@sjcrh/proteinpaint-shared 2.186.0 → 2.188.0

package/dist/src/common.js

@@ -0,0 +1,1302 @@
+import { rgb } from "d3-color";
+import * as d3scale from "d3-scale";
+import * as d3 from "d3";
+import { getWrappedTvslst } from "./filter.js";
+class TermTypeGroups {
+  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 = "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);
+const defaultcolor = rgb("#8AB1D4").darker();
+const default_text_color = rgb("#aaa").darker().darker();
+const exoncolor = "#4F8053";
+const plotColor = "#ce768e";
+const IN_frame = true;
+const OUT_frame = false;
+const dtsnvindel = 1;
+const dtfusionrna = 2;
+const dtgeneexpression = 3;
+const dtcnv = 4;
+const dtsv = 5;
+const dtitd = 6;
+const dtdel = 7;
+const dtnloss = 8;
+const dtcloss = 9;
+const dtloh = 10;
+const dtmetaboliteintensity = 11;
+const dtssgsea = 12;
+const dtdnamethylation = 13;
+const dtproteomeabundance = 14;
+const 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]: "Proteome Abundance"
+};
+const 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" }]
+  }
+};
+const optionToDt = {
+  snvindelOptions: dtsnvindel,
+  cnvOptions: dtcnv,
+  fusionOptions: dtfusionrna,
+  svOptions: dtsv
+};
+const 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" }
+};
+const mclassitd = "ITD";
+mclass[mclassitd] = {
+  label: "ITD",
+  color: "#ff70ff",
+  dt: dtitd,
+  desc: "In-frame internal tandem duplication.",
+  key: mclassitd
+};
+const mclassdel = "DEL";
+mclass[mclassdel] = {
+  label: "DELETION, intragenic",
+  color: "#858585",
+  dt: dtdel,
+  desc: "Intragenic deletion.",
+  key: mclassdel
+};
+const mclassnloss = "NLOSS";
+mclass[mclassnloss] = {
+  label: "N-terminus loss",
+  color: "#545454",
+  dt: dtnloss,
+  desc: "N-terminus loss due to translocation",
+  key: mclassnloss
+};
+const mclasscloss = "CLOSS";
+mclass[mclasscloss] = {
+  label: "C-terminus loss",
+  color: "#545454",
+  dt: dtcloss,
+  desc: "C-terminus loss due to translocation",
+  key: mclasscloss
+};
+const mclassutr3 = "Utr3";
+mclass[mclassutr3] = {
+  label: "UTR_3",
+  color: "#998199",
+  dt: dtsnvindel,
+  desc: "A variant in the 3' untranslated region.",
+  key: mclassutr3
+};
+const mclassutr5 = "Utr5";
+mclass[mclassutr5] = {
+  label: "UTR_5",
+  color: "#819981",
+  dt: dtsnvindel,
+  desc: "A variant in the 5' untranslated region.",
+  key: mclassutr5
+};
+const 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
+};
+const mclassnoncoding = "noncoding";
+mclass[mclassnoncoding] = {
+  label: "NONCODING",
+  color: "black",
+  dt: dtsnvindel,
+  desc: "Noncoding mutation.",
+  key: mclassnoncoding
+};
+const 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]
+];
+const class2SOterm = /* @__PURE__ */ new Map();
+for (const [csq, cls] of SOterms) {
+  if (!class2SOterm.has(cls)) class2SOterm.set(cls, []);
+  class2SOterm.get(cls).push(csq);
+}
+const 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;
+  }
+}
+const 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
+};
+const 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
+};
+const mclasscnvgain = "CNV_amp";
+mclass[mclasscnvgain] = {
+  label: "Copy number gain",
+  // TODO change to 'Gain'
+  color: "#e9a3c9",
+  dt: dtcnv,
+  desc: "Copy number gain",
+  key: mclasscnvgain
+};
+const mclasscnvloss = "CNV_loss";
+mclass[mclasscnvloss] = {
+  label: "Copy number loss",
+  color: "#a1d76a",
+  dt: dtcnv,
+  desc: "Copy number loss",
+  key: mclasscnvloss
+};
+const mclasscnvAmp = "CNV_amplification";
+mclass[mclasscnvAmp] = {
+  label: "Copy number amplification",
+  color: "#ff0000",
+  dt: dtcnv,
+  desc: "Copy number amplification",
+  key: mclasscnvAmp
+};
+const mclasscnvHomozygousDel = "CNV_homozygous_deletion";
+mclass[mclasscnvHomozygousDel] = {
+  label: "Copy number homozygous deletion",
+  color: "#0000ff",
+  dt: dtcnv,
+  desc: "Copy number homozygous deletion",
+  key: mclasscnvHomozygousDel
+};
+const mclasscnvloh = "CNV_loh";
+mclass[mclasscnvloh] = { label: "LOH", color: "#12EDFC", dt: dtcnv, desc: "Loss of heterozygosity", key: mclasscnvloh };
+const mclasssnv = "snv";
+mclass[mclasssnv] = {
+  label: "SNV",
+  color: "#92a2d4",
+  dt: dtsnvindel,
+  desc: "Single nucleotide variation",
+  key: mclasssnv
+};
+const mclassmnv = "mnv";
+mclass[mclassmnv] = {
+  label: "MNV",
+  color: "#92a2d4",
+  dt: dtsnvindel,
+  desc: "Multiple nucleotide variation",
+  key: mclassmnv
+};
+const mclassinsertion = "insertion";
+mclass[mclassinsertion] = {
+  label: "Sequence insertion",
+  color: "#bd8e91",
+  dt: dtsnvindel,
+  desc: "Sequence insertion",
+  key: mclassinsertion
+};
+const 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];
+}
+const 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];
+      }
+    }
+  }
+}
+const 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];
+};
+const 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>';
+const morigin = {};
+const 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>'
+};
+const 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];
+const 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>'
+};
+const morigingermlinepathogenic = "GP";
+morigin[morigingermlinepathogenic] = {
+  label: "Germline pathogenic",
+  desc: "A constitutional variant with pathogenic allele.",
+  legend: germlinelegend
+};
+const morigingermlinenonpathogenic = "GNP";
+morigin[morigingermlinenonpathogenic] = {
+  label: "Germline non-pathogenic",
+  desc: "A constitutional variant with non-pathogenic allele.",
+  legend: germlinelegend,
+  hidden: true
+};
+const 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;
+}
+const mdsvcftype = {
+  vcf: "vcf"
+};
+const custommdstktype = {
+  vcf: "vcf",
+  svcnvitd: "svcnvitd",
+  geneexpression: "geneexpression"
+};
+const 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"
+};
+const 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");
+}
+const 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;
+}
+const 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;
+}
+const 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;
+  };
+}
+const schemeCategory20 = [
+  "#1f77b4",
+  "#aec7e8",
+  "#ff7f0e",
+  "#ffbb78",
+  "#2ca02c",
+  "#98df8a",
+  "#d62728",
+  "#ff9896",
+  "#9467bd",
+  "#c5b0d5",
+  "#8c564b",
+  "#c49c94",
+  "#e377c2",
+  "#f7b6d2",
+  "#7f7f7f",
+  "#c7c7c7",
+  "#bcbd22",
+  "#dbdb8d",
+  "#17becf",
+  "#9edae5"
+];
+const schemeCategory2 = ["#e75480", "blue"];
+function getColorScheme(number) {
+  if (number > 20) {
+    const scheme = [];
+    for (let i = 0; i < number; i++) scheme.push(d3.interpolateRainbow(i / number));
+    return scheme;
+  }
+  if (number > 12) return schemeCategory20;
+  else if (number > 8) return d3.schemePaired;
+  else if (number > 2) return d3.schemeDark2;
+  else return schemeCategory2;
+}
+function getColors(number) {
+  const scheme = getColorScheme(number);
+  return d3scale.scaleOrdinal(scheme);
+}
+const proteinDomainColors = [
+  "#8dd3c7",
+  "#bebada",
+  "#fb8072",
+  "#80b1d3",
+  "#E8E89E",
+  "#a6d854",
+  "#fdb462",
+  "#ffd92f",
+  "#e5c494",
+  "#b3b3b3"
+];
+function proteinDomainColorScale() {
+  return d3scale.scaleOrdinal().range(proteinDomainColors);
+}
+const truncatingMutations = ["F", "N", "L", "P"];
+const proteinChangingMutations = ["F", "N", "L", "P", "D", "I", "ProteinAltering", "M"];
+const synonymousMutations = ["S", "Intron", "Utr3", "Utr5", "noncoding", "E"];
+const mutationClasses = Object.values(mclass).filter((m) => m.dt == dtsnvindel).map((m) => m.key);
+const CNVClasses = Object.values(mclass).filter((m) => m.dt == dtcnv).map((m) => m.key);
+const 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: {}
+  }
+];
+const 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));
+  }
+}
+const dtTerms = dtTerms_temp2;
+const 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 {
+  CNVClasses,
+  IN_frame,
+  OUT_frame,
+  SOterm2class,
+  TermTypeGroups,
+  alleleInGenotypeStr,
+  applyOverrides,
+  basecolor,
+  basecompliment,
+  bplen,
+  class2SOterm,
+  codon,
+  codon_stop,
+  colorScaleMap,
+  contigNameNoChr,
+  contigNameNoChr2,
+  custommdstktype,
+  default_text_color,
+  defaultcolor,
+  dt2color,
+  dt2label,
+  dt2lesion,
+  dtTerms,
+  dtcloss,
+  dtcnv,
+  dtdel,
+  dtdnamethylation,
+  dtfusionrna,
+  dtgeneexpression,
+  dtitd,
+  dtloh,
+  dtmetaboliteintensity,
+  dtnloss,
+  dtproteomeabundance,
+  dtsnvindel,
+  dtssgsea,
+  dtsv,
+  exoncolor,
+  fasta2gmframecheck,
+  germlinelegend,
+  getColorScheme,
+  getColors,
+  getMax_byiqr,
+  gmmode,
+  invalidcoord,
+  kernelDensityEstimator,
+  kernelEpanechnikov,
+  mclass,
+  mclasscloss,
+  mclasscnvAmp,
+  mclasscnvHomozygousDel,
+  mclasscnvgain,
+  mclasscnvloh,
+  mclasscnvloss,
+  mclassdel,
+  mclassdeletion,
+  mclassfusionrna,
+  mclassinsertion,
+  mclassitd,
+  mclassmnv,
+  mclassnloss,
+  mclassnoncoding,
+  mclassnonstandard,
+  mclasssnv,
+  mclasssv,
+  mclasstester,
+  mclassutr3,
+  mclassutr5,
+  mds3tkMclass,
+  mdsvcftype,
+  morigin,
+  morigingermline,
+  morigingermlinenonpathogenic,
+  morigingermlinepathogenic,
+  moriginrelapse,
+  moriginsomatic,
+  mutationClasses,
+  not_annotated,
+  nt2aa,
+  optionToDt,
+  plotColor,
+  proteinChangingMutations,
+  proteinDomainColorScale,
+  reversecompliment,
+  schemeCategory2,
+  schemeCategory20,
+  spliceeventchangegmexon,
+  string2pos,
+  synonymousMutations,
+  tkt,
+  truncatingMutations,
+  validate_vcfinfofilter,
+  validtkt,
+  vcfcopymclass,
+  vepinfo
+};
+//# sourceMappingURL=common.js.map