@sjcrh/proteinpaint-client 2.200.0 → 2.202.0

package/dist/chunk-UUKSL7QC.js

@@ -1,134 +0,0 @@
-import {
-  addGeneSearchbox,
-  isoformSelect,
-  pickCollectionFraction,
-  sayerror
-} from "./chunk-TKW5TW4Z.js";
-import {
-  Menu
-} from "./chunk-HYOEWQ5P.js";
-import {
-  dofetch3
-} from "./chunk-JVPWIVDT.js";
-import {
-  ISOFORM_EXPRESSION,
-  getColors
-} from "./chunk-6PNPHACF.js";
-
-// termdb/handlers/isoformExpression.ts
-var SearchHandler = class {
-  constructor() {
-    this.currentGene = null;
-  }
-  init(opts) {
-    this.callback = opts.callback;
-    this.app = opts.app;
-    this.termCollectionSelectionMode = opts.termCollectionSelectionMode;
-    const holder = opts.holder.append("div").style("padding", "10px 0px");
-    this.dom = {
-      errDiv: holder.append("div").style("margin", "5px 0px").style("display", "none")
-    };
-    const geneSearch = addGeneSearchbox({
-      tip: new Menu({ padding: "0px" }),
-      genome: opts.genomeObj,
-      row: holder,
-      searchOnly: "gene",
-      callback: async () => {
-        try {
-          this.dom.errDiv.style("display", "none");
-          if (!geneSearch.geneSymbol) throw new Error("No gene selected");
-          if (geneSearch.geneSymbol === this.currentGene) return;
-          this.currentGene = geneSearch.geneSymbol;
-          if (this.dom.isoformDiv) this.dom.isoformDiv.remove();
-          this.dom.isoformDiv = holder.append("div");
-          await this.showIsoforms(geneSearch.geneSymbol, opts.genomeObj);
-        } catch (e) {
-          this.dom.errDiv.style("display", "block");
-          sayerror(this.dom.errDiv, "Error: " + (e instanceof Error ? e.message : String(e)));
-        }
-      }
-    });
-  }
-  async showIsoforms(gene, genomeObj) {
-    if (!gene) throw new Error("No gene selected");
-    const data = await dofetch3("genelookup", { body: { genome: genomeObj.name, input: gene, deep: 1 } });
-    if (!data.gmlst?.length) throw new Error(`No isoforms found for ${gene}`);
-    const enstCandidates = data.gmlst.filter((gm) => gm.isoform?.startsWith("ENST"));
-    if (enstCandidates.length === 0) throw new Error(`No Ensembl transcript isoforms found for ${gene}`);
-    const { available } = await dofetch3("termdb/isoformAvailability", {
-      body: {
-        genome: genomeObj.name,
-        dslabel: this.app.vocabApi.vocab.dslabel,
-        isoforms: enstCandidates.map((gm) => gm.isoform)
-      }
-    });
-    const availableSet = new Set(available || []);
-    const enstModels = enstCandidates.filter((gm) => availableSet.has(gm.isoform));
-    if (enstModels.length === 0) throw new Error(`No isoforms with data found for ${gene}`);
-    if (gene !== this.currentGene) return;
-    const div = this.dom.isoformDiv;
-    div.append("div").style("margin-bottom", "8px").style("opacity", 0.65).text(`${gene} \u2014 select isoform(s):`);
-    isoformSelect({
-      holder: div,
-      allgm: enstModels,
-      multiSelect: true,
-      // a single checked isoform yields an individual term, 2+ yield a collection
-      getSubmitLabel: (selectedCount) => selectedCount === 1 ? "Select One Isoform" : `Create Collection (${selectedCount})`,
-      onMultiSelect: (selected) => {
-        if (selected.length === 1) {
-          this.selectIsoform(selected[0].isoform, gene);
-        } else {
-          this.selectCollection(selected, gene);
-        }
-      }
-    });
-  }
-  getUnit() {
-    return this.app.vocabApi.termdbConfig.queries.isoformExpression?.unit || "TPM";
-  }
-  selectIsoform(isoform, gene) {
-    const name = `${isoform} ${this.getUnit()}`;
-    this.callback({ isoform, gene, name, type: ISOFORM_EXPRESSION });
-  }
-  selectCollection(gms, gene) {
-    const unit = this.getUnit();
-    const termlst = gms.map((gm) => ({
-      id: gm.isoform,
-      name: gm.isoform,
-      type: ISOFORM_EXPRESSION,
-      isoform: gm.isoform
-    }));
-    const colorScale = getColors(termlst.length);
-    const term = {
-      type: "termCollection",
-      isCustom: true,
-      memberType: "numeric",
-      name: `${gene} Isoforms (${unit})`,
-      termlst,
-      propsByTermId: Object.fromEntries(termlst.map((term2) => [term2.id, { color: colorScale(term2.id) }])),
-      isleaf: true
-    };
-    if (this.termCollectionSelectionMode === "fraction") {
-      if (!this.dom?.isoformDiv) throw new Error("isoform result holder is missing");
-      this.dom.fractionDiv?.remove();
-      this.dom.fractionDiv = this.dom.isoformDiv.append("div").style("margin-top", "10px");
-      pickCollectionFraction({
-        holder: this.dom.fractionDiv,
-        term,
-        callback: (tw) => this.callback(tw)
-      });
-      return;
-    }
-    this.callback(term);
-  }
-};
-function filterIsoforms(gmlst, availableItems) {
-  const itemSet = new Set(availableItems);
-  return gmlst.filter((gm) => gm.isoform?.startsWith("ENST") && (itemSet.size === 0 || itemSet.has(gm.isoform)));
-}
-
-export {
-  SearchHandler,
-  filterIsoforms
-};
-//# sourceMappingURL=chunk-UUKSL7QC.js.map

package/dist/chunk-VUPWQCDR.js

@@ -1,194 +0,0 @@
-import {
-  sample_match_termvaluesetting
-} from "./chunk-GNS6CQMA.js";
-import {
-  isDictionaryType
-} from "./chunk-7JRDJNLR.js";
-import {
-  __export
-} from "./chunk-HFNDKYVF.js";
-
-// plots/matrix/matrix.data.js
-var matrix_data_exports = {};
-__export(matrix_data_exports, {
-  applyLegendValueFilter: () => applyLegendValueFilter,
-  getMatrixRequestOpts: () => getMatrixRequestOpts,
-  mayRequireToken: () => mayRequireToken,
-  setData: () => setData
-});
-function mayRequireToken(tokenMessage = "") {
-  const message = tokenMessage || this.state.tokenVerificationMessage;
-  if (!message && this.state.hasVerifiedToken) {
-    this.dom.errdiv.style("display", "none").html();
-    this.dom.controls.style("display", this.opts.controls ? "inline-block" : "");
-    this.dom.svg.style("display", "");
-    return false;
-  } else {
-    this.dom.errdiv.style("display", "").html(message || "Requires login");
-    this.dom.controls.style("display", "none");
-    this.dom.svg.style("display", "none");
-    return true;
-  }
-}
-function getMatrixRequestOpts(state, config) {
-  const terms = [];
-  const termgroups = this.chartType == "hierCluster" ? config.termgroups.filter((grp) => grp.type != "hierCluster") : config.termgroups;
-  for (const grp of termgroups) {
-    terms.push(...getNormalizedTwLstCopy(grp.lst));
-  }
-  if (config.divideBy) terms.push(normalizeTwForRequest(structuredClone(config.divideBy)));
-  const opts = {
-    terms,
-    filter: state.filter,
-    filter0: state.filter0,
-    maxGenes: state.config.settings.matrix.maxGenes,
-    /*********** quick fix
-    when the flag is true, set artificially large number to ensure all genes are sent in one query
-    this avoids changing getAnnotatedSampleData()
-    additional non-matrix app that calls getAnnotatedSampleData will NEED THE SAME FIX
-    */
-    termsPerRequest: this.app.vocabApi.termdbConfig.queries?.snvindel?.byisoform?.processTwsInOneQuery ? 1e3 : 1
-  };
-  if (this.chartType == "hierCluster") {
-    opts.isHierCluster = 1;
-  }
-  return opts;
-}
-function getNormalizedTwLstCopy(twlst) {
-  const lst = [];
-  for (const tw of twlst) {
-    if (tw.type && tw.constructor.name != "Object") lst.push(tw);
-    else lst.push(normalizeTwForRequest(tw));
-  }
-  lst.forEach(normalizeTwForRequest);
-  lst.sort(sortTwLst);
-  return lst;
-}
-function normalizeTwForRequest(_tw) {
-  const tw = structuredClone(_tw);
-  if (!tw?.term) return;
-  delete tw.term.category2samplecount;
-  if (isDictionaryType(tw.term.type) && tw.term.type !== "samplelst") delete tw.term.values;
-  return tw;
-}
-function sortTwLst(twa, twb) {
-  const a = twa?.$id || twa.term?.id || twa?.term?.name;
-  const b = twb?.$id || twb.term?.id || twb?.term?.name;
-  return a < b ? -1 : 1;
-}
-async function setData(_data) {
-  const opts = this.currRequestOpts?.matrix || this.getMatrixRequestOpts(this.state, this.config);
-  this.numTerms = opts.terms.length;
-  opts.loadingDiv = this.chartType != "hierCluster" && this.dom.loadingDiv;
-  opts.signal = this.api.getAbortSignal();
-  const data = await this.app.vocabApi.getAnnotatedSampleData(opts, _data);
-  this.data = data;
-  this.origData = structuredClone(this.data);
-  this.sampleIdMap = {};
-  for (const d of this.data.lst) {
-    this.sampleIdMap[d.sample] = d._ref_.label;
-  }
-}
-function applyLegendValueFilter() {
-  const self = this;
-  if (!self.config.legendValueFilter.lst.length && !self.config.legendGrpFilter.lst.length) return;
-  for (const grpFilter of self.config.legendGrpFilter.lst) {
-    if (grpFilter.dt) {
-      const filteredOutCats = /* @__PURE__ */ new Set();
-      for (const oneSampleData of self.origData.lst) {
-        for (const annoForOneTerm of Object.values(oneSampleData)) {
-          if (annoForOneTerm.values) {
-            const newValues = [];
-            for (const v of annoForOneTerm.values) {
-              if (!(grpFilter.dt.includes(v.dt) && (!grpFilter.origin || v.origin == grpFilter.origin))) {
-                newValues.push(v);
-              } else {
-                filteredOutCats.add(v.class);
-              }
-            }
-            annoForOneTerm.values = newValues;
-          }
-        }
-      }
-      grpFilter.filteredOutCats = [...filteredOutCats];
-      for (const oneSampleData of Object.values(self.origData.samples)) {
-        for (const annoForOneTerm of Object.values(oneSampleData)) {
-          if (annoForOneTerm.values)
-            annoForOneTerm.values = annoForOneTerm.values.filter(
-              (v) => !(grpFilter.dt.includes(v.dt) && (!grpFilter.origin || v.origin == grpFilter.origin))
-            );
-        }
-      }
-    }
-  }
-  const geneVariant$ids = Object.values(self.data.refs.byTermId).filter((v) => v.term?.type == "geneVariant").map((v) => v.$id);
-  const data = { samples: {}, lst: [], refs: self.data.refs };
-  const onlyHardFilter = structuredClone(self.config.legendValueFilter);
-  onlyHardFilter.lst = onlyHardFilter.lst.filter(
-    (l) => !l.tvs.legendFilterType || l.tvs.legendFilterType !== "geneVariant_soft"
-  );
-  for (const row of self.origData.lst) {
-    const include = sample_match_termvaluesetting(row, onlyHardFilter, geneVariant$ids);
-    if (include || self.chartType == "hierCluster") {
-      data.samples[row.sample] = row;
-      data.lst.push(row);
-    }
-  }
-  for (const valFilter of self.config.legendValueFilter.lst) {
-    if (valFilter.tvs.legendFilterType !== "geneVariant_soft") continue;
-    const tvsV = valFilter.tvs.values[0];
-    const filteredOutCats = /* @__PURE__ */ new Set();
-    for (const oneSampleData of data.lst) {
-      for (const annoForOneTerm of Object.values(oneSampleData)) {
-        if (annoForOneTerm.values) {
-          const newValues = [];
-          for (const v of annoForOneTerm.values) {
-            if (!(v.dt == tvsV.dt && (!tvsV.origin || v.origin == tvsV.origin) && tvsV.mclasslst.includes(v.class))) {
-              newValues.push(v);
-            } else {
-              filteredOutCats.add(v.class);
-            }
-          }
-          annoForOneTerm.values = newValues;
-        }
-      }
-    }
-    valFilter.filteredOutCats = [...filteredOutCats];
-    for (const oneSampleData of Object.values(data.samples)) {
-      for (const annoForOneTerm of Object.values(oneSampleData)) {
-        if (annoForOneTerm.values)
-          annoForOneTerm.values = annoForOneTerm.values.filter(
-            (v) => !(v.dt == tvsV.dt && (!tvsV.origin || v.origin == tvsV.origin) && tvsV.mclasslst.includes(v.class))
-          );
-      }
-    }
-  }
-  if (self.chartType !== "hierCluster" && geneVariant$ids.length && self.app.vocabApi.termdbConfig?.matrix?.removeEmptySamples)
-    remove_empty_sample(data, geneVariant$ids);
-  self.data = data;
-}
-function remove_empty_sample(data) {
-  for (const oneSampleData of data.lst) {
-    let removeSample = true;
-    for (const [key, annoForOneTerm] of Object.entries(oneSampleData)) {
-      if (!annoForOneTerm.values) continue;
-      const annoType = data.refs.byTermId[key].term.type;
-      if (annoType != "geneVariant") continue;
-      if (annoForOneTerm.values.length) removeSample = false;
-    }
-    if (removeSample) {
-      data.lst = data.lst.filter((dl) => dl.sample !== oneSampleData.sample);
-      delete data.samples[parseInt(oneSampleData.sample)];
-    }
-  }
-  return data;
-}
-
-export {
-  mayRequireToken,
-  getMatrixRequestOpts,
-  setData,
-  applyLegendValueFilter,
-  matrix_data_exports
-};
-//# sourceMappingURL=chunk-VUPWQCDR.js.map

package/dist/chunk-W76X6W73.js

@@ -1,100 +0,0 @@
-import {
-  SearchHandler,
-  fillTermWrapper,
-  table2col,
-  termsettingInit
-} from "./chunk-TKW5TW4Z.js";
-
-// plots/summarizeMutationDiagnosis.ts
-async function makeChartBtnMenu(holder, chartsInstance) {
-  let dictTw;
-  {
-    const t = chartsInstance.app.vocabApi.termdbConfig.defaultTw4correlationPlot?.disease;
-    if (!t) throw "defaultTw4correlationPlot missing";
-    dictTw = structuredClone(t);
-    await fillTermWrapper(dictTw, chartsInstance.app.vocabApi);
-  }
-  const table = table2col({
-    holder: holder.append("div"),
-    margin: "0px 10px 10px 10px",
-    cellPadding: "10px"
-  });
-  {
-    const [td1, td2] = table.addRow();
-    td1.text("Mutation Variable");
-    const searchDiv = td2.append("div");
-    const geneSearchInst = new SearchHandler();
-    geneSearchInst.init({
-      holder: searchDiv,
-      app: chartsInstance.app,
-      // required to supply "opts.app.vocabApi" for the search ui
-      genomeObj: chartsInstance.app.opts.genome,
-      msg: "Hit ENTER to launch plot.",
-      callback: async (geneTw) => {
-        await fillTermWrapper(geneTw, chartsInstance.app.vocabApi);
-        launchPlot({
-          tw1: dictTw,
-          tw2: geneTw,
-          chartsInstance,
-          holder
-        });
-      }
-    });
-    searchDiv.style("padding", "0px 0px 5px 0px");
-  }
-  {
-    const [td1, td2] = table.addRow();
-    td1.text("Compare Mutations Against");
-    const pillDiv = td2.append("div"), waitDiv = td2.append("div").style("font-size", ".7em").text("LOADING ...");
-    const pill = await termsettingInit({
-      menuOptions: "{edit,replace}",
-      /** presumably this usecase let it restrict to dictionary term ui, and hide genomic queries
-      target="filter" works for gdc since in gdc ds it is overriding filter to dict
-      but is not a general fix for non-gdc ds, which Replace menu will launch genomic+dict options
-      maybe this is okay for non-gdc ds as the default dictTw is meaningful
-      */
-      usecase: { target: "filter" },
-      vocabApi: chartsInstance.app.vocabApi,
-      holder: pillDiv,
-      callback: async (tw) => {
-        waitDiv.text("LOADING ...");
-        try {
-          await pill.main(tw);
-          dictTw = tw;
-          waitDiv.text("Click to edit/replace the variable before searching gene.");
-        } catch (e) {
-          waitDiv.text("Error: " + (e.message || e));
-        }
-      }
-    });
-    try {
-      await fillTermWrapper(dictTw, chartsInstance.app.vocabApi);
-      await pill.main(dictTw);
-      waitDiv.text("Click to edit/replace the variable before searching gene.");
-    } catch (e) {
-      waitDiv.text("Error: " + (e.message || e));
-    }
-  }
-}
-function launchPlot({ tw1, tw2, chartsInstance, holder }) {
-  const chart = {
-    config: {
-      chartType: tw1?.term?.type == "survival" ? "survival" : "summary",
-      // TODO define sandbox header with gene+term name
-      term: tw1,
-      term2: tw2
-    }
-  };
-  chartsInstance.plotCreate(chart);
-  holder.selectAll("*").remove();
-  holder.append("div").style("margin", "20px").text("LOADING CHART ...");
-  setTimeout(() => {
-    holder.style("display", "none");
-  }, 1e3);
-}
-
-export {
-  makeChartBtnMenu,
-  launchPlot
-};
-//# sourceMappingURL=chunk-W76X6W73.js.map

package/dist/chunk-W7OS7BNM.js

@@ -1,203 +0,0 @@
-import {
-  tkt
-} from "./chunk-TKW5TW4Z.js";
-import {
-  stratinput
-} from "./chunk-PF4DSFDR.js";
-import {
-  stratify_default
-} from "./chunk-VQZ2Z5YU.js";
-
-// src/vcf.tkconvert.js
-function vcf2dstk(arg) {
-  const ds = {
-    id2vcf: {},
-    label: arg.name || "Unnamed VCF file"
-  };
-  let vcfobj;
-  if (arg.file) {
-    const id = Math.random().toString();
-    vcfobj = {
-      file: arg.file,
-      indexURL: arg.indexURL,
-      vcfid: id
-    };
-    ds.id2vcf[id] = vcfobj;
-  } else if (arg.url) {
-    const id = Math.random().toString();
-    vcfobj = {
-      url: arg.url,
-      indexURL: arg.indexURL,
-      vcfid: id
-    };
-    ds.id2vcf[id] = vcfobj;
-  } else {
-    return ["no .file or .url"];
-  }
-  vcfobj.headernotloaded = true;
-  if (arg.samplenamemap) {
-    vcfobj.samplenamemap = arg.samplenamemap;
-  }
-  if (arg.variant2img) {
-    if (!arg.variant2img.path) return [".path missing from .variant2img{}"];
-  }
-  const tk = {
-    type: tkt.ds,
-    // to be loaded by loadvcftk() as a custom track, rather than "/dsdata" for official ds
-    isvcf: true,
-    name: ds.label,
-    ds,
-    populationfrequencyfilter: arg.populationfrequencyfilter,
-    vcfinfofilter: arg.vcfinfofilter,
-    itemlabelname: arg.itemlabelname,
-    viewrangeupperlimit: arg.viewrangeupperlimit,
-    variant2img: arg.variant2img,
-    axisheight: arg.axisheight
-  };
-  if (arg.url4variant) {
-    const err = check_url4variant(arg.url4variant);
-    if (err) return [".url4variant error: " + err];
-    tk.url4variant = arg.url4variant;
-  }
-  if (arg.button4variant) {
-    const err = check_button4variant(arg.button4variant);
-    if (err) return [".button4variant error: " + err];
-    tk.button4variant = arg.button4variant;
-  }
-  if (arg.sampleannotation) {
-    const sn = arg.sampleannotation;
-    if (!sn.annotation) return [".annotation{} missing from .sampleannotation"];
-    if (sn.levels) {
-      if (!Array.isArray(sn.levels)) return [".sampleannotation.levels should be array"];
-      const lst = [];
-      for (const sample in sn.annotation) {
-        const o = { sample_name: sample };
-        for (const k in sn.annotation[sample]) {
-          o[k] = sn.annotation[sample][k];
-        }
-        lst.push(o);
-      }
-      const nodes = stratinput(lst, sn.levels);
-      sn.root = stratify_default()(nodes);
-      sn.root.sum((i) => i.value);
-    }
-    if (sn.variantsunburst) {
-      if (!sn.levels) return [".levels missing when .variantsunburst is on from .sampleannotation"];
-    }
-    tk.ds.cohort = sn;
-  }
-  if (arg.vcfcohorttrack) {
-    if (!arg.vcfcohorttrack.file && !arg.vcfcohorttrack.url) return ["no .file or .url provided from .vcfcohorttrack"];
-    tk.ds.vcfcohorttrack = arg.vcfcohorttrack;
-  }
-  if (arg.germline2dvafplot) {
-    if (!arg.germline2dvafplot.individualkey) return [".individualkey missing from germline2dvafplot"];
-    if (!arg.germline2dvafplot.sampletypekey) return [".sampletypekey missing from germline2dvafplot"];
-    if (!arg.germline2dvafplot.xsampletype) return [".xsampletype missing from germline2dvafplot"];
-    if (!arg.germline2dvafplot.yleftsampletype) return [".yleftsampletype missing from germline2dvafplot"];
-    if (arg.germline2dvafplot.yrightsampletype) {
-      if (arg.germline2dvafplot.yrightsampletype == arg.germline2dvafplot.yleftsampletype)
-        return [".yrightsampletype should not be same as yleftsampletype"];
-    }
-    tk.ds.germline2dvafplot = arg.germline2dvafplot;
-  }
-  if (arg.vaf2coverageplot) {
-    if (arg.vaf2coverageplot.categorykey) {
-      if (!arg.vaf2coverageplot.categories)
-        return [".categories missing when .categorykey is in use for .vaf2coverageplot"];
-    }
-    tk.ds.vaf2coverageplot = arg.vaf2coverageplot;
-  }
-  if (arg.genotype2boxplot) {
-    if (arg.genotype2boxplot.boxplotvaluekey) {
-    } else if (arg.genotype2boxplot.sampleannotationkey) {
-      if (!tk.ds.cohort) return ["sampleannotation missing when using genotype2boxplot.sampleannotationkey"];
-      if (!tk.ds.cohort.annotation)
-        return ["sampleannotation.annotation missing when using genotype2boxplot.sampleannotationkey"];
-      let found = false;
-      for (const k in tk.ds.cohort.annotation) {
-        if (arg.genotype2boxplot.sampleannotationkey in tk.ds.cohort.annotation[k]) {
-          found = true;
-          break;
-        }
-      }
-      if (!found) return [arg.genotype2boxplot.sampleannotationkey + " not found in any sample annotation"];
-    } else {
-      return ["incomplete instruction for genotype2boxplot"];
-    }
-    tk.ds.genotype2boxplot = arg.genotype2boxplot;
-  }
-  if (arg.discardsymbolicallele) {
-    tk.ds.discardsymbolicallele = true;
-  }
-  if (arg.samplebynumericvalue) {
-    if (!arg.samplebynumericvalue.attrkey) return ["attrkey missing from samplebynumericvalue"];
-    if (!tk.ds.cohort) return ["sampleannotation missing when using samplebynumericvalue"];
-    if (!tk.ds.cohort.annotation) return ["sampleannotation.annotation missing when using samplebynumericvalue"];
-    let found = false;
-    for (const k in tk.ds.cohort.annotation) {
-      if (Number.isFinite(tk.ds.cohort.annotation[k][arg.samplebynumericvalue.attrkey])) {
-        found = true;
-        break;
-      }
-    }
-    if (!found) return ["samplebynumericvalue.attrkey not found in any sample annotation"];
-    tk.ds.samplebynumericvalue = arg.samplebynumericvalue;
-  }
-  {
-    const g = arg.genotypebynumericvalue;
-    if (g) {
-      if (!g.refref) return [tk.name + ": refref missing from genotypebynumericvalue"];
-      if (!g.refalt) return [tk.name + ": refalt missing from genotypebynumericvalue"];
-      if (!g.altalt) return [tk.name + ": altalt missing from genotypebynumericvalue"];
-      if (!g.refref.infokey) return [tk.name + ": refref.infokey missing from genotypebynumericvalue"];
-      if (!g.refalt.infokey) return [tk.name + ": refalt.infokey missing from genotypebynumericvalue"];
-      if (!g.altalt.infokey) return [tk.name + ": altalt.infokey missing from genotypebynumericvalue"];
-      if (g.refref.genotypeCountInfokey || g.refalt.genotypeCountInfokey || g.altalt.genotypeCountInfokey) {
-        if (!g.refref.genotypeCountInfokey)
-          return [tk.name + ": genotypeCountInfokey missing from genotypebynumericvalue.refref{}"];
-        if (!g.refalt.genotypeCountInfokey)
-          return [tk.name + ": genotypeCountInfokey missing from genotypebynumericvalue.refalt{}"];
-        if (!g.altalt.genotypeCountInfokey)
-          return [tk.name + ": genotypeCountInfokey missing from genotypebynumericvalue.altalt{}"];
-      }
-      tk.ds.genotypebynumericvalue = g;
-    }
-  }
-  if (arg.pointdown) {
-    tk.aboveprotein = false;
-  }
-  if (arg.dstk_novcferror) {
-    tk.dstk_novcferror = true;
-  }
-  return [null, tk];
-}
-function check_url4variant(lst) {
-  if (!Array.isArray(lst)) return "value is not an array";
-  for (const item of lst) {
-    if (!item.makeurl) {
-      return ".makeurl missing";
-    }
-    if (typeof item.makeurl != "function") {
-      return ".makeurl must be a function";
-    }
-  }
-  return false;
-}
-function check_button4variant(lst) {
-  if (!Array.isArray(lst)) return "value is not an array";
-  for (const item of lst) {
-    if (!item.makebutton) {
-      return ".makebutton missing";
-    }
-    if (typeof item.makebutton != "function") {
-      return ".makebutton must be a function";
-    }
-  }
-  return false;
-}
-
-export {
-  vcf2dstk
-};
-//# sourceMappingURL=chunk-W7OS7BNM.js.map

package/dist/chunk-WKNI3HRQ.js

@@ -1,39 +0,0 @@
-import {
-  isNumeric
-} from "./chunk-JNITUVXP.js";
-
-// common/urlmap.js
-function urlmap_default(search = "", log = console.warn) {
-  const location = search ? { search } : window.location;
-  const urlp = /* @__PURE__ */ new Map();
-  for (const s of location.search.substr(1).split("&")) {
-    if (!s) continue;
-    const l = s.split("=");
-    if (l.length == 2 && l[0] != "" && l[1] != "") {
-      let value = decodeURIComponent(l[1]);
-      if (
-        // assume JSON encoding when the string is enclosed by matching characters below
-        value.startsWith('"') && value.endsWith('"') || value.startsWith("{") && value.endsWith("}") || value.startsWith("[") && value.endsWith("]")
-      ) {
-        try {
-          value = JSON.parse(value);
-        } catch (e) {
-          log(e);
-        }
-      } else if (isNumeric(value)) {
-        value = Number(value);
-      }
-      urlp.set(l[0].toLowerCase(), value);
-    } else if (l.length > 2) {
-      log(`unexpected '=' character in the URL parameter value for '${l[0]}'`);
-    } else {
-      log(`Invalid url parameter: '${s}'`);
-    }
-  }
-  return urlp;
-}
-
-export {
-  urlmap_default
-};
-//# sourceMappingURL=chunk-WKNI3HRQ.js.map