@sjcrh/proteinpaint-client 2.183.0 → 2.183.1

package/dist/chunk-GZJ7GDZ4.js

@@ -0,0 +1,2327 @@
+import {
+  vcf2dstk
+} from "./chunk-TTGDA3MA.js";
+import {
+  getsjcharts
+} from "./chunk-MKAF2BHB.js";
+import {
+  parseheader,
+  parseline
+} from "./chunk-I2M62STM.js";
+import {
+  bulk_badline,
+  disappear2 as disappear,
+  filetypeselect,
+  newpane,
+  newpane3,
+  renderSandboxFormDiv,
+  sayerror,
+  tkt
+} from "./chunk-2LCTMDCS.js";
+import {
+  invalidcoord,
+  string2pos
+} from "./chunk-HJ6L54YS.js";
+import {
+  dofetch,
+  init_bulk_flag,
+  parsesample
+} from "./chunk-RCYTUKAJ.js";
+import {
+  dtcloss,
+  dtcnv,
+  dtdel,
+  dtfusionrna,
+  dtitd,
+  dtnloss,
+  dtsnvindel,
+  dtsv,
+  mclasscloss,
+  mclasscnvgain,
+  mclasscnvloh,
+  mclasscnvloss,
+  mclassdel,
+  mclassfusionrna,
+  mclassitd,
+  mclassnloss,
+  mclasssv,
+  mclasstester,
+  validtkt
+} from "./chunk-XRVBHNCW.js";
+import {
+  category10_default
+} from "./chunk-IH7ILDJS.js";
+import {
+  ordinal
+} from "./chunk-OAWQ6LOO.js";
+import {
+  select_default
+} from "./chunk-NDWTN4U5.js";
+
+// ../shared/utils/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, flag2.snv.badlines)) {
+    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 {
+      let 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 {
+      let 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/src/bulk.svjson.js
+function parseheader3(line, flag2) {
+  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, badlines)) {
+    return;
+  }
+  let json;
+  try {
+    json = JSON.parse(m.jsontext);
+  } catch (e) {
+    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/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, flag2.cnv.badlines)) {
+    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/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, flag2.itd.badlines)) {
+    return;
+  }
+  m.dt = dtitd;
+  m.class = mclassitd;
+  m.mname = "ITD";
+  flag2.good++;
+  var n = flag2.geneToUpper ? m.gene.toUpperCase() : m.gene;
+  if (!(n in flag2.data)) {
+    flag2.data[n] = [];
+  }
+  flag2.data[n].push(m);
+}
+
+// ../shared/utils/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, flag2.del.badlines)) {
+    return;
+  }
+  m.dt = dtdel;
+  m.class = mclassdel;
+  m.mname = "DEL";
+  flag2.good++;
+  var n = flag2.geneToUpper ? m.gene.toUpperCase() : m.gene;
+  if (!(n in flag2.data)) {
+    flag2.data[n] = [];
+  }
+  flag2.data[n].push(m);
+}
+
+// ../shared/utils/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, flag2.truncation.badlines)) {
+    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-4ESL6SCH.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",
+          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",
+          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",
+          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",
+          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",
+          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",
+          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",
+          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",
+          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-4ESL6SCH.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",
+    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-4ESL6SCH.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-GZJ7GDZ4.js.map