@sjcrh/proteinpaint-client 2.181.0 → 2.182.0

package/dist/chunk-5ZICCKEH.js

@@ -1,4952 +0,0 @@
-import {
-  rehydrateFilter
-} from "./chunk-SKMFMGCD.js";
-import {
-  showLDlegend
-} from "./chunk-AYDXOUFX.js";
-import {
-  legend_newrow
-} from "./chunk-VIYGTRUZ.js";
-import {
-  urlmap_default
-} from "./chunk-AQ4OP4GR.js";
-import {
-  ColorScale,
-  Tabs,
-  axisstyle,
-  fillTermWrapper,
-  fillbar,
-  makeNumericAxisConfig,
-  makeSsmLink,
-  make_radios,
-  newSandboxDiv,
-  renderCnvConfig,
-  renderTable,
-  shapeSelector,
-  shapes,
-  table2col,
-  to_textfile
-} from "./chunk-XZZLEHWC.js";
-import {
-  genomic2gm
-} from "./chunk-HJ6L54YS.js";
-import {
-  Menu
-} from "./chunk-2SRMRC6L.js";
-import {
-  dofetch3,
-  guessSsmid,
-  ssmIdFieldsSeparator,
-  summarize_mclass
-} from "./chunk-QEHUEG4X.js";
-import {
-  icons
-} from "./chunk-5EF5U7MX.js";
-import {
-  niceNumLabels
-} from "./chunk-SEQLC4AD.js";
-import {
-  bplen,
-  dt2label,
-  dtTerms,
-  dtcloss,
-  dtcnv,
-  dtdel,
-  dtfusionrna,
-  dtitd,
-  dtnloss,
-  dtsnvindel,
-  dtsv,
-  getColors,
-  gmmode,
-  mclass,
-  mds3tkMclass
-} from "./chunk-ZLH4PJKX.js";
-import {
-  convertUnits
-} from "./chunk-TV74I3Y5.js";
-import {
-  arc_default
-} from "./chunk-IH7ILDJS.js";
-import {
-  axisLeft,
-  axisRight
-} from "./chunk-LOZEKOES.js";
-import {
-  format,
-  linear
-} from "./chunk-OAWQ6LOO.js";
-import {
-  select_default
-} from "./chunk-NDWTN4U5.js";
-import {
-  rgb,
-  rgb_default
-} from "./chunk-OMR2DT66.js";
-
-// mds3/itemtable.js
-async function itemtable(arg) {
-  if (arg.mlst.find((m) => m.dt != dtsnvindel && m.dt != dtfusionrna && m.dt != dtsv && m.dt != dtcnv)) {
-    throw "mlst[] contains unknown dt";
-  }
-  if (arg.mlst.length == 1) {
-    await itemtable_oneItem(arg);
-  } else {
-    await itemtable_multiItems(arg);
-  }
-  mayMoveTipDiv2left(arg);
-}
-function mayMoveTipDiv2left(arg) {
-  if (!arg.tipDiv) {
-    return;
-  }
-  const tableDoms = [];
-  for (const d of arg.div.selectAll("div").selectAll("table")) {
-    if (d) tableDoms.push(d);
-  }
-  if (!tableDoms.length) return;
-  let maxColumnCount = 0;
-  for (const table of tableDoms) {
-    const thead = table.firstChild;
-    if (thead.tagName != "THEAD") continue;
-    const tr = thead.firstChild;
-    if (tr.tagName != "TR") continue;
-    maxColumnCount = Math.max(maxColumnCount, tr.childNodes?.length);
-  }
-  if (maxColumnCount > 5) {
-    arg.tipDiv.style("left", "50px");
-  }
-}
-async function itemtable_oneItem(arg) {
-  const table = table2col({ holder: arg.div });
-  const m = arg.mlst[0];
-  if (m.dt == dtsnvindel) {
-    table_snvindel(arg, table);
-  } else if (m.dt == dtsv || m.dt == dtfusionrna) {
-    await table_svfusion(arg, table);
-  } else if (m.dt == dtcnv) {
-    table_cnv(arg, table);
-  } else {
-    throw "itemtable_oneItem: unknown dt";
-  }
-  arg.singleSampleDiv = table;
-  if (arg.tk.mds.variant2samples) {
-    if (m.occurrence) {
-      await init_sampletable(arg);
-    }
-  }
-}
-async function itemtable_multiItems(arg) {
-  const goBackButton = arg.div.append("div").style("margin", "10px").append("button").style("display", "none");
-  goBackButton.html("≪ Back to list").on("click", () => {
-    tableDiv.style("display", "");
-    goBackButton.style("display", "none");
-    singleVariantDiv.style("display", "none");
-  });
-  const singleVariantDiv = arg.div.append("div").style("display", "none");
-  const columns = [
-    {
-      label: `Click a ${dt2label[arg.mlst[0].dt]} to see details`,
-      fillCell: (td, i) => {
-        const m = arg.mlst[i];
-        if (m.dt == dtsnvindel) {
-          td.append("span").text(arg.tk.mnamegetter(m));
-          td.append("span").text(mclass[m.class].label).style("font-size", ".8em").style("margin-left", "10px").style("color", mclass[m.class].color);
-          td.append("span").text(`${m.chr}:${m.pos + 1}${m.ref ? ", " + m.ref + ">" + m.alt : ""}`).style("font-size", ".8em").style("margin-left", "10px");
-        } else if (m.dt == dtsv || m.dt == dtfusionrna) {
-          td.append("span").text(mclass[m.class].label).style("font-size", ".7em").style("margin-right", "8px");
-          printSvPair(m.pairlst[0], td);
-        } else if (m.dt == dtcnv) {
-          const cs = cnv2str(m, arg.tk);
-          td.html(cs.value + "  " + cs.pos);
-        } else {
-          td.text("error: unknown m.dt");
-        }
-      }
-    }
-  ];
-  const hasOccurrence = arg.mlst.some((i) => i.occurrence);
-  if (hasOccurrence) {
-    columns.push({ label: "Occurrence" });
-  }
-  let infoFields = null;
-  if (arg.tk.mds.bcf?.info) {
-    infoFields = [];
-    for (const k in arg.tk.mds.bcf.info) {
-      if (arg.tk.mds.bcf.info[k].categories) {
-        infoFields.push(k);
-        columns.push({ label: arg.tk.mds.bcf.info[k].name || k });
-      }
-    }
-    if (infoFields.length == 0) infoFields = null;
-  }
-  let numViewMode;
-  if (arg.tk.skewer) {
-    numViewMode = arg.tk.skewer.viewModes.find((i) => i.inuse && i.type == "numeric" && i.byAttribute != "occurrence");
-    if (numViewMode) {
-      columns.push({ label: numViewMode.label });
-    }
-  }
-  arg.mlst.sort((i, j) => i.__x - j.__x);
-  const rows = [];
-  for (const m of arg.mlst) {
-    const row = [{}];
-    if (hasOccurrence) {
-      row.push({ value: "occurrence" in m ? m.occurrence : "" });
-    }
-    if (infoFields) {
-      for (const k of infoFields) {
-        const v = m.info?.[k];
-        if (v == void 0) {
-          row.push({});
-        } else {
-          const o = arg.tk.mds.bcf.info[k].categories[v];
-          if (o?.color) {
-            row.push({ html: `<span style="background:${o.color}">&nbsp;&nbsp;</span> ${o.label || v}` });
-          } else {
-            row.push({ value: v });
-          }
-        }
-      }
-    }
-    if (numViewMode) {
-      row.push({ value: m.__value_use });
-    }
-    rows.push(row);
-  }
-  const tableDiv = arg.div.append("div");
-  renderTable({
-    div: tableDiv,
-    columns,
-    rows,
-    resize: true,
-    noButtonCallback: (i) => {
-      tableDiv.style("display", "none");
-      goBackButton.style("display", "");
-      singleVariantDiv.style("display", "").selectAll("*").remove();
-      const a2 = Object.assign({}, arg);
-      a2.mlst = [arg.mlst[i]];
-      a2.div = singleVariantDiv;
-      itemtable(a2);
-    },
-    singleMode: true,
-    noRadioBtn: true
-  });
-  if (!arg.doNotListSample4multim && arg.tk.mds.variant2samples) {
-    const totalOccurrence = arg.mlst.reduce((i, j) => i + (j.occurrence || 0), 0);
-    if (totalOccurrence) {
-      arg.div.append("div").style("margin-top", "10px").append("span").attr("class", "sja_clbtext").text("List all samples").on("click", async (event2) => {
-        event2.target.remove();
-        tableDiv.remove();
-        await init_sampletable(arg);
-        mayMoveTipDiv2left(arg);
-      });
-    }
-  }
-}
-async function table_snvindel({ mlst, tk, block }, table) {
-  const m = mlst[0];
-  {
-    const [td1, td2] = table.addRow();
-    td1.text(block.mclassOverride ? block.mclassOverride.className : "Consequence");
-    print_mname(td2, m);
-  }
-  {
-    const [td1, td2] = table.addRow();
-    td1.text(m.ref && m.alt ? "Mutation" : "Position");
-    print_snv(td2, m, tk, block);
-  }
-  if (m.occurrence > 1) {
-    const [td1, td2] = table.addRow();
-    td1.text("Occurrence");
-    td2.text(m.occurrence);
-  }
-  table_snvindel_mayInsertNumericValueRow(m, tk, table);
-  table_snvindel_mayInsertHtmlSections(m, tk, table);
-  table_snvindel_mayInsertLD(m, tk, table);
-  if (m.info) {
-    for (const key in m.info) {
-      if (key == "CSQ") {
-        continue;
-      }
-      const [td1, td2] = table.addRow();
-      td1.text(key).attr("data-testid", "sjpp-mds3tk-singlemtablerow4infokey");
-      const infoValue = m.info[key];
-      const infoField = tk.mds?.bcf?.info?.[key];
-      if (Array.isArray(infoValue)) {
-        for (const v of infoValue) {
-          renderInfoTd(m, infoField, v, td2, tk);
-        }
-      } else {
-        renderInfoTd(m, infoField, infoValue, td2, tk);
-      }
-      if (infoField?.Description) {
-        td2.append("span").style("margin-left", "10px").style("font-size", ".8em").style("opacity", 0.6).text(infoField.Description);
-      }
-    }
-  }
-}
-function table_snvindel_mayInsertNumericValueRow(m, tk, table) {
-  const currentMode = tk.skewer.viewModes.find((i) => i.inuse);
-  if (currentMode.type != "numeric" || currentMode.byAttribute == "occurrence") return;
-  if (currentMode.tooltipPrintValue) {
-    const tmp = currentMode.tooltipPrintValue(m);
-    if (Array.isArray(tmp)) {
-      for (const s of tmp) {
-        const [td12, td22] = table.addRow();
-        td12.text(s.k);
-        td22.text(s.v);
-      }
-    } else {
-      console.log("unknown return value");
-    }
-    return;
-  }
-  const [td1, td2] = table.addRow();
-  td1.text(currentMode.label);
-  td2.text(m.__value_missing ? "NA" : m.__value_use);
-}
-function table_snvindel_mayInsertHtmlSections(m, tk, table) {
-  if (!m.htmlSections) return;
-  if (!Array.isArray(m.htmlSections)) throw "htmlSections[] is not array";
-  for (const section of m.htmlSections) {
-    const [td1, td2] = table.addRow();
-    if (section.key && section.html) {
-      td1.text(section.key);
-      td2.html(section.html);
-    }
-  }
-}
-function renderInfoTd(m, infoField, infoValue, td, tk) {
-  if (!infoField) {
-    td.append("span").text(infoValue);
-    return;
-  }
-  if (infoField.urlBase) {
-    td.append("a").text(infoValue).attr("href", infoField.urlBase + infoValue).attr("target", "_blank");
-    return;
-  }
-  const color = infoField.categories?.[infoValue]?.color;
-  if (color) {
-    td.append("span").html("&nbsp;&nbsp;").style("background", color).style("margin-right", "5px");
-  }
-  td.append("span").text(infoField.categories?.[infoValue]?.label || infoValue);
-}
-function print_mname(div, m) {
-  div.append("span").text(m.mname);
-  div.append("span").style("margin-left", "5px").style("color", mclass[m.class].color).style("font-size", ".8em").text(mclass[m.class].label.toUpperCase());
-}
-function print_snv(holder, m, tk, block) {
-  const ssmNameDom = holder.append("span").text(`${m.chr}:${m.pos + 1} ${m.ref && m.alt ? m.ref + ">" + m.alt : ""}`);
-  const urlConfig = tk.mds.termdbConfig?.urlTemplates?.ssm || tk.mds.queries?.snvindel?.ssmUrl;
-  if (urlConfig) {
-    const separateUrls = makeSsmLink(urlConfig, m, ssmNameDom, block.genome.name);
-    if (separateUrls?.length) {
-      holder.append("span").style("margin-left", "10px").html(separateUrls.join(" "));
-    }
-  }
-}
-async function table_svfusion(arg, table) {
-  await makeSvgraph(
-    arg.mlst[0],
-    table.scrollDiv.insert("div", ":first-child"),
-    // insert to top
-    arg.block
-  );
-  {
-    const [c1, c2] = table.addRow();
-    c1.text("Data type");
-    c2.text(mclass[arg.mlst[0].class].label);
-  }
-  {
-    const [c1, c2] = table.addRow();
-    c1.text("Break points");
-    for (const pair of arg.mlst[0].pairlst) {
-      printSvPair(pair, c2.append("div"));
-    }
-  }
-}
-function table_cnv(arg, table) {
-  const cs = cnv2str(arg.mlst[0], arg.tk);
-  {
-    const [c1, c2] = table.addRow();
-    c1.text("Copy number change");
-    c2.html(cs.value);
-  }
-  {
-    const [c1, c2] = table.addRow();
-    c1.text("Position");
-    c2.html(cs.pos);
-  }
-}
-function cnv2str(m, tk) {
-  const cs = {};
-  if (Number.isFinite(m.value)) {
-    if (tk.cnv.colorScale) {
-      cs.value = `<span style="background:${tk.cnv.colorScale(m.value)}">&nbsp;&nbsp;</span> ${m.value}`;
-    } else {
-      cs.value = m.value;
-    }
-  } else {
-    cs.value = `<span style="background:${mclass[m.class].color}">&nbsp;&nbsp;</span> 
-			${tk.mds.termdbConfig?.mclass?.[m.class]?.label || mclass[m.class].label}`;
-  }
-  cs.pos = `${m.chr}:${m.start}-${m.stop} <span style="font-size:.8em">${bplen(m.stop - m.start)}</span>`;
-  return cs;
-}
-function printSvPair(pair, div) {
-  if (pair.a.name) div.append("span").text(pair.a.name).style("font-weight", "bold").style("margin-right", "5px");
-  div.append("span").text(
-    `${pair.a.chr}:${pair.a.pos + 1} ${pair.a.strand == "+" ? "forward" : "reverse"} > ${pair.b.chr}:${pair.b.pos + 1} ${pair.b.strand == "+" ? "forward" : "reverse"}`
-  );
-  if (pair.b.name) div.append("span").text(pair.b.name).style("font-weight", "bold").style("margin-left", "5px");
-}
-async function makeSvgraph(m, div, block) {
-  div.attr("data-testid", "sjpp-mds3tk-singlesvfusiongraph");
-  const wait = div.append("div").text("Loading...");
-  try {
-    if (!m.pairlst) throw ".pairlst[] missing";
-    const svpair = {
-      a: {
-        chr: m.pairlst[0].a.chr,
-        position: m.pairlst[0].a.pos,
-        strand: m.pairlst[0].a.strand
-      },
-      b: {
-        chr: m.pairlst[0].b.chr,
-        position: m.pairlst[0].b.pos,
-        strand: m.pairlst[0].b.strand
-      }
-    };
-    await getGm(svpair.a, block, m.pairlst[0].a.name);
-    await getGm(svpair.b, block, m.pairlst[0].b.name);
-    wait.remove();
-    const _ = await import("./svgraph-D23WG3UE.js");
-    _.default({
-      pairlst: [svpair],
-      genome: block.genome,
-      holder: div
-    });
-  } catch (e) {
-    wait.text(e.message || e);
-  }
-}
-async function getGm(p, block, name) {
-  const d = await dofetch3("isoformbycoord", { body: { genome: block.genome.name, chr: p.chr, pos: p.position } });
-  if (d.error) throw d.error;
-  const u = d.lst.find((i) => i.isdefault && name == i.name) || d.lst[0];
-  if (u) {
-    p.name = u.name;
-    p.gm = { isoform: u.isoform };
-  }
-}
-function table_snvindel_mayInsertLD(m, tk, table) {
-  if (!tk.mds.queries?.ld) return;
-  const [td1, td2] = table.addRow();
-  td1.text("LD overlay");
-  const m0 = tk.mds.queries.ld.mOverlay?.m;
-  if (m0) {
-    const row = td2.append("div").style("margin-bottom", "5px");
-    if (m.ssm_id == m0.ssm_id) {
-      row.html(
-        tk.mds.queries.ld.mOverlay.ldtkname + " r<sup>2</sup> values against this variant are displayed on all the other variants."
-      );
-    } else {
-      let r2 = null;
-      for (const v of tk.mds.queries.ld.mOverlay.data || []) {
-        if (v.pos == m.pos && v.alleles == m.ref + "." + m.alt) {
-          r2 = v.r2;
-          break;
-        }
-      }
-      if (r2 == null) {
-        row.html("No r<sup>2</sup> value is found.");
-      } else {
-        row.html(tk.mds.queries.ld.mOverlay.ldtkname + " r<sup>2</sup> = " + r2);
-      }
-    }
-  }
-  td2.append("div").html("Click a button to overlay LD r<sup>2</sup> values against this variant:").style("font-size", ".8em").style("opacity", 0.5);
-  for (const o of tk.mds.queries.ld.tracks) {
-    const btn = td2.append("button").text(o.name);
-    if (m0 && m0.ssm_id == m.ssm_id) {
-      if (o.name == tk.mds.queries.ld.mOverlay.ldtkname) {
-        btn.property("disabled", true);
-        continue;
-      }
-    }
-    btn.on("click", () => {
-      tk.itemtip.hide();
-      tk.mds.queries.ld.mOverlay = {
-        ldtkname: o.name,
-        m: {
-          chr: m.chr,
-          pos: m.pos,
-          ref: m.ref,
-          alt: m.alt,
-          ssm_id: m.ssm_id
-          // required for highlighting
-        }
-      };
-      tk.load();
-    });
-  }
-}
-
-// mds3/sampletable.js
-async function init_sampletable(arg) {
-  const wait = arg.div.append("div").text("Loading...").style("padding", "10px").style("color", "#8AB1D4").style("font-size", "1.25em").style("font-weight", "bold");
-  arg.tid2value_orig = /* @__PURE__ */ new Set();
-  if (arg.tid2value) Object.keys(arg.tid2value).forEach(arg.tid2value_orig.add, arg.tid2value_orig);
-  try {
-    arg.querytype = arg.tk.mds.variant2samples.type_samples;
-    const out = await arg.tk.mds.variant2samples.get(arg);
-    await displaySampleTable(out.samples, arg);
-    wait.remove();
-  } catch (e) {
-    wait.text("Error: " + (e.message || e));
-    if (e.stack) console.log(e.stack);
-  }
-}
-async function displaySampleTable(samples, args) {
-  if (samples.length == 1) {
-    return await make_singleSampleTable(samples[0], args);
-  }
-  const [columns, rows] = await samples2columnsRows(samples, args.tk);
-  const params = { rows, columns, div: args.div, resize: rows.length > 10, dataTestId: "sjpp_mds3tk_sampletable" };
-  params.columnButtons = [];
-  if (args.tk.mds.queries?.singleSampleMutation) {
-    const width = window.innerWidth;
-    const height = screen.height;
-    const colButton = {
-      text: "Disco",
-      dataTestId: "sja_sample_table_disco_button",
-      callback: async (event2, i) => {
-        args.tk.itemtip.hide();
-        args.tk.menutip.hide();
-        let thisMutation;
-        if (samples[i].ssm_id_lst?.[0]) {
-          thisMutation = (args.tk.skewer.rawmlst || args.tk.custom_variants).find(
-            (m) => m.ssm_id == samples[i].ssm_id_lst[0]
-          );
-        }
-        await createDiscoInSandbox(args.tk, args.block, samples[i], thisMutation);
-      }
-    };
-    params.columnButtons.push(colButton);
-  }
-  if (args.tk.mds.queries?.singleSampleGenomeQuantification) {
-    for (const k in args.tk.mds.queries.singleSampleGenomeQuantification) {
-      const btn = {
-        text: k,
-        dataTestId: `${k}_button`,
-        callback: async (event2, i) => {
-          const sandbox = newSandboxDiv(args.tk.newChartHolder || args.block.holder0);
-          sandbox.header.text(samples[i].sample_id);
-          await (await import("./plot.ssgq-MU3BRTMC.js")).plotSingleSampleGenomeQuantification(
-            args.tk.mds,
-            args.tk.mds.label,
-            k,
-            samples[i],
-            sandbox.body.append("div").style("margin", "20px"),
-            args.block.genome,
-            args.block.usegm?.name
-          );
-        }
-      };
-      params.columnButtons.push(btn);
-    }
-  }
-  if (args.tk.allow2selectSamples) {
-    params.buttons = [
-      {
-        text: args.tk.allow2selectSamples.buttonText,
-        class: args.tk.allow2selectSamples.class,
-        callback: (sampleIdxLst) => {
-          feedSample2selectCallback(args.tk, args.block, samples, sampleIdxLst);
-          args.tk.itemtip.hide();
-          args.tk.menutip.hide();
-        }
-      }
-    ];
-  }
-  return renderTable(params);
-}
-async function feedSample2selectCallback(tk, block, _samples, sampleIdxLst) {
-  const s = [..._samples];
-  const samples = sampleIdxLst.map((i) => s[i]);
-  tk.allow2selectSamples.callback({
-    samples: await tk.mds.termdb.vocabApi.convertSampleId(samples, tk.allow2selectSamples.attributes),
-    source: "Samples with " + block2source(block)
-  });
-}
-async function make_singleSampleTable(s, arg) {
-  const table = arg.singleSampleDiv || table2col({ holder: arg.div });
-  if (s.sample_id) {
-    const [cell1, cell2] = table.addRow();
-    cell1.text(arg.tk.mds.termdbConfig?.lollipop?.sample || "Sample");
-    let m;
-    if (s.ssm_id_lst?.[0]) {
-      m = arg.tk.skewer.rawmlst.find((i) => i.ssm_id == s.ssm_id_lst[0]);
-    }
-    printSampleName(s, arg.tk, cell2, arg.block, m);
-  }
-  if ("caseIsOpenAccess" in s) {
-    const [cell1, cell2] = table.addRow();
-    cell1.text("Access");
-    cell2.text(s.caseIsOpenAccess ? "Open" : "Controlled");
-  }
-  if (arg.tk.mds.variant2samples.twLst) {
-    for (const tw of arg.tk.mds.variant2samples.twLst) {
-      const [cell1, cell2] = table.addRow();
-      cell1.text(tw.term.name).style("text-overflow", "ellipsis");
-      cell2.style("text-overflow", "ellipsis");
-      if (tw.term.id in s) {
-        if (Array.isArray(s[tw.term.id])) {
-          cell2.html(value2urlsOrText(s[tw.term.id], tw));
-        } else {
-          const v = twDisplayValueFromSample(s, tw);
-          cell2.html(value2urlsOrText(v, tw));
-        }
-      }
-    }
-  }
-  if (s.ssmid2format) {
-    for (const ssmid of s.ssm_id_lst) {
-      if (s.ssm_id_lst.length > 1) {
-        const [td1, td] = table.addRow();
-        td.style("padding-top", "20px");
-        const m = arg.tk.skewer.rawmlst.find((i) => i.ssm_id == ssmid);
-        if (m) {
-          if (m.dt == dtsnvindel) {
-            print_snv(td, m, arg.tk, arg.block);
-          } else if (m.dt == dtsv || m.dt == dtfusionrna) {
-            printSvPair(m.pairlst[0], td);
-          } else {
-            td.text(ssmid);
-          }
-        } else {
-          td.text(ssmid);
-        }
-      } else {
-      }
-      for (const formatkey in s.ssmid2format[ssmid]) {
-        const value = s.ssmid2format[ssmid][formatkey];
-        const [t1, t2] = table.addRow();
-        const fobj = arg.tk.mds?.bcf?.format?.[formatkey];
-        t1.text(fobj?.Description || formatkey).attr("data-testid", "sjpp-mds3tk-singlemtablerow4formatkey").attr("__key__", formatkey);
-        t2.html(printFormat(fobj, value));
-      }
-    }
-  }
-}
-function twDisplayValueFromSample(s, tw) {
-  if (!(tw.term.id in s)) return "";
-  const v = s[tw.term.id];
-  if (tw.term.values?.[v]?.label) return tw.term.values[v].label;
-  const vc = tw.term.valueConversion;
-  if (vc) return convertUnits(v, vc.fromUnit, vc.toUnit, vc.scaleFactor);
-  return v;
-}
-function printSampleName(sample, tk, div, block, thisMutation) {
-  const temp = tk.mds.termdbConfig?.urlTemplates?.sample;
-  if (temp) {
-    const a = div.append("a");
-    a.attr("href", temp.base + (sample[temp.namekey] || sample.sample_id));
-    a.attr("target", "_blank");
-    a.text(sample.sample_id);
-    a.style("word-break", "break-word");
-  } else {
-    div.append("span").attr("class", "pp_mds3_singleSampleNameSpan").text(sample.sample_id);
-  }
-  const extraRow = div.append("div");
-  if (tk.allow2selectSamples) {
-    const t = tk.allow2selectSamples.buttonText;
-    const btn = extraRow.append("button").attr("data-testid", "sjpp-mds3tk-selectsamplebtn").style("margin-right", "10px").text(t.endsWith("s") ? t.substring(0, t.length - 1) : t).on("click", () => {
-      feedSample2selectCallback(tk, block, [sample], [0]);
-      tk.itemtip.hide();
-      tk.menutip.hide();
-    });
-    if (tk.allow2selectSamples.class) btn.attr("class", tk.allow2selectSamples.class);
-  }
-  if (tk.mds.queries?.singleSampleMutation) {
-    extraRow.append("button").style("margin-right", "10px").text("Disco plot").attr("data-testid", "proteinpaint_disc_table_disco_button").on("click", async () => {
-      tk.itemtip.hide();
-      await createDiscoInSandbox(tk, block, sample, thisMutation);
-    });
-  }
-  if (tk.mds.queries?.singleSampleGenomeQuantification) {
-    for (const k in tk.mds.queries.singleSampleGenomeQuantification) {
-      extraRow.append("button").text(k).on("click", async () => {
-        const sandbox = newSandboxDiv(tk.newChartHolder || block.holder0);
-        sandbox.header.text(sample.sample_id);
-        await (await import("./plot.ssgq-MU3BRTMC.js")).plotSingleSampleGenomeQuantification(
-          tk.mds,
-          tk.mds.label,
-          k,
-          sample,
-          sandbox.body.append("div").style("margin", "20px"),
-          block.genome,
-          block.usegm?.name
-          /* to pass current gene name to launch ssgb at that gene
-          do not use thisMutation.gene, as "gene" is not guaranteed attribute on mutations
-          */
-        );
-      });
-    }
-  }
-}
-async function createDiscoInSandbox(tk, block, sample, thisMutation) {
-  const sandbox = newSandboxDiv(tk.newChartHolder || block.holder0);
-  const headerTexts = [sample.sample_id];
-  if (thisMutation) {
-    headerTexts.push(", with ");
-    if (block.usegm) {
-      headerTexts.push(block.usegm.name);
-    } else {
-      headerTexts.push(thisMutation.isoform);
-    }
-    headerTexts.push(" " + thisMutation.mname);
-  }
-  sandbox.header.text(headerTexts.join(""));
-  try {
-    ;
-    (await import("./plot.disco-VGOEQYRL.js")).default(
-      tk.mds.termdbConfig,
-      tk.mds.label,
-      sample,
-      sandbox.body,
-      block.genome,
-      {
-        downloadImgName: headerTexts.join("") + " Disco"
-        // file name of svg downloaded from disco
-      }
-    );
-  } catch (e) {
-    sandbox.body.append("div").text("Error: " + (e.message || e));
-    if (e.stack) console.log(e.stack);
-  }
-}
-async function samples2columnsRows(samples, tk) {
-  const has_caseAccess = samples.some((i) => "caseIsOpenAccess" in i), has_ssm = samples.some((i) => i.ssm_id) || samples.some((i) => i.ssm_id_lst), has_format = samples.some((i) => i.ssmid2format) && tk.mds?.bcf?.format;
-  const displayedFormatKeySet = /* @__PURE__ */ new Set();
-  const columns = [{ label: tk.mds.termdbConfig?.lollipop?.sample || "Sample" }], rows = [];
-  if (has_caseAccess) {
-    columns.push({ label: "Access" });
-  }
-  if (tk.mds.variant2samples.twLst) {
-    for (const tw of tk.mds.variant2samples.twLst) {
-      const cell = { label: tw.term.name };
-      columns.push(cell);
-    }
-  }
-  if (has_ssm) {
-    columns.push({
-      label: "Mutations",
-      isSsm: true
-      // flag for text file downloader to do detect and do special treatment on this field
-    });
-  }
-  if (has_format) {
-    for (const s of samples) {
-      if (!s.ssmid2format) continue;
-      for (const sm in s.ssmid2format) {
-        for (const k in s.ssmid2format[sm]) displayedFormatKeySet.add(k);
-      }
-    }
-    for (const f in tk.mds.bcf.format) {
-      if (!displayedFormatKeySet.has(f)) continue;
-      const fobj = tk.mds.bcf.format[f];
-      columns.push({
-        label: fobj.Description || f
-      });
-    }
-  }
-  for (const sample of samples) {
-    const row = [{ value: sample.sample_id }];
-    let ssm_id_lst = sample.ssm_id_lst;
-    if (!ssm_id_lst && sample.ssm_id) ssm_id_lst = [sample.ssm_id];
-    {
-      const temp = tk.mds.termdbConfig?.urlTemplates?.sample;
-      if (temp) {
-        row[0].url = temp.base + (sample[temp.namekey] || sample.sample_id);
-      }
-    }
-    if (has_caseAccess) {
-      row.push({ value: sample.caseIsOpenAccess ? "Open" : "Controlled" });
-    }
-    if (tk.mds.variant2samples.twLst) {
-      for (const tw of tk.mds.variant2samples.twLst) {
-        const v = twDisplayValueFromSample(sample, tw);
-        const v2 = value2urlsOrText(v, tw);
-        if (tw.baseURL || tw.pmidOrDoi) {
-          row.push({ html: v2 });
-        } else {
-          row.push({ value: v });
-        }
-      }
-    }
-    if (has_ssm) {
-      if (ssm_id_lst) {
-        const htmls = [];
-        for (const ssm_id of ssm_id_lst) {
-          const m = findMbyId(ssm_id, tk);
-          const oneHtml = [];
-          if (m) {
-            let showClass;
-            if (m.dt == dtsnvindel) {
-              if (tk.mds.queries && tk.mds.queries.snvindel && tk.mds.queries.snvindel.url) {
-                oneHtml.push(`<a href=${tk.mds.queries.snvindel.url.base + m.ssm_id} target=_blank>${m.mname}</a>`);
-              } else {
-                oneHtml.push(m.mname);
-              }
-              showClass = true;
-            } else if (m.dt == dtsv || m.dt == dtfusionrna) {
-              const p = sample._pairlst?.[0] || m.pairlst[0];
-              oneHtml.push(
-                `${p.a.name || ""} ${p.a.chr}:${p.a.pos} ${p.a.strand == "+" ? "forward" : "reverse"} > ${p.b.name || ""} ${p.b.chr}:${p.b.pos} ${p.b.strand == "+" ? "forward" : "reverse"}`
-              );
-              showClass = true;
-            } else if (m.dt == dtcnv) {
-              const v = cnv2str(m, tk);
-              oneHtml.push(v.value + " " + v.pos);
-              showClass = Number.isFinite(m.value);
-            } else {
-              throw "unknown dt";
-            }
-            if (showClass) {
-              oneHtml.push(
-                `<span style="color:${rgb(mclass[m.class].color).darker()};font-size:0.8em;">${mclass[m.class].label}</span>`
-              );
-            }
-            htmls.push(`<span style="white-space:nowrap">${oneHtml.join(" ")}</span>`);
-          } else {
-            htmls.push(ssm_id + "?");
-          }
-        }
-        row.push({ html: htmls.join("<br>") });
-      } else {
-        row.push({ value: "" });
-      }
-    }
-    if (has_format) {
-      if (!ssm_id_lst) throw "ssm_id_lst missing, cannot show format";
-      for (const fkey in tk.mds.bcf.format) {
-        if (!displayedFormatKeySet.has(fkey)) continue;
-        if (!sample.ssmid2format) {
-          row.push({ value: "" });
-          continue;
-        }
-        const fobj = tk.mds.bcf.format[fkey];
-        const htmls = [];
-        for (const ssmid of ssm_id_lst) {
-          const value = sample.ssmid2format?.[ssmid]?.[fkey];
-          if (value == void 0) {
-            htmls.push("&nbsp;");
-          } else {
-            htmls.push(printFormat(fobj, value));
-          }
-        }
-        row.push({ html: `<span style="white-space:nowrap">${htmls.join("<br>")}</span>` });
-      }
-    }
-    rows.push(row);
-  }
-  return [columns, rows];
-}
-function value2urlsOrText(v, tw) {
-  if (tw.baseURL) {
-    if (Array.isArray(v)) return v.map((i) => `<a href=${tw.baseURL + i} target=_blank>${i}</a>`).join("<br>");
-    return `<a href=${tw.baseURL + v} target=_blank>${v}</a>`;
-  }
-  if (tw.pmidOrDoi) {
-    const h = [];
-    for (const i of Array.isArray(v) ? v : [v]) {
-      if (i.startsWith("doi: ")) {
-        h.push(`<a href=https://doi.org/${i.slice(5)} target=_blank>${i}</a>`);
-      } else {
-        h.push(`<a href=https://pubmed.ncbi.nlm.nih.gov/${i} target=_blank>${i}</a>`);
-      }
-    }
-    return h.join("<br>");
-  }
-  if (Array.isArray(v)) return v.join("<br>");
-  return v;
-}
-function findMbyId(str, tk) {
-  const lst = tk.skewer?.rawmlst || tk.custom_variants;
-  if (lst) {
-    const m = lst.find((i) => i.ssm_id == str);
-    if (m) return m;
-  }
-  if (tk.cnv) {
-    if (tk.cnv.cnvLst) {
-      const m = tk.cnv.cnvLst.find((i) => i.ssm_id == str);
-      if (m) return m;
-    } else {
-      const m = guessSsmid(str);
-      if (m.dt == dtcnv) {
-        return {
-          dt: dtcnv,
-          chr: m.l[0],
-          start: m.l[1],
-          stop: m.l[2],
-          class: m.l[3],
-          value: m.l[4]
-        };
-      }
-    }
-  }
-  return null;
-}
-function printFormat(fobj, value) {
-  if (fobj && value && fobj.Number == "R" && fobj.Type == "Integer") {
-    const lst = value.split(",").map(Number);
-    if (lst.length == 2) {
-      const [ref, alt] = lst;
-      if (ref >= 0 && alt >= 0 && ref + alt > 0) {
-        return `${fillbar(null, { f: alt / (alt + ref) })} <span style="font-size:.8em">${alt}/${alt + ref}</span>`;
-      }
-    }
-  }
-  return value;
-}
-function block2source(b) {
-  if (b.gmmode == "genomic") {
-    const r = b.rglst[0];
-    return "mutations from " + r.chr + ":" + r.start + "-" + r.stop;
-  }
-  if (b.usegm) return "mutations in " + b.usegm.name;
-  return "mutations";
-}
-
-// mds3/clickVariant.js
-var minoccur4sunburst = 10;
-async function click_variant(d, tk, block, tippos, eventTarget) {
-  try {
-    if (tk.click_snvindel) {
-      tk.skewer.hlssmid = new Set(d.mlst.map((i) => i.ssm_id));
-      mayHighlightDiskBySsmid(tk);
-      tk.click_snvindel(d.mlst[0]);
-      return;
-    }
-    if ("occurrence" in d && d.occurrence >= minoccur4sunburst && tk.mds.variant2samples && tk.mds.variant2samples.sunburst_twLst) {
-      await click2sunburst(d, tk, block, tippos);
-      return;
-    }
-    await variant_details({ mlst: d.mlst, tk, block, tippos });
-  } catch (e) {
-    block.error(e.message || e);
-    if (e.stack) console.log(e.stack);
-  }
-}
-async function click2sunburst(d, tk, block, tippos) {
-  tk.glider.style("cursor", "wait");
-  const data = await tk.mds.variant2samples.get({
-    mlst: d.mlst,
-    querytype: tk.mds.variant2samples.type_sunburst
-  });
-  tk.glider.style("cursor", "auto");
-  if (!dataGood4sunburst(data)) {
-    await variant_details({ mlst: d.mlst, tk, block, tippos });
-    return;
-  }
-  const arg = {
-    nodes: data.nodes,
-    occurrence: d.occurrence,
-    boxyoff: tk.yoff,
-    boxheight: Math.min(800, tk.height),
-    // guard against very tall track
-    boxwidth: block.width,
-    svgheight: Number.parseFloat(block.svg.attr("height")),
-    g: tk.skewer.g.append("g"),
-    pica: tk.pica,
-    click_listbutton: (x, y) => {
-      variant_details({ mlst: d.mlst, tk, block, tippos });
-    },
-    click_ring: async (event2, d2) => {
-      tk.itemtip.clear();
-      const param = {
-        mlst: d.mlst,
-        tk,
-        block,
-        div: tk.itemtip.d,
-        tid2value: {}
-      };
-      param.tid2value[d2.data.id0] = d2.data.v0;
-      if (d2.data.id1) param.tid2value[d2.data.id1] = d2.data.v1;
-      if (d2.data.id2) param.tid2value[d2.data.id2] = d2.data.v2;
-      param.mlst = d.mlst.map((m) => {
-        if (tk.mds.variant2samples.variantkey == "ssm_id") {
-          return { ssm_id: m.ssm_id, occurrence: 0 };
-        }
-        throw "unknown variant2samples.variantkey";
-      });
-      param.mlst[0].occurrence = d2.value;
-      const x = event2.clientX;
-      const y = event2.clientY;
-      await init_sampletable(param);
-      tk.itemtip.show2(x, y);
-    }
-  };
-  if (d.aa) {
-    arg.cx = d.aa.x;
-    arg.cy = skewer_sety(d, tk) + d.yoffset * (tk.skewer.pointup ? -1 : 1);
-  } else {
-    arg.cx = d.x;
-    arg.cy = d.y + (tk.skewer.pointup ? 1 : -1) * tk.skewer.stem1 / 2;
-  }
-  if (d.mlst.length == 1) {
-    arg.chartlabel = d.mlst[0].mname;
-  } else {
-    const mnameSet = new Set(d.mlst.map((i) => i.mname));
-    if (mnameSet.size == 1) {
-      arg.chartlabel = [...mnameSet][0];
-    } else {
-      arg.chartlabel = d.mlst.reduce((i, j) => j.occurrence > i.occurrence ? j : i).mname + " etc";
-    }
-  }
-  const _ = await import("./sunburst-HPDML45I.js");
-  _.default(arg);
-}
-function dataGood4sunburst(data) {
-  if (!Array.isArray(data.nodes)) throw "nodes not array";
-  if (data.nodes.length == 0) throw "nodes empty array";
-  if (data.nodes.length == 1) return false;
-  for (let i = 1; i < data.nodes.length; i++) {
-    const n = data.nodes[i];
-    if (!n.name) throw "node name missing";
-    if (!Number.isInteger(n.cohortsize)) {
-    }
-  }
-  return true;
-}
-async function variant_details(arg) {
-  arg.tk.itemtip.clear().show(arg.tippos.left - 10, arg.tippos.top - 10);
-  arg.div = arg.tk.itemtip.d;
-  arg.tipDiv = arg.tk.itemtip.d;
-  await itemtable(arg);
-}
-
-// mds3/skewer.render.shapes.ts
-function renderSkewerShapes(tk, skewer, shapeG) {
-  shapeG.filter((d) => d.dt == dtsnvindel || d.dt == dtsv || d.dt == dtfusionrna).append("path").attr("d", (d) => shapes[d.shape].calculatePath(getPathDimensions(d.shape, d.radius, skewer.pointup))).attr("fill", (d) => !shapes[d.shape].isFilled ? "none" : d.mlst?.[0] ? tk.color4disc(d.mlst[0]) : tk.color4disc(d)).attr(
-    "stroke",
-    (d) => (d.dt == dtfusionrna || d.dt == dtsv) && d?.mlst[0] ? tk.color4disc(d.mlst[0]) : shapes[d.shape].isFilled ? "white" : d.mlst?.[0] ? tk.color4disc(d.mlst[0]) : tk.color4disc(d)
-  );
-  const defs = shapeG.append("defs").selectAll("clipPath").data(shapeG.data()).enter().append("clipPath").attr(
-    "id",
-    (d) => `clip-path-${d?.mlst ? `${d.mlst[0].mname}-${d.mlst[0].__x}-${d.yoffset}` : `${d.mname}-${d.__x}-${d._y}`}`
-  );
-  defs.each(function(d) {
-    const { width, height } = getPathDimensions(d.shape, d.radius, skewer.pointup);
-    if (!width || !height) return;
-    select_default(this).append("rect").attr("x", d.useNterm != shapes[d.shape].isFilled ? -(width / 2) : 0).attr("y", -(height / 2)).attr("width", d.useNterm != shapes[d.shape].isFilled ? width / 2 : width).attr("height", height);
-  });
-  shapeG.filter((d) => d.dt == dtfusionrna || d.dt == dtsv).append("g").attr(
-    "clip-path",
-    (d) => `url(#clip-path-${d?.mlst ? `${d.mlst[0].mname}-${d.mlst[0].__x}-${d.yoffset}` : `${d.mname}-${d.__x}-${d._y}`}`
-  ).append("path").attr("d", (d) => shapes[d.shape].calculatePath(getPathDimensions(d.shape, d.radius, skewer.pointup))).attr("fill", (d) => shapes[d.shape].isFilled ? "white" : tk.color4disc(d.mlst[0])).attr("stroke", "none");
-}
-function renderShapeKick(skewer, elem) {
-  const kick = elem.append("path").attr("d", (d) => {
-    if (!d.shape) d.shape = d.groups[0].shape;
-    const radius = d.radius * 1.01 || d.maxradius + 2;
-    return shapes[d.shape].calculatePath(getPathDimensions(d.shape, radius, skewer.pointup));
-  }).attr("stroke-width", 1.75);
-  return kick;
-}
-function getPathDimensions(key, radius, pointup = true) {
-  switch (key) {
-    case "filledCircle":
-      return { radius: radius * 0.95 };
-    case "emptyCircle":
-      return { radius };
-    case "filledVerticalRectangle":
-      return { width: radius * 1.5, height: radius * 2.1 };
-    case "emptyVerticalRectangle":
-      return { width: radius * 1.4, height: radius * 2 };
-    case "filledTriangle":
-      return { width: radius * 2.1, height: radius * 2.1, isUp: pointup };
-    case "emptyTriangle":
-      return { width: radius * 2, height: radius * 2, isUp: pointup };
-    case "filledSquare":
-      return { width: radius * 1.7, height: radius * 1.7 };
-    case "emptySquare":
-      return { width: radius * 1.7, height: radius * 1.7 };
-    default:
-      throw "Invalid shape key. Add shape [getPathDimensions() skewer.render.shapes.ts]";
-  }
-}
-function setNumBaseline(key, pointup) {
-  if (key.includes("Triangle")) {
-    if (pointup) return "central";
-    else return `text-after-edge`;
-  } else return "";
-}
-
-// mds3/skewer.render.js
-var modefold = 0;
-var modeshow = 1;
-var middlealignshift = 0.3;
-var disclabelspacing = 1;
-var textlensf = 0.6;
-function skewer_make(tk, block) {
-  const ss = tk.skewer;
-  for (const d of ss.data) {
-    d.x0 = d.x;
-    if (d.xoffset != void 0) {
-      d.x = d.x0 + d.xoffset;
-    }
-    for (const g of d.groups) {
-      g.aa = d;
-    }
-  }
-  const dotwidth = Math.max(14, block.width / 110);
-  let mdc = 0;
-  for (const d of ss.data) {
-    for (const g of d.groups) {
-      mdc = Math.max(mdc, g.occurrence);
-    }
-  }
-  let mrd = 0;
-  const w = Math.pow(dotwidth / 2, 2) * Math.PI;
-  if (mdc <= 10) mrd = w * mdc * 0.9;
-  else if (mdc <= 100) mrd = w * 10;
-  else if (mdc <= 1e3) mrd = w * 14;
-  else mrd = w * 20;
-  const sf_discradius = linear().domain([1, mdc * 0.5, mdc * 0.6, mdc * 0.7, mdc * 0.8, mdc]).range([w, w + (mrd - w) * 0.8, w + (mrd - w) * 0.85, w + (mrd - w) * 0.9, w + (mrd - w) * 0.95, mrd]);
-  let globalmaxradius = dotwidth / 2;
-  ss.maxheight = 0;
-  for (const d of ss.data) {
-    if (d.showmode == void 0) d.showmode = modefold;
-    if (d.slabelrotate == void 0) d.slabelrotate = false;
-    d.maxradius = 0;
-    d.maxrimwidth = 0;
-    d.width = 0;
-    d.slabelwidth = 0;
-    for (const r of d.groups) {
-      if (r.occurrence <= 1) {
-        r.radius = dotwidth / 2;
-      } else {
-        const digc = r.occurrence.toString().length;
-        r.radius = Math.max(Math.sqrt(sf_discradius(r.occurrence) / Math.PI), digc * 5);
-      }
-      d.maxradius = Math.max(d.maxradius, r.radius);
-      globalmaxradius = Math.max(globalmaxradius, r.radius);
-      r.rimwidth = r.rim1count + r.rim2count == 0 ? 0 : Math.max(2, r.radius / 6);
-      d.maxrimwidth = Math.max(d.maxrimwidth, r.rimwidth);
-    }
-    let totalheight = 0;
-    for (const r of d.groups) {
-      r.yoffset = totalheight + r.radius + r.rimwidth;
-      totalheight += (r.radius + r.rimwidth) * 2;
-    }
-    ss.maxheight = Math.max(ss.maxheight, totalheight);
-  }
-  if (!tk.shapes) {
-    if (!tk.shapeBy) {
-      tk.shapes = {};
-      Object.keys(mclass).forEach((v) => tk.shapes[v] = "filledCircle");
-    }
-  }
-  ss.selection = ss.g.selectAll().data(ss.data).enter().append("g").attr("class", "sja_skg").each(function(d) {
-    d.skewer = this;
-  });
-  const discg = ss.selection.selectAll().data((d) => d.groups).enter().append("g").attr(
-    "transform",
-    (d) => "translate(0," + (d.aa.showmode == modefold ? 0 : d.yoffset * (tk.skewer.pointup ? -1 : 1)) + ")"
-  ).attr("class", "sja_aa_discg").each(function(d) {
-    d.g = this;
-    if (!d.shape) {
-      d.shape = tk.shapes[d.mlst[0].class];
-    }
-    if (!d.shape.includes("Circle")) {
-      renderSkewerShapes(tk, ss, select_default(this));
-    } else {
-      const discdot = select_default(this).append("circle");
-      discdot.filter((d2) => d2.dt == dtsnvindel || d2.dt == dtsv || d2.dt == dtfusionrna).attr("fill", (d2) => !shapes[d2.shape].isFilled ? "white" : tk.color4disc(d2.mlst[0])).attr("stroke", (d2) => !shapes[d2.shape].isFilled ? tk.color4disc(d2.mlst[0]) : "white").attr("r", (d2) => d2.radius - 0.5);
-      select_default(this).filter((d2) => d2.dt == dtfusionrna || d2.dt == dtsv).append("path").attr("fill", (d2) => !shapes[d2.shape].isFilled ? tk.color4disc(d2.mlst[0]) : "white").attr("stroke", "none").attr(
-        "d",
-        (d2) => arc_default()({
-          innerRadius: 0,
-          outerRadius: d2.radius - 2,
-          /**** Always show the colored area on the correct side ****
-           * Preserves showing the colored:white areas regardless if
-           * the shape is filled or not
-           */
-          startAngle: d2.useNterm == shapes[d2.shape].isFilled ? 0 : Math.PI,
-          endAngle: d2.useNterm == shapes[d2.shape].isFilled ? Math.PI : Math.PI * 2
-        })
-      );
-    }
-  });
-  const textslc = discg.filter((d) => d.occurrence > 1).append("text").text((d) => d.occurrence).attr("class", "sja_aa_discnum").attr("fill-opacity", (d) => d.aa.showmode == modefold ? 0 : 1).attr("stroke-opacity", (d) => d.aa.showmode == modefold ? 0 : 1).attr("dominant-baseline", (d) => tk.shapes ? setNumBaseline(d.shape, tk.skewer.pointup) : "").attr("text-anchor", "middle").each((d) => {
-    const s = d.radius * 1.5;
-    d.discnumfontsize = Math.min(s / (d.occurrence.toString().length * textlensf), s);
-  }).attr("font-size", (d) => d.discnumfontsize).attr("y", (d) => d.discnumfontsize * middlealignshift);
-  textslc.filter((d) => d.dt == dtsnvindel).attr("fill", (d) => tk.shapes && !shapes[d.shape].isFilled ? "black" : "white");
-  textslc.filter((d) => d.dt == dtsv || d.dt == dtfusionrna).attr("stroke", (d) => tk.color4disc(d.mlst[0])).attr("stroke-width", 0.8).attr("font-weight", "bold").attr("fill", "white");
-  const textlab = discg.append("text").text((d) => d.mnameCompact || tk.mnamegetter(d.mlst[0])).attr("font-size", (d) => {
-    d._labfontsize = Math.max(12, d.radius * 1.2);
-    return d._labfontsize;
-  }).each(function(d) {
-    const lw = this.getBBox().width;
-    d._label_width = lw;
-    if (d.aa.groups.length == 1) {
-      d.aa.slabelrotate = true;
-      d.aa.slabelwidth = lw;
-      ss.maxheight = Math.max(ss.maxheight, (d.radius + d.rimwidth) * 2 + 2 + lw);
-    }
-  }).attr("fill", (d) => tk.color4disc(d.mlst[0])).attr("x", (d) => d.radius + d.rimwidth + 1).attr("y", (d) => d._labfontsize * middlealignshift).classed("sja_aa_disclabel", true).attr("fill-opacity", (d) => d.aa.showmode == modefold ? 0 : 1).attr("transform", "scale(1) rotate(0)").on("mousedown", (event2) => {
-    event2.stopPropagation();
-  }).on("click", (event2, d) => {
-    fold_glyph([d.aa], tk);
-    unfold_update(tk, block);
-  }).on("mouseover", (event2, d) => {
-    event2.target.setAttribute("font-size", d._labfontsize * 1.1);
-    showHoverTipOnDisk(event2, d, tk);
-  }).on("mouseout", (event2, d) => {
-    event2.target.setAttribute("font-size", d._labfontsize);
-    tk.hovertip.hide();
-  });
-  ss.hlBoxG = discg.append("g");
-  for (const d of ss.data) {
-    let leftw = 0, rightw = 0;
-    for (const g of d.groups) {
-      leftw = Math.max(leftw, g.radius + g.rimwidth);
-      rightw = Math.max(rightw, g.radius + g.rimwidth + disclabelspacing + g._label_width);
-    }
-    d.width = leftw + rightw;
-  }
-  let kick;
-  if (tk.shapes) {
-    kick = renderShapeKick(ss, discg);
-  } else {
-    kick = discg.append("circle").attr("r", (d) => d.radius - 0.5);
-  }
-  kick.attr("stroke", (d) => tk.color4disc(d.mlst[0])).classed("sja_aa_disckick", true).attr("fill", "white").attr("fill-opacity", 0).attr("stroke-opacity", 0).attr("data-testid", (d) => `sjpp-mds3skewerdisckick-${d.mlst[0].mname}`).on("mousedown", (event2) => {
-    event2.stopPropagation();
-  }).on("mouseover", (event2, d) => {
-    showHoverTipOnDisk(event2, d, tk);
-    if (tk.disc_mouseover) {
-      tk.disc_mouseover(d, event2.target);
-    }
-  }).on("mouseout", (event2, d) => {
-    tk.hovertip.hide();
-    if (tk.disc_mouseout) {
-      tk.disc_mouseout(d);
-    }
-  }).on("click", async (event2, d) => {
-    click_variant(d, tk, block, event2.target.getBoundingClientRect(), event2.target);
-  });
-  const rimfunc = arc_default().innerRadius((d) => d.radius).outerRadius((d) => d.radius + d.rimwidth).startAngle(0).endAngle((d) => {
-    d.rim1_startangle = Math.PI * 2 * d.rim1count / d.occurrence;
-    return d.rim1_startangle;
-  });
-  discg.filter((d) => d.rim1count > 0).append("path").attr("d", rimfunc).attr("fill", (d) => tk.color4disc(d.mlst[0])).attr("class", "sja_aa_discrim").attr("fill-opacity", 0);
-  const rimfunc2 = arc_default().innerRadius((d) => d.radius + 0.5).outerRadius((d) => d.radius + 0.5 + d.rimwidth).startAngle((d) => d.rim1_startangle).endAngle((d) => d.rim1_startangle + Math.PI * 2 * d.rim2count / d.occurrence);
-  discg.filter((d) => d.rim2count > 0).append("path").attr("d", rimfunc2).attr("stroke", (d) => tk.color4disc(d.mlst[0])).attr("fill", "none").attr("class", "sja_aa_discrim").attr("stroke-opacity", 0);
-  {
-    let lapcount = 0;
-    let lastx = 0;
-    for (const d of ss.data) {
-      if (d.x - d.maxradius - d.maxrimwidth < lastx) {
-        lapcount++;
-      }
-      lastx = Math.max(lastx, d.x + d.width - d.maxradius - d.maxrimwidth);
-    }
-    ss.stem1 = lapcount == 0 ? 0 : dotwidth;
-    ss.stem2 = linear().domain([0, 1, ss.data.length]).range([0, dotwidth, dotwidth * 3])(lapcount);
-  }
-  const hbaseline = dotwidth * 0.7;
-  let maxm = 0;
-  for (const d of ss.data) {
-    for (const g of d.groups) {
-      maxm = Math.max(maxm, g.occurrence);
-    }
-  }
-  ss.stem3 = Math.max(2, hbaseline + dotwidth * Math.min(5, maxm));
-  let foldedKick;
-  if (tk.shapes) {
-    foldedKick = renderShapeKick(ss, ss.selection);
-    foldedKick.attr(
-      "transform",
-      (d) => `translate(0, ${(tk.skewer.pointup ? -1 : 1) * d.maxradius})
-			scale(${d.showmode == modefold ? "1,1" : "0.01,0.01"})`
-    );
-  } else {
-    foldedKick = ss.selection.append("circle").attr("r", (d) => d.maxradius + 1).attr("cy", (d) => (tk.skewer.pointup ? -1 : 1) * d.maxradius).attr("transform", (d) => `scale(${d.showmode == modefold ? "1,1" : "0.01,0.01"})`);
-  }
-  foldedKick.attr("class", "sja_aa_skkick").attr("fill", "white").attr("fill-opacity", 0).attr("stroke", "none").on("mouseover", (event2, d) => {
-    let cumh = 0;
-    let boxw = 0;
-    const hpad = 5;
-    const tiph = tk.skewer.pointup ? 7 : 14;
-    for (const g of d.groups) {
-      g.pica_fontsize = Math.max(11, g.radius);
-      cumh += g.pica_fontsize + 1;
-      tk.pica.g.append("text").text((g.mnameCompact || g.mlst[0].mname) + (g.occurrence > 1 ? " x" + g.occurrence : "")).attr("font-size", g.pica_fontsize).each(function() {
-        boxw = Math.max(boxw, this.getBBox().width);
-      }).remove();
-    }
-    boxw += hpad * 2;
-    const boxh = cumh + 5;
-    tk.pica.g.append("rect").attr("y", tk.skewer.pointup ? -boxh : 0).attr("width", boxw).attr("height", boxh).attr("fill", "white").attr("fill-opacity", 0.8).attr("stroke", "#ccc").attr("shape-rendering", "crispEdges");
-    cumh = 0;
-    const _g = tk.pica.g.selectAll().data(d.groups).enter().append("g").attr("transform", (g, i) => {
-      cumh += g.pica_fontsize + 1;
-      return "translate(" + hpad + "," + cumh * (tk.skewer.pointup ? -1 : 1) + ")";
-    });
-    _g.append("text").text((g) => g.mnameCompact || g.mlst[0].mname).attr("font-size", (g) => g.pica_fontsize).each(function(g) {
-      g.pica_mlabelwidth = this.getBBox().width;
-    }).attr("fill", (d2) => tk.color4disc(d2.mlst[0])).attr("dominant-baseline", tk.skewer.pointup ? "hanging" : "auto");
-    const firstlabw = d.groups[0].pica_mlabelwidth;
-    tk.pica.x = d.x - hpad - firstlabw / 2;
-    tk.pica.y = d.y + (tk.skewer.pointup ? -1 : 1) * (d.maxradius * 2 + tiph + 2);
-    tk.pica.g.attr("transform", "translate(" + tk.pica.x + "," + tk.pica.y + ")");
-    _g.filter((g) => g.occurrence > 1).append("text").text((g) => "x" + g.occurrence).attr("x", (g) => g.pica_mlabelwidth + 5).attr("font-size", (g) => g.pica_fontsize).attr("dominant-baseline", tk.skewer.pointup ? "hanging" : "auto").attr("fill", "#9e9e9e");
-    const handle = tk.pica.g.append("g").attr("transform", "translate(" + (hpad + firstlabw / 2) + "," + (tk.skewer.pointup ? 1 : -1) + ")");
-    handle.append("line").attr("y2", (tk.skewer.pointup ? 1 : -1) * tiph).attr("stroke", "#858585").attr("shape-rendering", "crispEdges");
-    handle.append("line").attr("x1", -1).attr("x2", -1).attr("y2", (tk.skewer.pointup ? 1 : -1) * tiph).attr("stroke", "white").attr("shape-rendering", "crispEdges");
-    handle.append("line").attr("x1", 1).attr("x2", 1).attr("y2", (tk.skewer.pointup ? 1 : -1) * tiph).attr("stroke", "white").attr("shape-rendering", "crispEdges");
-  }).on("mouseout", (event2, d) => {
-    tk.pica.g.selectAll("*").remove();
-  }).on("click", (event2, d) => {
-    tk.pica.g.selectAll("*").remove();
-    unfold_glyph([d], tk, block);
-  });
-  let mm = 0;
-  for (const d of ss.data) {
-    mm = Math.max(mm, d.occurrence);
-  }
-  const sf_foldyoff = linear().domain([1, mm]).range([hbaseline, ss.stem3 - globalmaxradius]);
-  ss.selection.attr("transform", (d) => {
-    d.foldyoffset = sf_foldyoff(d.occurrence);
-    d.y = skewer_sety(d, tk);
-    return "translate(" + d.x + "," + d.y + ")";
-  });
-  ss.selection.append("path").attr("class", "sja_aa_stem").attr("d", (d) => skewer_setstem(d, tk)).attr("stroke", (d) => tk.color4disc(d.groups[0].mlst[0])).attr("fill", "none");
-  const mgsk = ss.selection.filter((d) => d.groups.length > 1);
-  mgsk.append("rect").attr("class", "sja_aa_ssk_bg").attr("shape-rendering", "crispEdges").attr("fill-opacity", 0).attr("height", ss.stem1).attr("fill", (d) => tk.color4disc(d.groups[0].mlst[0])).attr("width", (d) => {
-    d.ssk_width = Math.max(d.occurrence.toString().length * 8 + 6, 2 * (d.maxradius + d.maxrimwidth));
-    return d.ssk_width;
-  }).attr("x", (d) => -d.ssk_width / 2);
-  mgsk.append("text").attr("class", "sja_aa_ssk_text").attr("fill", "white").attr("fill-opacity", 0).attr("font-weight", "bold").attr("text-anchor", "middle").attr("dominant-baseline", "central").text((d) => d.occurrence).each((d) => {
-    d.ssk_fontsize = Math.min(ss.stem1, d.ssk_width / (d.occurrence.toString().length * textlensf));
-  }).attr("font-size", (d) => d.ssk_fontsize);
-  mgsk.append("rect").attr("class", "sja_aa_ssk_kick").attr("fill", "white").attr("fill-opacity", 0).attr("stroke", "none").attr("height", ss.stem1).attr("x", (d) => -d.ssk_width / 2).attr("width", (d) => d.ssk_width).on("mouseover", (event2, d) => {
-    const p = select_default(event2.target.parentNode);
-    p.selectAll(".sja_aa_disckick").transition().attr("stroke-opacity", 1);
-    p.select(".sja_aa_ssk_bg").transition().attr("fill-opacity", 1).attr("stroke-opacity", 1);
-    p.select(".sja_aa_ssk_text").transition().attr("fill-opacity", 1);
-  }).on("mouseout", function(event2, d) {
-    const p = select_default(event2.target.parentNode);
-    p.selectAll(".sja_aa_disckick").transition().attr("stroke-opacity", 0);
-    p.select(".sja_aa_ssk_bg").transition().attr("fill-opacity", 0).attr("stroke-opacity", 0);
-    p.select(".sja_aa_ssk_text").transition().attr("fill-opacity", 0);
-  }).on("click", async (event2, d) => {
-    click_variant(d, tk, block, event2.target.getBoundingClientRect(), null, event2.target);
-  });
-}
-function skewer_sety(d, tk) {
-  if (tk.skewer.pointup) {
-    if (d.showmode == modefold) {
-      return tk.skewer.maxheight + tk.skewer.stem1 + tk.skewer.stem2 + tk.skewer.stem3 - d.foldyoffset;
-    }
-    return tk.skewer.maxheight;
-  }
-  if (d.showmode == modefold) return d.foldyoffset;
-  return tk.skewer.stem1 + tk.skewer.stem2 + tk.skewer.stem3;
-}
-function skewer_setstem(d, tk) {
-  if (tk.skewer.pointup) {
-    if (d.showmode == modefold) {
-      return "M0,0v0l0,0v" + d.foldyoffset;
-    }
-    return "M0,0v" + tk.skewer.stem1 + "l" + (d.x0 - d.x) + "," + tk.skewer.stem2 + "v" + tk.skewer.stem3;
-  }
-  if (d.showmode == modefold) {
-    return "M0,0v0l0,0v-" + d.foldyoffset;
-  }
-  return "M0,0v-" + tk.skewer.stem1 + "l" + (d.x0 - d.x) + ",-" + tk.skewer.stem2 + "v-" + tk.skewer.stem3;
-}
-function settle_glyph(tk, block) {
-  if (tk.skewer.data.length == 0) return;
-  const x1 = 0;
-  const x2 = block.width;
-  let sumwidth = 0;
-  const allinview = [];
-  const beyondviewitems = [];
-  for (const d of tk.skewer.data) {
-    if (d.x0 < x1 || d.x0 > x2) {
-      delete d.xoffset;
-      beyondviewitems.push(d);
-    } else {
-      sumwidth += d.slabelrotate ? (d.groups[0].radius + d.groups[0].rimwidth) * 2 : d.width;
-      allinview.push(d);
-    }
-  }
-  fold_glyph(beyondviewitems, tk);
-  let expandlst = [];
-  const foldlst = [];
-  if (sumwidth < x2 - x1) {
-    expandlst = allinview;
-  } else {
-    allinview.sort((a, b) => {
-      if (b.occurrence == a.occurrence) {
-        if (b.groups.length == a.groups.length) {
-          return Math.abs(a.x0 * 2 - x1 - x2) - Math.abs(b.x0 * 2 - x1 - x2);
-        } else {
-          return b.groups.length - a.groups.length;
-        }
-      }
-      return b.occurrence - a.occurrence;
-    });
-    let width = 0;
-    let allowpx = (x2 - x1) * 0.8;
-    let stop = false;
-    for (const d of allinview) {
-      if (stop) {
-        delete d.xoffset;
-        foldlst.push(d);
-        d.showmode = modefold;
-      } else {
-        if (width + d.width < allowpx) {
-          expandlst.push(d);
-          width += d.width;
-        } else {
-          stop = true;
-          delete d.xoffset;
-          foldlst.push(d);
-          d.showmode = modefold;
-        }
-      }
-    }
-  }
-  fold_glyph(foldlst, tk);
-  unfold_glyph(expandlst, tk, block);
-}
-function unfold_glyph(newlst, tk, block) {
-  const dur = 1e3;
-  const expanded = /* @__PURE__ */ new Set();
-  const folded = /* @__PURE__ */ new Set();
-  for (const d of newlst) {
-    if (d.showmode == modeshow) {
-      expanded.add(d.x0);
-    } else {
-      d.showmode = modeshow;
-      folded.add(d.x0);
-      d.y = skewer_sety(d, tk);
-    }
-  }
-  if (expanded.size) {
-    const set = tk.skewer.selection.filter((d) => expanded.has(d.x0));
-    set.selectAll(".sja_aa_discrim").attr("fill-opacity", 1).attr("stroke-opacity", 1);
-  }
-  if (folded.size) {
-    const set = tk.skewer.selection.filter((d) => folded.has(d.x0));
-    set.transition().duration(dur).attr("transform", (d) => "translate(" + d.x + "," + d.y + ")");
-    set.selectAll(".sja_aa_discg").transition().duration(dur).attr("transform", (d) => {
-      d.y = d.yoffset * (tk.skewer.pointup ? -1 : 1);
-      return "translate(0," + d.y + ")";
-    });
-    set.selectAll(".sja_aa_disckick").transition().duration(dur).attr("transform", "scale(1)").on("end", () => {
-      set.selectAll(".sja_aa_ssk_kick").attr("transform", "scale(1)").attr("y", tk.skewer.pointup ? 0 : -tk.skewer.stem1);
-      set.selectAll(".sja_aa_disckick").classed("sjpp-active", true);
-    });
-    set.selectAll(".sja_aa_discnum").transition().duration(dur).attr("fill-opacity", 1).attr("stroke-opacity", 1);
-    set.filter((d) => d.groups.length > 1).selectAll(".sja_aa_disclabel").transition().duration(dur).attr("fill-opacity", 1).attr("transform", "scale(1)");
-    set.selectAll(".sja_aa_discrim").transition().duration(dur).attr("fill-opacity", 1).attr("stroke-opacity", 1);
-    set.selectAll(".sja_aa_ssk_bg").attr("transform", "scale(1)").attr("y", tk.skewer.pointup ? 0 : -tk.skewer.stem1);
-    set.selectAll(".sja_aa_ssk_text").attr("transform", "scale(1)").attr("y", (tk.skewer.pointup ? 1 : -1) * tk.skewer.stem1 / 2);
-    set.selectAll(".sja_aa_skkick").transition().duration(0).attr(
-      "transform",
-      (d) => `${d.shape && !d.shape.includes("Circle") ? `translate(0, ${(tk.skewer.pointup ? -1 : 1) * d.maxradius})` : ""} scale(0.01, 0.01)`
-      // safari fix
-    ).on("end", () => {
-      set.selectAll(".sja_aa_skkick").classed("sjpp-active", false);
-    });
-    let counter = 0;
-    set.selectAll(".sja_aa_stem").transition().duration(dur).attr("d", (d) => skewer_setstem(d, tk)).each(() => ++counter).on("end", () => {
-      if (!--counter) {
-        unfold_update(tk, block);
-      }
-    });
-  } else {
-    unfold_update(tk, block);
-  }
-}
-function unfold_update(tk, block) {
-  const dur = 1e3;
-  const alllst = [];
-  const hash = /* @__PURE__ */ new Set();
-  const x1 = 0;
-  const x2 = block.width;
-  for (const d of tk.skewer.data) {
-    if (d.x0 < x1 || d.x0 > x2) continue;
-    if (d.showmode == modeshow) {
-      d.x = d.x0;
-      alllst.push(d);
-      hash.add(d.x0);
-    }
-  }
-  if (alllst.length == 0) {
-    return;
-  }
-  horiplace(alllst, tk, block);
-  for (const d of alllst) {
-    d.xoffset = d.x - d.x0;
-  }
-  for (let i = 0; i < alllst.length; i++) {
-    const d = alllst[i];
-    if (d.groups.length > 1) continue;
-    const disc = d.groups[0];
-    if (tk.slabel_forcerotate) {
-      d.slabelrotate = true;
-    } else {
-      const next = alllst[i + 1];
-      const rightx = next ? next.x - next.maxradius - next.maxrimwidth : x2;
-      d.slabelrotate = rightx - d.x - disc.radius - disc.rimwidth - 1 < d.slabelwidth;
-    }
-    d.width = (disc.radius + disc.rimwidth) * 2 + (d.slabelrotate ? 0 : 2 + d.slabelwidth);
-  }
-  const set = tk.skewer.selection.filter((d) => hash.has(d.x0));
-  set.transition().duration(dur).attr("transform", (d) => "translate(" + d.x + "," + d.y + ")");
-  set.selectAll(".sja_aa_stem").transition().duration(dur).attr("d", (d) => skewer_setstem(d, tk));
-  set.filter((d) => d.groups.length == 1).selectAll(".sja_aa_disclabel").transition().duration(dur).attr("fill-opacity", 1).attr(
-    "transform",
-    (d) => "scale(1) rotate(" + (d.aa.slabelrotate ? (tk.skewer.pointup ? "-" : "") + "90" : "0") + ")"
-  );
-  tk.slabel_forcerotate = false;
-}
-function horiplace(items, tk, block) {
-  const xoffset0 = 0;
-  const x2 = block.width;
-  let xoffset = xoffset0;
-  let overlap = false;
-  for (const i of items) {
-    if (i.x0 < xoffset0 || i.x0 > x2) continue;
-    if (i.groups.length == 1) {
-      i.slabelrotate = true;
-      const disc = i.groups[0];
-      i.width = (disc.radius + disc.rimwidth) * 2;
-    }
-    const x = i.x - i.maxradius - i.maxrimwidth;
-    if (x < xoffset) {
-      overlap = true;
-    }
-    if (x + i.width > x2) {
-      overlap = true;
-    }
-    xoffset = Math.max(xoffset, x + i.width);
-  }
-  if (!overlap) {
-    return false;
-  }
-  xoffset = xoffset0;
-  for (const i of items) {
-    if (i.x0 < xoffset0 || i.x0 > x2) continue;
-    i.x = xoffset + i.maxradius + i.maxrimwidth;
-    xoffset += i.width;
-  }
-  horiplace0(items, block.width);
-}
-function horiplace0(items, allwidth) {
-  for (let i = 0; i < items.length; i++) {
-    if (items[i].x0 < 0) continue;
-    if (items[i].x0 > allwidth) break;
-    while (1) {
-      let currsum = 0, newsum = 0;
-      for (let j = i; j < items.length; j++) {
-        const t = items[j];
-        if (t.x0 > allwidth) {
-          return;
-        }
-        currsum += Math.abs(t.x - t.x0);
-        t.x++;
-        newsum += Math.abs(t.x - t.x0);
-      }
-      if (items[i].x >= items[i].x0) {
-        for (let j = i; j < items.length; j++) {
-          items[j].x--;
-        }
-        break;
-      }
-      const z = items[items.length - 1];
-      if (z.x + z.width / 2 >= allwidth) {
-        return;
-      }
-      if (newsum <= currsum) {
-      } else {
-        for (let j = i; j < items.length; j++) {
-          if (items[j].x0 > allwidth) {
-            break;
-          }
-          items[j].x--;
-        }
-        break;
-      }
-    }
-  }
-}
-function fold_glyph(lst, tk) {
-  if (lst.length == 0) return;
-  const dur = 1e3;
-  const hash = /* @__PURE__ */ new Set();
-  for (const d of lst) {
-    d.x = d.x0;
-    hash.add(d.x0);
-    d.showmode = modefold;
-    d.y = skewer_sety(d, tk);
-  }
-  const set = tk.skewer.selection.filter((d) => hash.has(d.x0));
-  set.transition().duration(dur).attr("transform", (d) => "translate(" + d.x + "," + d.y + ")");
-  set.selectAll(".sja_aa_stem").transition().duration(dur).attr("d", (d) => skewer_setstem(d, tk));
-  set.selectAll(".sja_aa_discg").transition().duration(dur).attr("transform", (d) => "translate(0," + (tk.skewer.pointup ? "-" : "") + d.aa.maxradius + ")");
-  set.selectAll(".sja_aa_disckick").transition().duration(0).attr("transform", "scale(0)").on("end", () => {
-    set.selectAll(".sja_aa_disckick").classed("sjpp-active", false);
-  });
-  set.selectAll(".sja_aa_discnum").transition().duration(dur).attr("fill-opacity", 0).attr("stroke-opacity", 0);
-  set.selectAll(".sja_aa_disclabel").transition().duration(dur).attr("fill-opacity", 0).attr("transform", "scale(0)");
-  set.selectAll(".sja_aa_discrim").transition().duration(dur).attr("fill-opacity", 0).attr("stroke-opacity", 0);
-  set.selectAll(".sja_aa_ssk_kick").attr("transform", "scale(0)");
-  set.selectAll(".sja_aa_ssk_bg").attr("transform", "scale(0)");
-  set.selectAll(".sja_aa_ssk_text").attr("transform", "scale(0)");
-  set.selectAll(".sja_aa_skkick").transition().duration(dur).attr("transform", (d) => `${d.shape ? `translate(0, ${(tk.skewer.pointup ? -1 : 1) * d.maxradius})` : ""} scale(1)`).on("end", () => {
-    set.selectAll(".sja_aa_skkick").classed("sjpp-active", true);
-  });
-}
-function mayHighlightDiskBySsmid(tk) {
-  tk.skewer.hlBoxG.selectAll("*").remove();
-  if (!tk.skewer.hlssmid) return;
-  tk.skewer.hlBoxG.filter((g) => {
-    if (g.mlst) {
-      return g.mlst.find((m) => tk.skewer.hlssmid.has(m.ssm_id));
-    }
-    return tk.skewer.hlssmid.has(g.ssm_id);
-  }).append("rect").attr("x", (g) => -g.radius).attr("y", (g) => -g.radius).attr("width", (g) => g.radius * 2).attr("height", (g) => g.radius * 2).attr("stroke", tk.skewer.hlBoxColor).attr("stroke-width", (g) => g.radius > 10 ? 1.5 : 1).attr("fill", "none").attr("class", "sja_mds3_skewer_ssmhlbox");
-}
-function showHoverTipOnDisk(event2, d, tk) {
-  tk.hovertip.clear().show(event2.clientX, event2.clientY);
-  if (!d.mlst?.[0]) {
-    tk.hovertip.d.append("div").text("d.mlst[] missing or blank");
-    return;
-  }
-  const m = mclass[d.mlst[0]?.class] || { color: "black", label: "_unknown" };
-  tk.hovertip.d.append("div").style("font-size", ".9em").html(`<span style="background:${m.color}">&nbsp;&nbsp;</span> ${m.label}`);
-  if (d.mlst[0].occurrence) {
-    const c = d.mlst.reduce((t, i) => t + i.occurrence, 0);
-    tk.hovertip.d.append("div").text(`${c} sample${c > 1 ? "s" : ""}`);
-  }
-  if (d.mlst.length > 1) {
-    tk.hovertip.d.append("div").text(`${d.mlst.length} ${d.mlst[0].dt == dtsnvindel ? "variants" : "alterations"}`);
-  }
-}
-
-// mds3/datagroup.js
-var minbpwidth = 4;
-function make_datagroup(tk, rawmlst, block) {
-  mlst_pretreat(rawmlst, tk, block);
-  const x2mlst = /* @__PURE__ */ new Map();
-  for (const m of rawmlst) {
-    if (m.__x == void 0) continue;
-    if (!x2mlst.has(m.__x)) {
-      x2mlst.set(m.__x, []);
-    }
-    x2mlst.get(m.__x).push(m);
-  }
-  const datagroup = [];
-  if (block.exonsf >= minbpwidth) {
-    for (const [x, mlst] of x2mlst) {
-      datagroup.push({
-        chr: mlst[0].chr,
-        pos: mlst[0].pos,
-        mlst,
-        x
-      });
-    }
-  } else {
-    if (block.usegm && block.usegm.coding && block.gmmode != gmmode.genomic) {
-      const aa2mlst = /* @__PURE__ */ new Map();
-      for (const [x, mlst] of x2mlst) {
-        if (mlst[0].chr != block.usegm.chr) {
-          continue;
-        }
-        let aapos = void 0;
-        for (const m of mlst) {
-          if (Number.isFinite(m.aapos)) aapos = m.aapos;
-        }
-        if (aapos == void 0) {
-          aapos = genomic2gm(mlst[0].pos, block.usegm).aapos;
-        }
-        if (aapos == void 0) {
-          console.error("data item cannot map to aaposition");
-          console.log(mlst[0]);
-          continue;
-        }
-        x2mlst.delete(x);
-        if (!aa2mlst.has(aapos)) {
-          aa2mlst.set(aapos, []);
-        }
-        let notmet = true;
-        for (const lst of aa2mlst.get(aapos)) {
-          if (Math.abs(lst[0].__x - mlst[0].__x) <= block.exonsf * 3) {
-            for (const m of mlst) {
-              lst.push(m);
-            }
-            notmet = false;
-            break;
-          }
-        }
-        if (notmet) {
-          aa2mlst.get(aapos).push(mlst);
-        }
-      }
-      for (const llst of aa2mlst.values()) {
-        for (const mlst of llst) {
-          let m = null;
-          for (const m2 of mlst) {
-            if (Number.isFinite(m2.rnapos)) m = m2;
-          }
-          if (m == null) {
-            console.log("trying to map mlst to codon, but no rnapos found");
-            for (const m2 of mlst) {
-              console.log(m2);
-            }
-            continue;
-          }
-          datagroup.push({
-            chr: mlst[0].chr,
-            pos: m.pos,
-            mlst,
-            x: mlst[0].__x
-          });
-        }
-      }
-    }
-    const pxbin = [];
-    const binpx = 2;
-    for (const [x, mlst] of x2mlst) {
-      const i = Math.floor(x / binpx);
-      if (!pxbin[i]) {
-        pxbin[i] = [];
-      }
-      pxbin[i] = [...pxbin[i], ...mlst];
-    }
-    for (const mlst of pxbin) {
-      if (!mlst) continue;
-      const xsum = mlst.reduce((i, j) => i + j.__x, 0);
-      datagroup.push({
-        isbin: true,
-        chr: mlst[0].chr,
-        pos: mlst[0].pos,
-        mlst,
-        x: xsum / mlst.length
-      });
-    }
-  }
-  datagroup.sort((a, b) => a.x - b.x);
-  return datagroup;
-}
-function mlst_pretreat(rawmlst, tk, block) {
-  let nogenomicpos = 0, outofcds = 0, nochr = 0;
-  const unmapped = [];
-  const usemlst = [];
-  for (const m of rawmlst) {
-    delete m.__x;
-    if (block.gmmode == gmmode.protein && block.usegm.codingstart && block.usegm.codingstop) {
-      if (m.pos < block.usegm.codingstart || m.pos > block.usegm.codingstop) {
-        outofcds++;
-        continue;
-      }
-    }
-    if (!m.chr) {
-      nochr++;
-      continue;
-    }
-    if (!Number.isInteger(m.pos)) {
-      nogenomicpos++;
-      continue;
-    }
-    const hits = block.seekcoord(m.chr, m.pos);
-    if (hits.length == 0) {
-      unmapped.push(m);
-      continue;
-    }
-    if (hits.length == 1) {
-      m.__x = hits[0].x;
-    } else {
-      m.__x = hits[0].x;
-    }
-    if (m.__x < -1 || m.__x > block.width + 1) {
-      continue;
-    }
-    usemlst.push(m);
-  }
-  if (nogenomicpos + nochr > 0) {
-    block.tkerror(tk, nogenomicpos + nochr + " items have no chromosome or genomic position");
-  }
-  if (unmapped.length) {
-    console.error(unmapped.length + " items not mapped to any region");
-    for (const m of unmapped) console.log(m);
-  }
-  dsqueryresult_snvindelfusionitd(usemlst, tk, block);
-}
-function dsqueryresult_snvindelfusionitd(lst, tk, block) {
-  for (const m of lst) {
-    if (block.usegm) {
-      const t = genomic2gm(m.pos, block.usegm);
-      m.rnapos = t.rnapos;
-      m.aapos = t.aapos;
-    }
-    if (m.dt == dtsnvindel) {
-      continue;
-    }
-    if (m.dt == dtsv || m.dt == dtfusionrna) {
-      if (m.pairlstIdx == 0) {
-        m.useNterm = true;
-      } else {
-        m.useNterm = false;
-      }
-      continue;
-    }
-    throw "unknown dt: " + m.dt;
-  }
-}
-
-// mds3/leftlabel.js
-var labyspace = 5;
-async function make_leftlabels(data, tk, block) {
-  let laby = 0;
-  makeVariantLabel(data, tk, block, laby);
-  if (tk.leftlabels.doms.variants) {
-    laby += labyspace + block.labelfontsize;
-  }
-  if ("sampleTotalNumber" in data || tk.leftlabels.doms.samples) {
-    const _ = await import("./leftlabel.sample-4JCKYXED.js");
-    _.makeSampleLabel(data, tk, block, laby);
-    laby += labyspace + block.labelfontsize;
-    if (tk.filterObj) {
-      _.makeSampleFilterLabel(data, tk, block, laby);
-    }
-    if (tk.leftlabels.doms.filterObj) {
-      laby += labyspace + block.labelfontsize;
-    }
-  }
-  if (tk.showCloseLeftlabel) {
-    if (!tk.leftlabels.doms.close) {
-      tk.leftlabels.doms.close = makelabel(tk, block, laby).text("Close").on("click", () => {
-        for (const [i, t] of block.tklst.entries()) {
-          if (t.tkid == tk.tkid) {
-            block.tk_remove(i);
-          }
-        }
-        tk.onClose?.();
-      });
-    }
-    laby += labyspace + block.labelfontsize;
-  }
-  tk.leftlabels.laby = laby;
-  positionLeftlabelg(tk, block);
-  setLeftlabelsMaxWidth(tk);
-  tk.subtk2height.leftlabels = laby + 20;
-}
-function setLeftlabelsMaxWidth(tk) {
-  tk.leftlabels.maxwidth = tk.tklabel.node().getBBox().width;
-  for (const k in tk.leftlabels.doms) {
-    tk.leftlabels.maxwidth = Math.max(tk.leftlabels.maxwidth, tk.leftlabels.doms[k].node().getBBox().width);
-  }
-}
-function positionLeftlabelg(tk, block) {
-  if (tk.leftlabels.laby == 0) {
-    return;
-  }
-  tk.leftlabels.xoff = 0;
-  if (tk.skewer) {
-    const nm = tk.skewer.viewModes.find((i) => i.inuse);
-    if (nm.type == "numeric") {
-      const lly = tk.leftlabels.laby + labyspace + block.labelfontsize;
-      if (lly > nm.toplabelheight + 5) {
-        tk.leftlabels.xoff = nm.axisWidth;
-      }
-    }
-  }
-  tk.leftlabels.g.transition().attr("transform", `translate(-${tk.leftlabels.xoff},${labyspace + block.labelfontsize})`);
-}
-function makelabel(tk, block, y) {
-  const text = tk.leftlabels.g.append("text").attr("font-size", block.labelfontsize).attr("y", block.labelfontsize / 2 + y).attr("text-anchor", "end").attr("dominant-baseline", "central").attr("class", "sja_clbtext2").attr("fill", "black").attr("x", block.tkleftlabel_xshift).attr("tabindex", 0).on("keydown", function(event2) {
-    if (event2.target != textElem) return;
-    if (event2.key == "Enter") textElem.dispatchEvent(new Event("click"));
-  });
-  const textElem = text.node();
-  return text;
-}
-
-// mds3/numericmode.js
-var disclabelspacing2 = 1;
-var middlealignshift2 = 0.3;
-var labyspace2 = 5;
-var clustercrowdlimit = 7;
-var maxclusterwidth = 100;
-var stemColor = "#ededed";
-var defaultLabel = "Numeric value";
-function renderNumericMode(nm, data, tk, block) {
-  const datagroup = make_datagroup(tk, data.skewer || tk.skewer.rawmlst, block).filter(
-    (g) => g.x >= 0 && g.x <= block.width
-  );
-  nm.data = datagroup;
-  if (!nm.axisg) nm.axisg = tk.gleft.append("g");
-  if (!nm.axisheight) nm.axisheight = 150;
-  clearTk(tk);
-  numeric_make(nm, tk, block);
-  mayHighlightByLDoverlay(tk);
-  return nm.toplabelheight + nm.maxradius + nm.axisheight + nm.maxradius + nm.stem1 + nm.stem2 + nm.stem3 + nm.bottomlabelheight;
-}
-function clearTk(tk) {
-  tk.skewer.g.selectAll("*").remove();
-  if (tk.skewer.nmg) tk.skewer.nmg.selectAll("*").remove();
-}
-function numeric_make(nm, tk, block) {
-  if (!nm.axisSetting) {
-    nm.axisSetting = { auto: 1 };
-  }
-  const data = nm.data;
-  for (const d of data) {
-    d.x0 = d.x;
-    if (d.xoffset != void 0) {
-      d.x = d.x0 + d.xoffset;
-    }
-  }
-  const dotwidth = Math.max(14, block.width / 110);
-  nm.dotwidth = dotwidth;
-  nm.maxradius = 0;
-  for (const d of data) {
-    for (const m of d.mlst) {
-      m.radius = dotwidth / 2;
-      nm.maxradius = Math.max(m.radius, nm.maxradius);
-      m.rimwidth = 0;
-      m.aa = d;
-    }
-  }
-  const showstem = adjustview(data, nm, tk, block);
-  setup_axis_scale(data, nm, tk);
-  const numscale = linear().domain([nm.minvalue, nm.maxvalue]).range([0, nm.axisheight]);
-  for (const d of data) {
-    for (const m of d.mlst) {
-      if (m.__value_missing) {
-        m._y = 0;
-      } else {
-        if (m.__value_use < nm.minvalue) {
-          m._y = 0;
-        } else if (m.__value_use > nm.maxvalue) {
-          m._y = nm.axisheight;
-        } else {
-          m._y = numscale(m.__value_use);
-        }
-      }
-    }
-  }
-  if (showstem) {
-    nm.stem1 = 5;
-    nm.stem2 = 20;
-    nm.stem3 = 10;
-  } else {
-    nm.stem1 = 0;
-    nm.stem2 = 0;
-    nm.stem3 = 0;
-  }
-  for (const d of data) {
-    for (const m of d.mlst) {
-      tk.glider.append("text").text(tk.mnamegetter(m)).attr("font-size", m.radius * 2 - 2).each(function() {
-        m.labwidth = this.getBBox().width;
-      }).remove();
-    }
-  }
-  for (const d of data) {
-    for (const m of d.mlst) {
-      delete m.labattop;
-      delete m.labatbottom;
-    }
-  }
-  if (!tk.skewer.hideDotLabels) {
-    if (showstem) {
-      for (const d of data) {
-        if (d.mlst.length == 1) {
-          const m = d.mlst[0];
-          m.labattop = true;
-        } else {
-          if ((d.width - d.fixedgew) / (d.mlst.length - 1) < clustercrowdlimit) {
-          } else {
-            for (const m of d.mlst) {
-              m.labattop = true;
-            }
-          }
-        }
-      }
-    } else {
-      verticallabplace(data);
-    }
-  }
-  nm.toplabelheight = 0;
-  nm.bottomlabelheight = 0;
-  if (nm.showsamplebar || nm.showgenotypebyvalue) {
-    for (const d of data) {
-      for (const m of d.mlst) {
-        nm.toplabelheight = Math.max(nm.toplabelheight, m.labwidth);
-      }
-    }
-  } else {
-    for (const d of data) {
-      for (const m of d.mlst) {
-        if (m.labattop) {
-          nm.toplabelheight = Math.max(nm.toplabelheight, m._y + m.labwidth - nm.axisheight);
-        } else if (m.labatbottom) {
-          nm.bottomlabelheight = Math.max(nm.bottomlabelheight, m.labwidth - m._y);
-        }
-        if (m.shapeCircle) {
-          m.shape = "emptyCircle";
-          delete m.shapeCircle;
-        } else if (m.shapeTriangle) {
-          m.shape = "filledTriangle";
-          delete m.shapeTriangle;
-        } else if (!m.shape) m.shape = "filledCircle";
-      }
-    }
-  }
-  {
-    let h = block.labelfontsize + labyspace2 + block.labelfontsize;
-    if (tk.label_stratify) {
-      h += tk.label_stratify.length * (labyspace2 + block.labelfontsize);
-    }
-    nm.toplabelheight = Math.max(nm.toplabelheight, h);
-  }
-  render_axis(tk, nm, block);
-  tk.skewer.g.append("line").attr("y1", nm.toplabelheight + nm.maxradius).attr("y2", nm.toplabelheight + nm.maxradius).attr("x2", block.width).attr("stroke", stemColor).attr("shape-rendering", "crispEdges");
-  tk.skewer.g.append("line").attr("y1", nm.toplabelheight + nm.maxradius + nm.axisheight).attr("y2", nm.toplabelheight + nm.maxradius + nm.axisheight).attr("x2", block.width).attr("stroke", stemColor).attr("shape-rendering", "crispEdges");
-  tk.skewer.nmg = tk.skewer.g.selectAll().data(data).enter().append("g").attr("class", "sja_skg2").each(function(d) {
-    d.g = this;
-  });
-  tk.skewer.nmg.attr(
-    "transform",
-    (d) => "translate(" + d.x + "," + (nm.toplabelheight + disclabelspacing2 + nm.maxradius + nm.axisheight + nm.maxradius) + ")"
-  );
-  if (showstem) {
-    tk.skewer.nmg.append("path").attr("class", "sja_aa_stem").attr("d", (d) => setStem(d, nm)).attr("stroke", (d) => tk.color4disc(d.mlst[0])).attr("fill", (d) => d.mlst.length == 1 ? "none" : stemColor);
-  }
-  const discg = tk.skewer.nmg.selectAll().data((d) => d.mlst).enter().append("g").attr("class", "sja_aa_discg").each(function(m) {
-    m.g = this;
-    if (!m.shape.includes("Circle")) {
-      renderSkewerShapes(tk, nm, select_default(this));
-    } else {
-      select_default(this).append("circle").attr("fill", (m2) => shapes[m2.shape].isFilled ? tk.color4disc(m2) : "none").attr("stroke", (m2) => shapes[m2.shape].isFilled ? "white" : tk.color4disc(m2)).attr("r", (m2) => m2.radius - 0.5).attr("class", "sja_aa_disk_fill");
-    }
-  });
-  discg.attr("transform", (m) => {
-    return "translate(" + m.xoff + "," + (m._y + nm.maxradius) * -1 + ")";
-  });
-  tk.skewer.hlBoxG = discg.append("g");
-  const kick = renderShapeKick(nm, discg);
-  kick.attr("stroke", (m) => tk.color4disc(m)).attr("fill", "white").attr("class", "sja_aa_disckick").attr("fill-opacity", 0).attr("stroke-opacity", 0).on("mousedown", (event2) => {
-    event2.preventDefault();
-  }).on("mouseover", (event2, m) => {
-    m_mouseover(m, nm, tk);
-  }).on("mouseout", (event2, m) => {
-    m_mouseout(m, tk);
-  }).on("click", (event2, m) => {
-    click_variant({ mlst: [m] }, tk, block, event2.target.getBoundingClientRect(), event2.target);
-  });
-  const textlabels = discg.filter((m) => m.labattop || m.labatbottom).append("text").each(function(m) {
-    m.__svg_textlabel = this;
-  }).text((m) => tk.mnamegetter(m)).attr("font-size", (m) => {
-    m._labfontsize = Math.max(12, m.radius * 1.2);
-    return m._labfontsize;
-  }).attr("fill", (m) => tk.color4disc(m)).attr(
-    "x",
-    (m) => nm.showsamplebar || nm.showgenotypebyvalue ? nm.axisheight + nm.maxradius + 4 : m.radius + m.rimwidth + disclabelspacing2
-  ).attr("y", (m) => m._labfontsize * middlealignshift2).attr("class", "sja_aa_disclabel").attr("transform", (m) => "rotate(" + (m.labattop ? "-" : "") + "90)").on("mousedown", (event2) => {
-    event2.preventDefault();
-  }).on("mouseover", (event2, m) => m_mouseover(m, nm, tk)).on("mouseout", (event2, m) => m_mouseout(m, tk)).on("click", (event2, m) => {
-    click_variant({ mlst: [m] }, tk, block, event2.target.getBoundingClientRect(), event2.target.previousSibling);
-  });
-}
-function adjustview(data, nm, tk, block) {
-  let sumwidth = 0;
-  for (const d of data) {
-    let w = 0;
-    for (const m of d.mlst) {
-      w += 2 * (m.radius + m.rimwidth);
-    }
-    if (d.mlst.length == 1) {
-      d.width = w;
-    } else {
-      d.width = Math.min(maxclusterwidth, w);
-      const m0 = d.mlst[0];
-      const m1 = d.mlst[d.mlst.length - 1];
-      d.fixedgew = m0.radius + m0.rimwidth + m1.radius + m1.rimwidth;
-    }
-    sumwidth += d.width;
-  }
-  if (sumwidth <= block.width) {
-    let cum = 0;
-    for (const d of data) {
-      d.x = cum + d.mlst[0].radius + d.mlst[0].rimwidth;
-      cum += d.width;
-      if (d.mlst.length == 1) {
-        d.stemw = 0;
-      } else {
-        d.stemw = d.width - d.fixedgew;
-      }
-    }
-    horiplace1(data, block.width);
-    for (const d of data) {
-      d.xoffset = d.x - d.x0;
-      if (d.mlst.length == 1) {
-        d.mlst[0].xoff = 0;
-        d.stemw = 0;
-      } else {
-        d.stemw = d.width - d.fixedgew;
-        const span = d.stemw / (d.mlst.length - 1);
-        for (let i = 0; i < d.mlst.length; i++) {
-          d.mlst[i].xoff = span * i;
-        }
-      }
-    }
-    return true;
-  }
-  for (const d of data) {
-    d.x = d.x0;
-    d.xoffset = 0;
-    for (const m of d.mlst) {
-      m.xoff = 0;
-    }
-  }
-  return false;
-}
-function horiplace1(items, allwidth) {
-  for (let i = 0; i < items.length; i++) {
-    if (items[i].x0 < 0) continue;
-    if (items[i].x0 > allwidth) break;
-    while (1) {
-      let currsum = 0, newsum = 0;
-      for (let j = i; j < items.length; j++) {
-        const t = items[j];
-        if (t.x0 > allwidth) {
-          return;
-        }
-        currsum += Math.abs(t.x - t.x0 - t.stemw / 2);
-        t.x++;
-        newsum += Math.abs(t.x - t.x0 - t.stemw / 2);
-      }
-      if (items[i].x > items[i].x0 - items[i].stemw / 2) {
-        for (let j = i; j < items.length; j++) {
-          items[j].x--;
-        }
-        break;
-      }
-      const z = items[items.length - 1];
-      if (z.x + z.width / 2 >= allwidth) {
-        return;
-      }
-      if (newsum <= currsum) {
-      } else {
-        for (let j = i; j < items.length; j++) {
-          if (items[j].x0 > allwidth) {
-            break;
-          }
-          items[j].x--;
-        }
-        break;
-      }
-    }
-  }
-}
-function verticallabplace(data) {
-  const mlst = [];
-  for (const d of data) {
-    for (const m of d.mlst) {
-      mlst.push({
-        m,
-        w: 2 * (m.radius + m.rimwidth),
-        x: d.x0,
-        y: m._y
-      });
-    }
-  }
-  mlst.sort((i, j) => j.y - i.y);
-  for (let i = 0; i < mlst.length; i++) {
-    const big = mlst[i];
-    let overlapwithdisc = false;
-    for (let j = 0; j < i; j++) {
-      const small = mlst[j];
-      if (Math.abs(big.x - small.x) < (big.w + small.w) / 2 - 2) {
-        overlapwithdisc = true;
-        break;
-      }
-    }
-    if (!overlapwithdisc) {
-      big.m.labattop = true;
-    }
-  }
-  for (let i = mlst.length - 1; i >= 0; i--) {
-    const big = mlst[i];
-    if (big.m.labattop) continue;
-    let overlapwithlabeleddisc = false;
-    for (let j = mlst.length - 1; j > i; j--) {
-      const small = mlst[j];
-      if (small.m.labatbottom && Math.abs(small.x - big.x) < (small.w + big.w) / 2 - 2) {
-        overlapwithlabeleddisc = true;
-        break;
-      }
-    }
-    if (!overlapwithlabeleddisc) {
-      big.m.labatbottom = true;
-    }
-  }
-}
-function setStem(d, nm) {
-  if (d.mlst.length == 1) {
-    return "M0,0v" + nm.stem1 + "l" + -d.xoffset + "," + nm.stem2 + "v" + nm.stem3;
-  }
-  return "M0,0v" + nm.stem1 + // vertical down
-  "l" + -d.xoffset + "," + nm.stem2 + // slope 1
-  "v" + nm.stem3 + // vertical down
-  //+'h1' // to right 1
-  "v-" + nm.stem3 + // veritical up
-  "l" + (d.stemw + d.xoffset - 1) + ",-" + nm.stem2 + // slope 2
-  "v-" + nm.stem1;
-}
-function m_mouseover(m, nm, tk) {
-  if (m.__svg_textlabel) {
-    select_default(m.__svg_textlabel).attr("font-size", m._labfontsize * 1.1);
-  }
-  tk.pica.g.attr(
-    "transform",
-    "translate(" + (m.aa.x + m.xoff) + "," + (nm.toplabelheight + nm.maxradius + nm.axisheight - m._y) + ")"
-  );
-  const linelen = 10;
-  const boxpad = 4;
-  const fontsize = m._labfontsize || 13;
-  const color = tk.color4disc(m);
-  const words = [];
-  if (nm.tooltipPrintValue) {
-    const out = nm.tooltipPrintValue(m);
-    if (Array.isArray(out)) {
-      words.push(...out.map((i) => `${i.k} = ${i.v}`));
-    }
-  } else {
-    words.push(nm.label + " = " + (m.__value_missing ? "NA" : m.__value_use));
-  }
-  if (tk.mds.queries?.ld?.mOverlay?.data) {
-    if (m.ssm_id == tk.mds.queries.ld.mOverlay.m.ssm_id) {
-    } else {
-      let r2 = "?";
-      for (const v of tk.mds.queries.ld.mOverlay.data) {
-        if (v.pos == m.pos && v.alleles == m.ref + "." + m.alt) {
-          r2 = v.r2;
-          break;
-        }
-      }
-      words.push("r2 = " + r2);
-    }
-  }
-  if (!m.labattop && !m.labatbottom) {
-    words.push(tk.mnamegetter(m));
-  }
-  let textw = 0;
-  for (const w of words) {
-    tk.pica.g.append("text").attr("font-size", fontsize).text(w).each(function() {
-      textw = Math.max(textw, this.getBBox().width);
-    }).remove();
-  }
-  const boxw = boxpad * 2 + textw;
-  let boxx, linex1, onleft = true;
-  if (boxw + linelen > m.aa.x + m.xoff) {
-    onleft = false;
-    linex1 = m.radius + m.rimwidth;
-    boxx = linex1 + linelen;
-  } else {
-    linex1 = -m.radius - m.rimwidth - linelen;
-    boxx = linex1 - boxw;
-  }
-  const boxh = fontsize * words.length;
-  tk.pica.g.append("rect").attr("x", boxx - 2).attr("y", -2 - boxpad - boxh / 2).attr("width", 4 + boxw).attr("height", 4 + boxpad * 2 + boxh).attr("fill", "white");
-  tk.pica.g.append("line").attr("x1", linex1).attr("x2", linex1 + linelen).attr("stroke", "white").attr("stroke-width", 3).attr("shape-rendering", "crispEdges");
-  tk.pica.g.append("line").attr("x1", linex1).attr("x2", linex1 + linelen).attr("stroke", color).attr("shape-rendering", "crispEdges");
-  tk.pica.g.append("rect").attr("x", boxx).attr("y", -boxpad - boxh / 2).attr("width", boxw).attr("height", boxpad * 2 + boxh).attr("fill", "none").attr("stroke", color).attr("shape-rendering", "crispEdges");
-  let y = (fontsize - boxh) / 2;
-  for (const w of words) {
-    tk.pica.g.append("text").text(w).attr("text-anchor", onleft ? "end" : "start").attr("font-size", fontsize).attr("x", onleft ? linex1 - boxpad : boxx + boxpad).attr("y", y).attr("fill", color).attr("dominant-baseline", "central");
-    y += fontsize;
-  }
-}
-function m_mouseout(m, tk) {
-  if (m.__svg_textlabel) {
-    select_default(m.__svg_textlabel).attr("font-size", m._labfontsize);
-  }
-  tk.pica.g.selectAll("*").remove();
-}
-function setup_axis_scale(data, nm, tk) {
-  for (const g of data) {
-    for (const m of g.mlst) {
-      delete m.__value_use;
-      delete m.__value_missing;
-    }
-  }
-  if (nm.byAttribute) {
-    for (const g of data) {
-      for (const m of g.mlst) {
-        const v = m[nm.byAttribute];
-        if (Number.isFinite(v)) {
-          m.__value_use = v;
-        } else {
-          m.__value_missing = true;
-        }
-      }
-    }
-  } else if (nm.byInfo) {
-    for (const g of data) {
-      for (const m of g.mlst) {
-        const v = m?.info?.[nm.byInfo];
-        if (Number.isFinite(v)) {
-          m.__value_use = v;
-        } else {
-          m.__value_missing = true;
-        }
-      }
-    }
-  } else {
-    throw "unknown method of getting value";
-  }
-  if (nm.axisSetting.auto) {
-    nm.minvalue = null;
-    nm.maxvalue = null;
-    for (const g of data) {
-      for (const m of g.mlst) {
-        if ("__value_use" in m) {
-          if (nm.minvalue == null) {
-            nm.minvalue = m.__value_use;
-            nm.maxvalue = m.__value_use;
-          } else {
-            nm.minvalue = Math.min(nm.minvalue, m.__value_use);
-            nm.maxvalue = Math.max(nm.maxvalue, m.__value_use);
-          }
-        }
-      }
-    }
-  } else if (nm.axisSetting.fixed) {
-    nm.minvalue = nm.axisSetting.fixed.min;
-    nm.maxvalue = nm.axisSetting.fixed.max;
-  } else {
-    throw "unknown axisSetting";
-  }
-}
-function render_axis(tk, nm, block) {
-  nm.axisg.attr("transform", "translate(0," + (nm.toplabelheight + nm.maxradius) + ")").selectAll("*").remove();
-  const thisscale = linear().domain([nm.minvalue, nm.maxvalue]).range([nm.axisheight, 0]);
-  const thisaxis = axisLeft().scale(thisscale).ticks(4);
-  if (nm.isinteger) {
-    thisaxis.tickFormat(format("d"));
-    if (nm.maxvalue - nm.minvalue < 3) {
-      thisaxis.ticks(nm.maxvalue - nm.minvalue);
-    }
-  }
-  axisstyle({
-    axis: nm.axisg.call(thisaxis),
-    showline: true,
-    fontsize: nm.dotwidth
-  });
-  nm.axisWidth = 0;
-  nm.axisg.selectAll("text").each(function() {
-    nm.axisWidth = Math.max(nm.axisWidth, this.getBBox().width);
-  });
-  nm.axisWidth += 15;
-  let w;
-  nm.axisg.append("text").attr("fill", "black").attr("font-size", nm.dotwidth).attr("dominant-baseline", "central").attr("text-anchor", "end").attr("class", "sjpp-mds3-nm-axislabel sja_clbtext2").attr("data-testid", "sjpp-mds3-nm-axislabel").attr("y", nm.axisheight / 2).attr("x", -nm.axisWidth).text(nm.label || defaultLabel).each(function() {
-    w = this.getBBox().width;
-  }).on("click", (event2) => {
-    tk.menutip.clear().showunder(event2.target).d.append("div").text("Cancel").attr("class", "sja_menuoption").attr("data-testid", "sjpp-cancel-numeric-axis-option").style("border-radius", "0px").on("click", () => {
-      tk.menutip.hide();
-      nm.inuse = false;
-      tk.skewer.viewModes.find((i) => i.type == "skewer").inuse = true;
-      may_render_skewer({ skewer: tk.skewer.rawmlst }, tk, block);
-      positionLeftlabelg(tk, block);
-      tk._finish();
-    });
-    makeNumericAxisConfig({
-      holder: tk.menutip.d.append("div").style("margin", "10px"),
-      noPercentile: true,
-      callback: (s) => {
-        nm.axisSetting = s;
-        clearTk(tk);
-        numeric_make(nm, tk, block);
-      },
-      setting: nm.axisSetting
-    });
-  });
-  tk.skewer.maxwidth = nm.axisWidth + w;
-}
-function mayHighlightByLDoverlay(tk) {
-  const m = tk.mds.queries?.ld?.mOverlay?.m;
-  if (!m) return;
-  tk.skewer.hlssmid = /* @__PURE__ */ new Set([m.ssm_id]);
-  mayHighlightDiskBySsmid(tk);
-}
-
-// mds3/skewer.js
-var minMnameCount2compact = 10;
-function may_render_skewer(data, tk, block) {
-  if (!tk.skewer) {
-    return;
-  }
-  tk.skewer.maxwidth = 0;
-  updateViewModes(tk, data.skewer);
-  hlaachange2ssmid(tk, data.skewer);
-  const currentMode = tk.skewer.viewModes.find((n) => n.inuse);
-  if (!currentMode) throw "no mode!!";
-  if (data.skewer) {
-    tk.skewer.rawmlst = data.skewer;
-    data.skewer.forEach((d) => {
-      if (!d.id) d.id = Math.random().toString();
-    });
-  } else {
-    tk.skewer.rawmlst.forEach((d) => {
-      if (!d.id) d.id = Math.random().toString();
-    });
-  }
-  if (currentMode.type == "numeric") {
-    tk.subtk2height.skewer = renderNumericMode(currentMode, data, tk, block);
-    mayHighlightDiskBySsmid(tk);
-    return;
-  }
-  if (currentMode.type != "skewer") throw 'mode.type is not "skewer"';
-  if (data && !data.skewer && block.usegm && block.gmmode != "genomic" && block.pannedpx != void 0) {
-    tkdata_update_x(tk, block);
-    tk.skewer.selection.attr("transform", (d) => "translate(" + d.x + "," + d.y + ")");
-    settle_glyph(tk, block);
-  } else {
-    tk.skewer.g.selectAll("*").remove();
-    tk.skewer.data = make_skewer_data(tk, block);
-    skewer_make(tk, block);
-  }
-  if (!tk.skewer.data || tk.skewer.data.length == 0) {
-    tk.subtk2height.skewer = 0;
-    tk.skewer.g.selectAll("*").remove();
-    return;
-  }
-  if (tk.skewer.hlssmid) {
-    const fold = [];
-    const unfold = [];
-    for (const d of tk.skewer.data) {
-      let has = false;
-      for (const g of d.groups) {
-        for (const m of g.mlst) {
-          if (tk.skewer.hlssmid.has(m.ssm_id)) {
-            has = true;
-            break;
-          }
-        }
-      }
-      if (has) {
-        unfold.push(d);
-      } else {
-        fold.push(d);
-      }
-    }
-    fold_glyph(fold, tk);
-    unfold_glyph(unfold, tk, block);
-    mayHighlightDiskBySsmid(tk);
-  } else {
-    settle_glyph(tk, block);
-  }
-  tk.subtk2height.skewer = tk.skewer.maxheight + tk.skewer.stem1 + tk.skewer.stem2 + tk.skewer.stem3;
-}
-function hlaachange2ssmid(tk, mlst) {
-  if (!tk.hlaachange || !mlst) return;
-  const set = new Set(tk.hlaachange.split(","));
-  delete tk.hlaachange;
-  tk.skewer.hlssmid = /* @__PURE__ */ new Set();
-  for (const m of mlst) {
-    if (set.has(m.mname)) tk.skewer.hlssmid.add(m.ssm_id);
-  }
-}
-function tkdata_update_x(tk, block) {
-  for (const d of tk.skewer.data) {
-    if (d.isbin) {
-      let sumx = 0;
-      for (const m of d.mlst) {
-        const hits = block.seekcoord(m.chr, m.pos);
-        if (m.usehitidx != void 0 && hits[m.usehitidx]) {
-          sumx += hits[m.usehitidx].x;
-        } else if (hits.length == 1) {
-          sumx += hits[0].x;
-        } else {
-          console.log("cannot map item");
-          console.log(m);
-        }
-      }
-      d.x0 = sumx / d.mlst.length;
-      d.x = d.x0 + (d.xoffset != void 0 ? d.xoffset : 0);
-    } else {
-      const hits = block.seekcoord(d.chr, d.pos);
-      if (hits.length > 0) {
-        d.x0 = hits[0].x;
-        d.x = d.x0 + (d.xoffset != void 0 ? d.xoffset : 0);
-      } else {
-        console.log("cannot map group of item");
-        console.log(d);
-      }
-    }
-  }
-}
-function make_skewer_data(tk, block) {
-  const datagroup = make_datagroup(tk, tk.skewer.rawmlst, block);
-  for (const g of datagroup) {
-    g.groups = mlst2disc(g.mlst, tk);
-  }
-  if (tk.skewer.data && block.pannedpx != void 0) {
-    const pastmode = {};
-    for (const g of tk.skewer.data) {
-      pastmode[g.chr + "." + g.pos] = {
-        mode: g.showmode,
-        xoffset: g.xoffset,
-        slabelrotate: g.slabelrotate
-        // no effect
-      };
-    }
-    for (const g of datagroup) {
-      const k = g.chr + "." + g.pos;
-      if (pastmode[k]) {
-        g.showmode = pastmode[k].mode;
-        g.xoffset = pastmode[k].xoffset;
-        g.slabelrotate = pastmode[k].slabelrotate;
-      }
-    }
-  }
-  for (const d of datagroup) {
-    d.occurrence = d.groups.reduce((i, j) => i + j.occurrence, 0);
-  }
-  return datagroup;
-}
-function mlst2disc(mlst, tk) {
-  const k2g = /* @__PURE__ */ new Map();
-  for (const m of mlst) {
-    if (!Number.isInteger(m.dt)) continue;
-    if (!k2g.has(m.dt)) k2g.set(m.dt, /* @__PURE__ */ new Map());
-    switch (m.dt) {
-      case dtsnvindel:
-        if (!k2g.get(m.dt).has(m.class)) k2g.get(m.dt).set(m.class, /* @__PURE__ */ new Map());
-        const n = m.mname || "";
-        if (!k2g.get(m.dt).get(m.class).has(n)) {
-          k2g.get(m.dt).get(m.class).set(n, []);
-        }
-        k2g.get(m.dt).get(m.class).get(n).push(m);
-        break;
-      case dtsv:
-      case dtfusionrna:
-        if (!k2g.get(m.dt).has(m.class)) {
-          k2g.get(m.dt).set(m.class, {
-            use5: /* @__PURE__ */ new Map(),
-            use3: /* @__PURE__ */ new Map()
-          });
-        }
-        if (m.useNterm) {
-          if (!k2g.get(m.dt).get(m.class).use5.has(m.mname)) {
-            k2g.get(m.dt).get(m.class).use5.set(m.mname, []);
-          }
-          k2g.get(m.dt).get(m.class).use5.get(m.mname).push(m);
-        } else {
-          if (!k2g.get(m.dt).get(m.class).use3.has(m.mname)) {
-            k2g.get(m.dt).get(m.class).use3.set(m.mname, []);
-          }
-          k2g.get(m.dt).get(m.class).use3.get(m.mname).push(m);
-        }
-        break;
-      case dtitd:
-      case dtdel:
-      case dtnloss:
-      case dtcloss:
-        if (!k2g.has(m.dt)) {
-          k2g.set(m.dt, []);
-        }
-        k2g.get(m.dt).push(m);
-        break;
-      default:
-        console.log("unknown datatype: " + m.dt);
-        console.log(m);
-        return;
-    }
-  }
-  const groups = [];
-  for (const [dt, tmp] of k2g) {
-    switch (dt) {
-      case dtsnvindel:
-        for (const [thisClass, mname2lst] of tmp) {
-          if (mname2lst.size > minMnameCount2compact) {
-            const mlst2 = [];
-            for (const l2 of mname2lst.values()) mlst2.push(...l2);
-            groups.push({
-              dt,
-              mlst: mlst2,
-              mnameCompact: mclass[thisClass].label
-            });
-          } else {
-            for (const mlst2 of mname2lst.values()) {
-              groups.push({ dt, mlst: mlst2 });
-            }
-          }
-        }
-        break;
-      case dtsv:
-      case dtfusionrna:
-        for (const classset of tmp.values()) {
-          if (classset.use5.size > minMnameCount2compact) {
-            const mlst2 = [];
-            for (const l2 of classset.use5.values()) mlst2.push(...l2);
-            groups.push({ dt, mlst: mlst2, useNterm: true, mnameCompact: dt == dtsv ? "SV" : "fusion" });
-          } else {
-            for (const mlst2 of classset.use5.values()) {
-              groups.push({ dt, mlst: mlst2, useNterm: true });
-            }
-          }
-          if (classset.use3.size > minMnameCount2compact) {
-            const mlst2 = [];
-            for (const l2 of classset.use3.values()) mlst2.push(...l2);
-            groups.push({ dt, mlst: mlst2, useNterm: false, mnameCompact: dt == dtsv ? "SV" : "fusion" });
-          } else {
-            for (const mlst2 of classset.use3.values()) {
-              groups.push({ dt, mlst: mlst2, useNterm: false });
-            }
-          }
-        }
-        break;
-      case dtitd:
-      case dtdel:
-      case dtnloss:
-      case dtcloss:
-        groups.push({
-          dt,
-          mlst: tmp
-        });
-    }
-  }
-  for (const g of groups) {
-    let rim1count = 0, rim2count = 0;
-    for (const m of g.mlst) {
-      rim1count += m.rim1count || 0;
-      rim2count += m.rim2count || 0;
-    }
-    g.rim1count = rim1count;
-    g.rim2count = rim2count;
-  }
-  if (mlst.some((m) => Number.isFinite(m.occurrence))) {
-    for (const g of groups) g.occurrence = g.mlst.reduce((i, j) => i + j.occurrence, 0);
-  } else {
-    for (const g of groups) g.occurrence = g.mlst.length;
-  }
-  groups.sort((a, b) => {
-    return b.occurrence - a.occurrence;
-  });
-  return groups;
-}
-function updateViewModes(tk, mlst) {
-  detectNumericMode(tk, mlst);
-  detectAlternativeSkewerModes(tk, mlst);
-  for (const n of tk.skewer.viewModes) {
-    if (n.type == "numeric" && !n.inuse && n.axisg) {
-      n.axisg.remove();
-      delete n.axisg;
-    }
-  }
-}
-function detectAlternativeSkewerModes(tk) {
-}
-function detectNumericMode(tk, mlst) {
-  if (mlst && mlst.find((i) => Number.isFinite(i.occurrence))) {
-    if (!tk.skewer.viewModes.find((n) => n.type == "numeric" && n.byAttribute == "occurrence")) {
-      tk.skewer.viewModes.push({
-        type: "numeric",
-        byAttribute: "occurrence",
-        label: "Occurrence",
-        isinteger: true
-      });
-    }
-  }
-}
-
-// mds3/leftlabel.variant.js
-function makeVariantLabel(data, tk, block, laby) {
-  if (!tk.skewer && !tk.cnv) return;
-  if (!tk.leftlabels.doms.variants) {
-    tk.leftlabels.doms.variants = makelabel(tk, block, laby);
-    tk.leftlabels.doms.variants.attr("data-testid", "sja_variants_label");
-    if (data.variantAlerts?.length) tk.leftlabels.doms.variants.attr("fill", "red");
-  }
-  const [labeltext, totalcount, showcount] = getVariantLabelText(data, tk, block);
-  if (totalcount == 0) {
-    tk.leftlabels.doms.variants.text(labeltext).attr("class", "").style("opacity", 0.7).on("click", null);
-    return;
-  }
-  if (showcount == 0) {
-    tk.leftlabels.doms.variants.text(labeltext).attr("class", "").style("opacity", 0.5).on("click", null);
-    return;
-  }
-  tk.leftlabels.doms.variants.style("opacity", 1).attr("class", "sja_clbtext2").text(labeltext).on("click", (event2) => {
-    tk.menutip.clear().showunder(event2.target);
-    menu_variants(data, tk, block);
-  });
-}
-function getVariantLabelText(data, tk, block) {
-  let totalcount = 0, showcount = 0;
-  const dtset = /* @__PURE__ */ new Set();
-  if (tk.custom_variants) {
-    totalcount = tk.custom_variants.length;
-    for (const m of tk.custom_variants) dtset.add(m.dt);
-  } else {
-    if (tk.skewer?.rawmlst) {
-      totalcount += tk.skewer.rawmlst.length;
-      for (const m of tk.skewer.rawmlst) dtset.add(m.dt);
-    }
-    if (data.cnv) {
-      totalcount += data.cnv.cnvs.length;
-      for (const m of data.cnv.cnvs) dtset.add(m.dt);
-    } else if (data.cnvDensity) {
-      totalcount += data.cnvDensity.segmentCount;
-      dtset.add(dtcnv);
-    }
-  }
-  if (totalcount == 0) return ["No data", 0, 0];
-  if (tk.skewer) {
-    const currentMode = tk.skewer.viewModes.find((i) => i.inuse);
-    if (currentMode.type == "skewer") {
-      showcount = tk.skewer.data.filter((i) => i.x >= 0 && i.x <= block.width).reduce((i, j) => i + j.mlst.length, 0);
-    } else if (currentMode.type == "numeric") {
-      showcount = currentMode.data.filter((i) => i.x >= 0 && i.x <= block.width).reduce((i, j) => i + j.mlst.length, 0);
-    } else {
-      throw "unknown mode type";
-    }
-  }
-  if (data.cnv) {
-    showcount += data.cnv.cnvs.length;
-  } else if (data.cnvDensity) {
-    showcount += data.cnvDensity.segmentCount;
-  }
-  let vn = "variant";
-  if (dtset.size == 1) {
-    const dt = [...dtset][0];
-    if (dt == dtsnvindel) {
-    } else {
-      vn = dt2label[dt];
-    }
-  }
-  if (showcount == 0) {
-    return [`0 out of ${totalcount} ${vn}${totalcount > 1 ? "s" : ""}`, totalcount, showcount];
-  }
-  return [
-    showcount < totalcount ? showcount + " of " + totalcount + " " + vn + "s" : showcount + " " + vn + (showcount > 1 ? "s" : ""),
-    totalcount,
-    showcount
-  ];
-}
-function menu_variants(data, tk, block) {
-  if (data.variantAlerts?.length) {
-    for (const m of data.variantAlerts) {
-      tk.menutip.d.append("div").style("margin", "10px").attr("data-testid", "sjpp-mds3tk-variantalerts").style("font-size", ".8em").style("color", "red").text(m);
-    }
-  }
-  if ((!tk.skewer?.rawmlst || tk.skewer.rawmlst?.length == 0) && tk.cnv?.cnvInDensity) {
-    tk.menutip.d.append("div").attr("data-testid", "sjpp-mds3tk-variantleftlabel-cnvdensitymsg").style("margin", "10px").text("Viewing CNV segment density, no information on individual segments.");
-    if (tk.cnv.cnvMsg) {
-      tk.menutip.d.append("div").style("margin", "10px").text(tk.cnv.cnvMsg);
-    }
-    return;
-  }
-  const listDiv = tk.menutip.d.append("div").text("List").attr("class", "sja_menuoption sja_sharp_border").attr("data-testid", "sjpp_mds3tk_variantleftlabel_list").attr("tabindex", 0).on("click", () => {
-    listVariantData(tk, block);
-  });
-  listDiv.node().focus();
-  setTimeout(() => listDiv.node().blur(), 2e3);
-  if (tk.skewer && !tk.hardcodeCnvOnly) {
-    if (tk.skewer.hlssmid) {
-      tk.menutip.d.append("div").text("Cancel highlight").attr("class", "sja_menuoption sja_sharp_border").attr("data-testid", "sjpp-cancel-highlight-option").attr("tabindex", 0).on("click", () => {
-        delete tk.skewer.hlssmid;
-        tk.skewer.hlBoxG.selectAll("*").remove();
-        const currentMode = tk.skewer.viewModes.find((i) => i.inuse);
-        if (currentMode.type == "skewer") {
-          settle_glyph(tk, block);
-        } else if (currentMode.type == "numeric") {
-        } else {
-          throw "unknown mode type";
-        }
-        tk.menutip.hide();
-      });
-    }
-    const vm = tk.skewer.viewModes.find((n) => n.inuse);
-    if (vm.type == "skewer") {
-      const expandCount = tk.skewer.data.reduce((i, j) => i + j.showmode, 0);
-      if (expandCount > 0) {
-        tk.menutip.d.append("div").text("Collapse").attr("class", "sja_menuoption sja_sharp_border").attr("data-testid", "sja_collapse_menuoption").attr("tabindex", 0).on("click", () => {
-          fold_glyph(tk.skewer.data, tk);
-          tk.menutip.hide();
-        });
-      } else if (expandCount == 0) {
-        tk.menutip.d.append("div").text("Expand").attr("class", "sja_menuoption sja_sharp_border").attr("data-testid", "sja_expand_menuoption").attr("tabindex", 0).on("click", () => {
-          settle_glyph(tk, block);
-          tk.menutip.hide();
-        });
-      }
-      tk.menutip.d.append("div").text(tk.skewer.pointup ? "Point down" : "Point up").attr("class", "sja_menuoption sja_sharp_border").attr("data-testid", "sjpp-pointup-option").attr("tabindex", 0).on("click", () => {
-        tk.skewer.pointup = !tk.skewer.pointup;
-        tk.load();
-        tk.menutip.hide();
-      });
-      if (tk.filterObj) {
-        let called = false;
-        const div = tk.menutip.d.append("div").text("Change variant shape").style("vertical-align", "middle").attr("class", "sja_menuoption sja_sharp_border").attr("data-testid", "sja-change-skewer-shape-option").attr("tabindex", 0).on("click", () => {
-          if (called == false) {
-            called = true;
-            renderShapePicker({
-              holder: div.append("div").style("margin-top", "10px"),
-              callback: (shape) => {
-                Object.keys(tk.shapes).forEach((key) => {
-                  tk.shapes[key] = shape;
-                });
-                tk.load();
-                tk.menutip.hide();
-              },
-              tk
-            });
-          }
-        });
-      }
-    } else if (vm.type == "numeric") {
-      tk.menutip.d.append("div").text(tk.skewer.hideDotLabels ? "Show all variant labels" : "Hide all variant labels").attr("class", "sja_menuoption sja_sharp_border").attr("data-testid", "sjpp-show-hide-variant-labels-option").attr("tabindex", 0).on("click", () => {
-        tk.skewer.hideDotLabels = !tk.skewer.hideDotLabels;
-        tk.load();
-        tk.menutip.hide();
-      });
-    }
-  }
-  if (!tk.custom_variants) {
-    tk.menutip.d.append("div").text("Download").attr("class", "sja_menuoption sja_sharp_border").attr("tabindex", 0).attr("data-testid", "sjpp_mds3tk_variantdownload_menuoption").on("click", () => {
-      downloadVariants(tk, block);
-      tk.menutip.hide();
-    });
-  }
-  tk.menutip.d.on("keydown", function(event2) {
-    if (event2.key != "Enter" || !event2.target.className.includes("sja_menuoption")) return;
-    event2.target.dispatchEvent(new KeyboardEvent("click"));
-  });
-  mayAddSkewerModeOption(tk, block);
-}
-async function listVariantData(tk, block) {
-  tk.menutip.clear();
-  const dt2mlst = /* @__PURE__ */ new Map();
-  if (tk.skewer) {
-    const currentMode = tk.skewer.viewModes.find((i2) => i2.inuse);
-    let data;
-    if (currentMode.type == "skewer") {
-      data = tk.skewer.data.filter((i2) => i2.x >= 0 && i2.x <= block.width);
-    } else if (currentMode.type == "numeric") {
-      data = currentMode.data;
-    } else {
-      throw "unknown mode type";
-    }
-    for (const g of data) {
-      for (const m of g.mlst) {
-        if (!dt2mlst.has(m.dt)) dt2mlst.set(m.dt, []);
-        dt2mlst.get(m.dt).push(m);
-      }
-    }
-  }
-  if (tk.cnv?.cnvLst?.length) {
-    dt2mlst.set(dtcnv, tk.cnv.cnvLst);
-  }
-  if (dt2mlst.size == 1) {
-    const div = tk.menutip.d.append("div").style("margin", "10px");
-    await itemtable({
-      div,
-      mlst: dt2mlst.get([...dt2mlst.keys()][0]),
-      tk,
-      block,
-      doNotListSample4multim: true
-    });
-    return;
-  }
-  const tabs = [];
-  for (const [dt, mlst] of dt2mlst) {
-    tabs.push({ label: mlst.length + " " + dt2label[dt] });
-  }
-  new Tabs({
-    holder: tk.menutip.d.append("div").attr("class", "sja_pp_vlb_dttabdiv").style("margin", "10px"),
-    tabs
-  }).main();
-  let i = 0;
-  for (const [dt, mlst] of dt2mlst) {
-    itemtable({
-      div: tabs[i++].contentHolder.append("div").style("margin-left", "10px"),
-      mlst,
-      tk,
-      block,
-      doNotListSample4multim: true
-    });
-  }
-}
-function renderShapePicker(arg) {
-  const lollipopShapes = {
-    filledCircle: shapes.filledCircle,
-    emptyCircle: shapes.emptyCircle,
-    filledVerticalRectangle: shapes.filledVerticalRectangle,
-    emptyVerticalRectangle: shapes.emptyVerticalRectangle,
-    filledTriangle: shapes.filledTriangle,
-    emptyTriangle: shapes.emptyTriangle,
-    filledSquare: shapes.filledSquare,
-    emptySquare: shapes.emptySquare
-  };
-  const { holder, callback, tk } = arg;
-  const shapePaths = Object.values(lollipopShapes).map((shape) => shape.path);
-  const selectorCallback = (val) => {
-    const shape = Object.keys(lollipopShapes)[val];
-    callback(shape, tk);
-  };
-  const opts = { backgroundColor: "" };
-  shapeSelector(holder, selectorCallback, shapePaths, opts);
-}
-function mayAddSkewerModeOption(tk, block) {
-  if (!tk.skewer) return;
-  if (tk.skewer.viewModes.length <= 1) {
-    return;
-  }
-  const options = [];
-  for (const [idx, v] of tk.skewer.viewModes.entries()) {
-    const o = {
-      label: getViewmodeName(v),
-      value: idx
-    };
-    if (v.inuse) o.checked = true;
-    options.push(o);
-  }
-  make_radios({
-    holder: tk.menutip.d.append("div").attr("class", "sja_pp_vlb_viewmoderadiodiv").style("margin", "10px"),
-    styles: {
-      display: "block"
-    },
-    options,
-    callback: async (idx) => {
-      for (const i of tk.skewer.viewModes) i.inuse = false;
-      tk.skewer.viewModes[idx].inuse = true;
-      may_render_skewer({ skewer: tk.skewer.rawmlst }, tk, block);
-      positionLeftlabelg(tk, block);
-      tk._finish();
-    }
-  });
-}
-function getViewmodeName(n) {
-  if (!n) return "MISSING!!";
-  if (n.type == "skewer") return "As lollipops";
-  if (n.type == "numeric") return n.label + " as Y axis";
-  return "unknown mode";
-}
-async function downloadVariants(tk, block) {
-  if (!tk.mds.variant2samples) {
-    console.log("TODO: variant-only");
-    return;
-  }
-  const arg = {
-    querytype: "samples"
-  };
-  rangequery_rglst(tk, block, arg);
-  const samples = (await tk.mds.variant2samples.get(arg)).samples;
-  const [columns, rows] = await samples2columnsRows(samples, tk);
-  const headerline = [];
-  for (const c of columns) {
-    if (c.isSsm) {
-      headerline.push("AAchange");
-      headerline.push("Consequence");
-      headerline.push("Mutation");
-      continue;
-    }
-    if (c.isMaf) {
-      headerline.push("Alternative allele depth in tumor");
-      headerline.push("Total depth in tumor");
-      continue;
-    }
-    headerline.push(c.label);
-  }
-  const lines = [];
-  for (const [sidx, sample] of samples.entries()) {
-    let ssm_id_lst;
-    if (Array.isArray(sample.ssm_id_lst)) {
-      ssm_id_lst = sample.ssm_id_lst;
-    } else if (sample.ssm_id) {
-      ssm_id_lst = [sample.ssm_id];
-    } else {
-      console.log("sample obj lacks ssm_id and ssm_id_lst");
-      continue;
-    }
-    for (const ssmid of ssm_id_lst) {
-      const m = findMbyId(ssmid, tk);
-      if (!m) {
-        console.log("ssm not found by id: " + ssmid);
-        continue;
-      }
-      const line = [];
-      for (const [cidx, c] of columns.entries()) {
-        if (c.isSsm) {
-          if (m.dt == dtsnvindel) {
-            line.push(m.mname);
-            line.push(mclass[m.class].label);
-            line.push(m.chr + ":" + (m.pos + 1) + " " + m.ref + ">" + m.alt);
-          } else if (m.dt == dtsv || m.dt == dtfusionrna) {
-            line.push("");
-            line.push(mclass[m.class].label);
-            line.push(
-              m.pairlst[0].a.chr + ":" + m.pairlst[0].a.pos + ">" + m.pairlst[0].b.chr + ":" + m.pairlst[0].b.pos
-            );
-          } else if (m.dt == dtcnv) {
-            line.push(Number.isFinite(m.value) ? m.value : "");
-            line.push(mclass[m.class].label);
-            line.push(m.chr + ":" + (m.start + 1) + "-" + (m.stop + 1));
-          } else {
-            throw "unknown m.dt";
-          }
-          continue;
-        }
-        const cell = rows[sidx][cidx];
-        if (cell.bySsmid) {
-          if (ssmid in cell.bySsmid) {
-            const v = cell.bySsmid[ssmid];
-            if (c.isMaf) {
-              line.push(v.altTumor);
-              line.push(v.totalTumor);
-            } else {
-              line.push(v);
-            }
-          } else {
-            line.push("");
-          }
-          continue;
-        }
-        if (c.isMaf) {
-          line.push(cell.altTumor);
-          line.push(cell.totalTumor);
-          continue;
-        }
-        line.push(cell.value);
-      }
-      lines.push(line.join("	"));
-    }
-  }
-  to_textfile(
-    block2source(block) + " " + (/* @__PURE__ */ new Date()).toLocaleDateString() + ".txt",
-    headerline.join("	") + "\n" + lines.join("\n")
-  );
-}
-
-// mds3/legend.js
-var unknown_infoCategory_color = "black";
-var unannotatedKey = "Unannotated";
-function initLegend(tk, block) {
-  if (!block.legend) return;
-  if (!tk.legend) tk.legend = {};
-  tk.legend.tip = new Menu({ padding: "0px" });
-  const [tr, td, td0] = legend_newrow(block, tk.name);
-  tk.legend.headTd = td0;
-  tk.tr_legend = tr;
-  const table = td.append("table").style("border-spacing", "5px").style("border-collapse", "separate");
-  tk.legend.table = table;
-  create_mclass(tk, block);
-  may_create_variantShapeName(tk);
-  may_create_infoFields(tk);
-  may_create_formatFilter(tk);
-  may_create_skewerRim(tk);
-  may_create_ld(tk);
-  may_create_cnv(tk);
-}
-function create_mclass(tk, block) {
-  if (!tk.legend.mclass) tk.legend.mclass = {};
-  if (!tk.legend.mclass.hiddenvalues) tk.legend.mclass.hiddenvalues = /* @__PURE__ */ new Set();
-  tk.legend.mclass.row = tk.legend.table.append("tr");
-  if (tk.hardcodeCnvOnly) {
-    tk.legend.mclass.row.style("display", "none");
-  }
-  tk.legend.mclass.row.append("td").attr("data-testid", "sjpp-mds3tk-legend-mclass").style("text-align", "right").style("opacity", 0.7).text(block.mclassOverride?.className || "Mutation");
-  tk.legend.mclass.holder = tk.legend.mclass.row.append("td");
-}
-function may_create_variantShapeName(tk) {
-  if (!tk.legend.customShapeLabels || !tk.custom_variants) return;
-  if (!tk.legend.variantShapeName) tk.legend.variantShapeName = [];
-  for (const data of tk.custom_variants) {
-    if (!data.shape) data.shape = "filledCircle";
-    const shapeObj = tk.legend.variantShapeName.find((v) => v.key == data.shape);
-    if (!shapeObj) {
-      tk.legend.variantShapeName.push({
-        key: data.shape,
-        origShape: data.shape,
-        num: 1
-      });
-    } else {
-      shapeObj.num = ++shapeObj.num;
-    }
-  }
-  if (tk.legend.customShapeLabels) {
-    for (const shape in tk.legend.customShapeLabels) {
-      if (!tk.legend.variantShapeName.find((i) => i.key == shape)) {
-        tk.legend.variantShapeName.push({
-          key: shape,
-          origShape: shape,
-          num: 0
-        });
-      }
-    }
-  }
-  tk.legend.variantShapeName.sort((a, b) => b.num - a.num);
-  const width = 12;
-  const height = 12;
-  const shapesWrapper = tk.legend.table.append("tr").append("td").attr("colspan", 2);
-  for (const shapeObj of Object.values(tk.legend.variantShapeName)) {
-    const getArgs = () => {
-      return shapeObj.key.includes("Circle") ? { radius: width / 2 - 0.5 } : shapeObj.key.includes("Rectangle") ? { width: width / 2 + 2.5, height: height - 0.5 } : { width: width - 0.5, height: height - 0.5 };
-    };
-    shapeObj.wrapper = shapesWrapper.append("div");
-    const svg = shapeObj.wrapper.append("span").append("svg").attr("width", width).attr("height", height);
-    shapeObj.shapeG = svg.append("g").attr("transform", `translate(${width / 2}, ${height / 2})`).append("path").attr("d", shapes[shapeObj.key].calculatePath(getArgs(shapeObj))).attr("fill", shapes[shapeObj.key].isFilled ? "grey" : "white").attr("stroke", shapes[shapeObj.key].isFilled ? "none" : "grey");
-    shapeObj.wrapper.append("span").html(`&nbsp;n=`);
-    shapeObj.numDiv = shapeObj.wrapper.append("span").text(shapeObj.num);
-    shapeObj.wrapper.append("span").text(`, ${tk.legend.customShapeLabels[shapeObj.key]}`);
-  }
-}
-function may_create_infoFields(tk) {
-  if (!tk.mds.bcf?.info) return;
-  const infoFields4legend = [];
-  for (const key in tk.mds.bcf.info) {
-    const field = tk.mds.bcf.info[key];
-    if (field.categories) {
-      infoFields4legend.push(key);
-    }
-  }
-  if (!infoFields4legend.length) return;
-  if (!tk.legend.bcfInfo) tk.legend.bcfInfo = {};
-  for (const key of infoFields4legend) {
-    const row = tk.legend.table.append("tr");
-    row.append("td").attr("data-testid", `sjpp-mds3tk-legend-bcfinfo-${key}`).style("text-align", "right").style("opacity", 0.7).text(tk.mds.bcf.info[key].name || key);
-    tk.legend.bcfInfo[key] = {
-      hiddenvalues: /* @__PURE__ */ new Set(),
-      row,
-      // column 2 <td>: content holder
-      holder: row.append("td")
-    };
-  }
-}
-function may_create_formatFilter(tk) {
-  if (!tk.mds.bcf?.format) return;
-  const formatFields4legend = [];
-  for (const k in tk.mds.bcf.format) {
-    if (tk.mds.bcf.format[k].isFilter) formatFields4legend.push(k);
-  }
-  if (!formatFields4legend.length) return;
-  if (!tk.legend.formatFilter) tk.legend.formatFilter = {};
-  for (const key of formatFields4legend) {
-    const row = tk.legend.table.append("tr");
-    row.append("td").attr("data-testid", `sjpp-mds3tk-legend-bcfformat-${key}`).style("text-align", "right").style("opacity", 0.7).text(tk.mds.bcf.format[key].Description);
-    tk.legend.formatFilter[key] = {
-      hiddenvalues: /* @__PURE__ */ new Set(),
-      row,
-      // column 2 <td>: content holder
-      holder: row.append("td")
-    };
-  }
-}
-function may_update_formatFilter(data, tk) {
-  if (!tk.legend.formatFilter) return;
-  if (!data.skewer) {
-    console.log("data.skewer[] is not present and cannot show INFO legend");
-    return;
-  }
-  for (const formatKey in tk.legend.formatFilter) {
-    tk.legend.formatFilter[formatKey].holder.selectAll("*").remove();
-    const category2variantCount = /* @__PURE__ */ new Map();
-    let unannotatedCount = 0;
-    for (const m of data.skewer) {
-      if (!m.formatK2count?.[formatKey]) continue;
-      for (const category in m.formatK2count[formatKey].v2c) {
-        category2variantCount.set(
-          category,
-          m.formatK2count[formatKey].v2c[category] + (category2variantCount.get(category) || 0)
-        );
-      }
-      unannotatedCount += m.formatK2count[formatKey].unannotatedCount || 0;
-    }
-    const show_lst = [...category2variantCount];
-    show_lst.sort((i, j) => j[1] - i[1]);
-    if (unannotatedCount) {
-      show_lst.push([unannotatedKey, unannotatedCount]);
-    }
-    for (const [category, count] of show_lst) {
-      const cell = tk.legend.formatFilter[formatKey].holder.append("div").attr("class", "sja_clb").style("display", "inline-block").on("click", () => {
-        const opts = [
-          {
-            label: "Hide",
-            isVisible: () => true,
-            callback: () => {
-              tk.legend.formatFilter[formatKey].hiddenvalues.add(category);
-            }
-          },
-          {
-            label: "Show only",
-            isVisible: () => true,
-            callback: () => {
-              for (const c2 of show_lst) {
-                tk.legend.formatFilter[formatKey].hiddenvalues.add(c2[0]);
-              }
-              tk.legend.formatFilter[formatKey].hiddenvalues.delete(category);
-            }
-          },
-          {
-            label: "Show all",
-            isVisible: () => tk.legend.formatFilter[formatKey].hiddenvalues.size,
-            callback: () => {
-              tk.legend.formatFilter[formatKey].hiddenvalues.clear();
-            }
-          }
-        ];
-        createLegendTipMenu(opts, tk, cell.node());
-      });
-      cell.append("div").style("display", "inline-block").attr("class", "sja_mcdot").style("background", "#aaa").style("margin-right", "5px").html(count > 1 ? count : "&nbsp;");
-      cell.append("div").style("display", "inline-block").text(category);
-    }
-    for (const c of tk.legend.formatFilter[formatKey].hiddenvalues) {
-      let loading = false;
-      tk.legend.formatFilter[formatKey].holder.append("div").style("display", "inline-block").attr("class", "sja_clb").style("text-decoration", "line-through").style("opacity", 0.7).text(c).on("click", async () => {
-        if (loading) return;
-        loading = true;
-        tk.legend.formatFilter[formatKey].hiddenvalues.delete(c);
-        reload(tk);
-      });
-    }
-  }
-}
-function reload(tk) {
-  tk.legend.tip.hide();
-  tk.load();
-}
-function updateLegend(data, tk, block) {
-  if (!tk.legend) {
-    return;
-  }
-  tk.legend.mclass.currentData = data.mclass2variantcount;
-  update_mclass(tk);
-  may_update_variantShapeName(data, tk);
-  may_update_infoFields(data, tk);
-  may_update_formatFilter(data, tk);
-  may_update_skewerRim(data, tk);
-  may_update_ld(tk);
-  may_update_cnv(tk);
-}
-function may_update_variantShapeName(data, tk) {
-  if (!tk.legend.customShapeLabels) return;
-  Object.values(tk.legend.variantShapeName).forEach((s) => {
-    if (!s.ids) {
-      s.ids = data.skewer.filter((d) => d.shape == s.key).map((i) => i.id);
-    }
-    s.num = 0;
-  });
-  for (const d of data.skewer) {
-    let shapeObj = tk.legend.variantShapeName.find((s) => s.ids.some((i) => i == d.id));
-    if (!shapeObj) {
-      shapeObj = tk.legend.variantShapeName.find((s) => s.key == d.shape || s.origShape == d.shape);
-      shapeObj.ids.push(d.id);
-    }
-    shapeObj.num = ++shapeObj.num;
-  }
-  Object.values(tk.legend.variantShapeName).forEach((s) => {
-    s.wrapper.style("display", s.num ? "block" : "none");
-    s.numDiv.text(s.num);
-  });
-}
-function may_update_infoFields(data, tk) {
-  if (!tk.legend.bcfInfo) return;
-  if (!data.skewer) {
-    console.log("data.skewer[] is not present and cannot show INFO legend");
-    return;
-  }
-  for (const infoKey in tk.legend.bcfInfo) {
-    tk.legend.bcfInfo[infoKey].holder.selectAll("*").remove();
-    if (tk.mds.bcf.info[infoKey].Type == "String") {
-      const category2variantCount = /* @__PURE__ */ new Map();
-      for (const m of data.skewer) {
-        const category = m.info?.[infoKey] || unannotatedKey;
-        if (Array.isArray(category)) {
-          for (const c of category) {
-            category2variantCount.set(c, 1 + (category2variantCount.get(c) || 0));
-          }
-        } else {
-          category2variantCount.set(category, 1 + (category2variantCount.get(category) || 0));
-        }
-      }
-      const show_lst = [...category2variantCount].sort((i, j) => j[1] - i[1]);
-      for (const [category, count] of show_lst) {
-        printCategory({
-          holder: tk.legend.bcfInfo[infoKey].holder,
-          key: category,
-          color: tk.mds.bcf.info[infoKey].categories?.[category]?.color || unknown_infoCategory_color,
-          label: tk.mds.bcf.info[infoKey].categories?.[category]?.label || category,
-          count,
-          click: (event2) => {
-            const opts = [
-              {
-                label: "Hide",
-                isVisible: () => true,
-                callback: () => {
-                  tk.legend.bcfInfo[infoKey].hiddenvalues.add(category);
-                }
-              },
-              {
-                label: "Show only",
-                isVisible: () => true,
-                callback: () => {
-                  for (const c2 of show_lst) {
-                    tk.legend.bcfInfo[infoKey].hiddenvalues.add(c2[0]);
-                  }
-                  tk.legend.bcfInfo[infoKey].hiddenvalues.delete(category);
-                }
-              },
-              {
-                label: "Show all",
-                isVisible: () => tk.legend.bcfInfo[infoKey].hiddenvalues.size,
-                callback: () => {
-                  tk.legend.bcfInfo[infoKey].hiddenvalues.clear();
-                }
-              }
-            ];
-            createLegendTipMenu(opts, tk, event2.target);
-            const desc = tk.mds.bcf.info[infoKey].categories?.[category]?.desc;
-            if (desc) {
-              tk.legend.tip.d.append("div").style("padding", "10px").style("font-size", ".8em").style("width", "150px").html(desc);
-            }
-          }
-        });
-      }
-      for (const c of tk.legend.bcfInfo[infoKey].hiddenvalues) {
-        let loading = false;
-        tk.legend.bcfInfo[infoKey].holder.append("div").style("display", "inline-block").attr("class", "sja_clb").style("text-decoration", "line-through").text(c).on("click", async () => {
-          if (loading) return;
-          loading = true;
-          tk.legend.bcfInfo[infoKey].hiddenvalues.delete(c);
-          reload(tk);
-        });
-      }
-    }
-  }
-}
-function update_mclass(tk) {
-  if (tk.hardcodeCnvOnly) return;
-  if (!tk.legend.mclass.currentData || tk.legend.mclass.currentData.length == 0) return;
-  tk.legend.mclass.holder.selectAll("*").remove();
-  const showlst = [], hiddenlst = [];
-  for (const [k, count] of tk.legend.mclass.currentData) {
-    const v = { k, count };
-    if (tk.legend.mclass.hiddenvalues.has(k)) {
-      hiddenlst.push(v);
-    } else {
-      showlst.push(v);
-    }
-  }
-  showlst.sort((i, j) => j.count - i.count);
-  hiddenlst.sort((i, j) => j.count - i.count);
-  for (const k of tk.legend.mclass.hiddenvalues) {
-    if (!hiddenlst.find((i) => i.k == k)) {
-      hiddenlst.push({ k });
-    }
-  }
-  for (const c of showlst) {
-    const { label, desc, color } = mds3tkMclass(c.k);
-    printCategory({
-      holder: tk.legend.mclass.holder,
-      key: c.k,
-      label: tk.mds.termdbConfig?.mclass?.[c.k]?.label || label,
-      color,
-      count: c.count,
-      click: () => {
-        const opts = [
-          {
-            label: "Hide",
-            isVisible: () => true,
-            callback: () => {
-              tk.legend.mclass.hiddenvalues.add(c.k);
-            }
-          },
-          {
-            label: "Show only",
-            isVisible: () => true,
-            callback: () => {
-              for (const c2 of showlst) {
-                tk.legend.mclass.hiddenvalues.add(c2.k);
-              }
-              tk.legend.mclass.hiddenvalues.delete(c.k);
-            }
-          },
-          {
-            label: "Show all",
-            isVisible: () => hiddenlst.length,
-            callback: () => {
-              tk.legend.mclass.hiddenvalues.clear();
-            }
-          },
-          {
-            isChangeShape: true,
-            isVisible: () => {
-              if (c.k == dtcnv) return false;
-              return !tk.skewer.viewModes.find((v) => v.type === "numeric")?.inuse ? tk.mds?.termdbConfig?.tracks?.allowSkewerChanges ?? true : false;
-            },
-            callback: (val, tk2) => {
-              tk2.shapes[c.k] = val;
-              tk2.load();
-              tk2.legend.tip.hide();
-            }
-          },
-          {
-            isChangeColor: true,
-            value: color,
-            isVisible: () => {
-              return c.k != dtcnv;
-            },
-            callback: (colorValue) => {
-              if (!mclass[c.k].origColor) mclass[c.k].origColor = mclass[c.k].color;
-              mclass[c.k].color = colorValue;
-            },
-            reset: {
-              isVisible: () => mclass[c.k].origColor,
-              callback: () => mclass[c.k].color = mclass[c.k].origColor
-            }
-          }
-        ];
-        createLegendTipMenu(opts, tk, event.target);
-        const descDiv = tk.legend.tip.d.append("div").style("padding", "10px").style("font-size", ".8em").style("width", "150px");
-        descDiv.append("span").style("color", color).text(label.toUpperCase());
-        descDiv.append("div").style("color", "black").html(desc);
-      }
-    });
-  }
-  for (const c of hiddenlst) {
-    let loading = false;
-    tk.legend.mclass.holder.append("div").style("display", "inline-block").attr("class", "sja_clb").style("text-decoration", "line-through").style("opacity", 0.7).text((c.count ? "(" + c.count + ") " : "") + (Number.isInteger(c.k) ? dt2label[c.k] : mclass[c.k].label)).on("click", async (event2) => {
-      if (loading) return;
-      loading = true;
-      tk.legend.mclass.hiddenvalues.delete(c.k);
-      event2.target.innerHTML = "Updating...";
-      await tk.load();
-    });
-  }
-}
-function may_create_skewerRim(tk, block) {
-  if (!tk.mds.queries?.snvindel?.skewerRim) return;
-  const R = tk.legend.skewerRim = {};
-  if (!tk.mds.queries.snvindel.skewerRim.hiddenvaluelst) tk.mds.queries.snvindel.skewerRim.hiddenvaluelst = [];
-  R.row = tk.legend.table.append("tr");
-  R.headerTd = R.row.append("td").attr("data-testid", `sjpp-mds3tk-legend-skewerRim`).style("text-align", "right").style("opacity", 0.7);
-  R.holder = R.row.append("td");
-}
-function getSkewerRimLegendHeaderName(tk) {
-  const sk = tk.mds.queries.snvindel.skewerRim;
-  if (sk.type == "format") {
-    if (!sk.formatKey) throw "skewerRim.formatKey missing";
-    return tk.mds.bcf?.format?.[sk.formatKey]?.Description || sk.formatKey;
-  }
-  return "unknown skewerRim.type";
-}
-function may_update_skewerRim(data, tk) {
-  if (!data.skewer) return;
-  const sk = tk.mds.queries?.snvindel?.skewerRim;
-  if (!sk) return;
-  let rim1total = 0, noRimTotal = 0;
-  for (const m of data.skewer) {
-    const r1 = m.rim1count || 0;
-    rim1total += r1;
-    noRimTotal += m.occurrence - r1;
-  }
-  const R = tk.legend.skewerRim;
-  R.headerTd.text(getSkewerRimLegendHeaderName(tk));
-  R.holder.selectAll("*").remove();
-  if (rim1total > 0) {
-    R.holder.append("div").attr("class", "sja_clb").style("display", "inline-block").html(`${getRimSvg(1)}${sk.rim1value}, n=${rim1total}`).on("click", (event2) => {
-      tk.legend.tip.clear().showunder(event2.target).d.append("div").attr("class", "sja_menuoption").attr("data-testid", `sjpp-hide-${sk.rim1value}-option`).text("Hide").on("click", () => {
-        sk.hiddenvaluelst.push(sk.rim1value);
-        reload(tk);
-      });
-    });
-  }
-  if (noRimTotal > 0) {
-    R.holder.append("div").attr("class", "sja_clb").style("display", "inline-block").html(`${getRimSvg()}${sk.noRimValue}, n=${noRimTotal}`).on("click", (event2) => {
-      tk.legend.tip.clear().showunder(event2.target).d.append("div").attr("class", "sja_menuoption").attr("data-testid", "sjpp-hide-no-rim-option").text("Hide").on("click", () => {
-        sk.hiddenvaluelst.push(sk.noRimValue);
-        reload(tk);
-      });
-    });
-  }
-  for (const c of sk.hiddenvaluelst) {
-    let loading = false;
-    R.holder.append("div").style("display", "inline-block").attr("class", "sja_clb").style("text-decoration", "line-through").style("opacity", 0.7).text(c).on("click", async (event2) => {
-      if (loading) return;
-      loading = true;
-      sk.hiddenvaluelst.splice(sk.hiddenvaluelst.indexOf(c), 1);
-      event2.target.innerHTML = "Updating...";
-      await tk.load();
-    });
-  }
-}
-function getRimSvg(rim) {
-  return '<svg width="19" height="19" style="margin-right: 5px;"><circle cx="7" cy="12" r="7" fill="#b1b1b1"></circle>' + (rim == 1 ? '<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>' : rim == 2 ? "" : "") + // blank for no rim
-  "</svg>";
-}
-function may_create_ld(tk, block) {
-  if (!tk.mds.queries?.ld) return;
-  tk.mds.queries.ld.colorScale = rgb_default(tk.mds.queries.ld.overlay.color_0, tk.mds.queries.ld.overlay.color_1);
-  const R = tk.legend.ld = {};
-  R.row = tk.legend.table.append("tr");
-  R.headerTd = R.row.append("td").attr("data-testid", `sjpp-mds3tk-legend-ld`).style("text-align", "right").style("opacity", 0.7);
-  R.holder = R.row.append("td");
-  R.showHolder = R.holder.append("div").style("display", "none");
-  showLDlegend(R.showHolder, tk.mds.queries.ld.colorScale);
-  R.showHolder.append("span").text("Cancel overlay").style("font-size", ".7em").attr("class", "sja_clbtext").on("click", () => {
-    delete tk.mds.queries.ld.mOverlay;
-    if (tk.skewer?.hlssmid) delete tk.skewer.hlssmid;
-    tk.load();
-  });
-}
-function may_update_ld(tk) {
-  if (!tk.mds.queries?.ld?.mOverlay) {
-    if (tk.legend.ld) {
-      tk.legend.ld.headerTd.html("");
-      tk.legend.ld.showHolder.style("display", "none");
-    }
-    return;
-  }
-  tk.legend.ld.headerTd.html(tk.mds.queries.ld.mOverlay.ldtkname + " LD r<sup>2</sup>");
-  tk.legend.ld.showHolder.style("display", "block");
-}
-function may_create_cnv(tk, block) {
-  if (!tk.cnv) return;
-  const R = tk.legend.cnv = {};
-  R.row = tk.legend.table.append("tr");
-  R.headerTd = R.row.append("td").attr("data-testid", `sjpp-mds3tk-legend-cnv`).style("text-align", "right").style("opacity", 0.7).text("CNV");
-  R.holder = R.row.append("td").style("padding-left", "10px");
-  if (Number.isFinite(tk.cnv.cnvGainCutoff)) {
-    R.colorscaleHolder = R.holder.append("div");
-    R.colorscaleHolder.append("span").text("Loss").style("font-size", ".8em").style("opacity", 0.6);
-    const csHolder = R.colorscaleHolder.append("span");
-    R.colorscaleHolder.append("span").text("Gain").style("font-size", ".8em").style("opacity", 0.6);
-    const axisheight = 20;
-    const barheight = 15;
-    const xpad = 10;
-    const axiswidth = 150;
-    R.colorScale = new ColorScale({
-      barwidth: axiswidth,
-      barheight,
-      colors: [tk.cnv.lossColor, "white", tk.cnv.gainColor],
-      domain: [-1, 0, 1],
-      // actual domain added during update
-      fontSize: 12,
-      holder: csHolder,
-      height: axisheight + barheight,
-      width: xpad * 2 + axiswidth,
-      position: `${xpad},${axisheight}`,
-      ticks: 4,
-      tickSize: 6,
-      topTicks: true,
-      numericInputs: {
-        callback: (obj) => {
-          if (obj.cutoffMode == "auto") {
-            delete tk.cnv.presetMax;
-          } else if (obj.cutoffMode == "fixed") {
-            tk.cnv.presetMax = Math.abs(obj.max);
-          } else {
-            throw "unknown cutoffMode value";
-          }
-          tk.load();
-        }
-      }
-    });
-  } else {
-    R.cnvCategoryHolder = R.holder.append("span").attr("data-testid", "sjpp-mds3cnvlegend-categoryholder");
-  }
-  R.noCnv = R.holder.append("div").text("No data").style("opacity", 0.6);
-  const menu = new Menu();
-  R.cnvFilterPrompt = R.holder.append("div").style("display", "inline-block").style("margin-left", "10px").style("font-size", ".9em").attr("class", "sja_clbtext").on("click", () => {
-    menu.clear().showunder(R.cnvFilterPrompt.node());
-    const arg = {
-      holder: menu.d.append("div"),
-      cnvGainCutoff: tk.cnv.cnvGainCutoff,
-      cnvLossCutoff: tk.cnv.cnvLossCutoff,
-      cnvMaxLength: tk.cnv.cnvMaxLength,
-      callback: (config) => {
-        Object.assign(tk.cnv, config);
-        menu.hide();
-        tk.load();
-      }
-    };
-    renderCnvConfig(arg);
-  });
-}
-function may_update_cnv(tk) {
-  if (!tk.cnv) return;
-  if (!tk.cnv.cnvLst || tk.cnv.cnvLst.length == 0) {
-    tk.legend.cnv.colorscaleHolder?.style("display", "none");
-    tk.legend.cnv.cnvCategoryHolder?.style("display", "none");
-    tk.legend.cnv.noCnv.style("display", tk.cnv.cnvInDensity ? "none" : "inline-block");
-  } else {
-    tk.legend.cnv.noCnv.style("display", "none");
-    if (Number.isFinite(tk.cnv.cnvGainCutoff)) {
-      tk.legend.cnv.colorscaleHolder.style("display", "inline-block");
-      tk.legend.cnv.colorScale.colors = [tk.cnv.lossColor, "white", tk.cnv.gainColor];
-      tk.legend.cnv.colorScale.domain = tk.cnv.presetMax ? [-tk.cnv.presetMax, 0, tk.cnv.presetMax] : [-tk.cnv.absoluteMax, 0, tk.cnv.absoluteMax];
-      tk.legend.cnv.colorScale.updateScale();
-    } else {
-      if (!tk.hardcodeCnvOnly) {
-      } else {
-        tk.legend.cnv.cnvCategoryHolder.style("display", "inline-block").selectAll("*").remove();
-        const class2count = /* @__PURE__ */ new Map();
-        for (const c of tk.cnv.cnvLst) {
-          if (!c.class) continue;
-          class2count.set(c.class, 1 + (class2count.get(c.class) || 0));
-        }
-        for (const [cls, count] of [...class2count].sort((i, j) => j[1] - i[1])) {
-          printCategory({
-            holder: tk.legend.cnv.cnvCategoryHolder,
-            key: cls,
-            label: mclass[cls].label,
-            color: mclass[cls].color,
-            count,
-            click: (event2) => {
-              const opts = [
-                {
-                  label: "Hide",
-                  isVisible: () => true,
-                  callback: () => {
-                    tk.legend.mclass.hiddenvalues.add(cls);
-                  }
-                },
-                {
-                  isChangeColor: true,
-                  value: mclass[cls].color,
-                  isVisible: () => true,
-                  callback: (colorValue) => {
-                    if (!mclass[cls].origColor) mclass[cls].origColor = mclass[cls].color;
-                    mclass[cls].color = colorValue;
-                  },
-                  reset: {
-                    isVisible: () => mclass[cls].origColor,
-                    callback: () => mclass[cls].color = mclass[cls].origColor
-                  }
-                }
-              ];
-              createLegendTipMenu(opts, tk, event2.target);
-            }
-          });
-        }
-        for (const cls of tk.legend.mclass.hiddenvalues) {
-          let loading = false;
-          tk.legend.cnv.cnvCategoryHolder.append("div").style("display", "inline-block").attr("class", "sja_clb").style("text-decoration", "line-through").style("opacity", 0.7).text(mclass[cls].label).on("click", async (event2) => {
-            if (loading) return;
-            loading = true;
-            tk.legend.mclass.hiddenvalues.delete(cls);
-            event2.target.innerHTML = "Updating...";
-            await tk.load();
-          });
-        }
-      }
-    }
-  }
-  const lst = [];
-  if (Number.isFinite(tk.cnv.cnvGainCutoff)) {
-    lst.push(`CNV gain \u2265 ${tk.cnv.cnvGainCutoff}`);
-  }
-  if (Number.isFinite(tk.cnv.cnvLossCutoff)) {
-    lst.push(`CNV loss \u2264 ${tk.cnv.cnvLossCutoff}`);
-  }
-  if (Number.isFinite(tk.cnv.cnvMaxLength)) {
-    lst.push(`CNV length \u2264 ${bplen(tk.cnv.cnvMaxLength)}`);
-  } else {
-    lst.push("no length limit");
-  }
-  tk.legend.cnv.cnvFilterPrompt.text(`Filter: ${lst.join("; ")}`);
-}
-function createLegendTipMenu(opts, tk, elem) {
-  tk.legend.tip.clear().showunder(elem);
-  for (const opt of opts) {
-    if (opt.isVisible()) {
-      if (opt.isChangeColor) {
-        tk.legend.tip.d.append("div").style("padding", "5px 10px").style("display", "inline-block").text("Color:").append("input").attr("type", "color").property("value", rgb(opt.value).formatHex()).on("change", (event2) => {
-          const color = event2.target.value;
-          opt.callback(color);
-          reload(tk);
-        });
-        if (opt.reset && opt.reset?.isVisible()) {
-          const resetDiv = tk.legend.tip.d.append("div").style("display", "inline-block");
-          const handler = () => {
-            opt.reset.callback();
-            reload(tk);
-          };
-          icons["restart"](resetDiv, { handler, title: "Reset to original color" });
-        }
-      } else if (opt.isChangeShape) {
-        let called = false;
-        const div = tk.legend.tip.d.append("div").text("Change shape").style("vertical-align", "middle").classed("sja_menuoption", true).attr("data-testid", "sjpp-change-shape-option").style("padding", "5px 10px").style("margin", "1px").style("border-radius", "0px").on("click", () => {
-          div.classed("sja_menuoption", false);
-          div.attr("data-testid", "sjpp-shape-picker");
-          div.style("background-color", "white");
-          if (called == false) {
-            called = true;
-            renderShapePicker({
-              holder: div.append("div").style("margin-top", "10px"),
-              callback: (val) => opt.callback(val, tk),
-              tk
-            });
-          }
-        });
-      } else {
-        tk.legend.tip.d.append("div").attr("class", "sja_menuoption").attr("data-testid", `sjpp-legend-option-${opt.label.toLowerCase().replace(/\s/g, "-")}`).style("border-radius", "0px").text(opt.label).on("click", () => {
-          opt.callback();
-          reload(tk);
-        });
-      }
-    }
-  }
-}
-function printCategory({ holder, key, color, count, label, click }) {
-  const div = holder.append("div").attr("class", "sja_clb").style("display", "inline-block").on("click", click);
-  div.append("div").style("display", "inline-block").attr("class", "sja_mcdot").style("background", color).html(count > 1 ? count : "&nbsp;");
-  div.append("div").style("display", "inline-block").style("color", color).style("padding-left", "5px").attr("data-testid", "sjpp-mds3tk-legenditemlabel").attr("__key__", key).text(label);
-}
-
-// mds3/filterName.js
-function getFilterName(f) {
-  if (!Array.isArray(f?.lst)) return "Invalid filter";
-  const lst = f.lst.filter((i) => i.tag != "cohortFilter");
-  if (lst.length == 0) return "No filter";
-  if (lst.length == 1 && lst[0].type == "tvs") {
-    const tvs = lst[0].tvs;
-    if (!tvs) throw "f.lst[0].tvs{} missing";
-    switch (tvs?.term?.type) {
-      case "categorical":
-        if (!Array.isArray(tvs.values)) throw "f.lst[0].tvs.values not array";
-        const catKey = tvs.values[0]?.key;
-        if (catKey == void 0) throw "f.lst[0].tvs.values[0].key missing";
-        const catValue = tvs.term.values?.[catKey]?.label || catKey;
-        if (tvs.values.length == 1) {
-          if ((tvs.term.name + catValue).length < 20) {
-            return tvs.term.name + (tvs.isnot ? "!=" : ": ") + catValue;
-          }
-          return (tvs.isnot ? "!" : "") + (catValue.length < 15 ? catValue : catValue.substring(0, 13) + "...");
-        }
-        return `${tvs.isnot ? "!" : ""}${catValue.length < 12 ? catValue : catValue.substring(0, 10) + "..."} (${tvs.values.length})`;
-      case "integer":
-      case "float":
-      case "geneExpression":
-      case "metaboliteIntensity":
-      case "proteomeAbundance":
-        return getNumericRangeLabel(tvs);
-      case "samplelst":
-        return Object.keys(tvs.term.values)[0];
-      default:
-        for (const dtt of dtTerms) {
-          if (dtt.type == tvs.term.type) {
-            return (tvs.term.parentTerm?.name || "?") + " " + dtt.name;
-          }
-        }
-        throw "unknown tvs term type";
-    }
-  }
-  return "Filter (" + lst.length + ")";
-}
-function getNumericRangeLabel(tvs) {
-  if (!Array.isArray(tvs.ranges)) throw "tvs.ranges not array";
-  if (!tvs.ranges[0]) throw "tvs.ranges[] blank array";
-  const r = tvs.ranges[0];
-  let startName, stopName;
-  const vc = tvs.term.valueConversion;
-  if (vc) {
-    if ("start" in r) startName = convertUnits(r.start, vc.fromUnit, vc.toUnit, vc.scaleFactor, true);
-    if ("stop" in r) stopName = convertUnits(r.stop, vc.fromUnit, vc.toUnit, vc.scaleFactor, true);
-  } else {
-    if (tvs.term.type == "integer") {
-      if ("start" in r) startName = Math.round(r.start);
-      if ("stop" in r) stopName = Math.round(r.stop);
-    } else {
-      if ("start" in r) startName = r.start;
-      if ("stop" in r) stopName = r.stop;
-      if ("start" in r && "stop" in r) {
-        ;
-        [startName, stopName] = niceNumLabels([startName, stopName]);
-      }
-    }
-  }
-  let label;
-  if (tvs.isnot) {
-    if (r.startunbounded) label = `x ${r.stopinclusive ? ">" : ">="} ${stopName}`;
-    else if (r.stopunbounded) label = `x ${r.startinclusive ? "<" : "<="} ${startName}`;
-    else label = `!(${startName} ${stopName})`;
-  } else {
-    if (r.startunbounded) label = `x ${r.stopinclusive ? "<=" : "<"} ${stopName}`;
-    else if (r.stopunbounded) label = `x ${r.startinclusive ? ">=" : ">"} ${startName}`;
-    else label = `${startName}${r.startinclusive ? "<=" : "<"}x${r.stopinclusive ? "<=" : "<"}${stopName}`;
-  }
-  if (tvs.ranges.length > 1) label += "...";
-  return label;
-}
-
-// mds3/makeTk.js
-var callbacknames = [
-  "onClose",
-  // this only takes effect if tk shows the "Close" handle, e.g. on subtk
-  "click_snvindel",
-  "callbackOnRender",
-  "disc_mouseover",
-  "disc_mouseout"
-];
-async function makeTk(tk, block) {
-  tk.subtk2height = {
-    skewer: 0,
-    leftlabels: 0,
-    cnv: 0
-  };
-  tk.leftlabels = {
-    g: tk.gleft.append("g"),
-    // all labels are rendered here, except track label
-    doms: {},
-    // keys: label name, value: label dom
-    // to avoid having to delete all labels upon tk rendering
-    laby: 0,
-    // cumulative height, 0 for no labels
-    xoff: 0,
-    maxwidth: 0
-    // set default 0 in case track runs into err, can still render tk
-  };
-  tk._finish = loadTk_finish_closure(tk, block);
-  tk.cache = {};
-  tk.itemtip = new Menu();
-  tk.hovertip = new Menu();
-  tk.menutip = new Menu({ padding: "" });
-  tk.load = _load(tk, block);
-  tk.mnamegetter = (m) => {
-    if (tk.mds.queries?.snvindel?.vcfid4skewerName && m.vcf_id) return m.vcf_id;
-    const s = m.mname;
-    if (!s) return "";
-    if (s.length > 25) {
-      return s.substr(0, 20) + "...";
-    }
-    return s;
-  };
-  await get_ds(tk, block);
-  await mayInitTermdb(tk, block);
-  await mayInit_variant2samples(tk, block);
-  mayaddGetter_m2csq(tk, block);
-  mayInitSkewer(tk);
-  mayInitCnv(tk);
-  if (tk.filterObj) await Promise.all(rehydrateFilter(tk.filterObj, tk.mds.termdb.vocabApi));
-  tk.tklabel.text(tk.mds.label || tk.name);
-  tk.clear = () => {
-    if (tk.skewer) tk.skewer.g.selectAll("*").remove();
-  };
-  initLegend(tk, block);
-  init_mclass(tk);
-  tk.color4disc = (m) => {
-    if (tk.mutationColorBy) {
-      if (tk.mutationColorBy == "hardcode") {
-        if (m.color) return m.color;
-      }
-    }
-    if (tk.mds.queries?.ld?.mOverlay?.data) {
-      const m0 = tk.mds.queries.ld.mOverlay.m;
-      if (m.chr == m0.chr && m.pos == m0.pos && m.ref == m0.ref && m.alt == m0.alt) {
-        return tk.mds.queries.ld.overlay.color_1;
-      }
-      for (const m1 of tk.mds.queries.ld.mOverlay.data) {
-        if (m1.pos == m.pos && m1.alleles == m.ref + "." + m.alt) {
-          return tk.mds.queries.ld.colorScale(m1.r2);
-        }
-      }
-      return tk.mds.queries.ld.overlay.color_0;
-    }
-    if (tk.vcfinfofilter && tk.vcfinfofilter.setidx4mclass != void 0) {
-      const mcset = tk.vcfinfofilter.lst[tk.vcfinfofilter.setidx4mclass];
-      const [err, vlst] = getter_mcset_key(mcset, m);
-      if (err || vlst == void 0) return "black";
-      for (const v of vlst) {
-        if (mcset.categories[v]) {
-          return mcset.categories[v].color;
-        } else {
-          return "black";
-        }
-      }
-    }
-    if (mclass[m.class]) {
-      return mclass[m.class].color;
-    }
-    return "black";
-  };
-  parseUrl(tk);
-  if (tk.hlssmid) {
-    tk.skewer.hlssmid = new Set(tk.hlssmid.split(","));
-    delete tk.hlssmid;
-  }
-  try {
-    validateSelectSamples(tk);
-  } catch (e) {
-    console.error(e);
-  }
-  tk.duplicateTk = (filter) => {
-    const tkarg = {
-      type: "mds3",
-      dslabel: tk.dslabel,
-      filter0: tk.filter0,
-      showCloseLeftlabel: true,
-      filterObj: filter || structuredClone(tk.filterObj),
-      allow2selectSamples: tk.allow2selectSamples,
-      onClose: tk.onClose,
-      callbackOnRender: tk.callbackOnRender,
-      hardcodeCnvOnly: tk.hardcodeCnvOnly,
-      token: tk.token
-      // for testing
-    };
-    if (tk.cnv?.presetMax) tkarg.cnv = { presetMax: tk.cnv.presetMax };
-    if (tk.legend.mclass?.hiddenvalues?.size) {
-      tkarg.legend = { mclass: { hiddenvalues: /* @__PURE__ */ new Set() } };
-      for (const v of tk.legend.mclass.hiddenvalues) tkarg.legend.mclass.hiddenvalues.add(v);
-    }
-    return tkarg;
-  };
-  for (const n of callbacknames) {
-    if (tk[n] && typeof tk[n] != "function") throw `.${n}() is not function`;
-  }
-}
-function loadTk_finish_closure(tk, block) {
-  return (data) => {
-    tk.legend?.headTd.text(tk.name + (tk.filterObj ? " - " + getFilterName(tk.filterObj) : ""));
-    if (tk.cnv) {
-      tk.cnv.g.transition().attr("transform", `translate(0,${tk.subtk2height.skewer})`);
-    }
-    if (data) {
-      if (data.error) {
-        tk.subtk2height.skewer = 40;
-      } else {
-        let totalCount = 0;
-        if (data.skewer) totalCount = data.skewer.length;
-        if (data.cnv) totalCount += data.cnv.length;
-        if (data.cnvDensity) totalCount += data.cnvDensity.segmentCount;
-        if (totalCount == 0) {
-          let context = "view range";
-          if (block.usegm && block.gmmode != "genomic") context = block.usegm.name || block.usegm.isoform;
-          tk.skewer.g.append("text").text("No data in " + context).attr("y", 25).attr("x", block.width / 2).attr("text-anchor", "middle").attr("dominant-baseline", "center");
-          tk.subtk2height.skewer = 40;
-        }
-      }
-    }
-    tk.height_main = Math.max(
-      tk.subtk2height.leftlabels,
-      // won't be added if tk crashed
-      tk.subtk2height.skewer + tk.subtk2height.cnv
-    ) + tk.toppad + tk.bottompad;
-    if (data) {
-      updateLegend(data, tk, block);
-    }
-    tk.leftLabelMaxwidth = Math.max(
-      tk.leftlabels.maxwidth + tk.leftlabels.xoff,
-      // tk.skewer.maxwidth is undefined if makeTk had exception. must yield valid value for leftLabelMaxwidth for block to show properly with err msg in tk body
-      Number.isFinite(tk.skewer?.maxwidth) ? tk.skewer.maxwidth : 0
-    );
-    block.tkcloakoff(tk, { error: data ? data.error : null });
-    block.block_setheight();
-    block.setllabel();
-    tk.callbackOnRender?.(tk, block);
-  };
-}
-function parseUrl(tk) {
-  const urlp = urlmap_default();
-  if (tk.skewer) {
-    if (urlp.has("hlaachange")) {
-      tk.hlaachange = urlp.get("hlaachange");
-    }
-    if (urlp.has("hlssmid")) {
-      tk.hlssmid = urlp.get("hlssmid").split(",");
-    }
-  }
-}
-function mayInitSkewer(tk) {
-  if (!tk.mds.has_skewer) return;
-  tk.skewer = {
-    // both skewer and numeric mode will render elements into tk.skewer.g
-    // will also attach skewer.discKickSelection
-    g: tk.glider.append("g"),
-    // border color of a box over a highlighted data
-    hlBoxColor: tk.mds.hlBoxColor || "red",
-    // default to show dot labels
-    hideDotLabels: false,
-    // true for pointing up
-    pointup: true
-  };
-  setSkewerMode(tk);
-}
-function mayInitCnv(tk) {
-  let cfg;
-  if (tk.mds.termdbConfig?.queries?.cnv) {
-    if (tk.mds.termdbConfig.queries.cnv.requiresHardcodeCnvOnlyFlag) {
-      if (tk.hardcodeCnvOnly) {
-        cfg = tk.mds.termdbConfig.queries.cnv;
-      } else {
-      }
-    } else {
-      cfg = tk.mds.termdbConfig.queries.cnv;
-    }
-  } else if (tk.custom_variants?.find((i) => i.dt == dtcnv)) {
-    let useValue = false, useCat = false;
-    for (const m of tk.custom_variants) {
-      if (m.dt == dtcnv) {
-        if (Number.isFinite(m.value)) useValue = true;
-        else useCat = true;
-      }
-    }
-    if (useValue && useCat) throw "custom cnv should be either using numeric value or not, but cannot be mixture";
-    if (useValue) {
-      cfg = {
-        cnvGainCutoff: 0,
-        // use 0 for not filtering and show all events
-        cnvLossCutoff: 0
-      };
-    } else if (useCat) {
-      cfg = {};
-    } else {
-      throw "custom cnv is neither value or category, should not happen";
-    }
-  }
-  if (!cfg) return;
-  if (!tk.cnv) tk.cnv = {};
-  tk.cnv.g = tk.glider.append("g");
-  tk.cnv.cnvMaxLength = cfg.cnvMaxLength;
-  tk.cnv.cnvGainCutoff = cfg.cnvGainCutoff;
-  tk.cnv.cnvLossCutoff = cfg.cnvLossCutoff;
-  tk.cnv.absoluteValueRenderMax = cfg.absoluteValueRenderMax || 5;
-  tk.cnv.gainColor = cfg.gainColor || "#D6683C";
-  tk.cnv.lossColor = cfg.lossColor || "#67a9cf";
-  tk.cnv.density = {
-    barheight: 60
-  };
-}
-function setSkewerMode(tk) {
-  tk.skewer.viewModes = tk.skewerModes;
-  delete tk.skewerModes;
-  if (!tk.skewer.viewModes) tk.skewer.viewModes = [];
-  const vm = tk.skewer.viewModes;
-  if (!Array.isArray(vm)) throw "skewerModes[] is not array";
-  if (tk.mds.skewerModes) {
-    for (const n of tk.mds.skewerModes) vm.push(n);
-  }
-  if (!vm.find((n) => n.type == "skewer")) vm.push({ type: "skewer" });
-  for (const n of vm) {
-    if (typeof n != "object") throw "one of skewerModes[] is not object";
-    if (n.type == "skewer") {
-      if (!n.label) n.label = "lollipops";
-    } else if (n.type == "numeric") {
-      if (n.byAttribute) {
-        if (!n.label) n.label = n.byAttribute;
-      } else if (n.byInfo) {
-      } else {
-        throw "unknown data method for a type=numeric mode";
-      }
-    } else {
-      throw "unknown type from a skewerModes[]";
-    }
-  }
-  if (!vm.find((n) => n.inuse)) vm[0].inuse = true;
-}
-function init_mclass(tk) {
-  if (tk.mds.hiddenmclass) {
-    for (const c of tk.mds.hiddenmclass) tk.legend.mclass.hiddenvalues.add(c);
-  }
-}
-async function get_ds(tk, block) {
-  if (tk.dslabel) {
-    const data = await dofetch3("getDataset", { body: { genome: block.genome.name, dsname: tk.dslabel } });
-    if (data.error) throw "Error: " + data.error;
-    if (!data.ds) throw "data.ds{} missing";
-    if (!data.ds.isMds3) throw "A legacy dataset cannot be loaded as a mds3 track";
-    tk.mds = data.ds;
-    tk.name = data.ds.label;
-    return;
-  }
-  if (!tk.name) tk.name = "Custom data";
-  tk.mds = {};
-  if (tk.bcf) {
-    if (!tk.bcf.file && !tk.bcf.url) throw "file or url missing for tk.bcf{}";
-    tk.mds.has_skewer = true;
-    await getbcfheader_customtk(tk, block.genome);
-  } else if (tk.custom_variants) {
-    validateCustomVariants(tk, block);
-    mayDeriveSkewerOccurrence4samples(tk);
-    mayAddInfoField(tk);
-  } else {
-    throw "unknown data source for custom track";
-  }
-  mayProcessSampleAnnotation(tk);
-}
-function mayProcessSampleAnnotation(tk) {
-  if (!tk.sampleAnnotation) return;
-  if (!Array.isArray(tk.sampleAnnotation.terms)) throw "sampleAnnotation.terms is not array";
-  if (!tk.mds.termdb) tk.mds.termdb = {};
-  tk.mds.termdb.terms = tk.sampleAnnotation.terms;
-  tk.mds.termdb.annotations = tk.sampleAnnotation.annotations;
-}
-async function mayInitTermdb(tk, block) {
-  const tdb = tk.mds.termdb;
-  if (!tdb) return;
-  {
-    const arg = {};
-    if (tk.mds.label) {
-      arg.vocab = {
-        genome: block.genome.name,
-        dslabel: tk.mds.label
-      };
-    } else if (tdb.terms) {
-      arg.vocab = {
-        terms: tdb.terms,
-        sampleannotation: tdb.annotations
-      };
-    } else {
-      throw "do not know how to init vocab";
-    }
-    const _ = await import("./vocabulary-KLWZ6LRP.js");
-    tdb.vocabApi = _.vocabInit(arg);
-    if (!tdb.vocabApi.app) {
-      tdb.vocabApi.app = { opts: { genome: block.genome } };
-    }
-  }
-  tk.mds.termdbConfig = await tdb.vocabApi.getTermdbConfig();
-  if (tk.mds.termdb.allowCaseDetails) {
-    tk.mds.termdb.allowCaseDetails.get = async (acase) => {
-    };
-  }
-}
-function mayaddGetter_m2csq(tk, block) {
-  if (!tk.mds.queries?.snvindel?.m2csq) return;
-  tk.mds.queries.snvindel.m2csq.get = async (m) => {
-    const body = { genome: block.genome.name, dslabel: tk.mds.label, m2csq: 1 };
-    if (tk.mds.queries.snvindel.m2csq.by == "ssm_id") {
-      body.ssm_id = m.ssm_id;
-    } else {
-      return { error: "unknown query method" };
-    }
-    const headers = { "Content-Type": "application/json", Accept: "application/json" };
-    if (tk.token) headers["X-Auth-Token"] = tk.token;
-    return await dofetch3("mds3", { body, headers }, { serverData: tk.cache });
-  };
-}
-async function mayInit_variant2samples(tk, block) {
-  if (!tk.mds.variant2samples) return;
-  if (tk.custom_variants) {
-    addV2Sgetter_custom(tk, block);
-  } else {
-    addV2Sgetter_native(tk, block);
-  }
-  if (tk.mds.variant2samples.twLst) {
-    if (!Array.isArray(tk.mds.variant2samples.twLst)) throw "v2s.twLst[] not array";
-    if (!tk.mds.termdb?.vocabApi) throw "mds.termdb.vocabApi should be present for initiating v2s.twLst";
-    for (const t of tk.mds.variant2samples.twLst) await fillTermWrapper(t, tk.mds.termdb.vocabApi);
-  }
-}
-function addV2Sgetter_custom(tk, block) {
-  tk.mds.variant2samples.get = (arg) => {
-    if (arg.querytype == tk.mds.variant2samples.type_samples) {
-      const samples = [];
-      for (const m of arg.mlst) {
-        if (!m.samples) continue;
-        for (const s of m.samples) {
-          const s2 = JSON.parse(JSON.stringify(s));
-          s2.ssm_id = m.ssm_id;
-          samples.push(s2);
-        }
-      }
-      return { samples };
-    }
-    if (arg.querytype == tk.mds.variant2samples.type_summary) {
-      throw "todo: summary";
-    }
-    if (arg.querytype == tk.mds.variant2samples.type_sunburst) {
-      throw "todo: sunburst";
-    }
-    throw "unknown querytype";
-  };
-  tk.mds.getSamples = () => {
-    const id2sample = /* @__PURE__ */ new Map();
-    for (const m of tk.custom_variants) {
-      if (!m.samples) continue;
-      for (const s of m.samples) {
-        if (id2sample.has(s.sample_id)) {
-          id2sample.get(s.sample_id).ssm_id_lst.push(m.ssm_id);
-        } else {
-          const s2 = JSON.parse(JSON.stringify(s));
-          s2.ssm_id_lst = [m.ssm_id];
-          id2sample.set(s.sample_id, s2);
-        }
-      }
-    }
-    return { samples: [...id2sample.values()] };
-  };
-}
-function addV2Sgetter_native(tk, block) {
-  tk.mds.variant2samples.get = async (arg) => {
-    const par = {
-      genome: block.genome.name,
-      variant2samples: 1,
-      get: arg.querytype,
-      hardcodeCnvOnly: tk.hardcodeCnvOnly
-    };
-    if (tk.cnv) {
-      if (tk.cnv.cnvMaxLength) par.cnvMaxLength = tk.cnv.cnvMaxLength;
-      if (tk.cnv.cnvGainCutoff) par.cnvGainCutoff = tk.cnv.cnvGainCutoff;
-      if (tk.cnv.cnvLossCutoff) par.cnvLossCutoff = tk.cnv.cnvLossCutoff;
-    }
-    if (tk.mds.label) {
-      par.dslabel = tk.mds.label;
-    } else if (tk.bcf) {
-      if (tk.bcf.file) par.bcffile = tk.bcf.file;
-      else if (tk.bcf.url) par.bcfurl = tk.bcf.url;
-      else throw "tk.bcf{}: file/url missing";
-    } else {
-      throw "no dslabel or tk.bcf";
-    }
-    if (arg.groupSsmBySample) {
-      par.groupSsmBySample = 1;
-    }
-    if (arg.mlst) {
-      if (tk.mds.variant2samples.variantkey == "ssm_id") {
-        par.ssm_id_lst = arg.mlst.map((i) => i.ssm_id).join(",");
-      } else {
-        throw "unknown variantkey for variant2samples";
-      }
-    }
-    if (arg.isoform) {
-      par.isoform = arg.isoform;
-    }
-    if (arg.rglst) {
-      par.rglst = arg.rglst;
-    }
-    const headers = { "Content-Type": "application/json", Accept: "application/json" };
-    if (tk.set_id) par.set_id = tk.set_id;
-    if (tk.token) headers["X-Auth-Token"] = tk.token;
-    if (tk.filter0) par.filter0 = tk.filter0;
-    if (tk.filterObj) par.filterObj = tk.filterObj;
-    if (arg.tid2value) par.tid2value = arg.tid2value;
-    if (arg.querytype == tk.mds.variant2samples.type_sunburst) {
-      if (tk.mds.variant2samples.sunburst_twLst) {
-        par.twLst = tk.mds.variant2samples.sunburst_twLst;
-      }
-    } else if (arg.querytype == tk.mds.variant2samples.type_samples) {
-      if (tk.mds.variant2samples.twLst) par.twLst = tk.mds.variant2samples.twLst;
-    } else if (arg.querytype == tk.mds.variant2samples.type_summary) {
-      if (tk.mds.variant2samples.twLst) par.twLst = tk.mds.variant2samples.twLst;
-    } else {
-      throw "unknown querytype";
-    }
-    par.skewerRim = tk.mds.queries.snvindel?.skewerRim;
-    if (tk.legend?.formatFilter) {
-      const filter = {};
-      for (const k in tk.legend.formatFilter) {
-        if (tk.legend.formatFilter[k].hiddenvalues.size) {
-          filter[k] = [...tk.legend.formatFilter[k].hiddenvalues];
-        }
-      }
-      if (Object.keys(filter).length) {
-        par.formatFilter = filter;
-      }
-    }
-    if (tk.legend?.mclass?.hiddenvalues?.size) {
-      par.hiddenmclasslst = JSON.stringify([...tk.legend.mclass.hiddenvalues]);
-    }
-    const data = await dofetch3("mds3", { body: par, headers }, { serverData: tk.cache });
-    if (data.error) throw data.error;
-    const r = data.variant2samples;
-    if (!r) throw "result error";
-    if (arg.querytype == tk.mds.variant2samples.type_sunburst) {
-      if (!Array.isArray(r.nodes)) throw "nodes[] not array from return";
-    } else if (arg.querytype == tk.mds.variant2samples.type_samples) {
-      if (!Array.isArray(r.samples)) throw "samples[] not array from return";
-    } else if (arg.querytype == tk.mds.variant2samples.type_summary) {
-      if (!Array.isArray(r.summary)) throw "summary[] not array from return";
-    } else {
-      throw "unknown querytype";
-    }
-    return r;
-  };
-  tk.mds.getSamples = async (arg = {}) => {
-    if (arg.isSummary) {
-      arg.querytype = tk.mds.variant2samples.type_summary;
-    } else {
-      arg.querytype = tk.mds.variant2samples.type_samples;
-      arg.groupSsmBySample = 1;
-    }
-    rangequery_rglst(tk, block, arg);
-    return await tk.mds.variant2samples.get(arg);
-  };
-}
-function _load(tk, block) {
-  return async () => {
-    return await loadTk(tk, block);
-  };
-}
-function getter_mcset_key(mcset, m) {
-  if (mcset.altalleleinfo) {
-    if (!m.altinfo) return ["no .altinfo"];
-    const value = m.altinfo[mcset.altalleleinfo.key];
-    if (value == void 0) {
-      if (mcset.numericfilter) {
-        return [null, [0]];
-      }
-      return [null, void 0];
-    }
-    let vlst = Array.isArray(value) ? value : [value];
-    if (mcset.altalleleinfo.separator) {
-      vlst = vlst[0].split(mcset.altalleleinfo.separator);
-    }
-    return [null, vlst];
-  }
-  if (mcset.locusinfo) {
-    if (!m.info) return ["no .info"];
-    const value = m.info[mcset.locusinfo.key];
-    if (value == void 0) {
-      if (mcset.numericfilter) {
-        return [null, [0]];
-      }
-      return [null, void 0];
-    }
-    let vlst = Array.isArray(value) ? value : [value];
-    if (mcset.locusinfo.separator) {
-      vlst = vlst[0].split(mcset.locusinfo.separator);
-    }
-    return [null, vlst];
-  }
-  return ["no trigger"];
-}
-function validateCustomVariants(tk, block) {
-  for (const m of tk.custom_variants) {
-    if (m.dt == dtsnvindel) {
-      tk.mds.has_skewer = true;
-      validateCustomSnvindel(m);
-      continue;
-    }
-    if (m.dt == dtfusionrna || m.dt == dtsv) {
-      tk.mds.has_skewer = true;
-      validateCustomSvfusion(m, block);
-      continue;
-    }
-    if (m.dt == dtcnv) {
-      m.ssm_id = [m.chr, m.start, m.stop, m.class].join(ssmIdFieldsSeparator);
-      continue;
-    }
-    throw "unknown dt for a custom variant";
-  }
-}
-function validateCustomSnvindel(m) {
-  if (!m.chr) throw ".chr missing for custom snvindel";
-  if (!Number.isInteger(m.pos)) throw ".pos not integer for custom snvindel";
-  if (!m.ssm_id) {
-    m.ssm_id = [m.chr, m.pos, m.ref && m.alt ? m.ref + ssmIdFieldsSeparator + m.alt : m.mname].join(
-      ssmIdFieldsSeparator
-    );
-  }
-}
-function validateCustomSvfusion(m, block) {
-  if (m.pairlst) {
-  } else {
-    if (!m.chr1) throw ".chr1 missing for custom sv/fusion";
-    if (!Number.isInteger(m.pos1)) throw ".pos1 not integer for custom svfusion";
-    if (m.strand1 != "+" && m.strand1 != "-") throw ".strand1 not +/- for custom svfusion";
-    if (!m.chr2) throw ".chr1 missing for custom sv/fusion";
-    if (!Number.isInteger(m.pos2)) throw ".pos1 not integer for custom svfusion";
-    if (m.strand2 != "+" && m.strand2 != "-") throw ".strand1 not +/- for custom svfusion";
-    m.pairlst = [
-      {
-        a: {
-          chr: m.chr1,
-          pos: m.pos1,
-          strand: m.strand1,
-          name: m.gene1 || ""
-        },
-        b: {
-          chr: m.chr2,
-          pos: m.pos2,
-          strand: m.strand2,
-          name: m.gene2 || ""
-        }
-      }
-    ];
-    delete m.chr1;
-    delete m.pos1;
-    delete m.strand1;
-    delete m.gene1;
-    delete m.chr2;
-    delete m.pos2;
-    delete m.strand2;
-    delete m.gene2;
-  }
-  const fields = [m.dt];
-  const hits = block.seekcoord(m.pairlst[0].a.chr, m.pairlst[0].a.pos);
-  if (hits.length && hits[0].x > 0 && hits[0].x < block.width) {
-    fields.push(...[m.pairlst[0].a.chr, m.pairlst[0].a.pos, m.pairlst[0].a.strand, 0, m.pairlst[0].a.name]);
-    m.mname = m.pairlst[0].b.name || "";
-    m.chr = m.pairlst[0].a.chr;
-    m.pos = m.pairlst[0].a.pos;
-    m.pairlstIdx = 0;
-  } else {
-    const hits2 = block.seekcoord(m.pairlst[0].b.chr, m.pairlst[0].b.pos);
-    if (hits2.length && hits2[0].x > 0 && hits2[0].x < block.width) {
-      fields.push(...[m.pairlst[0].b.chr, m.pairlst[0].b.pos, m.pairlst[0].b.strand, 1, m.pairlst[0].b.name]);
-      m.mname = m.pairlst[0].a.name || "";
-      m.chr = m.pairlst[0].b.chr;
-      m.pos = m.pairlst[0].b.pos;
-      m.pairlstIdx = 1;
-    } else {
-    }
-  }
-  m.ssm_id = fields.join(ssmIdFieldsSeparator);
-}
-function mayDeriveSkewerOccurrence4samples(tk) {
-  if (tk.custom_variants.find((i) => i.occurrence != void 0)) {
-    return;
-  }
-  for (const i of tk.custom_variants) {
-    if (i.sample) {
-      i.sample_id = i.sample;
-      delete i.sample;
-    }
-  }
-  if (!tk.custom_variants.find((i) => i.sample_id)) {
-    return;
-  }
-  const ungrouped = [];
-  const key2m = /* @__PURE__ */ new Map();
-  for (const m of tk.custom_variants) {
-    if (m.dt != dtsnvindel) {
-      m.occurrence = 1;
-      m.samples = [{ sample_id: m.sample_id }];
-      delete m.sample_id;
-      ungrouped.push(m);
-      continue;
-    }
-    const key = [m.mname, m.chr, m.pos, m.ref, m.alt].join(ssmIdFieldsSeparator);
-    const m2 = key2m.get(key);
-    if (m2) {
-      m2.occurrence++;
-      m2.samples.push({
-        sample_id: m.sample_id
-      });
-    } else {
-      m.occurrence = 1;
-      m.samples = [
-        {
-          sample_id: m.sample_id
-        }
-      ];
-      delete m.sample_id;
-      key2m.set(key, m);
-    }
-  }
-  tk.custom_variants = ungrouped;
-  for (const m of key2m.values()) tk.custom_variants.push(m);
-  if (!tk.mds.variant2samples) tk.mds.variant2samples = {};
-  const v = tk.mds.variant2samples;
-  v.type_samples = "samples";
-  v.type_summary = "summary";
-  v.type_sunburst = "sunburst";
-}
-function mayAddInfoField(tk) {
-  if (!tk.custom_variants.some((i) => i.info)) return;
-  const info = {};
-  for (const m of tk.custom_variants) {
-    if (typeof m.info != "object") continue;
-    for (const k in m.info) {
-      const v = m.info[k];
-      if (v == null || v == void 0) continue;
-      if (!info[k]) info[k] = { ID: k, Number: ".", Type: "String", categories: {} };
-      if (!info[k].categories[v]) info[k].categories[v] = {};
-    }
-  }
-  for (const k in info) {
-    const colors = getColors(Object.keys(info[k].categories).length);
-    for (const c in info[k].categories) {
-      info[k].categories[c].color = colors(c);
-    }
-  }
-  tk.mds.bcf = { info };
-}
-async function getbcfheader_customtk(tk, genome) {
-  const arg = { genome: genome.name };
-  if (tk.bcf.file) {
-    arg.file = tk.bcf.file;
-  } else {
-    arg.url = tk.bcf.url;
-    if (tk.bcf.indexURL) arg.indexURL = tk.bcf.indexURL;
-  }
-  const data = await dofetch3("bcfheader", { body: arg });
-  if (data.error) throw data.error;
-  const [info, format2, samples, errs] = data.header;
-  if (errs) throw "Error parsing VCF meta lines: " + errs.join("; ");
-  tk.mds.bcf = {
-    info,
-    format: format2
-    // can be null
-  };
-  if (samples?.length) {
-    tk.mds.bcf.samples = samples;
-    tk.mds.variant2samples = {
-      //twLst:[], // TODO should not be required
-      type_samples: "samples",
-      variantkey: "ssm_id"
-    };
-  }
-  if (!tk.mds.queries) tk.mds.queries = {};
-  tk.mds.queries.snvindel = { forTrack: true };
-}
-function validateSelectSamples(tk) {
-  const a = tk.allow2selectSamples;
-  if (!a) return;
-  if (!a.buttonText) a.buttonText = "Select samples";
-  if (typeof a.buttonText != "string") throw "allow2selectSamples.buttonText value is not string";
-  if (!a.attributes) a.attributes = [{ from: "sample_id", to: "sample_id" }];
-  if (!Array.isArray(a.attributes)) throw "allow2selectSamples.attributes[] is not array";
-  if (a.attributes.length == 0) throw "allow2selectSamples.attributes[] blank array";
-  for (const i of a.attributes) {
-    if (typeof i.from != "string" || !i.from) throw "allow2selectSamples.attributes.from is not string";
-    if (typeof i.to != "string" || !i.to) throw "allow2selectSamples.attributes.to is not string";
-  }
-  if (typeof a.callback != "function") throw "allow2selectSamples.callback() is not function";
-  a._cart = [];
-}
-
-// mds3/cnv.js
-var maxRowHeight = 10;
-var maxTkHeight = 200;
-function getRowHeight(rows, tk) {
-  let maxh = maxTkHeight;
-  if (tk.subtk2height.skewer == 0) {
-    maxh *= 2;
-  }
-  const v = maxh / rows.length;
-  if (v > maxRowHeight) return [maxRowHeight, 1];
-  if (v > 3) return [Math.floor(v), 1];
-  if (v > 1) return [Math.floor(v), 0];
-  return [v, 0];
-}
-function may_render_cnv(data, tk, block) {
-  if (!tk.cnv) return;
-  tk.cnv?.g.selectAll("*").remove();
-  delete tk.cnv.cnvLst;
-  delete tk.cnv.cnvInDensity;
-  delete tk.cnv.cnvMsg;
-  if (data.cnv) {
-    if (!Array.isArray(data.cnv.cnvs)) throw "data.cnv.cnvs[] not array";
-    tk.cnv.cnvMsg = data.cnv.cnvMsg;
-    renderSegments(data, tk, block);
-    return;
-  }
-  if (data.cnvDensity) {
-    tk.cnv.cnvInDensity = true;
-    tk.cnv.cnvMsg = data.cnvDensity.cnvMsg;
-    renderDensity(data, tk, block);
-    return;
-  }
-  tk.subtk2height.cnv = 0;
-  if (tk.cnv) tk.cnv.cnvLst = [];
-}
-function renderDensity(data, tk, block) {
-  tk.cnv.g.append("image").attr("width", block.width).attr("height", tk.cnv.density.barheight).attr("xlink:href", data.cnvDensity.gain.src).attr("data-testid", "sjpp-mds3tk-cnvdensityimg");
-  tk.cnv.g.append("image").attr("width", block.width).attr("height", tk.cnv.density.barheight).attr("xlink:href", data.cnvDensity.loss.src).attr("y", tk.cnv.density.barheight);
-  axisstyle({
-    axis: tk.cnv.g.append("g").attr("transform", `translate(-1,0)`).call(
-      axisRight().scale(linear().domain([0, data.cnvDensity.max]).range([tk.cnv.density.barheight, 0])).tickValues([0, data.cnvDensity.max])
-    ),
-    color: "black",
-    showline: true
-  });
-  axisstyle({
-    axis: tk.cnv.g.append("g").attr("transform", `translate(-1,${tk.cnv.density.barheight})`).call(
-      axisRight().scale(linear().domain([0, data.cnvDensity.max]).range([0, tk.cnv.density.barheight])).tickValues([0, data.cnvDensity.max])
-    ),
-    color: "black",
-    showline: true
-  });
-  tk.cnv.g.append("text").text("Gain").attr("font-size", block.labelfontsize * 0.9).attr("x", 5).attr("y", tk.cnv.density.barheight / 2);
-  tk.cnv.g.append("text").text("Loss").attr("font-size", block.labelfontsize * 0.9).attr("x", 5).attr("y", tk.cnv.density.barheight * 1.5);
-  tk.subtk2height.cnv = tk.cnv.density.barheight * 2;
-}
-function renderSegments(data, tk, block) {
-  const [cnvBySample, cnvLst, absoluteMax] = prepData(data, tk, block);
-  tk.cnv.cnvLst = cnvLst;
-  tk.cnv.absoluteMax = absoluteMax;
-  tk.cnv.colorScale = linear(
-    tk.cnv.presetMax ? [-tk.cnv.presetMax, 0, tk.cnv.presetMax] : [-absoluteMax, 0, absoluteMax],
-    [tk.cnv.lossColor, "white", tk.cnv.gainColor]
-  ).clamp(true);
-  const [rowheight, rowspace] = getRowHeight(cnvBySample || cnvLst, tk);
-  if (cnvBySample) {
-    for (const sample of cnvBySample) {
-      for (const c of sample.cnvs) {
-        plotOneSegment(c, sample.y * (rowheight + rowspace), rowheight, tk, block, sample);
-      }
-    }
-  } else {
-    for (const c of cnvLst) {
-      plotOneSegment(c, c.y * (rowheight + rowspace), rowheight, tk, block);
-    }
-  }
-  const rowc = (cnvBySample || cnvLst).length;
-  tk.subtk2height.cnv = rowc * rowheight + (rowc - 1) * rowspace;
-}
-function prepData(data, tk, block) {
-  let maxAbsoluteValue = 0;
-  const sample2cnv = /* @__PURE__ */ new Map();
-  const cnvLst = [];
-  for (const v of data.cnv.cnvs) {
-    if (!v.chr) continue;
-    if (!Number.isInteger(v.start) || !Number.isInteger(v.stop)) continue;
-    const t1 = block.seekcoord(v.chr, v.start)[0];
-    if (!t1) continue;
-    const t2 = block.seekcoord(v.chr, v.stop)[0];
-    if (!t2) continue;
-    const j = structuredClone(v);
-    if (t1.x > t2.x) {
-      j.x1 = t2.x;
-      j.x2 = t1.x;
-    } else {
-      j.x1 = t1.x;
-      j.x2 = t2.x;
-    }
-    if (Number.isFinite(v.value)) maxAbsoluteValue = Math.max(maxAbsoluteValue, Math.abs(v.value));
-    cnvLst.push(j);
-    if (Array.isArray(v.samples)) {
-      for (const s of v.samples) {
-        if (!sample2cnv.has(s.sample_id)) sample2cnv.set(s.sample_id, []);
-        sample2cnv.get(s.sample_id).push(structuredClone(j));
-      }
-    }
-  }
-  let samples;
-  if (sample2cnv.size) {
-    samples = [];
-    for (const [s, cnvs] of sample2cnv) {
-      cnvs.sort((a, b) => a.x1 - b.x1);
-      samples.push({
-        sample_id: s,
-        cnvs,
-        x1: Math.min(...cnvs.map((i) => i.x1)),
-        x2: Math.max(...cnvs.map((i) => i.x2))
-      });
-    }
-    samples.sort((a, b) => a.x1 - b.x1);
-    for (let i = 0; i < samples.length; i++) samples[i].y = i;
-  } else {
-    cnvLst.sort((a, b) => a.x1 - b.x1);
-    stackRows(cnvLst, 0);
-  }
-  return [samples, cnvLst, Math.min(tk.cnv.absoluteValueRenderMax, maxAbsoluteValue)];
-}
-function plotOneSegment(c, y, rowheight, tk, block, sample) {
-  const x1 = Math.max(0, c.x1), x2 = Math.min(c.x2, block.width);
-  tk.cnv.g.append("rect").attr("x", x1).attr("y", y).attr("width", x2 - x1).attr("height", Math.max(rowheight, 1)).attr("fill", Number.isFinite(c.value) ? tk.cnv.colorScale(c.value) : mclass[c.class].color).on("mouseover", (event2) => {
-    event2.target.setAttribute("stroke", "black");
-    tk.hovertip.clear().show(event2.clientX, event2.clientY);
-    const table = table2col({ holder: tk.hovertip.d });
-    table_cnv({ mlst: [c], tk }, table);
-    if (sample) {
-      const [t1, t2] = table.addRow();
-      t1.text("Sample");
-      t2.text(sample.sample_id);
-    }
-  }).on("mouseout", (event2) => {
-    event2.target.setAttribute("stroke", "");
-    tk.hovertip.hide();
-  }).on("click", async (event2) => {
-    tk.itemtip.clear().show(event2.clientX, event2.clientY);
-    await itemtable_oneItem({
-      mlst: [c],
-      tk,
-      block,
-      div: tk.itemtip.d
-    });
-    return;
-    const table = table2col({ holder: tk.itemtip.d });
-    const cnv = structuredClone(c);
-    if (sample) {
-      cnv.samples = [{ sample_id: sample.sample_id }];
-    }
-    table_cnv({ mlst: [cnv], tk }, table, true);
-  });
-}
-function stackRows(lst, spacing) {
-  const stacks = [];
-  for (const item of lst) {
-    for (let i = 0; i < stacks.length; i++) {
-      if (stacks[i] + spacing < item.x1) {
-        stacks[i] = item.x2;
-        item.y = i;
-        break;
-      }
-    }
-    if (!("y" in item)) {
-      item.y = stacks.length;
-      stacks.push(item.x2);
-    }
-  }
-}
-
-// mds3/tk.js
-async function loadTk(tk, block) {
-  block.tkcloakon(tk);
-  block.block_setheight();
-  try {
-    if (!tk.mds || tk.uninitialized) {
-      await makeTk(tk, block);
-    }
-    const data = await getTkData(tk, block);
-    if (tk.uninitialized) {
-      tk.clear();
-      delete tk.uninitialized;
-    }
-    may_render_skewer(data, tk, block);
-    may_render_cnv(data, tk, block);
-    await make_leftlabels(data, tk, block);
-    tk._finish(data);
-  } catch (e) {
-    if (tk.clear) tk.clear();
-    if (tk.subtk2height) tk.subtk2height.skewer = 50;
-    if (tk._finish) tk._finish({ error: e.message || e });
-    if (e.stack) console.log(e.stack);
-    return;
-  }
-}
-function getParameter(tk, block) {
-  const par = {
-    genome: block.genome.name,
-    // instructs server to return data types associated with tracks
-    // including skewer or non-skewer
-    forTrack: 1,
-    // may not pass skewerRim if it is not in use (turn off)
-    skewerRim: tk.mds.queries?.snvindel?.skewerRim,
-    // instructions for counting rim counts per variant
-    hardcodeCnvOnly: tk.hardcodeCnvOnly
-  };
-  const headers = { "Content-Type": "application/json", Accept: "application/json" };
-  par.skewer = 1;
-  if (tk.set_id) {
-    par.set_id = tk.set_id;
-  }
-  if (tk.filter0) {
-    par.filter0 = tk.filter0;
-  }
-  if (tk.filterObj) {
-    if (tk.filterObj?.lst.length) {
-      par.filterObj = tk.filterObj;
-    }
-  }
-  if (tk.token) {
-    headers["X-Auth-Token"] = tk.token;
-  }
-  if (tk.mds.label) {
-    par.dslabel = tk.mds.label;
-  } else {
-    if (tk.bcf) {
-      if (tk.bcf.file) {
-        par.bcffile = tk.bcf.file;
-      } else if (tk.bcf.url) {
-        par.bcfurl = tk.bcf.url;
-        if (tk.bcf.indexURL) par.bcfindexURL = tk.bcf.indexURL;
-      } else {
-        throw ".file and .url missing for tk.bcf{}";
-      }
-    }
-  }
-  rangequery_rglst(tk, block, par);
-  if (tk.legend?.mclass.hiddenvalues.size) {
-    par.hiddenmclasslst = JSON.stringify([...tk.legend.mclass.hiddenvalues]);
-  }
-  if (tk.legend?.bcfInfo) {
-    const infoFilter = {};
-    for (const k in tk.legend.bcfInfo) {
-      if (tk.legend.bcfInfo[k].hiddenvalues.size) {
-        infoFilter[k] = [...tk.legend.bcfInfo[k].hiddenvalues];
-      }
-    }
-    if (Object.keys(infoFilter).length) {
-      par.infoFilter = infoFilter;
-    }
-  }
-  if (tk.legend?.formatFilter) {
-    const filter = {};
-    for (const k in tk.legend.formatFilter) {
-      if (tk.legend.formatFilter[k].hiddenvalues.size) {
-        filter[k] = [...tk.legend.formatFilter[k].hiddenvalues];
-      }
-    }
-    if (Object.keys(filter).length) {
-      par.formatFilter = filter;
-    }
-  }
-  if (tk.cnv) {
-    if (tk.cnv.cnvMaxLength) par.cnvMaxLength = tk.cnv.cnvMaxLength;
-    if (tk.cnv.cnvGainCutoff) par.cnvGainCutoff = tk.cnv.cnvGainCutoff;
-    if (tk.cnv.cnvLossCutoff) par.cnvLossCutoff = tk.cnv.cnvLossCutoff;
-    par.cnvDensity = {
-      width: block.width,
-      barheight: tk.cnv.density.barheight,
-      pcolor: tk.cnv.gainColor,
-      ncolor: tk.cnv.lossColor
-    };
-  }
-  return [par, headers];
-}
-async function getTkData(tk, block) {
-  let data;
-  if (tk.custom_variants) {
-    data = await dataFromCustomVariants(tk, block);
-  } else {
-    const [body, headers] = getParameter(tk, block);
-    data = await dofetch3("mds3", { body, headers });
-  }
-  if (data.error) throw data.error;
-  return data;
-}
-function rangequery_rglst(tk, block, par) {
-  if (typeof par != "object") throw "par{} is not object";
-  let rglst = [];
-  if (block.usegm) {
-    const r = {
-      chr: block.rglst[0].chr,
-      reverse: block.rglst[0].reverse,
-      width: 0,
-      start: null,
-      stop: null
-    };
-    for (let i = block.startidx; i <= block.stopidx; i++) {
-      const j = block.rglst[i];
-      r.width += j.width + block.regionspace;
-      r.start = r.start == null ? j.start : Math.min(r.start, j.start);
-      r.stop = r.stop == null ? j.stop : Math.max(r.stop, j.stop);
-    }
-    rglst.push(r);
-    if (block.gmmode == "genomic") {
-    } else {
-      par.isoform = block.usegm.isoform;
-      par.gene = block.usegm.name;
-    }
-  } else {
-    rglst = block.tkarg_rglst(tk);
-  }
-  let xoff = 0;
-  for (const r of rglst) {
-    r.xoff = 0;
-    xoff += r.width + block.regionspace;
-  }
-  if (block.subpanels.length == tk.subpanels.length) {
-    for (const r of block.subpanels) {
-      rglst.push({
-        chr: r.chr,
-        start: r.start,
-        stop: r.stop,
-        width: r.width,
-        exonsf: r.exonsf,
-        xoff
-      });
-      xoff += r.width + r.leftpad;
-    }
-  }
-  par.rglst = rglst;
-  par.regionspace = block.regionspace;
-  par.devicePixelRatio = window.devicePixelRatio > 1 ? window.devicePixelRatio : 1;
-}
-async function dataFromCustomVariants(tk, block) {
-  const data = {
-    // these holder will contain subset of tk.custom_variants[] that are in view range
-    skewer: [],
-    // for non-cnv data
-    cnv: {
-      cnvs: []
-      // for cnv segments
-    }
-    // adds mclass2variantcount[] later
-  };
-  let bbstart = null, bbstop;
-  for (let i = block.startidx; i <= block.stopidx; i++) {
-    if (bbstart == null) {
-      bbstart = block.rglst[i].start;
-      bbstop = block.rglst[i].stop;
-    } else {
-      bbstart = Math.min(bbstart, block.rglst[i].start);
-      bbstop = Math.max(bbstop, block.rglst[i].stop);
-    }
-  }
-  for (const m of tk.custom_variants) {
-    if (tk.legend?.bcfInfo) {
-      let skip = false;
-      for (const infoKey in tk.legend.bcfInfo) {
-        if (tk.legend.bcfInfo[infoKey].hiddenvalues?.size) {
-          const v = m.info?.[infoKey] || unannotatedKey;
-          if (tk.legend?.bcfInfo[infoKey].hiddenvalues.has(v)) {
-            skip = true;
-            break;
-          }
-        }
-      }
-      if (skip) continue;
-    }
-    if (m.dt == dtcnv) {
-      if (m.chr != block.rglst[0].chr) continue;
-      if (Math.max(m.start, bbstart) > Math.min(m.stop, bbstop)) continue;
-      data.cnv.cnvs.push(m);
-    } else if (m.dt == dtsnvindel || m.dt == dtsv || m.dt == dtfusionrna) {
-      if (m.chr != block.rglst[0].chr) continue;
-      if (m.pos <= bbstart || m.pos >= bbstop) continue;
-      if (!m.class) m.class = "X";
-      if (!mclass[m.class]) m.class = "X";
-      if (tk.legend?.mclass.hiddenvalues.has(m.class)) continue;
-      data.skewer.push(m);
-    } else {
-      throw "unknown custom data dt";
-    }
-  }
-  data.mclass2variantcount = summarize_mclass([...data.skewer, ...data.cnv.cnvs]);
-  if (data.cnv.cnvs.length == 0) delete data.cnv;
-  const set = /* @__PURE__ */ new Set();
-  if (data.skewer?.some((i) => i.samples)) {
-    for (const m of data.skewer) {
-      if (m.samples) {
-        for (const s of m.samples) set.add(s.sample_id);
-      }
-    }
-  }
-  if (data.cnv?.cnvs?.some((i) => i.samples)) {
-    for (const m of data.cnv.cnvs) {
-      if (m.samples) {
-        for (const s of m.samples) set.add(s.sample_id);
-      }
-    }
-  }
-  if (set.size) data.sampleTotalNumber = set.size;
-  await mayDoLDoverlay(tk, data.skewer);
-  return data;
-}
-async function mayDoLDoverlay(tk) {
-  if (!tk.mds.queries?.ld?.mOverlay) return;
-  if (!tk.mds.termdb?.vocabApi) return;
-  delete tk.mds.queries.ld.mOverlay.data;
-  const data = await tk.mds.termdb.vocabApi.getLDdata(tk.mds.queries.ld.mOverlay.ldtkname, tk.mds.queries.ld.mOverlay.m);
-  if (data.error || !Array.isArray(data.lst)) return;
-  tk.mds.queries.ld.mOverlay.data = data.lst;
-}
-
-export {
-  displaySampleTable,
-  getFilterName,
-  makelabel,
-  loadTk,
-  rangequery_rglst
-};
-//# sourceMappingURL=chunk-5ZICCKEH.js.map