typeof value == "string" && !isNumeric(value) && !reserved.includes(value) && !delimiters.includes(value[0])) {
-      params.push(`${key}=${encodeURIComponent(value)}`);
-    } else if (value !== void 0) {
-      params.push(`${key}=${encodeURIComponent(JSON.stringify(value))}`);
-    }
-  }
-  return params.join("&");
-}
-
-// ../shared/utils/src/fetch-helpers.js
-async function processResponse(r) {
-  const ct = r.headers.get("content-type");
-  if (!ct) throw `missing response.header['content-type']`;
-  if (ct.includes("/json")) {
-    const payload = await r.json();
-    return payload;
-  }
-  if (ct.includes("/text") || ct.includes("text/")) {
-    return r.text();
-  }
-  if (ct.includes("multipart")) {
-    if (ct.startsWith("multipart/form-data")) return processFormData(r);
-    else throw `cannot handle response content-type: '${ct}'`;
-  }
-  if (ct == "application/x-ndjson-nestedkey") {
-    return processNDJSON_nestedKey(r);
-  }
-  return r.blob();
-}
-async function processFormData(res) {
-  const decoder = new TextDecoder();
-  const data = {};
-  try {
-    const form = await res.formData();
-    for (const [key, value] of form.entries()) {
-      if (value.type) {
-        data[key] = { headers: { "content-type": value.type }, body: value };
-      } else {
-        const body = !value ? [] : value.trim().split("\n").map(JSON.parse);
-        data[key] = { headers: { "content-type": "application/json" }, body };
-      }
-    }
-    return data;
-  } catch (e) {
-    throw e;
-  }
-}
-async function processNDJSON_nestedKey(r) {
-  const stream = r.body.pipeThrough(new TextDecoderStream());
-  const reader = stream.getReader();
-  let rootObj = {};
-  let buffer = "";
-  while (true) {
-    const { value, done } = await reader.read();
-    if (done) break;
-    buffer += value;
-    let parts = buffer.split("\n");
-    buffer = parts.pop();
-    for (const line of parts) {
-      if (line.trim()) {
-        const [keys, data] = JSON.parse(line);
-        if (!keys.length) rootObj = data;
-        else {
-          const lastKey = keys.pop();
-          let target = rootObj;
-          for (const k of keys) target = target[k];
-          target[lastKey] = data;
-        }
-      }
-    }
-  }
-  return rootObj;
-}
-var cacheLifetime = 1e3 * 60 * 5;
-async function getDataName(url, init) {
-  const dataName = url + " | " + init.method + " | " + init.body + " | " + JSON.stringify(init.headers);
-  return await hash(dataName);
-}
-
-// ../shared/utils/src/termdb.usecase.js
-var graphableTypes = /* @__PURE__ */ new Set([
-  "categorical",
-  "integer",
-  "float",
-  "condition",
-  "survival",
-  "snplst",
-  "snplocus",
-  "geneVariant",
-  "samplelst",
-  "geneExpression",
-  ISOFORM_EXPRESSION,
-  "dtcnv",
-  "dtsnvindel",
-  "dtfusion",
-  "dtsv",
-  "date",
-  TermTypes.SSGSEA,
-  TermTypes.DNA_METHYLATION,
-  TermTypes.METABOLITE_INTENSITY,
-  TermTypes.PROTEOME_ABUNDANCE,
-  SINGLECELL_GENE_EXPRESSION,
-  SINGLECELL_CELLTYPE,
-  TermTypes.SNP,
-  TermTypes.TERM_COLLECTION
-]);
-function isUsableTerm(term, _usecase, termdbConfig, ds) {
-  const usecase = _usecase || {};
-  if (typeof ds?.usecase?.[usecase.target] == "function") {
-    return ds.usecase[usecase.target](term, usecase);
-  }
-  const uses = /* @__PURE__ */ new Set();
-  const child_types = term.child_types || [];
-  switch (usecase.target) {
-    case "barchart":
-    case "violin":
-    case "boxplot":
-    case "summary":
-      if (term.type && term.type !== "survival") uses.add("plot");
-      if (hasAllowedChildTypes(child_types, ["survival"])) uses.add("branch");
-      return uses;
-    case "summaryInput":
-      if (usecase.detail === "term2" || usecase.detail == "term0") {
-        if (term.type && term.type !== "survival") uses.add("plot");
-        if (hasAllowedChildTypes(child_types, ["survival"])) uses.add("branch");
-        return uses;
-      } else {
-        if (graphableTypes.has(term.type)) uses.add("plot");
-        if (!term.isleaf) uses.add("branch");
-        return uses;
-      }
-    case "matrix":
-      if (term.type) uses.add("plot");
-      if (!term.isleaf) uses.add("branch");
-      return uses;
-    case "table":
-      if (usecase.detail == "term") uses.add("plot");
-      if (child_types.length > 1) uses.add("branch");
-      return uses;
-    case "sampleScatter":
-      if (usecase.detail == "numeric") {
-        if (isNumericTerm(term)) {
-          uses.add("plot");
-        }
-        if (hasNumericChild(child_types)) uses.add("branch");
-      } else {
-        if (graphableTypes.has(term.type)) uses.add("plot");
-        if (!term.isleaf) uses.add("branch");
-      }
-      return uses;
-    case "runChart2":
-      if (usecase.detail == "date" || usecase.detail == "xtw") {
-        if (term.type == "date") {
-          uses.add("plot");
-        }
-        if (child_types.includes("date")) uses.add("branch");
-      } else if (usecase.detail == "numeric") {
-        if (isNumericTerm(term) && term.type != "date") {
-          uses.add("plot");
-        }
-        if (hasNumericChild(child_types)) uses.add("branch");
-      } else {
-        if (graphableTypes.has(term.type)) uses.add("plot");
-        if (!term.isleaf) uses.add("branch");
-      }
-      return uses;
-    case "termCollections":
-      if (usecase.detail?.termIds?.includes(term.id)) uses.add("plot");
-      if (usecase.detail?.branchIds?.includes(term.id)) uses.add("branch");
-      return uses;
-    case "profileForms":
-      if (!term.isleaf) {
-        const ancestors = term.id.split("__").length;
-        if (ancestors == 3) {
-          uses.add("plot");
-        } else if (ancestors < 3) uses.add("branch");
-      }
-      return uses;
-    // case 'boxplot':
-    // 	if (term.type == 'float' || term.type == 'integer') uses.add('plot')
-    // 	if (usecase.detail === 'term2' && hasNumericChild(child_types)) uses.add('branch')
-    // 	return uses
-    case "cuminc":
-      if (usecase.detail == "term") {
-        if (term.type == "condition") uses.add("plot");
-        if (child_types.includes("condition")) uses.add("branch");
-        return uses;
-      }
-      if (usecase.detail === "term2" || usecase.detail == "term0") {
-        if (term.type && term.type != "condition" && term.type != "survival") uses.add("plot");
-        if (hasAllowedChildTypes(child_types, ["condition", "survival"])) uses.add("branch");
-        return uses;
-      }
-      return uses;
-    case "survival":
-      if (usecase.detail == "term") {
-        if (term.type == "survival") uses.add("plot");
-        if (child_types.includes("survival")) uses.add("branch");
-        return uses;
-      }
-      if (usecase.detail === "term2" || usecase.detail == "term0") {
-        if (term.type && term.type != "survival") uses.add("plot");
-        if (hasAllowedChildTypes(child_types, ["survival"])) uses.add("branch");
-        return uses;
-      }
-      return uses;
-    case "regression":
-      if (usecase.detail == "outcome") {
-        if (usecase.regressionType == "linear") {
-          if (term.type == "float" || term.type == "integer") uses.add("plot");
-          if (hasNumericChild(child_types)) uses.add("branch");
-          return uses;
-        }
-        if (usecase.regressionType == "logistic") {
-          if (term.type && term.type != "survival") uses.add("plot");
-          if (hasAllowedChildTypes(child_types, ["survival"])) uses.add("branch");
-          return uses;
-        } else if (usecase.regressionType == "cox") {
-          if (term.type == "condition" || term.type == "survival") uses.add("plot");
-          if (child_types.includes("condition") || child_types.includes("survival")) uses.add("branch");
-          return uses;
-        }
-      }
-      if (usecase.detail == "independent") {
-        if (term.type == "float" || term.type == "integer" || term.type == "categorical" || term.type == "samplelst")
-          uses.add("plot");
-        if (hasChildTypes(child_types, ["categorical", "float", "integer"])) uses.add("branch");
-        return uses;
-      }
-      return uses;
-    case "filter": {
-      const exlst = termdbConfig?.excludedTermtypeByTarget?.filter;
-      if (exlst) {
-        if (graphableTypes.has(term.type) && !exlst.includes(term.type)) uses.add("plot");
-        if (child_types.find((t) => !exlst.includes(t))) uses.add("branch");
-        return uses;
-      }
-      if (graphableTypes.has(term.type)) uses.add("plot");
-      if (!term.isleaf) uses.add("branch");
-      return uses;
-    }
-    case "correlationVolcano":
-      if (usecase.detail == "numeric") {
-        if (isNumericTerm(term)) {
-          uses.add("plot");
-        }
-        if (hasNumericChild(child_types)) uses.add("branch");
-      } else {
-        if (graphableTypes.has(term.type)) uses.add("plot");
-        if (!term.isleaf) uses.add("branch");
-      }
-      return uses;
-    case "proteinView":
-      if (term.type == TermTypes.PROTEOME_ABUNDANCE) uses.add("plot");
-      if (child_types.includes(TermTypes.PROTEOME_ABUNDANCE)) uses.add("branch");
-      return uses;
-    default:
-      if (graphableTypes.has(term.type)) uses.add("plot");
-      if (!term.isleaf) uses.add("branch");
-      return uses;
-  }
-}
-function hasAllowedChildTypes(child_types, excluded_types) {
-  if (!child_types.length) {
-    return false;
-  }
-  if (!excluded_types?.length) {
-    return true;
-  }
-  if (child_types.some((type) => !excluded_types.includes(type))) {
-    return true;
-  }
-}
-function hasNumericChild(child_types) {
-  return child_types.includes("float") || child_types.includes("integer");
-}
-function hasChildTypes(child_types, expected_types) {
-  for (const a of expected_types) {
-    if (child_types.includes(a)) return true;
-  }
-}
-
-// ../shared/utils/src/time.js
-function formatElapsedTime(ms, precision = 2) {
-  if (typeof ms !== "number" || isNaN(ms)) {
-    return typeof ms !== "number" ? "Invalid time: not a number" : "Invalid time: NaN";
-  }
-  if (!isFinite(ms)) {
-    return ms > 0 ? "Infinite time" : "-Infinite time";
-  }
-  const absMs = Math.abs(ms);
-  const sign = ms < 0 ? "-" : "";
-  if (absMs < 1e3) {
-    return `${sign}${absMs}ms`;
-  }
-  if (absMs < 6e4) {
-    return `${sign}${(absMs / 1e3).toFixed(precision)}s`;
-  }
-  const minutes = Math.floor(absMs / 6e4);
-  const seconds = (absMs % 6e4 / 1e3).toFixed(precision);
-  return `${sign}${minutes}m ${seconds}s`;
-}
-
-// common/auth.js
-var jwtByDsRouteStr = localStorage.getItem("jwtByDsRoute") || `{}`;
-var jwtByDsRoute = JSON.parse(jwtByDsRouteStr);
-function setTokenByDsRoute(dslabel, route, jwt) {
-  if (!jwtByDsRoute[dslabel]) jwtByDsRoute[dslabel] = {};
-  if (jwt) jwtByDsRoute[dslabel][route] = jwt;
-  else delete jwtByDsRoute[dslabel][route];
-  localStorage.setItem("jwtByDsRoute", JSON.stringify(jwtByDsRoute));
-}
-function getSavedToken(dslabel, route) {
-  return jwtByDsRoute[dslabel]?.[route] || jwtByDsRoute[dslabel]?.["/**"];
-}
-function mayAddJwtToRequest(init, body, url) {
-  if (init.headers.authorization) return;
-  let dslabel = body?.dslabel;
-  if (!dslabel) {
-    const param = url.split("?")[1]?.split("&").find((kv) => kv.includes("dslabel"));
-    if (!param) return;
-    let value = decodeURIComponent(param.split("=")[1]);
-    if (value.startsWith("{") && value.endsWith("}")) {
-      value = JSON.parse(value);
-      dslabel = value.dslabel || value.mass?.vocab.dslabel || value.tracks?.find((t) => t.dslabel)?.dslabel;
-    } else {
-      dslabel = value;
-    }
-  }
-  if (!dslabel || !jwtByDsRoute[dslabel]) return;
-  const h = url.split("//");
-  const postProtocolStr = h[1] || h[0];
-  const preQuestionMarkStr = postProtocolStr.split("?")[0];
-  const pathSegments = preQuestionMarkStr.split("/");
-  let route = pathSegments.find((p) => p != "" && !p.includes(":") && !p.includes("."));
-  const jwt = jwtByDsRoute[dslabel][route] || jwtByDsRoute[dslabel]["/**"];
-  if (jwt) init.headers.authorization = "Bearer " + btoa(jwt);
-}
-var dsAuthOk = /* @__PURE__ */ new Set();
-var dsAuth;
-var authUi;
-var authUiHolder;
-var includeEmbedder = false;
-async function setDsAuthOk(opts, dofetch32) {
-  dsAuth = opts.dsAuth;
-  authUi = opts.ui || defaultAuthUi;
-  authUiHolder = opts.holder || select_default("body");
-  for (const auth of dsAuth) {
-    if (auth.insession) dsAuthOk.add(auth);
-    else {
-      const { dslabel, route } = auth;
-      const jwt = getSavedToken(dslabel, route);
-      if (jwt) {
-        const payload = JSON.parse(atob(jwt.split(".")[1]));
-        if (payload.exp && Math.ceil(Date.now() / 1e3) > payload.exp) continue;
-        const data = await dofetch32("/jwt-status", {
-          method: "POST",
-          headers: {
-            //authorization: `Bearer ${btoa(jwt)}`
-            [auth.headerKey]: jwt
-          },
-          body: {
-            dslabel,
-            route,
-            embedder: location.hostname
-          }
-        });
-        if (data.ok || data.status == "ok") {
-          dsAuthOk.add(auth);
-          auth.insession = true;
-        }
-      }
-    }
-  }
-  includeEmbedder = opts.dsAuth?.length > 0 || false;
-}
-function getRequiredAuth(dslabel, route) {
-  if (!dsAuth || !Array.isArray(dsAuth)) return;
-  for (const a of dsAuth) {
-    if (a.dslabel == dslabel && (a.route == route || a.route == "*" || a.route == "/**")) return a;
-  }
-}
-function isInSession(dslabel, route) {
-  if (!dslabel) return false;
-  for (const a of dsAuthOk) {
-    if (a.dslabel == dslabel && (a.route == route || a.route == "/**")) return true;
-  }
-  return false;
-}
-async function mayShowAuthUi(init, path, opts = {}) {
-  const ok = { status: "ok" };
-  if (!dsAuth || path.endsWith("jwt-status")) return ok;
-  const body = JSON.parse(init.body || `{}`);
-  const params = (path.split("?")[1] || "").split("&").reduce((obj, kv) => {
-    const [key, value] = kv.split("=");
-    obj[key] = value;
-    return obj;
-  }, {});
-  const q = Object.assign({}, body, params);
-  const route = ((path.split("?")[0] || "").split("//")[1] || "").split("/").slice(1).join("/");
-  for (const a of dsAuth) {
-    if (q.dslabel == a.dslabel && (a.route == "/**" || route == a.route)) {
-      if (dsAuthOk.has(a)) return ok;
-      else if (a.route != "/**") return ok;
-      else if (a.type == "basic") return await authUi(a.dslabel, a, opts);
-      else if (a.type == "jwt") {
-      } else if (a.type == "forbidden") {
-        alert("Forbidden access");
-      } else throw `unsupported dsAuth type='${a.type}'`;
-    }
-  }
-  return ok;
-}
-async function defaultAuthUi(dslabel, auth, opts = {}) {
-  const mask = authUiHolder.append("div").style("position", "fixed").style("top", 0).style("left", 0).style("height", "100%").style("width", "100%").style("margin", 0).style("padding", "20px").style("background-color", "rgb(150,150,150)");
-  const form = mask.append("div").style("opacity", 1);
-  form.append("div").html(`Restricted dataset '${dslabel}'`);
-  form.append("span").html("Please enter password ");
-  const pwd = form.append("input").attr("type", "password");
-  pwd.node().focus();
-  const btn = form.append("button").html("Submit");
-  return new Promise((resolve, reject) => {
-    function login() {
-      fetch("/dslogin", {
-        method: "POST",
-        headers: {
-          authorization: `Basic ${btoa(pwd.property("value"))}`
-        },
-        body: JSON.stringify({ dslabel, route: auth.route, embedder: window.location.hostname })
-      }).then((res) => res.json()).then((res) => {
-        if (res.error) throw res.error;
-        mask.remove();
-        dsAuthOk.add(auth);
-        if (res.jwt) {
-          setTokenByDsRoute(dslabel, res.route, res.jwt);
-        }
-        if (!opts.setDomRefs) window.location.reload();
-        else resolve(dslabel);
-      }).catch((e) => {
-        alert("login error: " + e);
-      });
-    }
-    btn.on("click", login);
-    pwd.on("change", login);
-    if (opts.setDomRefs)
-      opts.setDomRefs({
-        pwd,
-        btn,
-        mask,
-        authUiHolder
-      });
-  });
-}
-
-// common/dofetch.js
-function dofetch(path, arg, opts = null) {
-  if (opts && typeof opts == "object") {
-    if (opts.serverData && typeof opts.serverData == "object") {
-      if (!dofetch.serverData) {
-        dofetch.serverData = opts.serverData;
-      } else if (!opts.serverData) {
-        opts.serverData = dofetch.serverData;
-      }
-    }
-    return dofetch2(
-      path,
-      {
-        method: "POST",
-        headers: {
-          "content-type": "application/json"
-        },
-        body: JSON.stringify(arg)
-      },
-      opts
-    );
-  } else {
-    if (path[0] == "/") {
-      path = path.slice(1);
-    }
-    const jwt = sessionStorage.getItem("jwt");
-    if (jwt) {
-      arg.jwt = jwt;
-    }
-    let url = path;
-    const host = sessionStorage.getItem("hostURL") || window.testHost || "";
-    if (host) {
-      if (host.endsWith("/")) {
-        url = host + path;
-      } else {
-        url = host + "/" + path;
-      }
-    }
-    return fetch(
-      new Request(url, {
-        method: "POST",
-        headers: {
-          "content-type": "application/json"
-        },
-        body: JSON.stringify(arg)
-      })
-    ).then((r) => r.json());
-  }
-}
-function dofetch2(path, init = {}, opts = {}) {
-  if (path[0] == "/") {
-    path = path.slice(1);
-  }
-  let url = path;
-  const host = sessionStorage.getItem("hostURL") || window.testHost || "";
-  if (host) {
-    if (host.endsWith("/")) {
-      url = host + path;
-    } else {
-      url = host + "/" + path;
-    }
-  }
-  const body = init.body || {};
-  url = mayAdjustRequest(url, init);
-  if (!init.headers) {
-    init.headers = {};
-  }
-  if (!init.headers["content-type"] && init.body) {
-    init.headers["content-type"] = "application/json";
-  }
-  const jwt = sessionStorage.getItem("jwt");
-  if (jwt) {
-    init.headers.authorization = "Bearer " + jwt;
-  }
-  return mayShowAuthUi(init, url).then(async () => {
-    if (!jwt) mayAddJwtToRequest(init, body, url);
-    if (opts.serverData) {
-      return namedFetch(url, init, opts);
-    } else {
-      return fetch(url, init).then(processResponse);
-    }
-  });
-}
-var optsServerDataNames2 = /* @__PURE__ */ new WeakMap();
-async function namedFetch(url, init, opts = {}) {
-  if (!opts.serverData) throw `use ezFetch() from fetch-helpers if a fetched response is not meant to be cached`;
-  if (typeof opts.serverData != "object") throw `opts.serverData is not an object`;
-  let result;
-  const dataName = await getDataName(url, init);
-  if (opts.serverData[dataName]) {
-    if (init.signal) {
-      await sleep(0);
-      if (init.signal.aborted) throw `stale sequenceId`;
-    }
-    result = structuredClone(opts.serverData[dataName]);
-  }
-  if (!result || typeof result != "object" && !(result instanceof Promise)) {
-    delete opts.serverData[dataName];
-    result = void 0;
-  }
-  if (!result) {
-    try {
-      const res = await fetch(url, init);
-      result = await processResponse(res);
-      if (typeof result == "object" && !(result instanceof Promise)) {
-        deepFreeze(result);
-        opts.serverData[dataName] = result;
-        result = structuredClone(result);
-      }
-    } catch (e) {
-      delete opts.serverData[dataName];
-      throw e;
-    }
-  }
-  if (!optsServerDataNames2.has(opts.serverData)) optsServerDataNames2.set(opts.serverData, []);
-  const keys = optsServerDataNames2.get(opts.serverData);
-  const i2 = keys.indexOf(dataName);
-  if (i2 > 0) {
-    keys.splice(i2, 1);
-  }
-  keys.unshift(dataName);
-  const maxKeys = 360;
-  while (keys.length > maxKeys) {
-    const oldestDataKey = keys.pop();
-    delete opts.serverData[oldestDataKey];
-  }
-  return result;
-}
-var defaultServerDataCache = {};
-function dofetch3(path, init = {}, opts = {}) {
-  if (!init.signal && typeof this?.app?.getAbortSignal == "function") init.signal = this.app.getAbortSignal();
-  opts.serverData = defaultServerDataCache;
-  return dofetch2(path, init, opts);
-}
-function clearServerDataCache(opts = {}) {
-  const cache = opts?.serverData || defaultServerDataCache;
-  if (!cache) return;
-  for (const k of Object.keys(cache)) {
-    delete cache[k];
-  }
-}
-var urlMaxLength = 2e3;
-function mayAdjustRequest(url, init) {
-  const hostname = window.location.hostname;
-  const method = init.method && init.method.toUpperCase() || "GET";
-  if (method == "POST") {
-    if (typeof init.body == "string") init.body = JSON.parse(init.body);
-    if (!init.body.embedder && includeEmbedder) init.body.embedder = hostname;
-    init.body = JSON.stringify(init.body);
-    return url;
-  }
-  if (method != "GET" && method != "DELETE" && method != "PUT") {
-    throw `unsupported init.method='${method}': must be undefined or GET or POST or DELETE or PUT`;
-  }
-  if (init.body) {
-    if (!init.body.embedder && includeEmbedder) init.body.embedder = hostname;
-    const params = encode(init.body);
-    if (!url.includes("?")) url += "?";
-    url += params;
-  }
-  if (!url.includes("embedder=") && includeEmbedder) {
-    const sep = url.includes("?") ? "&" : "?";
-    url += `${sep}embedder=${hostname}`;
-  }
-  if (url.length < urlMaxLength) {
-    if (init.body) delete init.body;
-    return url;
-  }
-  init.method = "POST";
-  const [hostpath, query] = url.split("?");
-  if (init.body) {
-    init.body = JSON.stringify(init.body);
-  } else {
-    const params = {};
-    if (query)
-      query.split("&").forEach((p) => {
-        const [k, v] = p.split("=");
-        const decodedVal = decodeURIComponent(v);
-        try {
-          params[k] = JSON.parse(decodedVal);
-        } catch {
-          params[k] = decodedVal;
-        }
-      });
-    if (!params.embedder && includeEmbedder) params.embedder = hostname;
-    init.body = JSON.stringify(params);
-  }
-  return hostpath;
-}
-function setAuth(opts) {
-  setDsAuthOk(opts, dofetch3);
-}
-
-export {
-  init_bulk_flag,
-  parsesample,
-  clusterMethodLst,
-  distanceMethodLst,
-  computePercentile,
-  fileSize,
-  ssmIdFieldsSeparator,
-  summarize_mclass,
-  guessSsmid,
-  initBinConfig,
-  isUsableTerm,
-  formatElapsedTime,
-  vcfparsemeta,
-  vcfparseline,
-  setTokenByDsRoute,
-  getSavedToken,
-  getRequiredAuth,
-  isInSession,
-  dofetch,
-  dofetch2,
-  dofetch3,
-  clearServerDataCache,
-  setAuth
-};
-//# sourceMappingURL=chunk-RCYTUKAJ.js.map