@sjcrh/proteinpaint-client 2.207.1 → 2.209.0

package/dist/chunk-EKQ7NYOU.js

@@ -1,276 +0,0 @@
-import {
-  parsesample
-} from "./chunk-52QHIKH2.js";
-import {
-  dtfusionrna,
-  dtsv,
-  mclassfusionrna,
-  mclasssv
-} from "./chunk-RUBZCKIX.js";
-
-// ../shared/utils/dist/src/bulk.sv.js
-function parseheader(line, flag, issv) {
-  const header = line.toLowerCase().split("	");
-  if (header.length <= 1) return "invalid file header for fusions";
-  const htry = (...lst) => {
-    for (const a of lst) {
-      const j = header.indexOf(a);
-      if (j != -1) return j;
-    }
-    return -1;
-  };
-  let i = htry("gene_a", "gene1", "genea");
-  if (i == -1) return "gene_a missing from header";
-  header[i] = "gene1";
-  i = htry("gene_b", "gene2", "geneb");
-  if (i == -1) return "gene_b missing from header";
-  header[i] = "gene2";
-  i = htry("chr_a", "chr1", "chra");
-  if (i == -1) return "chr_a missing from header";
-  header[i] = "chr1";
-  i = htry("chr_b", "chr2", "chrb");
-  if (i == -1) return "chr_b missing from header";
-  header[i] = "chr2";
-  i = htry("pos_a", "position_a", "position1", "posa");
-  if (i == -1) return "pos_a missing from header";
-  header[i] = "position1";
-  i = htry("pos_b", "position_b", "position2", "posb");
-  if (i == -1) return "pos_b missing from header";
-  header[i] = "position2";
-  i = htry("isoform_a", "refseq_a", "refseq1", "isoform1", "sv_refseqa");
-  if (i == -1) return "isoform_a missing from header";
-  header[i] = "isoform1";
-  i = htry("isoform_b", "refseq_b", "refseq2", "isoform2", "sv_refseqb");
-  if (i == -1) return "isoform_b missing from header";
-  header[i] = "isoform2";
-  i = htry("strand_a", "orta");
-  if (i == -1) return "strand_a missing from header";
-  header[i] = "strand1";
-  i = htry("strand_b", "ortb");
-  if (i == -1) return "strand_b missing from header";
-  header[i] = "strand2";
-  i = htry("sample", "sample_name", "tumor_sample_barcode");
-  if (i != -1) header[i] = "sample";
-  i = htry("patient", "donor", "target_case_id");
-  if (i != -1) header[i] = "patient";
-  i = htry("sampletype", "sample type", "sample_type");
-  if (i != -1) header[i] = "sampletype";
-  i = htry("disease");
-  if (i != -1) header[i] = "disease";
-  i = htry("origin");
-  if (i != -1) header[i] = "origin";
-  if (issv) {
-    flag.sv.loaded = true;
-    flag.sv.header = header;
-  } else {
-    flag.fusion.loaded = true;
-    flag.fusion.header = header;
-  }
-  return false;
-}
-function parseline(i, line, flag, issv) {
-  if (line == "" || line[0] == "#") return;
-  const lst = line.split("	");
-  const m = {};
-  const header = issv ? flag.sv.header : flag.fusion.header;
-  const badlines = issv ? flag.sv.badlines : flag.fusion.badlines;
-  for (let j = 0; j < header.length; j++) {
-    m[header[j]] = lst[j];
-  }
-  if (!m.chr1) {
-    badlines.push([i, "missing chr1", lst]);
-    return;
-  }
-  if (m.chr1.toLowerCase().indexOf("chr") != 0) {
-    m.chr1 = "chr" + m.chr1;
-  }
-  if (!m.chr2) {
-    badlines.push([i, "missing chr2", lst]);
-    return;
-  }
-  if (m.chr2.toLowerCase().indexOf("chr") != 0) {
-    m.chr2 = "chr" + m.chr2;
-  }
-  let v = m.position1;
-  if (!v) {
-    badlines.push([i, "missing position1", lst]);
-    return;
-  }
-  let v2 = Number.parseInt(v);
-  if (Number.isNaN(v2) || v2 <= 0) {
-    badlines.push([i, "invalid value for position1", lst]);
-    return;
-  }
-  m.position1 = v2;
-  v = m.position2;
-  if (!v) {
-    badlines.push([i, "missing position2", lst]);
-    return;
-  }
-  v2 = Number.parseInt(v);
-  if (Number.isNaN(v2) || v2 <= 0) {
-    badlines.push([i, "invalid value for position2", lst]);
-    return;
-  }
-  m.position2 = v2;
-  if (parsesample(m, flag, i, lst)) {
-    return;
-  }
-  if (m.isoform1 && m.isoform1.indexOf(",") != -1) {
-    const lst2 = m.isoform1.split(",");
-    m.isoform1 = void 0;
-    for (const t of lst2) {
-      if (t != "") m.isoform1 = t;
-    }
-  }
-  if (m.isoform2 && m.isoform2.indexOf(",") != -1) {
-    const lst2 = m.isoform2.split(",");
-    m.isoform2 = void 0;
-    for (const t of lst2) {
-      if (t != "") m.isoform2 = t;
-    }
-  }
-  if (!m.gene1) {
-    m.isoform1 = void 0;
-  }
-  if (!m.gene2) {
-    m.isoform2 = void 0;
-  }
-  if (m.gene1) {
-    flag.good++;
-    const m2 = {
-      dt: issv ? dtsv : dtfusionrna,
-      class: issv ? mclasssv : mclassfusionrna,
-      isoform: m.isoform1,
-      mname: m.gene2 || m.chr2,
-      sample: m.sample,
-      patient: m.patient,
-      sampletype: m.sampletype,
-      origin: m.origin,
-      disease: m.disease,
-      pairlst: [
-        {
-          a: {
-            name: m.gene1,
-            isoform: m.isoform1,
-            strand: m.strand1,
-            chr: m.chr1,
-            position: m.position1
-          },
-          b: {
-            name: m.gene2,
-            isoform: m.isoform2,
-            strand: m.strand2,
-            chr: m.chr2,
-            position: m.position2
-          }
-        }
-      ]
-    };
-    const n = flag.geneToUpper ? m.gene1.toUpperCase() : m.gene1;
-    if (!flag.data[n]) {
-      flag.data[n] = [];
-    }
-    flag.data[n].push(m2);
-  }
-  if (m.gene2 && m.gene2 != m.gene1) {
-    flag.good++;
-    const m2 = {
-      dt: issv ? dtsv : dtfusionrna,
-      class: issv ? mclasssv : mclassfusionrna,
-      isoform: m.isoform2,
-      mname: m.gene1 || m.chr1,
-      sample: m.sample,
-      patient: m.patient,
-      sampletype: m.sampletype,
-      origin: m.origin,
-      disease: m.disease,
-      pairlst: [
-        {
-          a: {
-            name: m.gene1,
-            isoform: m.isoform1,
-            strand: m.strand1,
-            chr: m.chr1,
-            position: m.position1
-          },
-          b: {
-            name: m.gene2,
-            isoform: m.isoform2,
-            strand: m.strand2,
-            chr: m.chr2,
-            position: m.position2
-          }
-        }
-      ]
-    };
-    const n = flag.geneToUpper ? m.gene2.toUpperCase() : m.gene2;
-    if (!flag.data[n]) {
-      flag.data[n] = [];
-    }
-    flag.data[n].push(m2);
-  }
-}
-function duplicate(m) {
-  const n = {};
-  for (const k in m) {
-    if (k == "pairlst") continue;
-    const v = m[k];
-    const type = typeof v;
-    if (type == "object") {
-      continue;
-    }
-    n[k] = v;
-  }
-  if (m.pairlst) {
-    n.pairlst = [];
-    for (const pair of m.pairlst) {
-      const p = {};
-      for (const k in pair) {
-        if (k == "a" || k == "b" || k == "interstitial") {
-          continue;
-        }
-        p[k] = pair[k];
-      }
-      if (pair.a) {
-        p.a = {};
-        for (const k in pair.a) {
-          const v = pair.a[k];
-          if (typeof v == "object") {
-            continue;
-          }
-          p.a[k] = v;
-        }
-      }
-      if (pair.b) {
-        p.b = {};
-        for (const k in pair.b) {
-          const v = pair.b[k];
-          if (typeof v == "object") {
-            continue;
-          }
-          p.b[k] = v;
-        }
-      }
-      if (pair.interstitial) {
-        p.interstitial = {};
-        for (const k in pair.interstitial) {
-          const v = pair.interstitial[k];
-          if (typeof v == "object") {
-            continue;
-          }
-          p.interstitial[k] = v;
-        }
-      }
-      n.pairlst.push(p);
-    }
-  }
-  return n;
-}
-
-export {
-  parseheader,
-  parseline,
-  duplicate
-};
-//# sourceMappingURL=chunk-EKQ7NYOU.js.map

package/dist/chunk-EUQEQOFE.js

@@ -1,141 +0,0 @@
-import {
-  skipPrevActionAbort,
-  storeInit
-} from "./chunk-LOWJQFCC.js";
-import {
-  recoverInit
-} from "./chunk-X46YA4CB.js";
-import {
-  AppBase,
-  sayerror,
-  vocabInit
-} from "./chunk-PC4MFDHP.js";
-import {
-  importPlot
-} from "./chunk-HPAW7XDM.js";
-import {
-  Menu
-} from "./chunk-ELJX3QIQ.js";
-import {
-  AppApi
-} from "./chunk-WINIL2KN.js";
-
-// plots/plot.app.ts
-var PlotApp = class _PlotApp extends AppBase {
-  constructor(opts, api) {
-    super(opts);
-    this.components = {};
-    this.wasDestroyed = false;
-    this.api = api;
-    this.type = _PlotApp.type;
-    this.dom = this.getDom(opts);
-  }
-  static {
-    this.type = "app";
-  }
-  getDom(opts) {
-    const dom = {
-      holder: opts.holder,
-      errdiv: opts.holder.append("div"),
-      plotDiv: opts.holder.append("div")
-    };
-    const controls = opts.violin?.mode == "minimal" ? null : opts.holder.append("div").style("white-space", "nowrap");
-    if (controls) {
-      dom.plotControls = controls.append("div").style("display", "inline-block");
-      dom.recoverControls = controls.append("div").style("display", "inline-block");
-    }
-    return dom;
-  }
-  async preApiFreeze(api) {
-    try {
-      api.tip = new Menu({ padding: "5px" });
-      api.printError = (e) => this.printError(e);
-      const vocab = this.opts.state.vocab;
-      api.vocabApi = this.opts.vocabApi ? this.opts.vocabApi : await vocabInit({
-        app: api,
-        state: {
-          vocab: {
-            // either (genome + dslabel) XOR (terms) can be undefined
-            genome: vocab?.genome || this.opts.state.genome,
-            dslabel: vocab?.dslabel || this.opts.state.dslabel,
-            terms: vocab?.terms
-          }
-        },
-        fetchOpts: this.opts.fetchOpts
-      });
-      this.opts.state.vocab = api.vocabApi.vocab;
-    } catch (e) {
-      console.log(`preApiFreeze error`, e);
-      throw e;
-    }
-  }
-  async init() {
-    try {
-      this.opts.state.nav = { header_mode: "hidden" };
-      this.store = await storeInit({ app: this.api, state: this.opts.state });
-      this.state = await this.store.copyState();
-      this.components = {
-        plots: {}
-      };
-      if (this.opts.app?.features?.includes("recover"))
-        this.components.recover = await recoverInit({
-          app: this.api,
-          holder: this.dom.recoverControls,
-          // TODO: ???? may limit the tracked state to only the filter, activeCohort ???
-          getState: (appState) => appState,
-          //reactsTo: action => true, //action.type != 'plot_edit' || action.type == 'app_refresh',
-          maxHistoryLen: 10
-        });
-      if (this.opts.app?.doNotAwaitInitRender) {
-        this.api.dispatch();
-      } else {
-        await this.api.dispatch();
-      }
-    } catch (e) {
-      this.printError(e);
-      throw e;
-    }
-  }
-  async main() {
-    this.api.vocabApi.main();
-    for (const id in this.components.plots) {
-      const plot = this.components.plots[id];
-      if (!this.state.plots.find((p) => p.id === plot.id)) {
-        plot.destroy();
-        delete this.components.plots[id];
-      }
-    }
-    for (const plot of this.state.plots.values()) {
-      if (plot.parentId) continue;
-      if (!this.components.plots[plot.id]) {
-        const holder = this.opts?.app?.getPlotHolder ? this.opts.app.getPlotHolder(plot, this.dom.holder) : this.dom.holder.append("div");
-        if (!this.dom.plotDiv) this.dom.plotDiv = holder;
-        const { componentInit } = await importPlot(plot.chartType);
-        const plotApi = await componentInit({
-          id: plot.id,
-          app: this.api,
-          holder,
-          controls: this.dom.plotControls
-        });
-        this.components.plots[plot.id] = plotApi;
-      }
-    }
-  }
-  printError(e) {
-    sayerror(this.dom.errdiv, "Error: " + (e.message || e));
-    if (e.stack) console.log(e.stack);
-    this.bus.emit("error");
-  }
-  skipPrevActionAbort(action) {
-    return skipPrevActionAbort(action);
-  }
-  destroy() {
-    if (this.dom?.holder) this.dom.holder.selectAll("*").remove();
-  }
-};
-var appInit = AppApi.getInitFxn(PlotApp);
-
-export {
-  appInit
-};
-//# sourceMappingURL=chunk-EUQEQOFE.js.map

package/dist/chunk-FKA55PHV.js

@@ -1,281 +0,0 @@
-import {
-  getMclassSorter,
-  getSampleGroupSorter,
-  getSampleSorter,
-  getTermSorter
-} from "./chunk-4KJSNR5E.js";
-import {
-  setRelatedSamples
-} from "./chunk-C2MCQZWH.js";
-import {
-  filterVariantValues,
-  sample_match_termvaluesetting
-} from "./chunk-A2ORIMUJ.js";
-import {
-  dtcnv,
-  dtfusionrna,
-  dtgeneexpression,
-  dtsnvindel
-} from "./chunk-RUBZCKIX.js";
-import {
-  __export
-} from "./chunk-HS5PO5ZQ.js";
-
-// plots/matrix/matrix.groups.js
-var matrix_groups_exports = {};
-__export(matrix_groups_exports, {
-  classifyValues: () => classifyValues,
-  getSampleGroups: () => getSampleGroups,
-  getSampleOrder: () => getSampleOrder,
-  getTermOrder: () => getTermOrder,
-  stackSiblingCellsByClass: () => stackSiblingCellsByClass
-});
-function getTermOrder(data) {
-  const s = this.settings.matrix;
-  this.termSorter = getTermSorter(this, s);
-  const termOrder = [];
-  let totalIndex = 0, visibleGrpIndex = 0, numClusterTerms = 0;
-  this.mclassSorter = getMclassSorter(this);
-  this.samplesByAncestorId = /* @__PURE__ */ new Map();
-  const seenAncestorSamples = /* @__PURE__ */ new Set();
-  for (const sd of data.lst) {
-    if (seenAncestorSamples.has(sd.sample)) continue;
-    seenAncestorSamples.add(sd.sample);
-    if (!sd._ref_?.ancestors) continue;
-    for (const a of sd._ref_.ancestors) {
-      const id = a.ancestor_id;
-      if (id === void 0) continue;
-      if (!this.samplesByAncestorId.has(id)) this.samplesByAncestorId.set(id, /* @__PURE__ */ new Set());
-      this.samplesByAncestorId.get(id).add(sd);
-    }
-  }
-  for (const [grpIndex, grp] of this.termGroups.entries()) {
-    const lst = [];
-    for (const [index, tw] of grp.lst.entries()) {
-      const counts = { samples: 0, hits: 0 };
-      const countedSamples = /* @__PURE__ */ new Set();
-      for (const sd of data.lst) {
-        if (countedSamples.has(sd.sample)) continue;
-        countedSamples.add(sd.sample);
-        const anno = sd[tw.$id];
-        if (anno) {
-          const { filteredValues, countedValues, renderedValues } = this.classifyValues(anno, tw, grp, s, sd);
-          anno.filteredValues = filteredValues;
-          anno.countedValues = countedValues;
-          anno.renderedValues = renderedValues;
-          if (anno.countedValues?.length) {
-            const v = tw.term.values?.[anno.value];
-            if (v?.uncountable) continue;
-            counts.samples += 1;
-            counts.hits += anno.countedValues.length;
-            if (tw.q?.mode == "continuous") {
-              const v2 = anno.value;
-              if (!("minval" in counts) || counts.minval > v2) counts.minval = v2;
-              if (!("maxval" in counts) || counts.maxval < v2) counts.maxval = v2;
-            }
-          }
-        }
-      }
-      if (grp.type != "hierCluster" || counts.samples) lst.push({ tw, counts, index });
-      if (grp.type == "hierCluster") numClusterTerms++;
-    }
-    const termSorter = grp.sortTermsBy || grp.type == "hierCluster" ? getTermSorter(this, s, grp) : this.termSorter;
-    const processedLst = lst.filter((t) => {
-      if ("minNumSamples" in t.tw) return t.tw.minNumSamples <= t.counts.samples;
-      if (!grp.settings) return true;
-      return !("minNumSamples" in grp.settings) || t.counts.samples >= grp.settings.minNumSamples;
-    }).sort(termSorter);
-    if (!processedLst.length) continue;
-    for (const [index, t] of processedLst.entries()) {
-      const { tw, counts } = t;
-      const ref = data.refs.byTermId[t.tw.$id] || {};
-      termOrder.push({
-        grp,
-        grpIndex,
-        visibleGrpIndex,
-        tw,
-        index,
-        // rendered index
-        lstIndex: t.index,
-        // as-listed index, before applying term filters
-        processedLst,
-        prevGrpTotalIndex: totalIndex,
-        totalIndex: totalIndex + index,
-        ref,
-        allCounts: counts
-        // note: term label will be assigned after sample counts are known
-        // label: t.tw.label || t.tw.term.name,
-      });
-    }
-    totalIndex += processedLst.length;
-    visibleGrpIndex += 1;
-  }
-  for (const [ancestor_id, samples] of this.samplesByAncestorId.entries()) {
-    if (samples.size < 2) this.samplesByAncestorId.delete(ancestor_id);
-  }
-  this.numTerms = termOrder.length;
-  this.numClusterTerms = numClusterTerms;
-  return termOrder;
-}
-function getSampleGroups(data) {
-  const s = this.settings.matrix;
-  const defaultSampleGrp = {
-    id: this.config.divideBy?.$id,
-    name: this.config.divideBy ? "Not annotated" : "",
-    lst: []
-  };
-  const sampleGroups = /* @__PURE__ */ new Map();
-  const term = this.config.divideBy?.term || {};
-  const $id = this.config.divideBy?.$id || "-";
-  const exclude = this.config.divideBy?.exclude || [];
-  const values = term.values || {};
-  const ref = data.refs.byTermId[$id] || {};
-  for (const row of data.lst) {
-    if ($id in row) {
-      const cell = row[$id];
-      const keys = term.type == "multivalue" && Array.isArray(cell.values) ? cell.values.map((v) => v.key) : [cell.key];
-      for (const key of keys) {
-        const name = key in values && values[key].label ? values[key].label : key;
-        if (!sampleGroups.has(key)) {
-          const grp = {
-            name: `${name}`,
-            // convert to a string
-            id: key,
-            lst: [],
-            tw: this.config.divideBy,
-            legendGroups: {},
-            isExcluded: exclude.includes(key)
-          };
-          if (ref.bins && s.sortSampleGrpsBy == "name") grp.order = ref.bins.findIndex((bin) => bin.name == key);
-          else delete grp.order;
-          sampleGroups.set(key, grp);
-        }
-        sampleGroups.get(key).lst.push(row);
-      }
-    } else {
-      defaultSampleGrp.lst.push(row);
-    }
-  }
-  const sampleGrpsArr = [...sampleGroups.values()];
-  const n = sampleGroups.size;
-  if (n > 100 && sampleGrpsArr.filter((sg) => sg.lst.length < 3).length > 0.8 * n) {
-    const l = s.controlLabels;
-    throw `Did not group ${l.samples} by "${term.name}": too many ${l.sample} groups (${n}), with the majority of groups having <= 2 ${l.samples} per group.`;
-  }
-  if (defaultSampleGrp.lst.length && !sampleGroups.size) {
-    sampleGroups.set(void 0, defaultSampleGrp);
-    sampleGrpsArr.push(...sampleGroups.values());
-  }
-  this.asListedSampleOrder = [];
-  for (const grp of sampleGrpsArr) {
-    this.asListedSampleOrder.push(...grp.lst.map((s2) => s2.sample));
-  }
-  const selectedDictTerms = this.termOrder.filter((t) => t.tw.sortSamples && t.tw.term.type != "geneVariant");
-  const noGrpSampleSorter = getSampleSorter(this, s, data.lst, {
-    skipSorter: (p, tw) => !p.types?.includes("geneVariant") && selectedDictTerms.find((t) => t.tw.$id === tw.$id)
-  });
-  const noGrpSampleOrder = data.lst.sort(noGrpSampleSorter);
-  const allowedSamples = noGrpSampleOrder.slice(0, s.maxSample);
-  const dataFilter = (d) => allowedSamples.includes(d);
-  const hitsPerSample = (t, c) => t + (typeof c == "object" && c.countedValues?.length ? 1 : 0);
-  const countHits = (total, d) => total + (Object.values(d).reduce(hitsPerSample, 0) ? 1 : 0);
-  const grpLstSampleSorter = getSampleSorter(this, s, data.lst);
-  for (const grp of sampleGrpsArr) {
-    grp.lst = grp.lst.filter(dataFilter);
-    grp.totalCountedValues = grp.lst.reduce(countHits, 0);
-    grp.lst.sort(grpLstSampleSorter);
-    if (this.config.chartType == "matrix" && s.sortBySampleAncestry) setRelatedSamples(grp);
-  }
-  const sampleGrpSorter = getSampleGroupSorter(this);
-  return sampleGrpsArr.sort(sampleGrpSorter);
-}
-function getSampleOrder(data) {
-  const s = this.settings.matrix;
-  this.visibleSampleGrps = /* @__PURE__ */ new Set();
-  const sampleOrder = [];
-  let total = 0, numHiddenGrps = 0;
-  for (const [grpIndex, grp] of this.sampleGroups.entries()) {
-    if (!grp.lst.length) continue;
-    if (grp.isExcluded) numHiddenGrps++;
-    let processedLst = grp.lst;
-    for (const [index, row] of processedLst.entries()) {
-      sampleOrder.push({
-        grp,
-        grpIndex: grpIndex - numHiddenGrps,
-        // : this.sampleGroups.length,
-        row,
-        index,
-        prevGrpTotalIndex: total,
-        totalIndex: total + index,
-        totalHtAdjustments: 0,
-        // may be required when transposed???
-        grpTotals: { htAdjustment: 0 },
-        // may be required when transposed???
-        processedLst
-      });
-    }
-    if (!grp.isExcluded) total += processedLst.length;
-    this.visibleSampleGrps.add(grp);
-  }
-  this.unfilteredSampleOrder = sampleOrder;
-  return sampleOrder.filter((so) => !so.grp.isExcluded);
-}
-function classifyValues(anno, tw, grp, s, sample) {
-  let values = "value" in anno ? [anno.value] : anno.values;
-  if (!values) return { filteredValues: null, countedValues: null, renderedValues: null };
-  if (tw.term.type == "geneVariant" && tw.q?.type == "values" && tw.q.variantFilter) {
-    values = filterVariantValues(values, tw.q.variantFilter);
-  }
-  const isSpecific = [tw.valueFilter || grp.valueFilter].filter((v) => v && true);
-  if (isSpecific.length && isSpecific[0].type !== "tvs" && isSpecific[0].type !== "tvslst")
-    throw `unknown matrix value filter type='${isSpecific.type}'`;
-  let filteredValues = !isSpecific.length ? values : values.filter((v) => sample_match_termvaluesetting(v, isSpecific[0], tw.term, sample));
-  const renderedValues = [];
-  if (tw.term.type == "geneVariant" && tw.q?.type == "values") {
-    filteredValues.sort(this.mclassSorter);
-    if (s.cellEncoding == "") renderedValues.push(...filteredValues);
-    else {
-      const sortedFilteredValues = [];
-      for (const dt of [dtcnv, dtsnvindel, dtfusionrna, dtgeneexpression]) {
-        const v = dt == dtgeneexpression ? filteredValues.find((v2) => v2.dt === dt) : filteredValues.find((v2) => v2.dt === dt && v2.class !== "WT" && v2.class !== "Blank");
-        if (v) renderedValues.push(v);
-        const oneDtV = filteredValues.filter((v2) => v2.dt === dt);
-        sortedFilteredValues.push(...oneDtV);
-      }
-      filteredValues = sortedFilteredValues;
-    }
-  } else {
-    renderedValues.push(...filteredValues);
-  }
-  return {
-    filteredValues,
-    countedValues: filteredValues.filter((v) => {
-      if (tw.term.type == "geneVariant") {
-        if (tw.q?.type == "predefined-groupset" || tw.q?.type == "custom-groupset") {
-          const groupset = tw.q.type == "predefined-groupset" ? tw.term.groupsetting.lst[tw.q.predefined_groupset_idx] : tw.q.customset;
-          if (!groupset) throw "groupset not found";
-          const group = groupset.groups[0];
-          if (v != group.name) return false;
-        } else {
-          if (v.class == "WT" || v.class == "Blank" || s.geneVariantCountSamplesSkipMclass.includes(v.class))
-            return false;
-        }
-      }
-      return true;
-    }),
-    renderedValues
-  };
-}
-function stackSiblingCellsByClass(a, b) {
-  return a.class === b.class ? 0 : a.class === "Blank" ? 1 : b.class == "Blank" ? -1 : a.class < b.class ? -1 : 1;
-}
-
-export {
-  getTermOrder,
-  getSampleGroups,
-  getSampleOrder,
-  classifyValues,
-  stackSiblingCellsByClass,
-  matrix_groups_exports
-};
-//# sourceMappingURL=chunk-FKA55PHV.js.map