@sjcrh/proteinpaint-client 2.220.0 → 2.222.0

package/dist/chunk-XHZ723K4.js

@@ -1,2334 +0,0 @@
-import {
-  vcf2dstk
-} from "./chunk-WTWHUZ4O.js";
-import {
-  getsjcharts
-} from "./chunk-MKAF2BHB.js";
-import {
-  parseheader,
-  parseline
-} from "./chunk-VLIOMJDR.js";
-import {
-  bulk_badline,
-  disappear2 as disappear,
-  filetypeselect,
-  newpane,
-  newpane3,
-  renderSandboxFormDiv,
-  sayerror,
-  tkt
-} from "./chunk-PEKCVKJK.js";
-import {
-  invalidcoord,
-  string2pos
-} from "./chunk-HJ6L54YS.js";
-import {
-  dofetch,
-  init_bulk_flag,
-  parsesample
-} from "./chunk-4TJO2DGU.js";
-import {
-  category10_default,
-  dtcloss,
-  dtcnv,
-  dtdel,
-  dtfusionrna,
-  dtitd,
-  dtnloss,
-  dtsnvindel,
-  dtsv,
-  mclasscloss,
-  mclasscnvgain,
-  mclasscnvloh,
-  mclasscnvloss,
-  mclassdel,
-  mclassfusionrna,
-  mclassitd,
-  mclassnloss,
-  mclasssv,
-  mclasstester,
-  validtkt
-} from "./chunk-WJLRU5OF.js";
-import {
-  ordinal
-} from "./chunk-4OLM3KSB.js";
-import {
-  select_default
-} from "./chunk-I6Y4O3RR.js";
-
-// ../shared/utils/dist/src/bulk.snv.js
-function parseheader2(line, flag2) {
-  const header = line.toLowerCase().split("	");
-  if (header.length <= 1) return "invalid file header for snv/indel";
-  const htry = (...args) => {
-    for (const s of args) {
-      const i2 = header.indexOf(s);
-      if (i2 != -1) return i2;
-    }
-    return -1;
-  };
-  let i = htry("annovar_gene", "annovar_sj_gene", "gene", "genename", "gene_symbol", "hugo_symbol");
-  if (i == -1) return "gene missing from header";
-  header[i] = "gene";
-  i = htry("annovar_aachange", "amino_acid_change", "annovar_sj_aachange", "aachange", "protein_change", "variant");
-  if (i == -1) return "amino_acid_change missing from header";
-  header[i] = "mname";
-  i = htry("annovar_class", "class", "mclass", "variant_class", "variant_classification", "annovar_sj_class");
-  if (i == -1) return "variant_class missing from header";
-  header[i] = "class";
-  i = htry("chromosome", "chr");
-  if (i == -1) return "chromosome missing from header";
-  header[i] = "chr";
-  i = htry("wu_hg19_pos", "start", "start_position", "chr_position", "position");
-  if (i == -1) return "start missing from header";
-  header[i] = "pos";
-  i = htry(
-    "annovar_isoform",
-    "mrna_accession",
-    "mrna accession",
-    "refseq_mrna_id",
-    "annovar_sj_filter_isoform",
-    "refseq",
-    "isoform"
-  );
-  if (i == -1) return "isoform missing from header";
-  header[i] = "isoform";
-  i = htry("sample", "sample_name", "tumor_sample_barcode");
-  if (i != -1) header[i] = "sample";
-  i = htry("patient", "donor", "target_case_id");
-  if (i != -1) header[i] = "patient";
-  i = htry("quantitative_measurements");
-  if (i != -1) header[i] = "qmset";
-  i = htry("mutant_reads_in_case", "mutant_in_tumor", "tumor_readcount_alt");
-  if (i != -1) header[i] = "maf_tumor_v1";
-  i = htry("total_reads_in_case", "total_in_tumor", "tumor_readcount_total");
-  if (i != -1) header[i] = "maf_tumor_v2";
-  i = htry("mutant_reads_in_control", "mutant_in_normal", "normal_readcount_alt");
-  if (i != -1) header[i] = "maf_normal_v1";
-  i = htry("total_reads_in_control", "total_in_normal", "normal_readcount_total");
-  if (i != -1) header[i] = "maf_normal_v2";
-  i = htry("cdna_change");
-  if (i != -1) header[i] = "cdna_change";
-  i = htry("sampletype", "sample type", "sample_type");
-  if (i != -1) header[i] = "sampletype";
-  i = htry("origin");
-  if (i != -1) header[i] = "origin";
-  i = htry("cancer", "disease", "diagnosis");
-  if (i != -1) header[i] = "disease";
-  flag2.snv.header = header;
-  flag2.snv.loaded = true;
-  return false;
-}
-function parseline2(linei, line, flag2) {
-  if (line == "" || line[0] == "#") return;
-  const lst = line.split("	");
-  const m = {};
-  for (let j = 0; j < flag2.snv.header.length; j++) {
-    if (lst[j] == void 0) break;
-    m[flag2.snv.header[j]] = lst[j];
-  }
-  if (!m.gene) {
-    flag2.snv.badlines.push([linei, "missing gene", lst]);
-    return;
-  }
-  if (m.gene.toUpperCase() == "UNKNOWN") {
-    flag2.snv.badlines.push([linei, "gene name is UNKNOWN", lst]);
-    return;
-  }
-  if (!m.isoform) {
-    flag2.snv.badlines.push([linei, "missing isoform", lst]);
-    return;
-  }
-  if (!m.mname) {
-    m.mname = m.cdna_change;
-    if (!m.mname) {
-      flag2.snv.badlines.push([linei, "missing amino acid change", lst]);
-      return;
-    }
-  } else {
-    if (m.mname.indexOf("p.") == 0) {
-      m.mname = m.mname.replace(/^p\./, "");
-    }
-  }
-  if (!m.class) {
-    flag2.snv.badlines.push([linei, "missing mutation class", lst]);
-    return;
-  }
-  let _c = flag2.mclasslabel2key[m.class.toUpperCase()];
-  if (_c) {
-    m.class = _c;
-  } else {
-    _c = mclasstester(m.class);
-    if (_c) {
-      m.class = _c;
-    } else {
-      flag2.snv.badlines.push([linei, "wrong mutation class: " + m.class, lst]);
-      return;
-    }
-  }
-  if (parsesample(m, flag2, linei, lst)) {
-    return;
-  }
-  if (!m.chr) {
-    flag2.snv.badlines.push([linei, "missing chromosome", lst]);
-    return;
-  }
-  if (m.chr.toLowerCase().indexOf("chr") != 0) {
-    m.chr = "chr" + m.chr;
-  }
-  if (!m.pos) {
-    flag2.snv.badlines.push([linei, "missing chromosome position", lst]);
-    return;
-  }
-  const v = Number.parseInt(m.pos);
-  if (Number.isNaN(v)) {
-    flag2.snv.badlines.push([linei, "invalid chromosome position", lst]);
-    return;
-  }
-  m.pos = v - 1;
-  if (m.maf_tumor_v2 != void 0 && m.maf_tumor_v1 != void 0) {
-    if (m.maf_tumor_v2 == "") {
-    } else {
-      const v1 = Number.parseInt(m.maf_tumor_v1), v2 = Number.parseInt(m.maf_tumor_v2);
-      if (Number.isNaN(v1) || Number.isNaN(v2)) {
-        flag2.snv.badlines.push([linei, "invalid maf_tumor mutant and/or total read count", lst]);
-        return;
-      }
-      m.maf_tumor = { f: v1 / v2, v1, v2 };
-    }
-    delete m.maf_tumor_v1;
-    delete m.maf_tumor_v2;
-  }
-  if (m.maf_normal_v1 != void 0 && m.maf_normal_v2 != void 0) {
-    if (m.maf_normal_v2 == "") {
-    } else {
-      const v1 = Number.parseInt(m.maf_normal_v1), v2 = Number.parseInt(m.maf_normal_v2);
-      if (Number.isNaN(v1) || Number.isNaN(v2)) {
-        flag2.snv.badlines.push([linei, "invalid maf_normal mutant and/or total read count", lst]);
-        return;
-      }
-      m.maf_normal = { f: v1 / v2, v1, v2 };
-    }
-    delete m.maf_normal_v1;
-    delete m.maf_normal_v2;
-  }
-  flag2.good++;
-  if (m.class == "M") {
-    flag2.snv.missense++;
-  } else if (m.class == "S") {
-    flag2.snv.silent++;
-  }
-  const n = flag2.geneToUpper ? m.gene.toUpperCase() : m.gene;
-  if (!flag2.data[n]) {
-    flag2.data[n] = [];
-  }
-  m.dt = dtsnvindel;
-  flag2.data[n].push(m);
-}
-
-// ../shared/utils/dist/src/bulk.svjson.js
-function parseheader3(line) {
-  const header = line.toLowerCase().split("	");
-  if (header.length <= 1) return "invalid file header for svjson";
-  const htry = (...lst) => {
-    for (const a of lst) {
-      const j = header.indexOf(a);
-      if (j != -1) return j;
-    }
-    return -1;
-  };
-  let i = htry("sample");
-  if (i != -1) header[i] = "sample";
-  i = htry("sampletype");
-  if (i != -1) header[i] = "sampletype";
-  i = htry("patient");
-  if (i != -1) header[i] = "patient";
-  i = htry("json", "jsontext");
-  if (i == -1) return ["json missing from header"];
-  header[i] = "jsontext";
-  return [null, header];
-}
-function parseline3(i, line, flag2, header) {
-  if (line == "" || line[0] == "#") return;
-  const lst = line.split("	");
-  const m = {};
-  const badlines = flag2.svjson.badlines;
-  for (let j = 0; j < header.length; j++) {
-    m[header[j]] = lst[j];
-  }
-  if (!m.jsontext) {
-    badlines.push([i, "missing jsontext", lst]);
-    return;
-  }
-  if (parsesample(m, flag2, i, lst)) {
-    return;
-  }
-  let json;
-  try {
-    json = JSON.parse(m.jsontext);
-  } catch (_) {
-    badlines.push([i, "invalid JSON text", lst]);
-    return;
-  }
-  if (Array.isArray(json)) {
-    for (const pair of json) {
-      if (pair.a && pair.a.name && pair.a.isoform) {
-        flag2.good++;
-        const m2 = {
-          dt: dtfusionrna,
-          class: mclassfusionrna,
-          isoform: pair.a.isoform,
-          mname: pair.b.name
-        };
-        for (const k in m) {
-          if (k != "jsontext") m2[k] = m[k];
-        }
-        m2.pairlst = duplicate(json);
-        const n = pair.a.name.toUpperCase();
-        if (!flag2.data[n]) {
-          flag2.data[n] = [];
-        }
-        flag2.data[n].push(m2);
-      }
-      if (pair.b && pair.b.name && pair.b.isoform) {
-        flag2.good++;
-        const m2 = {
-          dt: dtfusionrna,
-          class: mclassfusionrna,
-          isoform: pair.b.isoform,
-          mname: pair.a.name
-        };
-        for (const k in m) {
-          if (k != "jsontext") m2[k] = m[k];
-        }
-        m2.pairlst = duplicate(json);
-        const n = pair.b.name.toUpperCase();
-        if (!flag2.data[n]) {
-          flag2.data[n] = [];
-        }
-        flag2.data[n].push(m2);
-      }
-    }
-  } else {
-    json.dt = json.typecode;
-    delete json.typecode;
-    switch (json.dt) {
-      case dtitd:
-        json.class = mclassitd;
-        json.mname = "ITD";
-        break;
-      case dtnloss:
-        json.class = mclassnloss;
-        json.mname = "N-loss";
-        break;
-      case dtcloss:
-        json.class = mclasscloss;
-        json.mname = "C-loss";
-        break;
-      case dtdel:
-        json.class = mclassdel;
-        json.mname = "Del";
-        break;
-      case dtsv:
-        json.class = mclasssv;
-        json.mname = "SV";
-        break;
-      default:
-        badlines.push([i, "unknown datatype", lst]);
-        return;
-    }
-    if (!json.gene) {
-      badlines.push([i, "json.gene missing", lst]);
-      return;
-    }
-    flag2.good++;
-    for (const k in m) {
-      if (k != "jsontext") {
-        json[k] = m[k];
-      }
-    }
-    const n = flag2.geneToUpper ? json.gene.toUpperCase() : json.gene.toUpperCase();
-    if (!flag2.data[n]) {
-      flag2.data[n] = [];
-    }
-    flag2.data[n].push(json);
-  }
-}
-function duplicate(lst) {
-  const d = [];
-  for (const pair of lst) {
-    const p = { a: {}, b: {} };
-    for (const k in pair) {
-      if (k != "a" && k != "b") p[k] = pair[k];
-    }
-    for (const k in pair.a) {
-      p.a[k] = pair.a[k];
-    }
-    for (const k in pair.b) {
-      p.b[k] = pair.b[k];
-    }
-    d.push(p);
-  }
-  return d;
-}
-
-// ../shared/utils/dist/src/bulk.cnv.js
-function parseheader4(line, flag2) {
-  const header = line.toLowerCase().split("	");
-  if (header.length <= 1) return "invalid file header for CNV";
-  const htry = (...lst) => {
-    for (const i2 of lst) {
-      const j = header.indexOf(i2);
-      if (j != -1) return j;
-    }
-    return -1;
-  };
-  let i = htry("gene");
-  if (i == -1) return "gene missing from header";
-  header[i] = "gene";
-  i = htry("cnv");
-  if (i == -1) return "CNV missing from header";
-  header[i] = "cnv";
-  i = htry("sample", "sample_name", "tumor_sample_barcode");
-  if (i != -1) header[i] = "sample";
-  i = htry("patient", "donor", "target_case_id");
-  if (i != -1) header[i] = "patient";
-  i = htry("disease");
-  if (i != -1) header[i] = "disease";
-  i = htry("origin");
-  if (i != -1) header[i] = "origin";
-  i = htry("sampletype", "sample type", "sample_type");
-  if (i != -1) header[i] = "sampletype";
-  flag2.cnv.header = header;
-  flag2.cnv.loaded = true;
-  return false;
-}
-function parseline4(i, line, flag2) {
-  if (line == "" || line[0] == "#") return;
-  const lst = line.split("	");
-  const m = {};
-  for (let j = 0; j < flag2.cnv.header.length; j++) {
-    m[flag2.cnv.header[j]] = lst[j];
-  }
-  if (!m.gene) {
-    flag2.cnv.badlines.push([i, "missing gene", lst]);
-    return;
-  }
-  if (!m.cnv) {
-    flag2.cnv.badlines.push([i, "missing cnv value", lst]);
-    return;
-  }
-  const value = m.cnv.toLowerCase();
-  switch (value) {
-    case "amplification":
-    case "gain":
-      m.class = mclasscnvgain;
-      break;
-    case "deletion":
-    case "loss":
-      m.class = mclasscnvloss;
-      break;
-    case "loh":
-      m.class = mclasscnvloh;
-      break;
-    default:
-      flag2.cnv.badlines.push([i, "invalid cnv value: " + m.cnv, lst]);
-      m.class = null;
-  }
-  if (!m.class) {
-    return;
-  }
-  if (parsesample(m, flag2, i, lst)) {
-    return;
-  }
-  m.dt = dtcnv;
-  flag2.good++;
-  const n = flag2.geneToUpper ? m.gene.toUpperCase() : m.gene;
-  if (!(n in flag2.data)) {
-    flag2.data[n] = [];
-  }
-  flag2.data[n].push(m);
-}
-
-// ../shared/utils/dist/src/bulk.itd.js
-function parseheader5(line, flag2) {
-  const header = line.toLowerCase().split("	");
-  if (header.length <= 1) return "invalid header line for ITD";
-  const htry = (...lst) => {
-    for (const i2 of lst) {
-      const j = header.indexOf(i2);
-      if (j != -1) return j;
-    }
-    return -1;
-  };
-  let i = htry("gene");
-  if (i == -1) return "gene missing from header";
-  header[i] = "gene";
-  i = htry(
-    "annovar_isoform",
-    "mrna_accession",
-    "mrna accession",
-    "refseq_mrna_id",
-    "annovar_sj_filter_isoform",
-    "refseq",
-    "isoform"
-  );
-  if (i == -1) return "isoform missing from header";
-  header[i] = "isoform";
-  i = htry("rnaposition");
-  if (i != -1) {
-    header[i] = "rnaposition";
-    i = htry("rnaduplength");
-    if (i == -1) return "rnaduplength is required when rnaposition is present";
-    header[i] = "rnaduplength";
-  }
-  i = htry("chromosome", "chr");
-  if (i != -1) {
-    header[i] = "chr";
-    i = htry("chr_start");
-    if (i == -1) return "chr_start is required when chr is present";
-    header[i] = "chrpos1";
-    i = htry("chr_stop");
-    if (i == -1) return "chr_stop is required when chr is present";
-    header[i] = "chrpos2";
-  }
-  i = htry("sample", "sample_name", "tumor_sample_barcode");
-  if (i != -1) header[i] = "sample";
-  i = htry("patient", "donor", "target_case_id");
-  if (i != -1) header[i] = "patient";
-  i = htry("disease");
-  if (i != -1) header[i] = "disease";
-  i = htry("origin");
-  if (i != -1) header[i] = "origin";
-  i = htry("sampletype", "sample type", "sample_type");
-  if (i != -1) header[i] = "sampletype";
-  flag2.itd.header = header;
-  flag2.itd.loaded = true;
-  return false;
-}
-function parseline5(i, line, flag2) {
-  if (line == "" || line[0] == "#") return;
-  const lst = line.split("	");
-  const m = {};
-  for (let j = 0; j < flag2.itd.header.length; j++) {
-    if (lst[j] == void 0) break;
-    m[flag2.itd.header[j]] = lst[j];
-  }
-  if (!m.gene) {
-    flag2.itd.badlines.push([i, "missing gene", lst]);
-    return;
-  }
-  if (m.rnaposition) {
-    let v = Number.parseInt(m.rnaposition);
-    if (Number.isNaN(v) || v < 0) {
-      flag2.itd.badlines.push([i, "invalid rnaPosition value", lst]);
-      return;
-    }
-    m.rnaposition = v;
-    if (!m.rnaduplength) {
-      flag2.itd.badlines.push([i, "missing rnaDuplength value", lst]);
-      return;
-    }
-    v = Number.parseInt(m.rnaduplength);
-    if (Number.isNaN(v) || v < 0) {
-      flag2.itd.badlines.push([i, "invalid rnaDuplength value", lst]);
-      return;
-    }
-    m.rnaduplength = v;
-  }
-  if (m.chr) {
-    let v = Number.parseInt(m.chrpos1);
-    if (Number.isNaN(v) || v < 0) {
-      flag2.itd.badlines.push([i, "invalid chr_start value", lst]);
-      return;
-    }
-    m.chrpos1 = v;
-    v = Number.parseInt(m.chrpos2);
-    if (Number.isNaN(v) || v < 0) {
-      flag2.itd.badlines.push([i, "invalid chr_stop value", lst]);
-      return;
-    }
-    m.chrpos2 = v;
-  }
-  if (parsesample(m, flag2, i, lst)) {
-    return;
-  }
-  m.dt = dtitd;
-  m.class = mclassitd;
-  m.mname = "ITD";
-  flag2.good++;
-  const n = flag2.geneToUpper ? m.gene.toUpperCase() : m.gene;
-  if (!(n in flag2.data)) {
-    flag2.data[n] = [];
-  }
-  flag2.data[n].push(m);
-}
-
-// ../shared/utils/dist/src/bulk.del.js
-function parseheader6(line, flag2) {
-  const header = line.toLowerCase().split("	");
-  if (header.length <= 1) return "invalid header line for intragenic deletion";
-  const htry = (...lst) => {
-    for (const i2 of lst) {
-      const j = header.indexOf(i2);
-      if (j != -1) return j;
-    }
-    return -1;
-  };
-  let i = htry("gene");
-  if (i == -1) return "gene missing from header";
-  header[i] = "gene";
-  i = htry(
-    "annovar_isoform",
-    "mrna_accession",
-    "mrna accession",
-    "refseq_mrna_id",
-    "annovar_sj_filter_isoform",
-    "refseq",
-    "isoform"
-  );
-  if (i == -1) return "isoform missing from header";
-  header[i] = "isoform";
-  i = htry("rnaposition");
-  if (i != -1) {
-    header[i] = "rnaposition";
-    i = htry("rnadellength");
-    if (i == -1) return "rnadellength is required when rnaPosition is used";
-    header[i] = "rnadellength";
-  }
-  i = htry("chromosome", "chr");
-  if (i != -1) {
-    header[i] = "chr";
-    i = htry("chr_start");
-    if (i == -1) return "chr_start is required when chr is used";
-    header[i] = "chrpos1";
-    i = htry("chr_stop");
-    if (i == -1) return "chr_stop is required when chr is used";
-    header[i] = "chrpos2";
-  }
-  i = htry("sample", "sample_name", "tumor_sample_barcode");
-  if (i != -1) header[i] = "sample";
-  i = htry("patient", "donor", "target_case_id");
-  if (i != -1) header[i] = "patient";
-  i = htry("disease");
-  if (i != -1) header[i] = "disease";
-  i = htry("origin");
-  if (i != -1) header[i] = "origin";
-  i = htry("sampletype", "sample type", "sample_type");
-  if (i != -1) header[i] = "sampletype";
-  flag2.del.header = header;
-  flag2.del.loaded = true;
-  return false;
-}
-function parseline6(i, line, flag2) {
-  if (line == "" || line[0] == "#") return;
-  const lst = line.split("	");
-  const m = {};
-  for (let j = 0; j < flag2.del.header.length; j++) {
-    if (lst[j] == void 0) break;
-    m[flag2.del.header[j]] = lst[j];
-  }
-  if (!m.gene) {
-    flag2.del.badlines.push([i, "missing gene", lst]);
-    return;
-  }
-  if (m.rnaposition) {
-    let v = Number.parseInt(m.rnaposition);
-    if (Number.isNaN(v) || v < 0) {
-      flag2.del.badlines.push([i, "invalid rnaPosition value", lst]);
-      return;
-    }
-    m.rnaposition = v;
-    if (!m.rnadellength) {
-      flag2.del.badlines.push([i, "missing rnaDellength value", lst]);
-      return;
-    }
-    v = Number.parseInt(m.rnadellength);
-    if (Number.isNaN(v) || v < 0) {
-      flag2.del.badlines.push([i, "invalid rnaDellength value", lst]);
-      return;
-    }
-    m.rnadellength = v;
-  }
-  if (m.chr) {
-    let v = Number.parseInt(m.chrpos1);
-    if (Number.isNaN(v) || v < 0) {
-      flag2.del.badlines.push([i, "invalid chr_start value", lst]);
-      return;
-    }
-    m.chrpos1 = v;
-    v = Number.parseInt(m.chrpos2);
-    if (Number.isNaN(v) || v < 0) {
-      flag2.del.badlines.push([i, "invalid chr_stop value", lst]);
-      return;
-    }
-    m.chrpos2 = v;
-  }
-  if (parsesample(m, flag2, i, lst)) {
-    return;
-  }
-  m.dt = dtdel;
-  m.class = mclassdel;
-  m.mname = "DEL";
-  flag2.good++;
-  const n = flag2.geneToUpper ? m.gene.toUpperCase() : m.gene;
-  if (!(n in flag2.data)) {
-    flag2.data[n] = [];
-  }
-  flag2.data[n].push(m);
-}
-
-// ../shared/utils/dist/src/bulk.trunc.js
-function parseheader7(line, flag2) {
-  const header = line.toLowerCase().split("	");
-  if (header.length <= 1) return "invalid header line for truncation";
-  const htry = (...lst) => {
-    for (const e of lst) {
-      const j = header.indexOf(e);
-      if (j != -1) return j;
-    }
-    return -1;
-  };
-  let i = htry("gene");
-  if (i == -1) return "gene missing from header";
-  header[i] = "gene";
-  i = htry(
-    "annovar_isoform",
-    "mrna_accession",
-    "mrna accession",
-    "refseq_mrna_id",
-    "annovar_sj_filter_isoform",
-    "refseq",
-    "isoform"
-  );
-  if (i == -1) return "isoform missing from header";
-  header[i] = "isoform";
-  let hasrnapos = false;
-  i = htry("rnaposition");
-  if (i != -1) {
-    header[i] = "rnaposition";
-    hasrnapos = true;
-  }
-  i = htry("losstype");
-  if (i == -1) return "lossType missing from header";
-  header[i] = "losstype";
-  let hasgenomic = false;
-  i = htry("chromosome", "chr");
-  if (i != -1) {
-    header[i] = "chr";
-    i = htry("start", "start_position", "wu_hg19_pos", "chr_position", "position");
-    if (i == -1) {
-      return "genomic position missing from header";
-    }
-    header[i] = "pos";
-    hasgenomic = true;
-  }
-  if (!hasrnapos && !hasgenomic) {
-    return "neither rnaposition nor genomic position is given";
-  }
-  i = htry("sample", "sample_name", "tumor_sample_barcode");
-  if (i != -1) header[i] = "sample";
-  i = htry("patient", "donor", "target_case_id");
-  if (i != -1) header[i] = "patient";
-  i = htry("disease");
-  if (i != -1) header[i] = "disease";
-  i = htry("origin");
-  if (i != -1) header[i] = "origin";
-  i = htry("sampletype", "sample type", "sample_type");
-  if (i != -1) header[i] = "sampletype";
-  flag2.truncation.header = header;
-  flag2.truncation.loaded = true;
-  return false;
-}
-function parseline7(i, line, flag2) {
-  if (line == "" || line[0] == "#") return;
-  const lst = line.split("	");
-  const m = {};
-  for (let j = 0; j < flag2.truncation.header.length; j++) {
-    m[flag2.truncation.header[j]] = lst[j];
-  }
-  if (!m.gene) {
-    flag2.truncation.badlines.push([i, "missing gene", lst]);
-    return;
-  }
-  if (m.rnaposition) {
-    const v = Number.parseInt(m.rnaposition);
-    if (Number.isNaN(v) || v < 0) {
-      flag2.truncation.badlines.push([i, "invalid rnaPosition value", lst]);
-      return;
-    }
-    m.rnaposition = v;
-  }
-  if (m.pos) {
-    const v = Number.parseInt(m.pos);
-    if (Number.isNaN(v) || v < 0) {
-      flag2.truncation.badlines.push([i, "invalid genomic position", lst]);
-      return;
-    }
-    m.pos = v;
-  }
-  if (!m.losstype) {
-    flag2.truncation.badlines.push([i, "missing lossType value", lst]);
-    return;
-  }
-  if (m.losstype != "n" && m.losstype != "c") {
-    flag2.truncation.badlines.push([i, 'lossType value not "n" or "c"', lst]);
-    return;
-  }
-  if (parsesample(m, flag2, i, lst)) {
-    return;
-  }
-  if (m.losstype == "n") {
-    m.dt = dtnloss;
-    m.class = mclassnloss;
-    m.mname = "N-loss";
-  } else {
-    m.dt = dtcloss;
-    m.class = mclasscloss;
-    m.mname = "C-loss";
-  }
-  flag2.good++;
-  const n = flag2.geneToUpper ? m.gene.toUpperCase() : m.gene;
-  if (!(n in flag2.data)) {
-    flag2.data[n] = [];
-  }
-  flag2.data[n].push(m);
-}
-
-// src/bulk.project.js
-var schemaNames = ["heatmapJSON", "piebarJSON", "survivalJSON", "discoJSON", "riverJSON"];
-var typeIndex = {
-  snvindel: 0,
-  si: 0,
-  sv: 1,
-  fusion: 2,
-  itd: 3,
-  deletion: 4,
-  truncation: 5,
-  cnv: 6
-};
-var urlProjectLoaded = false;
-var ProjectHandler = class {
-  /*
-  		Create a handler for multiple uploaded or fetched
-  		files in a project
-  
-  		bt = {
-  			flag: closured flag inside bulkui.bulkui,
-  			bulkin: bulkui.bulkin,
-  			content2flag: bulkui.content2flag,
-  			flag2tp: closured flat2tp,
-  			filediv: (optional) d3-wrapped container for file-input
-  		}
-  	*/
-  constructor(bt) {
-    this.bt = bt;
-    this.err = this.errHandler();
-    if (!urlProjectLoaded) {
-      const params = getParams();
-      if (params.project) {
-        this.getData(params.project);
-        urlProjectLoaded = true;
-      }
-    }
-    if (bt.filediv) {
-      this.projectByInput(bt.filediv);
-    }
-  }
-  /*
-  		Process data files sequentially for rendering
-  		into a TP div
-  
-  		data = {
-  			schemas: object {
-  				heatmapJSON (optional),
-  				piebarJSON (optional),
-  				survivalJSON (optional)
-  			},
-  			files: [] array of {
-  				name: string
-  				typeL one of the typeIndex values 
-  				content: string
-  			}
-  		}
-  	*/
-  processData(data) {
-    const file = data.files.pop();
-    const i = data.expectedFileNames.indexOf(file.name);
-    if (i == -1) {
-      if (data.files.length)
-        setTimeout(() => {
-          this.processData(data);
-        }, 1);
-      return;
-    }
-    data.expectedFileNames.splice(i, 1);
-    this.cohort = {
-      name: "project",
-      genome: this.bt.genomes[this.bt.gselect.options[this.bt.gselect.selectedIndex].innerHTML]
-    };
-    if (!this.flag) {
-      this.flag = this.bt.init_bulk_flag(this.cohort.genome);
-    }
-    const error = this.bt.content2flag(file.content, file.type, this.flag);
-    if (error) {
-      this.err(error);
-      this.processData(data);
-    } else if (!data.files.length) {
-      if (data.expectedFileNames.length) {
-        this.err('These referenced files were not found: "' + data.expectedFileNames.join('", "') + '".');
-      }
-      this.bt.flag2tp(this.flag, { name: "project" }, Object.assign(this.cohort, data.schema), this.ds);
-      return;
-    } else {
-      if (!this.ds) {
-        for (const k in this.cohort.dsset) {
-          this.ds = this.cohort.dsset[k];
-          break;
-        }
-      }
-      const error1 = this.bt.bulkin(
-        {
-          flag: this.flag,
-          cohort: this.cohort,
-          flag2thisds: this.ds,
-          filename: "project"
-        },
-        () => {
-          this.processData(data);
-        }
-      );
-      if (error1) {
-        this.err("Error with " + file.name + ": " + error1);
-        return;
-      }
-      if (this.flag.good === 0) {
-        this.err(file.name + ": no data loaded");
-        return;
-      }
-    }
-  }
-  getData(project) {
-    const [projectname, _refname] = project.split("/");
-    const refname = _refname && _refname.trim() ? _refname.trim() : "ref.txt";
-    this.gettext("/data/projects/" + projectname + "/" + refname, (text) => {
-      const fileNameToType = {};
-      const nameToSchemaType = {};
-      const data = { schema: {}, files: [], expectedFileNames: [] };
-      let schemaFileName = "";
-      let numProcessedFiles = 0;
-      let numFiles = 0;
-      text.trim().split("\n").forEach((line) => {
-        const [type, filename] = line.trim().split("	");
-        if (schemaNames.includes(type)) {
-          nameToSchemaType[filename] = type;
-          numFiles += 1;
-        } else if (!typeIndex[type] && typeIndex[type] !== 0) {
-          this.err("Unrecognized type " + type + " for file " + filename + " in reference.txt.");
-        } else {
-          fileNameToType[filename] = typeIndex[type];
-          numFiles += 1;
-        }
-      });
-      data.expectedFileNames = Object.keys(fileNameToType);
-      const tracker = this.getTracker(numFiles, () => this.processData(data));
-      Object.keys(nameToSchemaType).forEach((filename) => {
-        this.getjson("/data/projects/" + projectname + "/" + filename, (json) => {
-          data.schema[nameToSchemaType[filename]] = json;
-          tracker();
-        });
-      });
-      Object.keys(fileNameToType).forEach((filename) => {
-        this.gettext("/data/projects/" + projectname + "/" + filename, (text2) => {
-          data.files.push({
-            name: filename,
-            type: fileNameToType[filename],
-            content: text2
-          });
-          tracker();
-        });
-      });
-    });
-  }
-  gettext(url, callback) {
-    fetch(url).then((response) => {
-      if (response.ok) return response.text();
-      else this.err("File request error: " + url);
-    }).then(callback).catch((error) => this.err("File request error: " + url + " " + error));
-  }
-  getjson(url, callback) {
-    fetch(url).then((response) => {
-      if (response.ok) return response.json();
-      else this.err("Network error for " + url);
-    }).then(callback).catch((error) => this.err("file request error: " + url + " " + error));
-  }
-  getTracker(numFiles, callback) {
-    let numProcessedFiles = 0;
-    return function tracker() {
-      numProcessedFiles += 1;
-      if (numProcessedFiles == numFiles) {
-        callback();
-      }
-    };
-  }
-  projectByInput(filediv) {
-    this.tp = null;
-    const advancedDiv = filediv.append("div");
-    advancedDiv.append("span").html("Project: reference &nbsp;");
-    this.refNameInput = advancedDiv.append("input").attr("type", "text").property("value", "ref.txt").style("margin-right", "20px").style("padding-left", "7px");
-    const buttlabel = advancedDiv.append("label").attr("for", "sja-pp-bulk-ui-project-btn").attr("class", "sja_btn").style("padding", "3px 5px").html("Choose folder");
-    const butt = advancedDiv.append("input").attr("type", "file").attr("id", "sja-pp-bulk-ui-project-btn").property("multiple", true).property("webkitdirectory", true).property("directory", true).on("change", (event) => this.readFiles(event));
-    advancedDiv.append("div").style("margin", "10px 10px 10px 0").html(`<a href="https://docs.google.com/document/d/1wlfGzyhxFYtWu9Fyf3FK7pgvS3rVb9_vrfYUBUOUrw4/edit?usp=sharing" target="new">Project user guide</a> | 
-			<a href='https://proteinpaint.stjude.org/ppdemo/projects/target-tall-project/ref.txt' target=_blank>Example project reference file</a>`);
-    advancedDiv.append("div").style("margin", "20px").style("width", "100%").html("-- OR --");
-  }
-  /* to be used as a file input (FileList) handler */
-  readFiles(event) {
-    const self = this;
-    const refFileName = self.refNameInput.property("value");
-    const files = Array.from(event.target.files);
-    const ref = files.filter((f) => f.name == refFileName)[0];
-    if (!ref) {
-      self.err("Missing reference file='" + refFileName + "'.");
-      return;
-    }
-    const fileNameToType = {};
-    const nameToSchemaType = {};
-    const data = { schema: {}, files: [], expectedFileNames: [] };
-    const reader = new FileReader();
-    let schemaFileName = "";
-    let numProcessedFiles = 0;
-    reader.onload = (event2) => {
-      event2.target.result.trim().split("\n").forEach((line) => {
-        const [type, filename] = line.trim().split("	");
-        if (schemaNames.includes(type)) {
-          nameToSchemaType[filename] = type;
-        } else if (!typeIndex[type] && typeIndex[type] !== 0) {
-          self.err("Unrecognized type " + type + " for file " + filename + " in reference.txt.");
-        } else {
-          fileNameToType[filename] = typeIndex[type];
-        }
-      });
-      data.expectedFileNames = Object.keys(fileNameToType);
-      const schemaFiles = files.filter((file) => file.name in nameToSchemaType);
-      let numProcessedSchemas = 0;
-      if (!schemaFiles.length) {
-        files.forEach(processFile);
-      } else {
-        schemaFiles.forEach((file) => {
-          const reader2 = new FileReader();
-          reader2.onload = (event3) => {
-            const schema = JSON.parse(event3.target.result);
-            numProcessedSchemas += 1;
-            if (!schema) {
-              self.err('Unable to parse schema file="' + file.name + '".');
-            } else {
-              data.schema[nameToSchemaType[file.name]] = schema;
-            }
-            if (numProcessedSchemas == schemaFiles.length) {
-              files.forEach(processFile);
-            }
-          };
-          reader2.onerror = () => {
-            self.err("Error reading schema.txt.");
-          };
-          reader2.readAsText(file, "utf8");
-        });
-      }
-      function processFile(file) {
-        if (!data.expectedFileNames.includes(file.name)) {
-          numProcessedFiles += 1;
-          return;
-        }
-        if (!file) {
-          self.err("Error reading file.");
-          numProcessedFiles += 1;
-          return;
-        }
-        if (file.size == 0) {
-          self.err("Wrong file: " + file.name);
-          numProcessedFiles += 1;
-          return;
-        }
-        if (!fileNameToType[file.name] && fileNameToType[file.name] !== 0 && file.name != schemaFileName) {
-          self.err("Missing or invalid type assigned to file " + file.name + ".");
-          numProcessedFiles += 1;
-          return;
-        }
-        const reader2 = new FileReader();
-        reader2.onload = (event3) => {
-          numProcessedFiles += 1;
-          data.files.push({
-            name: file.name,
-            type: fileNameToType[file.name],
-            content: event3.target.result
-          });
-          if (numProcessedFiles == files.length) {
-            self.processData(data);
-          }
-        };
-        reader2.onerror = () => {
-          numProcessedFiles += 1;
-          self.err("Error reading file " + file.name);
-          if (numProcessedFiles == files.length) {
-            self.processData(data);
-          }
-        };
-        reader2.readAsText(file, "utf8");
-      }
-    };
-    reader.onerror = () => {
-      self.err("Error reading reference.txt.");
-    };
-    reader.readAsText(ref, "utf8");
-  }
-  // function to track and display accumulated error messages
-  errHandler() {
-    const errdiv = select_default("body").append("div");
-    let mssg = "";
-    return function(m) {
-      if (!m) return;
-      sayerror(errdiv, m);
-    };
-  }
-};
-function getParams() {
-  const params = {};
-  window.location.search.substr(1).split("&").forEach((kv) => {
-    const [key, value] = kv.split("=");
-    params[key] = value;
-  });
-  return params;
-}
-
-// src/bulk.ui.js
-function bulkui(x, y, genomes, hostURL, holder, header) {
-  let pane, inputdiv, gselect, filediv, saydiv, visualdiv;
-  if (holder !== void 0) [inputdiv, gselect, filediv, saydiv, visualdiv] = renderSandboxFormDiv(holder, genomes);
-  else {
-    ;
-    [pane, inputdiv, gselect, filediv, saydiv, visualdiv] = newpane3(x, y, genomes);
-    pane.header.text("Load mutation from text files");
-  }
-  inputdiv.append("div").style("margin", "20px 0px").style("color", "#858585").html(`
-	<p>Choose one file and upload to initiate the display panel.<br>From there you can add additional files.</p>
-	<div>Supported data types:</div>
-	<ul>
-	  <li>SNV and indel</li>
-	  <ul>
-	    <li><a href=https://drive.google.com/open?id=1OJ9aXq2_-a3BfIQdKLYCYzrJRTpu4_9i3gephTY-Z38 target=_blank>Format</a>,
-	        <a href=https://proteinpaint.stjude.org/ppdemo/hg19/heatmap/exampleFiles/example.snvindel.txt target=_blank>example file</a></li>
-	  </ul>
-	  <li>SV or fusion transcript</li>
-	  <ul>
-	    <li><a href=https://drive.google.com/open?id=1klDZ0MHVkQTW2-lCu_AvpRE4_FcbhdB-yI17wNdPaOM target=_blank>Tabular format</a>,
-	        <a href=https://proteinpaint.stjude.org/ppdemo/hg19/heatmap/exampleFiles/example.svfusion.txt target=_blank>example file</a>
-		</li>
-		<li>JSON-format, to come</li>
-	  </ul>
-	  <li>CNV, gene-level</li>
-	  <ul>
-	    <li><a href=https://drive.google.com/open?id=1WHptqOWNf96V0bYEDpj-EsKZGYnbBNc9aQIrhzdEJaU target=_blank>Format</a>, 
-	        <a href=https://proteinpaint.stjude.org/ppdemo/hg19/heatmap/exampleFiles/example.cnv.txt target=_blank>example file</a>
-		</li>
-	  </ul>
-	  <li>ITD</li>
-	  <ul>
-	  	<li>Internal tandem duplication, in-frame</li>
-	    <li><a href=https://drive.google.com/open?id=1Bh9awBsraoHbV8iWXv_3oDeXMsjIAHaOKHr973IJyZc target=_blank>Format</a>, 
-	        <a href=https://proteinpaint.stjude.org/ppdemo/hg19/heatmap/exampleFiles/example.itd.txt target=_blank>example file</a>
-		</li>
-	  </ul>
-	  <li>Intragenic deletion, in-frame</li>
-	  <ul>
-	    <li><a href=https://drive.google.com/open?id=1tWbf3rg3BmVIZPGGPk023P0aBkDw_ry5XuZLGyGodyg target=_blank>Format</a>, 
-	        <a href=https://proteinpaint.stjude.org/ppdemo/hg19/heatmap/exampleFiles/example.deletion.txt target=_blank>example file</a>
-		</li>
-	  </ul>
-	  <li>Truncation</li>
-	  <ul>
-	  	<li>Either N-terminus loss or C-terminus loss</li>
-	    <li><a href=https://drive.google.com/open?id=1P1g-Y8r30pSKfan1BhYZcsUtSk7wRb4plaO1S-JCJr4 target=_blank>Format</a>, 
-	        <a href=https://proteinpaint.stjude.org/ppdemo/hg19/heatmap/exampleFiles/example.truncation.txt target=_blank>example file</a>
-		</li>
-	  </ul>
-	</ul>`);
-  const fileui = () => {
-    filediv.selectAll("*").remove();
-    new ProjectHandler({
-      bulkin,
-      genomes,
-      gselect,
-      content2flag,
-      flag2tp,
-      filediv,
-      init_bulk_flag
-    });
-    filediv.append("span").html("Select data type&nbsp;");
-    const typeselect = filetypeselect(filediv).style("margin-right", "20px");
-    const butt = filediv.append("input").attr("type", "file").on("change", (event) => {
-      const flag2 = init_bulk_flag(genomes[gselect.options[gselect.selectedIndex].innerHTML]);
-      flag2.geneToUpper = geneToUpper.property("checked");
-      saydiv.text("");
-      const file = event.target.files[0];
-      if (!file) {
-        fileui();
-        return;
-      }
-      if (file.size == 0) {
-        saydiv.text("Wrong file: " + file.name);
-        fileui();
-        return;
-      }
-      const reader = new FileReader();
-      reader.onload = (event2) => {
-        const error = content2flag(event2.target.result, typeselect.node().selectedIndex, flag2);
-        if (error) {
-          saydiv.text("Error: " + error);
-          fileui();
-          return;
-        }
-        flag2tp(flag2, file);
-      };
-      reader.onerror = function() {
-        saydiv.text("Error reading file " + file.name);
-        fileui();
-        return;
-      };
-      saydiv.text("Parsing file " + file.name + " ...");
-      reader.readAsText(file, "utf8");
-    });
-    setTimeout(() => butt.node().focus(), 1100);
-  };
-  fileui();
-  filediv.append("span").html("<br/>Convert gene name to uppercase &nbsp;");
-  const geneToUpper = filediv.append("span").append("input").attr("type", "checkbox").property("checked", true);
-  function flag2tp(flag2, file, _cohort = null, ds = null) {
-    if (typeof flag2 == "string") {
-      saydiv.text(flag2);
-      fileui();
-      return;
-    }
-    saydiv.text("");
-    fileui();
-    const cohort = _cohort ? _cohort : Object.assign({
-      genome: flag2.genome,
-      name: file.name
-    });
-    const err2 = bulkin({
-      flag: flag2,
-      filename: file.name,
-      cohort,
-      flag2thisds: ds
-    });
-    if (err2) {
-      saydiv.text("Error with " + file.name + ": " + err2);
-      return;
-    }
-    if (flag2.good == 0) {
-      saydiv.text("No mutations can be loaded");
-      return;
-    }
-    let visual_holder;
-    if (pane) {
-      disappear(pane.pane);
-      const pane2 = newpane({ x: 100, y: 100, toshrink: true });
-      pane2.header.html('<span style="opacity:.5">FILE</span> ' + file.name);
-      visual_holder = pane2.body;
-    }
-    if (holder !== void 0) {
-      visual_holder = visualdiv.append("div").html('<span style="opacity:.5">FILE</span> ' + file.name);
-    }
-    inputdiv.selectAll("*").remove();
-    import("./tp.ui-KBFYUSWS.js").then((tpui) => {
-      tpui.default(cohort, visual_holder, hostURL);
-    });
-    return cohort;
-  }
-  return function content2flag2tp(file, type) {
-    const error = content2flag(file.content, type, flag);
-    if (error) {
-      saydiv.text("Error: " + error);
-      fileui();
-      return;
-    }
-    flag2tp(flag, file);
-  };
-}
-function content2flag(text, type, flag2) {
-  if (!flag2) return "should not happen!";
-  let err2;
-  switch (type) {
-    case 0:
-      err2 = parse_snvindel(text, flag2);
-      if (err2) return err2;
-      break;
-    case 1:
-      err2 = parse_sv(text, flag2, true);
-      if (err2) return err2;
-      break;
-    case 2:
-      err2 = parse_sv(text, flag2, false);
-      if (err2) return err2;
-      break;
-    case 3:
-      err2 = parse_itd(text, flag2);
-      if (err2) return err2;
-      break;
-    case 4:
-      err2 = parse_del(text, flag2);
-      if (err2) return err2;
-      break;
-    case 5:
-      err2 = parse_trunc(text, flag2);
-      if (err2) return err2;
-      break;
-    case 6:
-      err2 = parse_cnv(text, flag2);
-      if (err2) return err2;
-      break;
-    default:
-      return "unknown option array index from file type <select>: " + type;
-  }
-}
-function bulkin(p, callback = null) {
-  const flag2 = p.flag;
-  const cohort = p.cohort;
-  if (!cohort.p2st) {
-    cohort.p2st = {};
-  }
-  if (!cohort.dsset) {
-    cohort.dsset = {};
-  }
-  if (!cohort.assaylst) {
-    cohort.assaylst = [];
-  }
-  if (flag2.variantgene) {
-    if (cohort.variantgene) {
-      return "variantgene already set for this cohort";
-    }
-    cohort.variantgene = flag2.variantgene;
-  }
-  if (flag2.snv.badlines.length > 0) {
-    bulk_badline(flag2.snv.header, flag2.snv.badlines);
-  }
-  if (flag2.fusion.badlines.length > 0) {
-    bulk_badline(flag2.fusion.header, flag2.fusion.badlines);
-  }
-  if (flag2.sv.badlines.length > 0) {
-    bulk_badline(flag2.sv.header, flag2.sv.badlines);
-  }
-  if (flag2.cnv.badlines.length > 0) {
-    bulk_badline(flag2.cnv.header, flag2.cnv.badlines);
-  }
-  if (flag2.itd.badlines.length > 0) {
-    bulk_badline(flag2.itd.header, flag2.itd.badlines);
-  }
-  if (flag2.del.badlines.length > 0) {
-    bulk_badline(flag2.del.header, flag2.del.badlines);
-  }
-  if (flag2.truncation.badlines.length > 0) {
-    bulk_badline(flag2.truncation.header, flag2.truncation.badlines);
-  }
-  if (flag2.good == 0) {
-    return false;
-  }
-  const tmp = {};
-  let hastumormaf = false;
-  if (flag2.snv.loaded) {
-    for (const i of flag2.snv.header) {
-      tmp[i] = 1;
-    }
-    if ("maf_tumor_v1" in tmp && "maf_tumor_v2" in tmp) {
-      hastumormaf = true;
-    }
-  }
-  if (flag2.cnv.loaded) {
-    for (const i of flag2.cnv.header) {
-      tmp[i] = 1;
-    }
-  }
-  if (flag2.fusion.loaded) {
-    for (const i of flag2.fusion.header) {
-      tmp[i] = 1;
-    }
-  }
-  if (flag2.sv.loaded) {
-    for (const i of flag2.sv.header) {
-      tmp[i] = 1;
-    }
-  }
-  if (flag2.itd.loaded) {
-    for (const i of flag2.itd.header) {
-      tmp[i] = 1;
-    }
-  }
-  if (flag2.del.loaded) {
-    for (const i of flag2.del.header) {
-      tmp[i] = 1;
-    }
-  }
-  if (flag2.truncation.loaded) {
-    for (const i of flag2.truncation.header) {
-      tmp[i] = 1;
-    }
-  }
-  const hassample = "sample" in tmp || "patient" in tmp;
-  const hasdisease = "disease" in tmp;
-  const hasst = "sampletype" in tmp;
-  let dsc;
-  if (p.flag2thisds) {
-    dsc = p.flag2thisds;
-    if (hassample && !dsc.hassample) {
-      return '"sample" column found in new data but not in existing data';
-    }
-    if (!hassample && dsc.hassample) {
-      return '"sample" column found in existing data but not in new data';
-    }
-    if (hasdisease && !dsc.hasdisease) {
-      return '"disease" column found in new data but not in existing data';
-    }
-    if (!hasdisease && dsc.hasdisease) {
-      return '"disease" column found in existing data but not in new data';
-    }
-    if (hasst && !dsc.hasst) {
-      return '"sampletype" column found in new data but not in existing data';
-    }
-    if (!hasst && dsc.hasst) {
-      return '"sampletype" column found in existing data but not in new data';
-    }
-    for (const genename in flag2.data) {
-      const lst = dsc.bulkdata[genename];
-      if (lst) {
-        dsc.bulkdata[genename] = lst.concat(flag2.data[genename]);
-      } else {
-        dsc.bulkdata[genename] = flag2.data[genename];
-      }
-    }
-  } else {
-    let dsname = p.filename + (flag2.tpsetname ? "_" + flag2.tpsetname : "");
-    if (dsname in flag2.genome.datasets) {
-      let j = 1;
-      let n2 = dsname + " " + j;
-      while (n2 in flag2.genome.datasets) {
-        j++;
-        n2 = dsname + " " + j;
-      }
-      dsname = n2;
-    }
-    dsc = {
-      label: dsname,
-      bulkdata: flag2.data,
-      // official dataset don't have this
-      hassample,
-      hasdisease,
-      hastumormaf,
-      hasst,
-      genome: cohort.genome,
-      import: {},
-      imported: {},
-      importsilent: flag2.snv.silent == 0 ? false : flag2.snv.missense / flag2.snv.silent >= 5 ? false : true
-    };
-    flag2.genome.datasets[dsname] = dsc;
-    cohort.dsset[dsname] = dsc;
-    if (cohort.dbexpression) {
-      if (cohort.dbexpression.tidy) {
-        try {
-          cohort.dbexpression.tidy = new Function(...cohort.dbexpression.tidy);
-        } catch (e) {
-          err("invalid JavaScript for dbexpression.tidy");
-          delete cohort.dbexpression;
-        }
-      }
-      dsc.dbexpression = cohort.dbexpression;
-    }
-    if (hasdisease) {
-      dsc.stratify = [
-        {
-          label: "disease",
-          attr1: { k: "disease", label: "disease" }
-        }
-      ];
-    }
-  }
-  if (hassample) {
-    for (const gene in flag2.data) {
-      for (const m of flag2.data[gene]) {
-        let pn = m.patient;
-        if (!pn) {
-          pn = m.sample;
-          if (!pn) {
-            continue;
-          }
-        }
-        if (!cohort.p2st[pn]) {
-          cohort.p2st[pn] = {};
-        }
-        let st = m.sampletype;
-        if (!st) {
-          st = pn;
-        }
-        if (!cohort.p2st[pn][st]) {
-          cohort.p2st[pn][st] = {
-            dsset: {},
-            tktemplate: []
-          };
-        }
-        if (!cohort.p2st[pn][st].dsset[dsc.label]) {
-          cohort.p2st[pn][st].dsset[dsc.label] = [];
-        }
-        cohort.p2st[pn][st].dsset[dsc.label].push(m);
-      }
-    }
-  }
-  if (callback) callback();
-  return false;
-}
-function bulkembed(arg) {
-  if (!arg.name) arg.name = "Unnamed dataset";
-  let holder = arg.holder;
-  if (!holder) {
-    const pane = newpane({ x: 100, y: 100 });
-    holder = pane.body;
-  }
-  const saydiv = holder.append("div");
-  new Promise((resolve, reject) => {
-    const cohort = {
-      dsset: {}
-    };
-    for (const k in arg) {
-      if (k == "snvindel" || k == "svjson" || k == "cnv" || k == "sv" || k == "mutationset") {
-        continue;
-      }
-      cohort[k] = arg[k];
-    }
-    resolve(cohort);
-  }).then((cohort) => {
-    if (!arg.snvindel && !arg.svjson && !arg.cnv && !arg.sv) return cohort;
-    const flag2 = init_bulk_flag(cohort.genome);
-    if (arg.snvindel) {
-      const e = parse_snvindel(arg.snvindel, flag2);
-      if (e) throw { message: "error in snvindel data: " + e };
-      delete arg.snvindel;
-    }
-    if (arg.svjson) {
-      const e = parse_svjson(arg.svjson, flag2);
-      if (e) throw { message: "error in svjson data: " + e };
-      delete arg.svjson;
-    }
-    if (arg.sv) {
-      const e = parse_sv(arg.sv, flag2);
-      if (e) throw { message: "error in svjson data: " + e };
-      delete arg.sv;
-    }
-    if (arg.cnv) {
-      const e = parse_cnv(arg.cnv, flag2);
-      if (e) throw { message: "error in cnv data: " + e };
-      delete arg.cnv;
-    }
-    const err2 = bulkin({
-      flag: flag2,
-      filename: arg.name,
-      cohort
-    });
-    if (err2) throw { message: "Error parsing data: " + err2 };
-    return cohort;
-  }).then((cohort) => {
-    if (!arg.mutationset) return cohort;
-    if (!Array.isArray(arg.mutationset)) throw { message: "mutationset is not an array" };
-    const tasks2 = [];
-    for (const mset of arg.mutationset) {
-      const flag2 = init_bulk_flag(cohort.genome);
-      const tasks = [];
-      if (mset.snvindel) {
-        const req = new Request(arg.hostURL + "/textfile", {
-          method: "POST",
-          headers: { "content-type": "application/json" },
-          body: '{"file":"' + mset.snvindel + '"}'
-        });
-        const task = fetch(req).then((data) => {
-          return data.json();
-        }).then((data) => {
-          if (data.error) throw { message: "error with snvindel file: " + data.error };
-          const e = parse_snvindel(data.text, flag2);
-          if (e) throw { message: "error with snvindel file: " + e };
-        });
-        tasks.push(task);
-      }
-      if (mset.snvindel_url) {
-        tasks.push(
-          dofetch("urltextfile", { url: mset.snvindel_url }).then((data) => {
-            if (data.error) throw { message: "cannot get snvindel file from url" };
-            const e = parse_snvindel(data.text, flag2);
-            if (e) throw { message: "error with snvindel file: " + e };
-          })
-        );
-      }
-      if (mset.cnv) {
-        const req = new Request(arg.hostURL + "/textfile", {
-          method: "POST",
-          headers: { "content-type": "application/json" },
-          body: '{"file":"' + mset.cnv + '"}'
-        });
-        const task = fetch(req).then((data) => {
-          return data.json();
-        }).then((data) => {
-          if (data.error) throw { message: "error with cnv file: " + data.error };
-          const e = parse_cnv(data.text, flag2);
-          if (e) throw { message: "error with cnv file: " + e };
-        });
-        tasks.push(task);
-      }
-      if (mset.cnv_url) {
-        tasks.push(
-          dofetch("urltextfile", { url: mset.cnv_url }).then((data) => {
-            if (data.error) throw { message: "cannot get cnv file from url" };
-            const e = parse_cnv(data.text, flag2);
-            if (e) throw { message: "error with cnv file: " + e };
-          })
-        );
-      }
-      if (mset.sv) {
-        const req = new Request(arg.hostURL + "/textfile", {
-          method: "POST",
-          headers: { "content-type": "application/json" },
-          body: '{"file":"' + mset.sv + '"}'
-        });
-        const task = fetch(req).then((data) => {
-          return data.json();
-        }).then((data) => {
-          if (data.error) throw { message: "error with sv file: " + data.error };
-          const e = parse_sv(data.text, flag2, true);
-          if (e) throw { message: "error with sv file: " + e };
-        });
-        tasks.push(task);
-      }
-      if (mset.sv_url) {
-        tasks.push(
-          dofetch("urltextfile", { url: mset.sv_url }).then((data) => {
-            if (data.error) throw { message: "cannot get sv file from url" };
-            const e = parse_sv(data.text, flag2);
-            if (e) throw { message: "error with sv file: " + e };
-          })
-        );
-      }
-      if (mset.fusion) {
-        const req = new Request(arg.hostURL + "/textfile", {
-          method: "POST",
-          headers: { "content-type": "application/json" },
-          body: '{"file":"' + mset.fusion + '"}'
-        });
-        const task = fetch(req).then((data) => {
-          return data.json();
-        }).then((data) => {
-          if (data.error) throw { message: "error with fusion file: " + data.error };
-          const e = parse_sv(data.text, flag2, false);
-          if (e) throw { message: "error with fusion file: " + e };
-        });
-        tasks.push(task);
-      }
-      if (mset.svjson) {
-        const req = new Request(arg.hostURL + "/textfile", {
-          method: "POST",
-          headers: { "content-type": "application/json" },
-          body: '{"file":"' + mset.svjson + '"}'
-        });
-        const task = fetch(req).then((data) => {
-          return data.json();
-        }).then((data) => {
-          if (data.error) throw { message: "error with svjson file: " + data.error };
-          const e = parse_svjson(data.text, flag2, false);
-          if (e) throw { message: "error with svjson file: " + e };
-        });
-        tasks.push(task);
-      }
-      if (mset.deletion) {
-        const req = new Request(arg.hostURL + "/textfile", {
-          method: "POST",
-          headers: { "content-type": "application/json" },
-          body: '{"file":"' + mset.deletion + '"}'
-        });
-        const task = fetch(req).then((data) => {
-          return data.json();
-        }).then((data) => {
-          if (data.error) throw { message: "error with deletion file: " + data.error };
-          const e = parse_del(data.text, flag2, false);
-          if (e) throw { message: "error with deletion file: " + e };
-        });
-        tasks.push(task);
-      }
-      if (mset.deletion_url) {
-        tasks.push(
-          dofetch("urltextfile", { url: mset.deletion_url }).then((data) => {
-            if (data.error) throw { message: "cannot get deletion file from url" };
-            const e = parse_del(data.text, flag2);
-            if (e) throw { message: "error with deletion file: " + e };
-          })
-        );
-      }
-      if (mset.truncation) {
-        const req = new Request(arg.hostURL + "/textfile", {
-          method: "POST",
-          headers: { "content-type": "application/json" },
-          body: '{"file":"' + mset.truncation + '"}'
-        });
-        const task = fetch(req).then((data) => {
-          return data.json();
-        }).then((data) => {
-          if (data.error) throw { message: "error with truncation file: " + data.error };
-          const e = parse_trunc(data.text, flag2, false);
-          if (e) throw { message: "error with truncation file: " + e };
-        });
-        tasks.push(task);
-      }
-      if (mset.truncation_url) {
-        tasks.push(
-          dofetch("urltextfile", { url: mset.truncation_url }).then((data) => {
-            if (data.error) throw { message: "cannot get truncation file from url" };
-            const e = parse_trunc(data.text, flag2, false);
-            if (e) throw { message: "error with truncation file: " + e };
-          })
-        );
-      }
-      if (mset.itd) {
-        const req = new Request(arg.hostURL + "/textfile", {
-          method: "POST",
-          headers: { "content-type": "application/json" },
-          body: '{"file":"' + mset.itd + '"}'
-        });
-        const task = fetch(req).then((data) => {
-          return data.json();
-        }).then((data) => {
-          if (data.error) throw { message: "error with itd file: " + data.error };
-          const e = parse_itd(data.text, flag2, false);
-          if (e) throw { message: "error with itd file: " + e };
-        });
-        tasks.push(task);
-      }
-      if (mset.itd_url) {
-        tasks.push(
-          dofetch("urltextfile", { url: mset.itd_url }).then((data) => {
-            if (data.error) throw { message: "cannot get itd file from url" };
-            const e = parse_itd(data.text, flag2, false);
-            if (e) throw { message: "error with itd file: " + e };
-          })
-        );
-      }
-      const task2 = Promise.all(tasks).then((data) => {
-        const err2 = bulkin({
-          flag: flag2,
-          filename: arg.name,
-          cohort
-        });
-        if (err2) throw { message: "Error parsing data from " + mset.name + ": " + err2 };
-      });
-      tasks2.push(task2);
-    }
-    return Promise.all(tasks2).then((data) => {
-      return cohort;
-    });
-  }).then((cohort) => {
-    const err2 = tpinit(cohort);
-    if (err2) throw { message: "Error parsing study: " + err2 };
-    saydiv.text("");
-    import("./tp.ui-KBFYUSWS.js").then((p) => {
-      p.default(cohort, holder, arg.hostURL);
-    });
-  }).catch((err2) => {
-    saydiv.text(err2.message);
-    if (err2.stack) {
-      console.log(err2.stack);
-    }
-  });
-}
-function parse_snvindel(text, flag2) {
-  const lines = text.trim().split(/\r?\n/);
-  let headerline = lines[0];
-  let lineidx = 0;
-  while (headerline[0] == "#") {
-    lineidx++;
-    headerline = lines[lineidx];
-  }
-  if (!headerline) return "no header line";
-  const err2 = parseheader2(headerline, flag2);
-  if (err2) return "header error: " + err2;
-  for (let i = lineidx + 1; i < lines.length; i++) {
-    if (lines[i] == "") continue;
-    if (lines[i][0] == "#") continue;
-    parseline2(i, lines[i], flag2);
-  }
-}
-function parse_svjson(text, flag2) {
-  const lines = text.split(/\r?\n/);
-  let headerline = lines[0];
-  let lineidx = 0;
-  while (headerline[0] == "#") {
-    lineidx++;
-    headerline = lines[lineidx];
-  }
-  if (!headerline) return "no header line";
-  const [err2, header] = parseheader3(headerline, flag2);
-  if (err2) return "header error: " + err2;
-  for (let i = lineidx + 1; i < lines.length; i++) {
-    if (lines[i] == "") continue;
-    if (lines[i][0] == "#") continue;
-    parseline3(i, lines[i], flag2, header);
-  }
-}
-function parse_cnv(text, flag2) {
-  const lines = text.split(/\r?\n/);
-  let headerline = lines[0];
-  let lineidx = 0;
-  while (headerline[0] == "#") {
-    lineidx++;
-    headerline = lines[lineidx];
-  }
-  if (!headerline) return "no header line";
-  const err2 = parseheader4(headerline, flag2);
-  if (err2) return "header error: " + err2;
-  for (let i = lineidx + 1; i < lines.length; i++) {
-    if (lines[i] == "") continue;
-    if (lines[i][0] == "#") continue;
-    parseline4(i, lines[i], flag2);
-  }
-}
-function parse_itd(text, flag2) {
-  const lines = text.split(/\r?\n/);
-  let headerline = lines[0];
-  let lineidx = 0;
-  while (headerline[0] == "#") {
-    lineidx++;
-    headerline = lines[lineidx];
-  }
-  if (!headerline) return "no header line";
-  const err2 = parseheader5(headerline, flag2);
-  if (err2) return "header error: " + err2;
-  for (let i = lineidx + 1; i < lines.length; i++) {
-    if (lines[i] == "") continue;
-    if (lines[i][0] == "#") continue;
-    parseline5(i, lines[i], flag2);
-  }
-}
-function parse_del(text, flag2) {
-  const lines = text.split(/\r?\n/);
-  let headerline = lines[0];
-  let lineidx = 0;
-  while (headerline[0] == "#") {
-    lineidx++;
-    headerline = lines[lineidx];
-  }
-  if (!headerline) return "no header line";
-  const err2 = parseheader6(headerline, flag2);
-  if (err2) return "header error: " + err2;
-  for (let i = lineidx + 1; i < lines.length; i++) {
-    if (lines[i] == "") continue;
-    if (lines[i][0] == "#") continue;
-    parseline6(i, lines[i], flag2);
-  }
-}
-function parse_trunc(text, flag2) {
-  const lines = text.split(/\r?\n/);
-  let headerline = lines[0];
-  let lineidx = 0;
-  while (headerline[0] == "#") {
-    lineidx++;
-    headerline = lines[lineidx];
-  }
-  if (!headerline) return "no header line";
-  const err2 = parseheader7(headerline, flag2);
-  if (err2) return "header error: " + err2;
-  for (let i = lineidx + 1; i < lines.length; i++) {
-    if (lines[i] == "") continue;
-    if (lines[i][0] == "#") continue;
-    parseline7(i, lines[i], flag2);
-  }
-}
-function parse_sv(text, flag2, isSv) {
-  const lines = text.split(/\r?\n/);
-  let headerline = lines[0];
-  let lineidx = 0;
-  while (headerline[0] == "#") {
-    lineidx++;
-    headerline = lines[lineidx];
-  }
-  if (!headerline) return "no header line";
-  const err2 = parseheader(headerline, flag2, isSv);
-  if (err2) return "header error: " + err2;
-  for (let i = lineidx + 1; i < lines.length; i++) {
-    if (lines[i] == "") continue;
-    if (lines[i][0] == "#") continue;
-    parseline(i, lines[i], flag2, isSv);
-  }
-}
-
-// src/tp.init.js
-function tpinit(cohort) {
-  if (!cohort.p2st) {
-    cohort.p2st = {};
-  }
-  if (!cohort.assays) {
-    cohort.assays = [];
-  }
-  if (!Array.isArray(cohort.assays)) {
-    return ".assays should be an array";
-  }
-  cohort.assaylst = [];
-  let assaynum = 0;
-  for (const assayname of cohort.assays) {
-    const rawassay = cohort[assayname];
-    if (!rawassay) {
-      return 'Assay "' + assayname + '" not found in cohort';
-    }
-    const config = rawassay.config;
-    if (!config) {
-      return '.config object missing for assay "' + assayname + '"';
-    }
-    delete rawassay.config;
-    if (!config.type) {
-      return '.config.type missing for assay "' + assayname + '"';
-    }
-    if (config.type.toLowerCase() == "vcf") {
-      config.type = tkt.ds;
-      config.isvcf = true;
-    } else {
-      if (!validtkt(config.type)) {
-        return 'unknown .config.type "' + config.type + '" for assay "' + assayname + '"';
-      }
-    }
-    config.id = (++assaynum).toString();
-    if (!config.name) {
-      config.name = assayname;
-    }
-    if (config.type == tkt.junction) {
-      if (config.readcountcutoff) {
-        if (!Number.isInteger(config.readcountcutoff) || config.readcountcutoff < 0) {
-          return 'invalid .config.readcountcutoff for assay "' + assayname + '"';
-        }
-      }
-    }
-    cohort.assaylst.push(config);
-    for (const pn in rawassay) {
-      if (!cohort.p2st[pn]) {
-        cohort.p2st[pn] = {};
-      }
-      for (const st in rawassay[pn]) {
-        if (!cohort.p2st[pn][st]) {
-          cohort.p2st[pn][st] = {
-            tktemplate: []
-          };
-        }
-        if (config.type == tkt.vafs1) {
-          for (const name in rawassay[pn][st]) {
-            const tk = rawassay[pn][st][name];
-            if (!tk.file && !tk.url) {
-              return "no file or URL for " + name + " vafs1 of " + pn + ", " + st;
-            }
-            tk.type = tkt.vafs1;
-            tk.patient = pn;
-            tk.sampletype = st;
-            tk.assayname = assayname;
-            tk.id = config.id;
-            tk.tkid = Math.random().toString();
-            if (!tk.name) {
-              tk.name = name + " vaf";
-            }
-            cohort.p2st[pn][st].tktemplate.push(tk);
-          }
-          continue;
-        }
-        let rawtklst = [];
-        if (Array.isArray(rawassay[pn][st])) {
-          rawtklst = rawassay[pn][st];
-        } else {
-          rawtklst.push(rawassay[pn][st]);
-        }
-        for (const _tk of rawtklst) {
-          let tk = _tk;
-          if (!tk.file && !tk.url) {
-            return "track has no file or url (sample: " + pn + ", assay: " + assayname + ")";
-          }
-          if (tk.name) {
-          } else if (tk.partname) {
-            tk.name = pn + (st == pn ? "" : " " + st) + " " + assayname + " " + tk.partname;
-          } else {
-            tk.name = pn + (st == pn ? "" : " " + st) + " " + assayname;
-          }
-          if (config.isvcf) {
-            const [err2, tk2] = vcf2dstk({
-              name: tk.name,
-              file: tk.file,
-              url: tk.url
-            });
-            if (err2) {
-              return "VCF track error: " + err2;
-            }
-            tk = tk2;
-          } else {
-            if (tk.type) {
-              if (!validtkt(tk.type)) {
-                return 'invalid track type "' + tk.type + '" (sample: ' + pn + ", assay: " + assayname + ")";
-              }
-            } else {
-              tk.type = config.type;
-            }
-          }
-          tk.patient = pn;
-          tk.sampletype = st;
-          tk.assayname = assayname;
-          tk.id = config.id;
-          tk.tkid = Math.random().toString();
-          cohort.p2st[pn][st].tktemplate.push(tk);
-          switch (config.type) {
-            case tkt.bigwig:
-              const e = tidy_qtk(tk, config);
-              if (e) {
-                return "Assay " + assayname + ": " + config.type + " track error: " + e;
-              }
-              break;
-            case tkt.junction:
-              tk.categories = config.categories;
-              tk.readcountcutoff = config.readcountcutoff;
-              break;
-          }
-        }
-      }
-    }
-  }
-  delete cohort.assays;
-  {
-    const err2 = cohort2genometkset(cohort);
-    if (err2) {
-      return "Error: " + err2;
-    }
-  }
-  if (cohort.patientannotation) {
-    const err2 = parse_patientannotation(cohort);
-    if (err2) return err2;
-  }
-  if (cohort.browserview) {
-    const err2 = parse_browserview(cohort);
-    if (err2) return err2;
-  }
-  if (cohort.e2pca) {
-    if (!cohort.e2pca.list) return ".list missing from e2pca";
-    if (!Array.isArray(cohort.e2pca.list)) return "e2pca.list should be an array";
-    if (cohort.e2pca.list.length == 0) return "e2pca.list[] length 0";
-    if (!cohort.e2pca.label) {
-      cohort.e2pca.label = "Expression - PCA";
-    }
-    for (const obj of cohort.e2pca.list) {
-      if (!obj.vectorfile) return "vectorfile missing from e2pca";
-      if (!obj.dbfile) return "dbfile missing from e2pca";
-    }
-  }
-  return;
-}
-function loadstudycohort(genomes, file, holder, hostURL, jwt, noshow, app) {
-  const wait = holder.append("div").style("color", "#858585");
-  wait.text("Loading " + file + " ...");
-  return fetch(hostURL + "/study", {
-    method: "POST",
-    headers: { "content-type": "application/json" },
-    body: JSON.stringify({ file, jwt })
-  }).then((res) => res.json()).then((data) => {
-    if (!data) {
-      wait.text("Server error!");
-      return;
-    }
-    if (data.error) {
-      wait.text("Error loading study: " + data.error);
-      return;
-    }
-    const cohort = data.cohort;
-    if (!cohort) {
-      wait.text(".cohort missing");
-      return;
-    }
-    if (!cohort.genome) {
-      wait.text("No genome specified in the cohort JSON content");
-      return;
-    }
-    const g = genomes[cohort.genome];
-    if (!g) {
-      wait.text("Invalid genome from cohort: " + cohort.genome);
-      return;
-    }
-    cohort.genome = g;
-    cohort.jwt = jwt;
-    if (!data.flagset) {
-      wait.text(".flagset missing");
-      return;
-    }
-    wait.text("");
-    cohort.dsset = {};
-    for (const k in data.flagset) {
-      const flag2 = data.flagset[k];
-      flag2.genome = g;
-      bulkin({
-        flag: flag2,
-        filename: file,
-        cohort,
-        err: (m) => sayerror(wait, m)
-      });
-    }
-    const err2 = tpinit(cohort);
-    if (err2) {
-      sayerror(wait, err2);
-    }
-    if (!noshow) {
-      return import("./tp.ui-KBFYUSWS.js").then(async (p) => {
-        getsjcharts().catch(console.error);
-        p.default(cohort, holder, hostURL, app);
-        return app;
-      });
-    }
-  });
-}
-function tidy_qtk(tk, config) {
-  if (!config) {
-    config = {};
-  }
-  if (!tk.file && !tk.url) {
-    return "no file or url";
-  }
-  if (!tk.pcolor) {
-    tk.pcolor = config.pcolor || "#0066CC";
-  }
-  if (!tk.pcolor2) {
-    tk.pcolor2 = config.pcolor2 || "#CC0000";
-  }
-  if (!tk.ncolor) {
-    tk.ncolor = config.ncolor || "#FF850A";
-  }
-  if (!tk.ncolor2) {
-    tk.ncolor2 = config.ncolor2 || "#0A85FF";
-  }
-  if (!tk.height) {
-    tk.height = config.height || 50;
-  }
-  const scale = {};
-  if (config.scale) {
-    for (const k in config.scale) {
-      scale[k] = config.scale[k];
-    }
-  }
-  if (tk.scale) {
-    for (const k in tk.scale) {
-      scale[k] = tk.scale[k];
-    }
-  }
-  scale.auto = true;
-  if (Number.isFinite(scale.min) && Number.isFinite(scale.max)) {
-    delete scale.auto;
-  } else if (Number.isFinite(scale.percentile)) {
-    delete scale.auto;
-  }
-  tk.scale = scale;
-}
-function cohort2genometkset(cohort) {
-  const lst = [];
-  for (const pn in cohort.p2st) {
-    for (const st in cohort.p2st[pn]) {
-      const templates = cohort.p2st[pn][st].tktemplate;
-      if (!templates) continue;
-      for (const t of templates) {
-        lst.push(t);
-      }
-    }
-  }
-  if (cohort.browserview && cohort.browserview.assays) {
-    for (const assayname in cohort.browserview.assays) {
-      const assayview = cohort.browserview.assays[assayname];
-      if (assayview.combined && assayview.combinetk) {
-        lst.push(assayview.combinetk);
-      }
-    }
-  }
-  if (!cohort.genome.tkset) {
-    cohort.genome.tkset = [];
-  }
-  const thisset = {
-    name: cohort.name,
-    tklst: lst
-  };
-  if (cohort.trackfacets) {
-    if (!Array.isArray(cohort.trackfacets)) {
-      return ".trackfacets is not an array";
-    }
-    const lst2 = [];
-    for (const fc of cohort.trackfacets) {
-      if (!fc.samples) {
-        return "trackfacets: .samples missing from facet " + fc.name;
-      }
-      if (!Array.isArray(fc.samples)) {
-        return "trackfacets: .samples is not array from facet " + fc.name;
-      }
-      if (!fc.assays) {
-        return "trackfacets: .assays missing from a facet " + fc.name;
-      }
-      if (!Array.isArray(fc.assays)) {
-        return "trackfacets: .assays is not array from a facet " + fc.name;
-      }
-      lst2.push(fc);
-    }
-    if (lst2.length) {
-      thisset.facetlst = lst2;
-    }
-  }
-  cohort.genome.tkset.push(thisset);
-  return null;
-}
-function parse_browserview(cohort) {
-  if (cohort.browserview.position) {
-    let pos;
-    if (typeof cohort.browserview.position == "string") {
-      pos = string2pos(cohort.browserview.position, cohort.genome);
-      if (!pos) {
-        return ".browserview.position invalid value";
-      }
-    } else {
-      pos = cohort.browserview.position;
-    }
-    const e = invalidcoord(cohort.genome, pos.chr, pos.start, pos.stop);
-    if (e) {
-      return ".browserview.position error: " + e;
-    }
-    cohort.browserview.position = pos;
-  } else {
-    cohort.browserview.position = {
-      chr: cohort.genome.defaultcoord.chr,
-      start: cohort.genome.defaultcoord.start,
-      stop: cohort.genome.defaultcoord.stop
-    };
-  }
-  if (cohort.browserview.assays) {
-    for (const assayname in cohort.browserview.assays) {
-      if (typeof cohort.browserview.assays[assayname] != "object") {
-        cohort.browserview.assays[assayname] = {};
-      }
-      const assayview = cohort.browserview.assays[assayname];
-      for (const a of cohort.assaylst) {
-        if (a.name == assayname) {
-          assayview.assayobj = a;
-          break;
-        }
-      }
-      if (!assayview.assayobj) {
-        console.log("missing assayobj for assayview of " + assayname);
-        continue;
-      }
-      if (assayview.sum_view) {
-        delete assayview.sum_view;
-        assayview.combined = true;
-      }
-      if (assayview.combined) {
-        const combinetk = {};
-        for (const k in assayview.assayobj) {
-          combinetk[k] = assayview.assayobj[k];
-        }
-        for (const k in assayview) {
-          if (k == "assayobj") continue;
-          combinetk[k] = assayview[k];
-        }
-        if (!combinetk.name) {
-          combinetk.name = assayname;
-        }
-        combinetk.tracks = [];
-        for (const pn in cohort.p2st) {
-          for (const st in cohort.p2st[pn]) {
-            for (const t of cohort.p2st[pn][st].tktemplate) {
-              if (t.id == assayview.assayobj.id) {
-                t.patient = pn;
-                t.sampletype = st;
-                combinetk.tracks.push(t);
-              }
-            }
-          }
-        }
-        if (combinetk.isvcf) {
-          combinetk.ds = {
-            id2vcf: {},
-            label: combinetk.name
-          };
-          for (const t of combinetk.tracks) {
-            for (const i in t.ds.id2vcf) {
-              t.__vcfobj = t.ds.id2vcf[i];
-            }
-            combinetk.ds.id2vcf[t.__vcfobj.vcfid] = t.__vcfobj;
-          }
-        }
-        assayview.combinetk = combinetk;
-      }
-    }
-  }
-  if (cohort.browserview.defaultassaytracks) {
-    if (!Array.isArray(cohort.browserview.defaultassaytracks)) return ".browserview.defaultassaytracks must be array";
-    for (let i = 0; i < cohort.browserview.defaultassaytracks.length; i++) {
-      const t = cohort.browserview.defaultassaytracks[i];
-      if (!t.assay) return ".assay missing from .defaultassaytracks #" + (i + 1);
-      if (!cohort[t.assay]) return "unknown assay name from .defaultassaytracks #" + (i + 1) + ": " + t.assay;
-      if (!t.level1) return ".level1 missing from .defaultassaytracks #" + (i + 1);
-      if (!cohort[t.assay][t.level1])
-        return "level1 not exist in assay from .defaultassaytracks #" + (i + 1) + ": " + t.level1;
-      if (t.level2) {
-        if (!cohort[t.assay][t.level1][t.level2])
-          return "level2 not exist in assay from .defaultassaytracks #" + (i + 1) + ": " + t.level2;
-      }
-    }
-  }
-  return null;
-}
-function parse_patientannotation(cohort) {
-  if (!cohort.patientannotation.annotation) {
-    return ".patientannotation.annotation missing";
-  }
-  if (!cohort.patientannotation.metadata) {
-    return ".patientannotation.metadata missing";
-  }
-  if (!Array.isArray(cohort.patientannotation.metadata)) {
-    return ".patientannotation.metadata should be an array";
-  }
-  const mdh = {};
-  for (const md of cohort.patientannotation.metadata) {
-    if (md.key == void 0) {
-      return "patientannotation: key missing for a metadata term";
-    }
-    if (!md.values) {
-      return "patientannotation: values missing for metadata term " + md.key;
-    }
-    if (!Array.isArray(md.values)) {
-      return "patientannotation: .values not an array for metadata term " + md.key;
-    }
-    if (!md.label) {
-      md.label = md.key;
-    }
-    mdh[md.key] = {
-      label: md.label,
-      values: {}
-    };
-    const colorfunc = ordinal(category10_default);
-    for (const at of md.values) {
-      if (at.key == void 0) {
-        return "key missing for an attribute of term " + md.key;
-      }
-      if (!at.label) {
-        at.label = at.key;
-      }
-      if (!at.color) {
-        at.color = colorfunc(at.key);
-      }
-      mdh[md.key].values[at.key] = at;
-    }
-  }
-  cohort.patientannotation.mdh = mdh;
-  return null;
-}
-
-export {
-  loadstudycohort,
-  bulkui,
-  content2flag,
-  bulkin,
-  bulkembed
-};
-//# sourceMappingURL=chunk-XHZ723K4.js.map