@sjcrh/proteinpaint-client 2.182.0 → 2.183.0

package/dist/chunk-IGEQI6MR.js

@@ -1,1561 +0,0 @@
-import {
-  Dark2_default,
-  Paired_default,
-  rainbow_default
-} from "./chunk-IH7ILDJS.js";
-import {
-  ordinal
-} from "./chunk-OAWQ6LOO.js";
-import {
-  rgb
-} from "./chunk-OMR2DT66.js";
-import {
-  __export
-} from "./chunk-HFNDKYVF.js";
-
-// ../shared/utils/src/filter.js
-function getFilteredSamples(sampleAnno, filter) {
-  setDatasetAnnotations(filter);
-  const samples = /* @__PURE__ */ new Set();
-  for (const anno of sampleAnno) {
-    if (samples.has(anno.sample)) continue;
-    const data = anno.s || anno.data;
-    if (data && sample_match_termvaluesetting(data, filter)) {
-      samples.add(anno.sample);
-    }
-  }
-  return samples;
-}
-function sample_match_termvaluesetting(row, filter, _term = null, sample = null) {
-  const lst = filter.type == "tvslst" ? filter.lst : [filter];
-  let numberofmatchedterms = 0;
-  for (const item of lst) {
-    if ("type" in item && item.type == "tvslst") {
-      if (sample_match_termvaluesetting(row, item, _term, sample)) {
-        numberofmatchedterms++;
-      }
-    } else {
-      const itemCopy = JSON.parse(JSON.stringify(item));
-      const t = itemCopy.tvs;
-      if (_term && t.term) {
-        if (!(_term.name == t.term.name && _term.type == t.term.type)) {
-          numberofmatchedterms++;
-          continue;
-        }
-      }
-      let samplevalue;
-      if (_term && !t.term) {
-        if (t.term$type && t.term$type !== _term.type) {
-          numberofmatchedterms++;
-          continue;
-        }
-        t.term = _term;
-        samplevalue = typeof row === "object" && t.term.id in row ? row[t.term.id] : row;
-      } else if (sample && t.term.$id) {
-        samplevalue = sample[t.term.$id].value;
-      } else {
-        samplevalue = t.term.id in row ? row[t.term.id] : row;
-      }
-      setDatasetAnnotations(itemCopy);
-      let thistermmatch;
-      if (t.term.type == "categorical") {
-        if (samplevalue === void 0) continue;
-        thistermmatch = t.valueset.has(samplevalue);
-      } else if (t.term.type == "integer" || t.term.type == "float") {
-        if (samplevalue === void 0) continue;
-        for (const range of t.ranges) {
-          if ("value" in range) {
-            thistermmatch = samplevalue === range.value;
-            if (thistermmatch) break;
-          } else if (samplevalue == range.name) {
-            thistermmatch = true;
-            break;
-          } else {
-            if (t.term.values) {
-              const v = t.term.values[samplevalue.toString()];
-              if (v && v.uncomputable) {
-                continue;
-              }
-            }
-            let left, right;
-            if (range.startunbounded) {
-              left = true;
-            } else if ("start" in range) {
-              if (range.startinclusive) {
-                left = samplevalue >= range.start;
-              } else {
-                left = samplevalue > range.start;
-              }
-            }
-            if (range.stopunbounded) {
-              right = true;
-            } else if ("stop" in range) {
-              if (range.stopinclusive) {
-                right = samplevalue <= range.stop;
-              } else {
-                right = samplevalue < range.stop;
-              }
-            }
-            thistermmatch = left && right;
-          }
-          if (thistermmatch) break;
-        }
-      } else if (t.term.type == "condition") {
-        const key = getPrecomputedKey(t);
-        const anno = samplevalue && samplevalue[key];
-        if (anno) {
-          thistermmatch = Array.isArray(anno) ? t.values.find((d) => anno.includes(d.key)) : t.values.find((d) => d.key == anno);
-        }
-      } else if (t.term.type == "geneVariant") {
-        const svalues = samplevalue.values || [samplevalue];
-        for (const sv of svalues) {
-          thistermmatch = t.values.find(
-            (v) => v.dt == sv.dt && (!v.origin || sv.origin == v.origin) && (!v.mclasslst || v.mclasslst.includes(sv.class))
-          ) && true;
-          if (thistermmatch) break;
-        }
-      } else {
-        throw "unknown term type [sample_match_termvaluesetting() shared/utils/src/filter.ts]";
-      }
-      if (t.isnot) {
-        thistermmatch = !thistermmatch;
-      }
-      if (thistermmatch) numberofmatchedterms++;
-    }
-    if (filter.join == "or") {
-      if (numberofmatchedterms && filter.in) return true;
-      if (!numberofmatchedterms && !filter.in) return true;
-    }
-  }
-  if (!("in" in filter)) filter.in = true;
-  return filter.in == (numberofmatchedterms == lst.length);
-}
-function setDatasetAnnotations(item, ds = null) {
-  if (item.type == "tvslst") {
-    for (const subitem of item.lst) {
-      setDatasetAnnotations(subitem, ds);
-    }
-  } else {
-    if (ds && typeof ds.setAnnoByTermId == "function") {
-      ds.setAnnoByTermId(item.tvs.term.id);
-    }
-    if (item.tvs.term.type == "categorical") {
-      const tvsAny = item.tvs;
-      tvsAny.valueset = new Set(tvsAny.values.map((i) => i.key));
-    }
-  }
-}
-function getPrecomputedKey(q) {
-  const precomputedKey = q.bar_by_children && q.value_by_max_grade ? "childrenAtMaxGrade" : q.bar_by_children && q.value_by_most_recent ? "childrenAtMostRecent" : q.bar_by_children && q.value_by_computable_grade ? "children" : q.bar_by_grade && q.value_by_max_grade ? "maxGrade" : q.bar_by_grade && q.value_by_most_recent ? "mostRecentGrades" : q.bar_by_grade && q.value_by_computable_grade ? "computableGrades" : "";
-  if (!precomputedKey) throw `unknown condition term bar_by_* and/or value_by_*`;
-  return precomputedKey;
-}
-function getWrappedTvslst(lst = [], join = "", $id = null) {
-  const filter = {
-    type: "tvslst",
-    in: true,
-    join,
-    lst
-  };
-  if ($id !== null) filter.$id = $id;
-  return filter;
-}
-function validateTermCollectionTvs(lst1, lst2) {
-  if (!Array.isArray(lst1)) throw new Error("numerator not array");
-  if (!Array.isArray(lst2)) throw new Error("denominator not array");
-  if (lst1.length == 0) throw new Error("numerator empty");
-  if (lst2.length == 0) throw new Error("denominator empty");
-  if (lst1.length > lst2.length) throw new Error("numerator longer than denominator");
-  for (const s of lst1) {
-    if (typeof s != "string") throw new Error("one of numerator not string");
-    if (!s) throw new Error("empty string in numerator");
-    if (!lst2.includes(s)) throw new Error("one of numerator not in denominator");
-  }
-}
-
-// ../shared/utils/src/common.js
-var common_exports = {};
-__export(common_exports, {
-  CNVClasses: () => CNVClasses,
-  IN_frame: () => IN_frame,
-  OUT_frame: () => OUT_frame,
-  SOterm2class: () => SOterm2class,
-  TermTypeGroups: () => TermTypeGroups,
-  alleleInGenotypeStr: () => alleleInGenotypeStr,
-  applyOverrides: () => applyOverrides,
-  basecolor: () => basecolor,
-  basecompliment: () => basecompliment,
-  bplen: () => bplen,
-  class2SOterm: () => class2SOterm,
-  codon: () => codon,
-  codon_stop: () => codon_stop,
-  colorScaleMap: () => colorScaleMap,
-  contigNameNoChr: () => contigNameNoChr,
-  contigNameNoChr2: () => contigNameNoChr2,
-  custommdstktype: () => custommdstktype,
-  default_text_color: () => default_text_color,
-  defaultcolor: () => defaultcolor,
-  dt2color: () => dt2color,
-  dt2label: () => dt2label,
-  dt2lesion: () => dt2lesion,
-  dtTerms: () => dtTerms,
-  dtcloss: () => dtcloss,
-  dtcnv: () => dtcnv,
-  dtdel: () => dtdel,
-  dtdnamethylation: () => dtdnamethylation,
-  dtfusionrna: () => dtfusionrna,
-  dtgeneexpression: () => dtgeneexpression,
-  dtitd: () => dtitd,
-  dtloh: () => dtloh,
-  dtmetaboliteintensity: () => dtmetaboliteintensity,
-  dtnloss: () => dtnloss,
-  dtproteomeabundance: () => dtproteomeabundance,
-  dtsnvindel: () => dtsnvindel,
-  dtssgsea: () => dtssgsea,
-  dtsv: () => dtsv,
-  exoncolor: () => exoncolor,
-  fasta2gmframecheck: () => fasta2gmframecheck,
-  germlinelegend: () => germlinelegend,
-  getColorScheme: () => getColorScheme,
-  getColors: () => getColors,
-  getMax_byiqr: () => getMax_byiqr,
-  gmmode: () => gmmode,
-  invalidcoord: () => invalidcoord,
-  kernelDensityEstimator: () => kernelDensityEstimator,
-  kernelEpanechnikov: () => kernelEpanechnikov,
-  mclass: () => mclass,
-  mclasscloss: () => mclasscloss,
-  mclasscnvAmp: () => mclasscnvAmp,
-  mclasscnvHomozygousDel: () => mclasscnvHomozygousDel,
-  mclasscnvgain: () => mclasscnvgain,
-  mclasscnvloh: () => mclasscnvloh,
-  mclasscnvloss: () => mclasscnvloss,
-  mclassdel: () => mclassdel,
-  mclassdeletion: () => mclassdeletion,
-  mclassfusionrna: () => mclassfusionrna,
-  mclassinsertion: () => mclassinsertion,
-  mclassitd: () => mclassitd,
-  mclassmnv: () => mclassmnv,
-  mclassnloss: () => mclassnloss,
-  mclassnoncoding: () => mclassnoncoding,
-  mclassnonstandard: () => mclassnonstandard,
-  mclasssnv: () => mclasssnv,
-  mclasssv: () => mclasssv,
-  mclasstester: () => mclasstester,
-  mclassutr3: () => mclassutr3,
-  mclassutr5: () => mclassutr5,
-  mds3tkMclass: () => mds3tkMclass,
-  mdsvcftype: () => mdsvcftype,
-  morigin: () => morigin,
-  morigingermline: () => morigingermline,
-  morigingermlinenonpathogenic: () => morigingermlinenonpathogenic,
-  morigingermlinepathogenic: () => morigingermlinepathogenic,
-  moriginrelapse: () => moriginrelapse,
-  moriginsomatic: () => moriginsomatic,
-  mutationClasses: () => mutationClasses,
-  not_annotated: () => not_annotated,
-  nt2aa: () => nt2aa,
-  optionToDt: () => optionToDt,
-  plotColor: () => plotColor,
-  proteinChangingMutations: () => proteinChangingMutations,
-  proteinDomainColorScale: () => proteinDomainColorScale,
-  reversecompliment: () => reversecompliment,
-  schemeCategory2: () => schemeCategory2,
-  schemeCategory20: () => schemeCategory20,
-  spliceeventchangegmexon: () => spliceeventchangegmexon,
-  string2pos: () => string2pos,
-  synonymousMutations: () => synonymousMutations,
-  tkt: () => tkt,
-  truncatingMutations: () => truncatingMutations,
-  validate_vcfinfofilter: () => validate_vcfinfofilter,
-  validtkt: () => validtkt,
-  vcfcopymclass: () => vcfcopymclass,
-  vepinfo: () => vepinfo
-});
-var TermTypeGroups = class {
-  static DICTIONARY_VARIABLES = "Dictionary Variables";
-  static DNA_METHYLATION = "DNA Methylation";
-  static GENE_DEPENDENCY = "Gene Dependency";
-  static GENE_EXPRESSION = "Gene Expression";
-  static ISOFORM_EXPRESSION = "Isoform Expression";
-  static GSEA = "GSEA";
-  static METABOLITE_INTENSITY = "Metabolite Intensity";
-  static PROTEOME_ABUNDANCE = "Whole Proteome Abundance";
-  static MUTATION_CNV_FUSION = "Mutation/CNV/Fusion";
-  static MUTATION_SIGNATURE = "Mutation Signature";
-  static PROTEIN_EXPRESSION = "Protein Expression";
-  static SINGLECELL_CELLTYPE = "Single-cell Cell Type";
-  static SINGLECELL_GENE_EXPRESSION = "Single-cell Gene Expression";
-  static SNP = "SNP Genotype";
-  static SNP_LIST = "SNP List";
-  static SNP_LOCUS = "SNP Locus";
-  static SPLICE_JUNCTION = "Splice Junction";
-  static SSGSEA = "Geneset Expression";
-  static TERM_COLLECTION = "Term Collection";
-  static VARIANT_GENOTYPE = "Variant Genotype";
-};
-Object.freeze(TermTypeGroups);
-var defaultcolor = rgb("#8AB1D4").darker();
-var default_text_color = rgb("#aaa").darker().darker();
-var exoncolor = "#4F8053";
-var plotColor = "#ce768e";
-var IN_frame = true;
-var OUT_frame = false;
-var dtsnvindel = 1;
-var dtfusionrna = 2;
-var dtgeneexpression = 3;
-var dtcnv = 4;
-var dtsv = 5;
-var dtitd = 6;
-var dtdel = 7;
-var dtnloss = 8;
-var dtcloss = 9;
-var dtloh = 10;
-var dtmetaboliteintensity = 11;
-var dtssgsea = 12;
-var dtdnamethylation = 13;
-var dtproteomeabundance = 14;
-var dt2label = {
-  [dtsnvindel]: "SNV/indel",
-  [dtfusionrna]: "Fusion RNA",
-  [dtcnv]: "CNV",
-  [dtsv]: "SV",
-  [dtitd]: "ITD",
-  [dtdel]: "Deletion",
-  [dtnloss]: "N-loss",
-  [dtcloss]: "C-loss",
-  [dtloh]: "LOH",
-  [dtgeneexpression]: "Gene Expression",
-  [dtmetaboliteintensity]: "Metabolite Intensity",
-  [dtproteomeabundance]: "Whole Proteome Abundance"
-};
-var dt2lesion = {
-  [dtsnvindel]: {
-    uilabel: "SNV/INDEL (Mutation)",
-    lesionTypes: [{ name: "Mutation", lesionType: "mutation", color: "#44AA44" }]
-  },
-  [dtcnv]: {
-    uilabel: "CNV (Copy Number Variation)",
-    lesionTypes: [
-      { name: "Loss", lesionType: "loss", color: "#4444FF" },
-      { name: "Gain", lesionType: "gain", color: "#FF4444" }
-    ]
-  },
-  [dtsv]: {
-    uilabel: "SV (Structural Variation)",
-    lesionTypes: [{ name: "SV", lesionType: "sv", color: "#9932CC" }]
-  },
-  [dtfusionrna]: {
-    uilabel: "Fusion (RNA Fusion)",
-    lesionTypes: [{ name: "Fusion", lesionType: "fusion", color: "#FFA500" }]
-  }
-};
-var optionToDt = {
-  snvindelOptions: dtsnvindel,
-  cnvOptions: dtcnv,
-  fusionOptions: dtfusionrna,
-  svOptions: dtsv
-};
-var mclass = {
-  M: {
-    label: "MISSENSE",
-    color: "#3987CC",
-    dt: dtsnvindel,
-    desc: "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved",
-    key: "M"
-  },
-  E: { label: "EXON", color: "#bcbd22", dt: dtsnvindel, desc: "A variant in the exon of a non-coding RNA.", key: "E" },
-  F: {
-    label: "FRAMESHIFT",
-    color: "rgb(200, 61, 61)",
-    dt: dtsnvindel,
-    desc: "A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three",
-    key: "F"
-  },
-  N: {
-    label: "NONSENSE",
-    color: "#ff7f0e",
-    dt: dtsnvindel,
-    desc: "A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript",
-    key: "N"
-  },
-  S: {
-    label: "SILENT",
-    color: "#2ca02c",
-    dt: dtsnvindel,
-    desc: "A sequence variant where there is no resulting change to the encoded amino acid",
-    key: "S"
-  },
-  D: {
-    label: "PROTEINDEL",
-    color: "rgb(100, 100, 100)",
-    dt: dtsnvindel,
-    desc: "An inframe non synonymous variant that deletes bases from the coding sequence",
-    key: "D"
-  },
-  I: {
-    label: "PROTEININS",
-    color: "#8c564b",
-    dt: dtsnvindel,
-    desc: "An inframe non synonymous variant that inserts bases into in the coding sequence",
-    key: "I"
-  },
-  ProteinAltering: {
-    label: "PROTEINALTERING",
-    color: "#5a0034",
-    dt: dtsnvindel,
-    desc: "An inframe complex change to the coding sequence",
-    key: "ProteinAltering"
-  },
-  P: {
-    label: "SPLICE_REGION",
-    color: "#9467bd",
-    dt: dtsnvindel,
-    desc: "A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron",
-    key: "P"
-  },
-  L: {
-    label: "SPLICE",
-    color: "#6633FF",
-    dt: dtsnvindel,
-    desc: "A variant near an exon edge that may affect splicing functionality",
-    key: "L"
-  },
-  Intron: { label: "INTRON", color: "#656565", dt: dtsnvindel, desc: "An intronic variant.", key: "Intron" },
-  StopLost: {
-    label: "Stop lost",
-    color: "#ff7f0e",
-    dt: dtsnvindel,
-    desc: "A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript",
-    key: "StopLost"
-  },
-  StartLost: {
-    label: "Start lost",
-    color: "#ff7f0e",
-    dt: dtsnvindel,
-    desc: "A codon variant that changes at least one base of the canonical start codon",
-    key: "StartLost"
-  },
-  // quick fix!! for showing genes that are not tested in samples (e.g. gene panels) in the heatmap
-  Blank: { label: "Not tested", color: "#fff", dt: dtsnvindel, desc: "This gene is not tested.", key: "Blank" },
-  WT: { label: "Wildtype", color: "#D3D3D3", dt: dtsnvindel, desc: "Wildtype", key: "WT" }
-};
-var mclassitd = "ITD";
-mclass[mclassitd] = {
-  label: "ITD",
-  color: "#ff70ff",
-  dt: dtitd,
-  desc: "In-frame internal tandem duplication.",
-  key: mclassitd
-};
-var mclassdel = "DEL";
-mclass[mclassdel] = {
-  label: "DELETION, intragenic",
-  color: "#858585",
-  dt: dtdel,
-  desc: "Intragenic deletion.",
-  key: mclassdel
-};
-var mclassnloss = "NLOSS";
-mclass[mclassnloss] = {
-  label: "N-terminus loss",
-  color: "#545454",
-  dt: dtnloss,
-  desc: "N-terminus loss due to translocation",
-  key: mclassnloss
-};
-var mclasscloss = "CLOSS";
-mclass[mclasscloss] = {
-  label: "C-terminus loss",
-  color: "#545454",
-  dt: dtcloss,
-  desc: "C-terminus loss due to translocation",
-  key: mclasscloss
-};
-var mclassutr3 = "Utr3";
-mclass[mclassutr3] = {
-  label: "UTR_3",
-  color: "#998199",
-  dt: dtsnvindel,
-  desc: "A variant in the 3' untranslated region.",
-  key: mclassutr3
-};
-var mclassutr5 = "Utr5";
-mclass[mclassutr5] = {
-  label: "UTR_5",
-  color: "#819981",
-  dt: dtsnvindel,
-  desc: "A variant in the 5' untranslated region.",
-  key: mclassutr5
-};
-var mclassnonstandard = "X";
-mclass[mclassnonstandard] = {
-  label: "NONSTANDARD",
-  color: "black",
-  dt: dtsnvindel,
-  desc: "A mutation class that either does not match our notation, or is unspecified.",
-  key: mclassnonstandard
-};
-var mclassnoncoding = "noncoding";
-mclass[mclassnoncoding] = {
-  label: "NONCODING",
-  color: "black",
-  dt: dtsnvindel,
-  desc: "Noncoding mutation.",
-  key: mclassnoncoding
-};
-var SOterms = [
-  //transcript_ablation // not supported: 1) do not expect this in maf/vcf 2) should be represented as cnv deletion but not the legacy unused value "dtdel"; if needed can reenable
-  ["splice_acceptor_variant", "L"],
-  ["splice_donor_variant", "L"],
-  ["stop_gained", "N"],
-  ["frameshift_variant", "F"],
-  ["stop_lost", "StopLost"],
-  ["start_lost", "StartLost"],
-  //transcript_amplification // not supported, should be represented by cnv instead
-  ["feature_elongation", mclassnoncoding],
-  ["feature_truncation", mclassnoncoding],
-  ["inframe_insertion", "I"],
-  ["inframe_deletion", "D"],
-  ["missense_variant", "M"],
-  ["protein_altering_variant", "ProteinAltering"],
-  ["splice_donor_5th_base_variant", "P"],
-  ["splice_region_variant", "P"],
-  ["splice_donor_region_variant", "P"],
-  ["splice_polypyrimidine_tract_variant", "P"],
-  ["incomplete_terminal_codon_variant", "N"],
-  ["start_retained_variant", "S"],
-  ["stop_retained_variant", "S"],
-  ["synonymous_variant", "S"],
-  ["coding_sequence_variant", "E"],
-  ["mature_miRNA_variant", "E"],
-  ["5_prime_UTR_variant", mclassutr5],
-  ["3_prime_UTR_variant", mclassutr3],
-  ["non_coding_transcript_exon_variant", "E"],
-  ["intron_variant", "Intron"],
-  ["NMD_transcript_variant", "F"],
-  ["non_coding_transcript_variant", "E"],
-  ["coding_transcript_variant", "E"],
-  ["upstream_gene_variant", mclassnoncoding],
-  ["downstream_gene_variant", mclassnoncoding],
-  ["TFBS_ablation", mclassnoncoding],
-  ["TFBS_amplification", mclassnoncoding],
-  ["TF_binding_site_variant", mclassnoncoding],
-  ["regulatory_region_ablation", mclassnoncoding],
-  ["regulatory_region_amplification", mclassnoncoding],
-  ["regulatory_region_variant", mclassnoncoding],
-  ["intergenic_variant", mclassnoncoding],
-  ["sequence_variant", mclassnonstandard]
-];
-var class2SOterm = /* @__PURE__ */ new Map();
-for (const [csq, cls] of SOterms) {
-  if (!class2SOterm.has(cls)) class2SOterm.set(cls, []);
-  class2SOterm.get(cls).push(csq);
-}
-var SOterm2class = /* @__PURE__ */ new Map();
-for (const [csq, cls] of SOterms) {
-  SOterm2class.set(csq, cls);
-}
-function mclasstester(s) {
-  switch (s.toLowerCase()) {
-    case "missense_mutation":
-      return "M";
-    case "nonsense_mutation":
-      return "N";
-    case "splice_site":
-      return "L";
-    case "splice_region":
-      return "P";
-    case "rna":
-      return mclassnoncoding;
-    case "frame_shift_del":
-      return "F";
-    case "frame_shift_ins":
-      return "F";
-    case "in_frame_del":
-      return "D";
-    case "in_frame_ins":
-      return "I";
-    case "protein_altering_variant":
-      return "ProteinAltering";
-    case "translation_start_site":
-      return mclassnonstandard;
-    case "nonstop_mutation":
-      return "N";
-    case "3'utr":
-      return mclassutr3;
-    case "3'flank":
-      return mclassnoncoding;
-    case "5'utr":
-      return mclassutr5;
-    case "5'flank":
-      return mclassnoncoding;
-    case "silent":
-      return "S";
-    case "blank":
-      return "Blank";
-    default:
-      return null;
-  }
-}
-var mclassfusionrna = "Fuserna";
-mclass[mclassfusionrna] = {
-  label: "Fusion transcript",
-  color: "#545454",
-  dt: dtfusionrna,
-  desc: `Marks the break points leading to fusion transcripts.<br><span style="font-size:150%">&#9680;</span> - 3' end of the break point is fused to the 5' end of another break point in a different gene.<br><span style="font-size:150%">&#9681;</span> - 5' end of the break point is fused to the 3' end of another break point in a different gene.`,
-  key: mclassfusionrna
-};
-var mclasssv = "SV";
-mclass[mclasssv] = {
-  label: "Structural variation",
-  color: "#858585",
-  dt: dtsv,
-  desc: `<span style="font-size:150%">&#9680;</span> - 3' end of the break point is fused to the 5' end of another break point in a different gene.<br><span style="font-size:150%">&#9681;</span> - 5' end of the break point is fused to the 3' end of another break point in a different gene.`,
-  key: mclasssv
-};
-var mclasscnvgain = "CNV_amp";
-mclass[mclasscnvgain] = {
-  label: "Copy number gain",
-  // TODO change to 'Gain'
-  color: "#e9a3c9",
-  dt: dtcnv,
-  desc: "Copy number gain",
-  key: mclasscnvgain
-};
-var mclasscnvloss = "CNV_loss";
-mclass[mclasscnvloss] = {
-  label: "Copy number loss",
-  color: "#a1d76a",
-  dt: dtcnv,
-  desc: "Copy number loss",
-  key: mclasscnvloss
-};
-var mclasscnvAmp = "CNV_amplification";
-mclass[mclasscnvAmp] = {
-  label: "Copy number amplification",
-  color: "#ff0000",
-  dt: dtcnv,
-  desc: "Copy number amplification",
-  key: mclasscnvAmp
-};
-var mclasscnvHomozygousDel = "CNV_homozygous_deletion";
-mclass[mclasscnvHomozygousDel] = {
-  label: "Copy number homozygous deletion",
-  color: "#0000ff",
-  dt: dtcnv,
-  desc: "Copy number homozygous deletion",
-  key: mclasscnvHomozygousDel
-};
-var mclasscnvloh = "CNV_loh";
-mclass[mclasscnvloh] = { label: "LOH", color: "#12EDFC", dt: dtcnv, desc: "Loss of heterozygosity", key: mclasscnvloh };
-var mclasssnv = "snv";
-mclass[mclasssnv] = {
-  label: "SNV",
-  color: "#92a2d4",
-  dt: dtsnvindel,
-  desc: "Single nucleotide variation",
-  key: mclasssnv
-};
-var mclassmnv = "mnv";
-mclass[mclassmnv] = {
-  label: "MNV",
-  color: "#92a2d4",
-  dt: dtsnvindel,
-  desc: "Multiple nucleotide variation",
-  key: mclassmnv
-};
-var mclassinsertion = "insertion";
-mclass[mclassinsertion] = {
-  label: "Sequence insertion",
-  color: "#bd8e91",
-  dt: dtsnvindel,
-  desc: "Sequence insertion",
-  key: mclassinsertion
-};
-var mclassdeletion = "deletion";
-mclass[mclassdeletion] = {
-  label: "Sequence deletion",
-  color: "#b5a174",
-  dt: dtsnvindel,
-  desc: "Sequence deletion",
-  key: mclassdeletion
-};
-function mds3tkMclass(k) {
-  if (k == dtcnv) {
-    return {
-      color: "#858585",
-      label: "CNV",
-      desc: "Copy number variation"
-    };
-  }
-  return mclass[k];
-}
-var dt2color = {
-  [dtsnvindel]: mclass.M.color
-  // general color for snvindel irrespective of class (when class is not available)
-  // add new dt as needed
-};
-function applyOverrides(overrides = {}) {
-  if (overrides.mclass) {
-    for (const key in overrides.mclass) {
-      if (!mclass[key]) mclass[key] = {};
-      for (const subkey in overrides.mclass[key]) {
-        mclass[key][subkey] = overrides.mclass[key][subkey];
-      }
-    }
-  }
-}
-var vepinfo = function(s) {
-  const l = s.toLowerCase().split(",");
-  let rank = 1;
-  if (l.indexOf("transcript_ablation") != -1) {
-    return [dtdel, mclassdel, rank];
-  }
-  rank++;
-  if (l.indexOf("splice_acceptor_variant") != -1) return [dtsnvindel, "L", rank];
-  rank++;
-  if (l.indexOf("splice_donor_variant") != -1) return [dtsnvindel, "L", rank];
-  rank++;
-  if (l.indexOf("stop_gained") != -1) return [dtsnvindel, "N", rank];
-  rank++;
-  if (l.indexOf("frameshift_variant") != -1) return [dtsnvindel, "F", rank];
-  rank++;
-  if (l.indexOf("stop_lost") != -1) return [dtsnvindel, "N", rank];
-  rank++;
-  if (l.indexOf("start_lost") != -1) return [dtsnvindel, "N", rank];
-  rank++;
-  if (l.indexOf("transcript_amplification") != -1) {
-    return [dtsnvindel, mclassnonstandard, rank];
-  }
-  rank++;
-  if (l.indexOf("inframe_insertion") != -1 || l.indexOf("conservative_inframe_insertion") != -1 || l.indexOf("disruptive_inframe_insertion") != -1)
-    return [dtsnvindel, "I", rank];
-  rank++;
-  if (l.indexOf("inframe_deletion") != -1 || l.indexOf("conservative_inframe_deletion") != -1 || l.indexOf("disruptive_inframe_deletion") != -1)
-    return [dtsnvindel, "D", rank];
-  rank++;
-  if (l.indexOf("missense_variant") != -1) return [dtsnvindel, "M", rank];
-  rank++;
-  if (l.indexOf("protein_altering_variant") != -1) return [dtsnvindel, "ProteinAltering", rank];
-  rank++;
-  if (l.indexOf("splice_region_variant") != -1) return [dtsnvindel, "P", rank];
-  rank++;
-  if (l.indexOf("incomplete_terminal_codon_variant") != -1) return [dtsnvindel, "N", rank];
-  rank++;
-  if (l.indexOf("stop_retained_variant") != -1) return [dtsnvindel, "S", rank];
-  rank++;
-  if (l.indexOf("synonymous_variant") != -1) return [dtsnvindel, "S", rank];
-  rank++;
-  if (l.indexOf("coding_sequence_variant") != -1) return [dtsnvindel, mclassnonstandard, rank];
-  rank++;
-  if (l.indexOf("mature_mirna_variant") != -1) return [dtsnvindel, "E", rank];
-  rank++;
-  if (l.indexOf("5_prime_utr_variant") != -1) return [dtsnvindel, mclassutr5, rank];
-  rank++;
-  if (l.indexOf("3_prime_utr_variant") != -1) return [dtsnvindel, mclassutr3, rank];
-  rank++;
-  if (l.indexOf("non_coding_transcript_exon_variant") != -1) return [dtsnvindel, "E", rank];
-  rank++;
-  if (l.indexOf("intron_variant") != -1) return [dtsnvindel, "Intron", rank];
-  rank++;
-  if (l.indexOf("nmd_transcript_variant") != -1) return [dtsnvindel, "S", rank];
-  rank++;
-  if (l.indexOf("non_coding_transcript_variant") != -1) return [dtsnvindel, "E", rank];
-  rank++;
-  if (l.indexOf("upstream_gene_variant") != -1) return [dtsnvindel, mclassnoncoding, rank];
-  rank++;
-  if (l.indexOf("downstream_gene_variant") != -1) return [dtsnvindel, mclassnoncoding, rank];
-  rank++;
-  if (l.indexOf("tfbs_ablation") != -1) return [dtsnvindel, mclassnoncoding, rank];
-  rank++;
-  if (l.indexOf("tfbs_amplification") != -1) return [dtsnvindel, mclassnoncoding, rank];
-  rank++;
-  if (l.indexOf("tf_binding_site_variant") != -1) return [dtsnvindel, mclassnoncoding, rank];
-  rank++;
-  if (l.indexOf("regulatory_region_ablation") != -1) return [dtsnvindel, mclassnoncoding, rank];
-  rank++;
-  if (l.indexOf("regulatory_region_amplification") != -1) return [dtsnvindel, mclassnoncoding, rank];
-  rank++;
-  if (l.indexOf("feature_elongation") != -1) return [dtsnvindel, mclassnoncoding, rank];
-  rank++;
-  if (l.indexOf("regulatory_region_variant") != -1) return [dtsnvindel, mclassnoncoding, rank];
-  rank++;
-  if (l.indexOf("feature_truncation") != -1) return [dtsnvindel, mclassnoncoding, rank];
-  rank++;
-  if (l.indexOf("intergenic_variant") != -1) return [dtsnvindel, mclassnoncoding, rank];
-  rank++;
-  return [dtsnvindel, mclassnonstandard, rank];
-};
-var germlinelegend = '<circle cx="7" cy="12" r="7" fill="#b1b1b1"></circle><path d="M6.735557395310443e-16,-11A11,11 0 0,1 11,0L9,0A9,9 0 0,0 5.51091059616309e-16,-9Z" transform="translate(7,12)" fill="#858585" stroke="none"></path>';
-var morigin = {};
-var moriginsomatic = "S";
-morigin[moriginsomatic] = {
-  label: "Somatic",
-  desc: "A variant found only in a tumor sample. The proportion is indicated by lack of any arc.",
-  legend: '<circle cx="7" cy="12" r="7" fill="#b1b1b1"></circle>'
-};
-var morigingermline = "G";
-morigin[morigingermline] = {
-  label: "Germline",
-  desc: "A constitutional variant found in a normal sample. The proportion is indicated by the span of the solid arc within the whole circle.",
-  legend: germlinelegend
-};
-morigin.germline = morigin[morigingermline];
-morigin.somatic = morigin[moriginsomatic];
-var moriginrelapse = "R";
-morigin[moriginrelapse] = {
-  label: "Relapse",
-  desc: "A somatic variant found only in a relapse sample. The proportion is indicated by the span of the hollow arc within the whole circle.",
-  legend: '<circle cx="7" cy="12" r="7" fill="#b1b1b1"></circle><path d="M6.735557395310443e-16,-11A11,11 0 0,1 11,0L9,0A9,9 0 0,0 5.51091059616309e-16,-9Z" transform="translate(7,12)" fill="none" stroke="#858585"></path>'
-};
-var morigingermlinepathogenic = "GP";
-morigin[morigingermlinepathogenic] = {
-  label: "Germline pathogenic",
-  desc: "A constitutional variant with pathogenic allele.",
-  legend: germlinelegend
-};
-var morigingermlinenonpathogenic = "GNP";
-morigin[morigingermlinenonpathogenic] = {
-  label: "Germline non-pathogenic",
-  desc: "A constitutional variant with non-pathogenic allele.",
-  legend: germlinelegend,
-  hidden: true
-};
-var tkt = {
-  usegm: "usegm",
-  ds: "dataset",
-  bigwig: "bigwig",
-  bigwigstranded: "bigwigstranded",
-  junction: "junction",
-  mdsjunction: "mdsjunction",
-  mdssvcnv: "mdssvcnv",
-  // replaced by mds3
-  mdsexpressionrank: "mdsexpressionrank",
-  mdsvcf: "mdsvcf",
-  // for snv/indels, currently vcf, may include MAF
-  //mdsgeneral:'mdsgeneral', // replaces mdssvcnv   ****** not ready yet
-  bedj: "bedj",
-  pgv: "profilegenevalue",
-  bampile: "bampile",
-  hicstraw: "hicstraw",
-  expressionrank: "expressionrank",
-  aicheck: "aicheck",
-  ase: "ase",
-  mds3: "mds3",
-  //
-  bedgraphdot: "bedgraphdot",
-  bam: "bam",
-  ld: "ld"
-};
-function validtkt(what) {
-  for (const k in tkt) {
-    if (what == tkt[k]) {
-      return true;
-    }
-  }
-  return false;
-}
-var mdsvcftype = {
-  vcf: "vcf"
-};
-var custommdstktype = {
-  vcf: "vcf",
-  svcnvitd: "svcnvitd",
-  geneexpression: "geneexpression"
-};
-var codon = {
-  GCT: "A",
-  GCC: "A",
-  GCA: "A",
-  GCG: "A",
-  CGT: "R",
-  CGC: "R",
-  CGA: "R",
-  CGG: "R",
-  AGA: "R",
-  AGG: "R",
-  AAT: "N",
-  AAC: "N",
-  GAT: "D",
-  GAC: "D",
-  TGT: "C",
-  TGC: "C",
-  CAA: "Q",
-  CAG: "Q",
-  GAA: "E",
-  GAG: "E",
-  GGT: "G",
-  GGC: "G",
-  GGA: "G",
-  GGG: "G",
-  CAT: "H",
-  CAC: "H",
-  ATT: "I",
-  ATC: "I",
-  ATA: "I",
-  TTA: "L",
-  TTG: "L",
-  CTT: "L",
-  CTC: "L",
-  CTA: "L",
-  CTG: "L",
-  AAA: "K",
-  AAG: "K",
-  ATG: "M",
-  TTT: "F",
-  TTC: "F",
-  CCT: "P",
-  CCC: "P",
-  CCA: "P",
-  CCG: "P",
-  TCT: "S",
-  TCC: "S",
-  TCA: "S",
-  TCG: "S",
-  AGT: "S",
-  AGC: "S",
-  ACT: "T",
-  ACC: "T",
-  ACA: "T",
-  ACG: "T",
-  TGG: "W",
-  TAT: "Y",
-  TAC: "Y",
-  GTT: "V",
-  GTC: "V",
-  GTA: "V",
-  GTG: "V"
-};
-var codon_stop = "*";
-function nt2aa(gm) {
-  if (!gm.genomicseq) return void 0;
-  const enlst = [];
-  if (gm.coding) {
-    for (const [i, e] of gm.coding.entries()) {
-      const s = gm.genomicseq.substr(e[0] - gm.start, e[1] - e[0]);
-      if (gm.strand == "-") {
-        enlst.push(reversecompliment(s));
-      } else {
-        enlst.push(s);
-      }
-    }
-  }
-  const nt = enlst.join("");
-  const pep = [];
-  const startntidx = gm.startCodonFrame ? 3 - gm.startCodonFrame : 0;
-  for (let i = startntidx; i < nt.length; i += 3) {
-    const a = codon[nt.substr(i, 3)];
-    pep.push(a || codon_stop);
-  }
-  gm.cdseq = nt;
-  return pep.join("");
-}
-function bplen(len, isfile) {
-  if (len >= 1e9) return (len / 1e9).toFixed(1) + " Gb";
-  if (len >= 1e7) return Math.ceil(len / 1e6) + " Mb";
-  if (len >= 1e6) return (len / 1e6).toFixed(1) + " Mb";
-  if (len >= 1e4) return Math.ceil(len / 1e3) + " Kb";
-  if (len >= 1e3) return (len / 1e3).toFixed(1) + " Kb";
-  return len + (isfile ? "bytes" : " bp");
-}
-var basecolor = {
-  A: "#ca0020",
-  T: "#f4a582",
-  C: "#92c5de",
-  G: "#0571b0"
-};
-function basecompliment(nt) {
-  switch (nt) {
-    case "A":
-      return "T";
-    case "T":
-      return "A";
-    case "C":
-      return "G";
-    case "G":
-      return "C";
-    case "a":
-      return "t";
-    case "t":
-      return "a";
-    case "c":
-      return "g";
-    case "g":
-      return "c";
-    default:
-      return nt;
-  }
-}
-function reversecompliment(s) {
-  const tmp = [];
-  for (let i = s.length - 1; i >= 0; i--) {
-    tmp.push(basecompliment(s[i]));
-  }
-  return tmp.join("");
-}
-function spliceeventchangegmexon(gm, evt) {
-  const gm2 = {
-    chr: gm.chr,
-    start: gm.start,
-    stop: gm.stop,
-    strand: gm.strand,
-    coding: []
-  };
-  if (evt.isskipexon || evt.isaltexon) {
-    for (let i = 0; i < gm.exon.length; i++) {
-      const codingstart = Math.max(gm.codingstart, gm.exon[i][0]);
-      const codingstop = Math.min(gm.codingstop, gm.exon[i][1]);
-      if (codingstart > codingstop) {
-        continue;
-      }
-      if (evt.skippedexon.indexOf(i) == -1) {
-        gm2.coding.push([codingstart, codingstop]);
-      } else {
-      }
-    }
-  } else if (evt.a5ss || evt.a3ss) {
-    const exons = gm.exon.map((e) => [e[0], e[1]]);
-    const forward = gm.strand == "+";
-    if (evt.a5ss) {
-      if (forward) {
-        exons[evt.exon5idx][1] = evt.junctionB.start;
-      } else {
-        exons[evt.exon5idx + 1][0] = evt.junctionB.stop;
-      }
-    } else {
-      if (forward) {
-        exons[evt.exon5idx + 1][0] = evt.junctionB.stop;
-      } else {
-        exons[evt.exon5idx][1] = evt.junctionB.start;
-      }
-    }
-    for (const e of exons) {
-      const codingstart = Math.max(gm.codingstart, e[0]);
-      const codingstop = Math.min(gm.codingstop, e[1]);
-      if (codingstart > codingstop) {
-        continue;
-      }
-      gm2.coding.push([codingstart, codingstop]);
-    }
-  }
-  return gm2;
-}
-function fasta2gmframecheck(gm, str) {
-  const lines = str.split("\n");
-  lines.shift();
-  gm.genomicseq = lines.join("").toUpperCase();
-  const aaseq = nt2aa(gm);
-  let thisframe = OUT_frame;
-  const stopcodonidx = aaseq.indexOf(codon_stop);
-  if (stopcodonidx == aaseq.length - 1) {
-    thisframe = IN_frame;
-  }
-  return thisframe;
-}
-function validate_vcfinfofilter(obj) {
-  if (!obj.lst) return ".lst missing";
-  if (!Array.isArray(obj.lst)) return "input is not an array";
-  for (const set of obj.lst) {
-    if (!set.name) return "name missing from a set of .vcfinfofilter.lst";
-    if (set.autocategory || set.categories) {
-      if (!set.autocategory) {
-        for (const k in set.categories) {
-          const v = set.categories[k];
-          if (!set.autocolor && !v.color)
-            return ".color missing for class " + k + " from .categories of set " + set.name;
-          if (!v.label) {
-            v.label = k;
-          }
-        }
-      }
-      if (set.categoryhidden) {
-        for (const k in set.categoryhidden) {
-          if (!set.categories[k]) return "unknown hidden-by-default category " + k + " from set " + set.name;
-        }
-      } else {
-        set.categoryhidden = {};
-      }
-    } else if (set.numericfilter) {
-      const lst = [];
-      for (const v of set.numericfilter) {
-        if (typeof v == "number") {
-          lst.push({ side: "<", value: v });
-        } else {
-          lst.push({
-            side: v.side || "<",
-            value: v.value
-          });
-        }
-      }
-      set.numericfilter = lst;
-    }
-    if (set.altalleleinfo) {
-      if (!set.altalleleinfo.key) {
-        return ".key missing from .altalleleinfo from set " + set.name;
-      }
-    } else if (set.locusinfo) {
-      if (!set.locusinfo.key) {
-        return ".key missing from .locusinfo from set " + set.name;
-      }
-    } else {
-      return "neither .altalleleinfo or .locusinfo is available from set " + set.name;
-    }
-  }
-}
-function contigNameNoChr(genome, chrlst) {
-  for (const n in genome.majorchr) {
-    if (chrlst.indexOf(n.replace("chr", "")) != -1) {
-      return true;
-    }
-  }
-  if (genome.minorchr) {
-    for (const n in genome.minorchr) {
-      if (chrlst.indexOf(n.replace("chr", "")) != -1) {
-        return true;
-      }
-    }
-  }
-  return false;
-}
-function contigNameNoChr2(genome, chrlst) {
-  let nochrcount = 0, haschrcount = 0;
-  for (const n in genome.majorchr) {
-    if (chrlst.includes(n)) {
-      haschrcount++;
-    } else if (chrlst.includes(n.replace("chr", ""))) {
-      nochrcount++;
-    }
-  }
-  if (genome.minorchr) {
-    for (const n in genome.minorchr) {
-      if (chrlst.includes(n)) {
-        haschrcount++;
-      } else if (chrlst.includes(n.replace("chr", ""))) {
-        nochrcount++;
-      }
-    }
-  }
-  return [nochrcount, haschrcount];
-}
-function getMax_byiqr(lst, novaluemax) {
-  if (lst.length == 0) return novaluemax;
-  lst.sort((i, j) => i - j);
-  const max = lst[lst.length - 1];
-  if (lst.length <= 5) return max;
-  const q1 = lst[Math.floor(lst.length / 4)];
-  const q2 = lst[Math.floor(lst.length * 3 / 4)];
-  return Math.min(q2 + (q2 - q1) * 1.5, max);
-}
-function alleleInGenotypeStr(genotype, allele) {
-  if (!genotype) return false;
-  if (genotype.indexOf("/") != -1) {
-    return genotype.split("/").indexOf(allele) != -1;
-  }
-  return genotype.split("|").indexOf(allele) != -1;
-}
-var gmmode = {
-  genomic: "genomic",
-  splicingrna: "splicing RNA",
-  // if just 1 exon, use "RNA" as label
-  exononly: "exon only",
-  protein: "protein",
-  gmsum: "aggregated exons"
-};
-function vcfcopymclass(m, block) {
-  if (m.csq) {
-    let useone;
-    if (block.usegm) {
-      useone = m.csq.find((i) => i._isoform == block.usegm.isoform);
-    }
-    if (!useone) {
-      useone = m.csq.find((i) => i.CANONICAL);
-      if (!useone) {
-        useone = m.csq[0];
-        for (const q of m.csq) {
-          if (q._csqrank < useone._csqrank) {
-            useone = q;
-          }
-        }
-      }
-    }
-    if (useone) {
-      m.gene = useone._gene;
-      m.isoform = useone._isoform;
-      m.class = useone._class;
-      m.dt = useone._dt;
-      m.mname = useone._mname;
-      if (m.class == mclassnoncoding) {
-        delete m.class;
-      }
-    }
-  } else if (m.ann) {
-    let useone = null;
-    if (block.usegm) {
-      for (const q of m.ann) {
-        if (q._isoform != block.usegm.isoform) continue;
-        if (useone) {
-          if (q._csqrank < useone._csqrank) {
-            useone = q;
-          }
-        } else {
-          useone = q;
-        }
-      }
-      if (!useone && block.gmmode == gmmode.genomic) {
-        useone = m.ann[0];
-      }
-    } else {
-      useone = m.ann[0];
-      for (const q of m.ann) {
-        if (q._csqrank < useone._csqrank) {
-          useone = q;
-        }
-      }
-    }
-    if (useone) {
-      m.gene = useone._gene;
-      m.isoform = useone._isoform;
-      m.class = useone._class;
-      m.dt = useone._dt;
-      m.mname = useone._mname;
-      if (m.class == mclassnoncoding) {
-        delete m.class;
-      }
-    }
-  }
-  if (m.class == void 0) {
-    if (mclass[m.type]) {
-      m.class = m.type;
-      m.dt = mclass[m.type].dt;
-      m.mname = m.id && m.id != "." ? m.id : m.ref + ">" + m.alt;
-      if (m.mname.length > 15) {
-        m.mname = m.type;
-      }
-    } else {
-      m.class = mclassnonstandard;
-      m.dt = dtsnvindel;
-      m.mname = m.type;
-    }
-  }
-  delete m.type;
-}
-var not_annotated = "Unannotated";
-function kernelDensityEstimator(kernel, X) {
-  return function(V) {
-    return X.map((x) => {
-      return [x, V.map((v) => kernel(x - v)).reduce((i, j) => i + j, 0) / V.length];
-    });
-  };
-}
-function kernelEpanechnikov(k) {
-  return function(v) {
-    return Math.abs(v /= k) <= 1 ? 0.75 * (1 - v * v) / k : 0;
-  };
-}
-var schemeCategory20 = [
-  "#1f77b4",
-  "#aec7e8",
-  "#ff7f0e",
-  "#ffbb78",
-  "#2ca02c",
-  "#98df8a",
-  "#d62728",
-  "#ff9896",
-  "#9467bd",
-  "#c5b0d5",
-  "#8c564b",
-  "#c49c94",
-  "#e377c2",
-  "#f7b6d2",
-  "#7f7f7f",
-  "#c7c7c7",
-  "#bcbd22",
-  "#dbdb8d",
-  "#17becf",
-  "#9edae5"
-];
-var schemeCategory2 = ["#e75480", "blue"];
-function getColorScheme(number) {
-  if (number > 20) {
-    const scheme = [];
-    for (let i = 0; i < number; i++) scheme.push(rainbow_default(i / number));
-    return scheme;
-  }
-  if (number > 12) return schemeCategory20;
-  else if (number > 8) return Paired_default;
-  else if (number > 2) return Dark2_default;
-  else return schemeCategory2;
-}
-function getColors(number) {
-  const scheme = getColorScheme(number);
-  return ordinal(scheme);
-}
-var proteinDomainColors = [
-  "#8dd3c7",
-  "#bebada",
-  "#fb8072",
-  "#80b1d3",
-  "#E8E89E",
-  "#a6d854",
-  "#fdb462",
-  "#ffd92f",
-  "#e5c494",
-  "#b3b3b3"
-];
-function proteinDomainColorScale() {
-  return ordinal().range(proteinDomainColors);
-}
-var truncatingMutations = ["F", "N", "L", "P"];
-var proteinChangingMutations = ["F", "N", "L", "P", "D", "I", "ProteinAltering", "M"];
-var synonymousMutations = ["S", "Intron", "Utr3", "Utr5", "noncoding", "E"];
-var mutationClasses = Object.values(mclass).filter((m) => m.dt == dtsnvindel).map((m) => m.key);
-var CNVClasses = Object.values(mclass).filter((m) => m.dt == dtcnv).map((m) => m.key);
-var dtTerms_temp = [
-  {
-    id: "snvindel",
-    query: "snvindel",
-    name: dt2label[dtsnvindel],
-    parent_id: null,
-    isleaf: true,
-    type: "dtsnvindel",
-    dt: dtsnvindel,
-    values: {}
-  },
-  {
-    id: "cnv",
-    query: "cnv",
-    name: dt2label[dtcnv],
-    parent_id: null,
-    isleaf: true,
-    type: "dtcnv",
-    dt: dtcnv,
-    values: {}
-  },
-  {
-    id: "fusion",
-    query: "svfusion",
-    name: dt2label[dtfusionrna],
-    parent_id: null,
-    isleaf: true,
-    type: "dtfusion",
-    dt: dtfusionrna,
-    values: {}
-  },
-  {
-    id: "sv",
-    query: "svfusion",
-    name: dt2label[dtsv],
-    parent_id: null,
-    isleaf: true,
-    type: "dtsv",
-    dt: dtsv,
-    values: {}
-  }
-];
-var dtTerms_temp2 = [];
-for (const dtTerm of dtTerms_temp) {
-  dtTerm.name_noOrigin = dtTerm.name;
-  dtTerms_temp2.push(dtTerm);
-  for (const origin of ["somatic", "germline"]) {
-    const addOrigin = {
-      id: `${dtTerm.id}_${origin}`,
-      name: `${dtTerm.name} (${origin})`,
-      origin
-    };
-    dtTerms_temp2.push(Object.assign({}, dtTerm, addOrigin));
-  }
-}
-var dtTerms = dtTerms_temp2;
-var colorScaleMap = {
-  blueWhiteRed: { domain: [0, 0.5, 1], range: ["blue", "white", "red"] },
-  greenWhiteRed: { domain: [0, 0.5, 1], range: ["green", "white", "red"] },
-  blueYellowRed: {
-    domain: [0, 0.17, 0.33, 0.5, 0.67, 0.83, 1],
-    range: ["#313695", "#649AC7", "#BCE1ED", "#FFFFBF", "#FDBE70", "#EA5839", "#A50026"]
-  },
-  greenBlackRed: {
-    domain: [0, 0.17, 0.33, 0.5, 0.67, 0.83, 1],
-    range: ["#00FF00", "#14E10C", "#1AAF10", "#000000", "#B01205", "#E20E03", "#FF0000"]
-  },
-  blueBlackYellow: {
-    domain: [0, 0.17, 0.33, 0.5, 0.67, 0.83, 1],
-    range: ["#0000FF", "#0000CC", "#000099", "#202020", "#999900", "#CCCC00", "#FFFF00"]
-  },
-  // when hierCluster z-score transformation is not performed, should use two-color scale
-  whiteRed: { domain: [0, 1], range: ["white", "red"] }
-};
-function invalidcoord(thisgenome, chrom, start, stop) {
-  if (!thisgenome) return "no genome";
-  if (!chrom) return "no chr name";
-  const chr = thisgenome.chrlookup[chrom.toUpperCase()];
-  if (!chr) return "Invalid chromosome name: " + chr;
-  if (!Number.isInteger(start)) return "Non-numerical position: " + start;
-  if (start < 0 || start >= chr.len) return "Position out of range: " + start;
-  if (!Number.isInteger(stop)) return "Non-numerical position: " + stop;
-  if (stop < 0 || stop > chr.len) return "Position out of range: " + stop;
-  if (start > stop) return "Start position is greater than stop";
-  return false;
-}
-function string2pos(s, genome, donotextend) {
-  s = s.replace(/,/g, "");
-  const chr = genome.chrlookup[s.toUpperCase()];
-  if (chr) {
-    return {
-      chr: chr.name,
-      chrlen: chr.len,
-      start: Math.max(0, Math.ceil(chr.len / 2) - 1e4),
-      stop: Math.min(chr.len, Math.ceil(chr.len / 2) + 1e4)
-    };
-  }
-  {
-    const tmp2 = s.split(".");
-    if (tmp2.length >= 2) {
-      const chr2 = genome.chrlookup[tmp2[0].toUpperCase()];
-      const pos = Number.parseInt(tmp2[1]);
-      const e = invalidcoord(genome, tmp2[0], pos, pos + 1);
-      if (!e) {
-        const bpspan = 400;
-        return {
-          chr: chr2.name,
-          chrlen: chr2.len,
-          start: Math.max(0, pos - Math.ceil(bpspan / 2)),
-          stop: Math.min(chr2.len, pos + Math.ceil(bpspan / 2)),
-          actualposition: { position: pos, len: 1 }
-        };
-      }
-    }
-  }
-  const tmp = s.split(/[-:\s]+/);
-  if (tmp.length == 2) {
-    const pos = Number.parseInt(tmp[1]);
-    const e = invalidcoord(genome, tmp[0], pos, pos + 1);
-    if (e) {
-      return null;
-    }
-    const chr2 = genome.chrlookup[tmp[0].toUpperCase()];
-    const bpspan = 400;
-    return {
-      chr: chr2.name,
-      chrlen: chr2.len,
-      start: Math.max(0, pos - Math.ceil(bpspan / 2)),
-      stop: Math.min(chr2.len, pos + Math.ceil(bpspan / 2)),
-      actualposition: { position: pos, len: 1 }
-    };
-  }
-  if (tmp.length == 3) {
-    let start = Number.parseInt(tmp[1]), stop = Number.parseInt(tmp[2]);
-    const e = invalidcoord(genome, tmp[0], start, stop);
-    if (e) {
-      return null;
-    }
-    const actualposition = { position: start, len: stop - start };
-    const chr2 = genome.chrlookup[tmp[0].toUpperCase()];
-    if (!donotextend) {
-      const minspan = 400;
-      if (stop - start < minspan) {
-        let center = Math.ceil((start + stop) / 2);
-        if (center + minspan / 2 >= chr2.len) {
-          center = chr2.len - Math.ceil(minspan / 2);
-        }
-        start = Math.max(0, center - Math.ceil(minspan / 2));
-        stop = start + minspan;
-      }
-    }
-    return {
-      chr: chr2.name,
-      chrlen: chr2.len,
-      start,
-      stop,
-      actualposition
-    };
-  }
-  return null;
-}
-
-export {
-  getFilteredSamples,
-  sample_match_termvaluesetting,
-  getWrappedTvslst,
-  validateTermCollectionTvs,
-  TermTypeGroups,
-  defaultcolor,
-  default_text_color,
-  exoncolor,
-  plotColor,
-  IN_frame,
-  OUT_frame,
-  dtsnvindel,
-  dtfusionrna,
-  dtgeneexpression,
-  dtcnv,
-  dtsv,
-  dtitd,
-  dtdel,
-  dtnloss,
-  dtcloss,
-  dtloh,
-  dtmetaboliteintensity,
-  dtssgsea,
-  dtdnamethylation,
-  dtproteomeabundance,
-  dt2label,
-  dt2lesion,
-  mclass,
-  mclassitd,
-  mclassdel,
-  mclassnloss,
-  mclasscloss,
-  mclassutr3,
-  mclassutr5,
-  mclassnonstandard,
-  class2SOterm,
-  mclasstester,
-  mclassfusionrna,
-  mclasssv,
-  mclasscnvgain,
-  mclasscnvloss,
-  mclasscnvAmp,
-  mclasscnvHomozygousDel,
-  mclasscnvloh,
-  mclasssnv,
-  mclassmnv,
-  mclassinsertion,
-  mclassdeletion,
-  mds3tkMclass,
-  dt2color,
-  applyOverrides,
-  vepinfo,
-  morigin,
-  moriginsomatic,
-  morigingermline,
-  moriginrelapse,
-  morigingermlinepathogenic,
-  morigingermlinenonpathogenic,
-  tkt,
-  validtkt,
-  codon_stop,
-  nt2aa,
-  bplen,
-  basecolor,
-  basecompliment,
-  spliceeventchangegmexon,
-  validate_vcfinfofilter,
-  contigNameNoChr,
-  contigNameNoChr2,
-  getMax_byiqr,
-  alleleInGenotypeStr,
-  gmmode,
-  vcfcopymclass,
-  getColors,
-  proteinDomainColorScale,
-  truncatingMutations,
-  proteinChangingMutations,
-  synonymousMutations,
-  mutationClasses,
-  CNVClasses,
-  dtTerms,
-  colorScaleMap,
-  common_exports
-};
-//# sourceMappingURL=chunk-IGEQI6MR.js.map