@sjcrh/proteinpaint-client 2.226.0 → 2.227.0

package/dist/chunk-HKR5R5YR.js

@@ -1,466 +0,0 @@
-import {
-  mayRunSnplstTask
-} from "./chunk-7OYOC7XY.js";
-import {
-  escapeHtml
-} from "./chunk-DPWSIN62.js";
-
-// termsetting/handlers/snplst.ts
-function getHandler(self) {
-  return {
-    getPillName() {
-      return escapeHtml(self.term.name);
-    },
-    getPillStatus() {
-      if (!self.term?.snps) return;
-      const invalid = self.term.snps.reduce((i, j) => i + (j.invalid || !j.alleles ? 1 : 0), 0);
-      if (invalid) return { text: invalid + " invalid" };
-    },
-    validateQ(data) {
-      validateQ(data);
-    },
-    async showEditMenu(div) {
-      await makeEditMenu(self, div);
-    }
-  };
-}
-async function makeEditMenu(self, div0) {
-  const div = div0.append("div").style("margin", "15px");
-  const select_ancestry = await mayRestrictAncestry(self, div);
-  const inputUIholder = div.append("div");
-  const textarea = inputUIholder.append("textarea").attr("rows", 5).attr("cols", 20).attr("placeholder", "Enter variants");
-  const prompt = inputUIholder.append("div").style("opacity", 0.8).style("font-size", ".8em");
-  prompt.append("div").html(
-    `Enter a list of variants (dbSNP accessions). One variant per line. Max 500 allowed.${self.usecase.target == "dataDownload" ? "" : "<br>Effect alleles (alleles tested against in the analysis) can be specified here or<br>after variant validation."}`
-  );
-  const exampleInput = [
-    { id: "rs1641548", effectAllele: "T" },
-    { id: "rs4968204", effectAllele: "C" },
-    { id: "rs9893249", effectAllele: "T" },
-    { id: "rs1042522", effectAllele: "G" }
-  ];
-  const example1 = prompt.append("ul").style("display", "inline-block").style("list-style-type", "none").style("padding", "0px");
-  const example2 = prompt.append("ul").style("display", self.usecase.target == "dataDownload" ? "none" : "inline-block").style("list-style-type", "none").style("padding", "0px").style("margin-left", "40px");
-  example1.append("li").style("text-decoration", "underline").text("Example:");
-  example2.append("li").style("text-decoration", "underline").text("Example (with effect alleles):");
-  for (const variant of exampleInput) {
-    example1.append("li").text(variant.id);
-    example2.append("li").html(`${variant.id}&nbsp;${variant.effectAllele}`);
-  }
-  const validateBtn = inputUIholder.append("div").style("margin-top", "15px").append("button").text("Validate variants").on("click", async () => {
-    const snps = parseSnpFromText(textarea);
-    if (!snps.length) return window.alert("No valid variants");
-    if (!self.term) {
-      self.term = { id: makeId(), type: "snplst" };
-    }
-    if (self.term.snps) {
-      for (const n of snps) {
-        if (self.term.snps.find((i) => i.rsid == n.rsid)) continue;
-        self.term.snps.push(n);
-      }
-    } else {
-      self.term.snps = snps;
-    }
-    self.term.name = getTermName(self.term.snps);
-    if (!self.q) self.q = {};
-    self.doNotHideTipInMain = true;
-    if (self.dom.pill_termname) {
-      self.dom.pill_termname.text(self.term.name);
-    }
-    validateBtn.text("Validating...").property("disabled", true);
-    try {
-      await validateInput(self);
-    } catch (e) {
-      alert("Error: " + (e.message || e));
-      validateBtn.text("Validate variants").property("disabled", false);
-      return;
-    }
-    if (!Number.isFinite(self.q.AFcutoff)) {
-      self.q.AFcutoff = 5;
-      input_AFcutoff.property("value", self.q.AFcutoff);
-    }
-    if (!Number.isInteger(self.q.alleleType)) {
-      self.q.alleleType = snps.find((snp) => snp.effectAllele) ? 2 : 0;
-      select_alleleType.property("selectedIndex", self.q.alleleType);
-      div.select(".sjpp-allele-type-hint").text(getAlleleTypeHint(select_alleleType));
-    }
-    if (!Number.isInteger(self.q.geneticModel)) {
-      self.q.geneticModel = 0;
-      select_geneticModel.property("selectedIndex", self.q.geneticModel);
-    }
-    if (!Number.isInteger(self.q.missingGenotype)) {
-      self.q.missingGenotype = 0;
-      select_missingGenotype.property("selectedIndex", self.q.missingGenotype);
-    }
-    if (select_ancestry) {
-      self.q.restrictAncestry = select_ancestry.node().options[select_ancestry.property("selectedIndex")].__ancestry_obj;
-    }
-    await makeSampleSummary(self);
-    inputUIholder.style("display", "none");
-    editUIholder.style("display", "");
-    if (self.dom.snplst_table) {
-      renderSnpEditTable(self, select_alleleType);
-    } else {
-      initSnpEditTable(snplstTableDiv, self, select_alleleType);
-    }
-  });
-  const editUIholder = div.append("div");
-  editUIholder.append("p").append("span").html("&laquo; Back to input").attr("class", "sja_clbtext").on("click", () => {
-    inputUIholder.style("display", "");
-    editUIholder.style("display", "none");
-    validateBtn.text("Validate variants").property("disabled", false);
-  });
-  const snplstTableDiv = editUIholder.append("div").style("margin-bottom", "25px");
-  const [input_AFcutoff, select_alleleType, select_geneticModel, select_missingGenotype] = makeSnpSelect(
-    editUIholder.append("div").attr("class", "sjpp-snp-select"),
-    self,
-    "snplst"
-  );
-  if (self.usecase.target == "dataDownload") editUIholder.select(".sjpp-snp-select").style("display", "none");
-  const btnRow = editUIholder.append("div").style("margin-top", "20px");
-  btnRow.append("button").text("Submit").on("click", async () => {
-    self.term.snps = self.term.snps.filter((i) => !i.tobe_deleted);
-    if (self.term.snps.find((snp) => !snp.effectAllele))
-      return window.alert("Effect allele not specified for one or more variants");
-    self.term.name = getTermName(self.term.snps);
-    if (self.dom.pill_termname) {
-      self.dom.pill_termname.text(self.term.name);
-    }
-    try {
-      await validateInput(self);
-    } catch (e) {
-      alert("Error: " + (e.message || e));
-    }
-    {
-      const v = Number(input_AFcutoff.property("value"));
-      self.q.AFcutoff = v < 0 || v >= 100 ? 5 : v;
-    }
-    self.q.alleleType = select_alleleType.property("selectedIndex");
-    self.q.geneticModel = select_geneticModel.property("selectedIndex");
-    self.q.missingGenotype = select_missingGenotype.property("selectedIndex");
-    if (select_ancestry) {
-      self.q.restrictAncestry = select_ancestry.node().options[select_ancestry.property("selectedIndex")].__ancestry_obj;
-    }
-    await makeSampleSummary(self);
-    if (self.dom.snplst_table) {
-      renderSnpEditTable(self, select_alleleType);
-    } else {
-      initSnpEditTable(snplstTableDiv, self, select_alleleType);
-    }
-    delete self.doNotHideTipInMain;
-    self.api.runCallback();
-    self.view.updateUI();
-  });
-  btnRow.append("span").style("padding-left", "15px").style("opacity", 0.8).style("font-size", ".8em").text(
-    self.usecase.target == "dataDownload" ? "" : "Variants will be treated as separate covariates in the regression model"
-  );
-  if (self.term?.snps?.length) {
-    initSnpEditTable(snplstTableDiv, self, select_alleleType);
-    inputUIholder.style("display", "none");
-  } else {
-    editUIholder.style("display", "none");
-  }
-}
-function initSnpEditTable(div, self, select_alleleType) {
-  self.dom.snplst_table = div.append("table");
-  renderSnpEditTable(self, select_alleleType);
-  div.append("p").style("opacity", 0.8).style("font-size", ".8em").style("display", self.usecase.target == "dataDownload" ? "none" : "block").html("Effect alleles are highlighted in red. Click on an allele to set as the effect allele.");
-}
-function renderSnpEditTable(self, select_alleleType) {
-  self.dom.snplst_table.selectAll("*").remove();
-  const title_tr = self.dom.snplst_table.append("tr").style("opacity", 0.4);
-  const col_titles = [
-    { title: "Variants" },
-    { title: "# genotyped<br>samples" },
-    { title: "Reference allele<br>(frequency)" },
-    { title: "Alternative allele(s)<br>(frequency)" },
-    { title: "Genotype<br>(frequency)" },
-    { title: "Delete" }
-  ];
-  if (self.usecase.target == "dataDownload") col_titles.splice(4, 1);
-  col_titles.forEach((c) => {
-    title_tr.append("td").html(c.title).style("font-size", ".8em").style("text-align", "center").style("padding", "8px");
-  });
-  if (!self.term.snps) throw `Missing term.snps [snplst.ts renderSnpEditTable()]`;
-  for (const [i, snp] of self.term.snps.entries()) {
-    let invalid_snp = false;
-    if (snp.invalid || !snp.alleles && !snp.gt2count) invalid_snp = "NOT ANNNOTATED IN COHORT";
-    const rowcolor = (i + 2) % 2 ? "#eee" : "#fff";
-    const tr = self.dom.snplst_table.append("tr").style("background", rowcolor);
-    tr.append("td").text(snp.rsid).style("padding", "8px");
-    const sample_count = invalid_snp ? invalid_snp : snp.gt2count ? Object.values(snp.gt2count).reduce((a, b) => a + b, 0) : `Missing sample count for snp`;
-    tr.append("td").style("text-align", "center").text(sample_count);
-    const ref_allele_td = tr.append("td");
-    const alt_allele_td = tr.append("td");
-    if (!invalid_snp) {
-      if (!snp.alleles) throw `Missing alleles for snp = ${snp} [snplst.ts renderSnpEditTable()]`;
-      const effectAllele = self.q.snp2effAle ? self.q.snp2effAle[snp.rsid] : void 0;
-      const refAllele = snp.alleles.find((s) => s.isRef);
-      const altAlleles = snp.alleles.filter((s) => !s.isRef);
-      if (self.usecase.target == "dataDownload") {
-        const allele_freq = (refAllele.count * 100 / (sample_count * 2)).toFixed(2);
-        const refAlleleText = `${refAllele.allele} (${allele_freq}%)`;
-        ref_allele_td.style("text-align", "center").style("padding", "8px").text(refAlleleText);
-        const altAllelesText = altAlleles.map((al) => {
-          const allele_freq2 = (al.count * 100 / (sample_count * 2)).toFixed(2);
-          return `${al.allele} (${allele_freq2}%)`;
-        }).join(", ");
-        alt_allele_td.style("text-align", "center").style("padding", "8px").text(altAllelesText);
-      } else {
-        createAlleleBtn(refAllele, ref_allele_td, effectAllele, sample_count, snp, rowcolor, tr);
-        for (const al of altAlleles.values()) {
-          createAlleleBtn(al, alt_allele_td, effectAllele, sample_count, snp, rowcolor, tr);
-        }
-      }
-    }
-    if (self.usecase.target != "dataDownload") {
-      const gt_td = tr.append("td");
-      if (!invalid_snp) {
-        const refGT = self.q.snp2refGrp ? self.q.snp2refGrp[snp.rsid] : void 0;
-        if (!snp.gt2count) throw `Missing gt2count for snp = ${snp} [snplst.ts renderSnpEditTable()]`;
-        for (const [gt, freq] of Object.entries(snp.gt2count)) {
-          const gt_freq = (freq * 100 / sample_count).toFixed(2);
-          const gt_div = gt_td.append("div").style("display", "inline-block").style("border", gt == refGT ? "3px solid #ff0000" : `3px solid ${rowcolor}`);
-          gt_div.append("div").style("display", "inline-block").style("padding", "3px 5px").text(`${gt}`);
-          gt_div.append("div").style("display", "inline-block").style("padding", "0px 6px 0px 2px").style("font-size", ".8em").text(`(${gt_freq}%)`);
-        }
-      }
-    }
-    const snp_checkbox = tr.append("td").style("text-align", "center").append("input").attr("type", "checkbox").on("change", () => {
-      snp.tobe_deleted = snp_checkbox.node().checked;
-    });
-  }
-  function createAlleleBtn(al, td, effectAllele, sample_count, snp, rowcolor, tr) {
-    const allele_freq = (al.count * 100 / (sample_count * 2)).toFixed(2);
-    const allele_div = td.style("text-align", "center").append("button").style("display", "inline-block").style("margin", "0px 3px").style("padding", "3px 7px").style("border-radius", "3px").style("background-color", "#d9ead3").style("border", al.allele == effectAllele ? "3px solid #ff0000" : `3px solid ${rowcolor}`).on("mouseover", () => {
-      if (snp.effectAllele && snp.effectAllele == al.allele) return;
-      else {
-        allele_div.style("background-color", "#fff2cc").style("cursor", "pointer");
-      }
-    }).on("mouseout", () => {
-      if (snp.effectAllele && snp.effectAllele == al.allele) return;
-      else {
-        allele_div.style("background", "#d9ead3");
-      }
-    }).on("click", () => {
-      snp.effectAllele = al.allele;
-      tr.selectAll("button").style("border", "none");
-      allele_div.style("border", "3px solid #ff0000").style("background", "#d9ead3");
-      select_alleleType.selectAll("option").nodes()[2].selected = "selected";
-    });
-    allele_div.append("div").style("display", "inline-block").text(`${al.allele}  `);
-    allele_div.append("div").style("display", "inline-block").style("margin", "0px 5px").style("font-size", ".8em").text(`(${allele_freq}%)`);
-  }
-}
-function getTermName(snps) {
-  if (snps.length == 1) {
-    const s = snps[0];
-    if (s.rsid) return s.rsid;
-    return s.chr + ":" + s.pos;
-  }
-  return snps.length + " variant" + (snps.length > 1 ? "s" : "");
-}
-function parseSnpFromText(textarea) {
-  const text = textarea.property("value");
-  const snps = [];
-  for (const tmp of text.trim().split("\n")) {
-    const [rsid, ale] = tmp.trim().split(/[\s\t]/);
-    if (!rsid) continue;
-    if (snps.find((i) => i.rsid == rsid)) continue;
-    const s = { rsid };
-    if (ale) s.effectAllele = ale;
-    snps.push(s);
-  }
-  if (snps.length > 500) return snps.slice(0, 500);
-  return snps;
-}
-function snp2text(self) {
-  if (!self.term || !self.term.snps) return "";
-  const lines = [];
-  for (const a of self.term.snps) {
-    const l = a.rsid + (a.effectAllele ? " " + a.effectAllele : "");
-    lines.push(l);
-  }
-  return lines.join("\n");
-}
-async function validateInput(self) {
-  const data = await self.vocabApi.validateSnps({ text: snp2text(self) });
-  if (data.error) throw data.error;
-  self.q.cacheid = data.cacheid;
-  if (!self.term.snps) throw `Missing term.snps [snplst.ts validateInput()]`;
-  for (const [i, s] of self.term.snps.entries()) {
-    const s1 = data.snps[i];
-    s.snpid = s1.snpid;
-    s.invalid = s1.invalid;
-  }
-}
-async function makeSampleSummary(self) {
-  const body = { cacheid: self.q.cacheid };
-  const extraFilters = [];
-  let f;
-  if (self.q.restrictAncestry) {
-    if (self.filter) {
-      f = structuredClone(self.filter);
-      const idx = f.lst.findIndex((i) => i.tvs?.term?.id == self.q.restrictAncestry.tvs.term.id);
-      if (idx != -1) {
-        f.lst[idx] = { type: "tvs", tvs: self.q.restrictAncestry.tvs };
-      } else {
-        extraFilters.push({ type: "tvs", tvs: self.q.restrictAncestry.tvs });
-      }
-    } else {
-      extraFilters.push({ type: "tvs", tvs: self.q.restrictAncestry.tvs });
-    }
-  } else {
-    if (self.filter) extraFilters.push(self.filter);
-  }
-  const filter = { type: "tvslst", join: "and", lst: [...extraFilters] };
-  if (f) filter.lst.push(f);
-  const data = await self.vocabApi.getCategories(self.term, filter, body);
-  mayRunSnplstTask(
-    {
-      term: self.term,
-      q: self.q
-    },
-    //quick fix for $id being required in BaseTw type
-    data
-  );
-}
-function validateQ(data) {
-  if (!Number.isFinite(data.q.AFcutoff)) throw "AFcutoff is not number";
-  if (data.q.AFcutoff < 0 || data.q.AFcutoff > 100) throw "AFcutoff is not within 0 to 100";
-  if (![0, 1, 2].includes(data.q.alleleType)) throw "alleleType value is not one of 0/1";
-  if (![0, 1, 2, 3].includes(data.q.geneticModel)) throw "geneticModel value is not one of 0/1";
-  if (![0, 1].includes(data.q.missingGenotype)) throw "missingGenotype value is not one of 0/1";
-}
-async function fillTW(tw, vocabApi) {
-  try {
-    validateQ(tw);
-  } catch (e) {
-    throw "snplst validateQ(): " + e;
-  }
-  if (!Array.isArray(tw.term.snps)) throw "tw.term.snps[] is not an array";
-  if (tw.term.snps.length == 0) throw "tw.term.snps[] array is 0 length";
-  if (!tw.term.name) tw.term.name = getTermName(tw.term.snps);
-  if (tw.id == void 0 || tw.id == "") {
-    if (tw.term.id == void 0 || tw.term.id == "") {
-      tw.term.id = makeId();
-    }
-    tw.id = tw.term.id;
-  } else {
-    if (tw.term.id == void 0 || tw.term.id == "") {
-      tw.term.id = tw.id;
-    }
-  }
-  await validateInput({
-    term: tw.term,
-    q: tw.q,
-    vocabApi
-  });
-}
-function makeId() {
-  return "snplst" + Math.random();
-}
-function makeSnpSelect(div, self, termtype) {
-  let input_AFcutoff_label, input_AFcutoff, select_missingGenotype;
-  {
-    input_AFcutoff_label = div.append("div").style("opacity", 0.5).style("font-size", ".8em").style("margin-bottom", "2px").text("EFFECT ALLELE FREQUENCY CUTOFF");
-    self.dom.input_AFcutoff_label = input_AFcutoff_label;
-    const row = div.append("div");
-    input_AFcutoff = row.append("input").attr("type", "number").attr("min", 0).attr("max", 100).property("value", 5).style("border-color", "#858585").style("margin", "0px");
-    row.append("span").text("%");
-    let text;
-    if (termtype == "snplst") {
-      text = "Variants below this cutoff are discarded";
-    } else {
-      if (self.usecase.regressionType == "linear") {
-        text = "Variants below this cutoff are analyzed by the Wilcoxon rank sum test";
-      } else if (self.usecase.regressionType == "logistic") {
-        text = "Variants below this cutoff are analyzed by the Fisher's exact test";
-      } else {
-        text = "Variants below this cutoff are analyzed by the cumulative incidence test";
-      }
-    }
-    row.append("span").style("margin-left", "10px").style("opacity", 0.5).style("font-size", ".7em").style("font-style", "italic").text(text);
-  }
-  div.append("div").style("margin-top", "15px").style("opacity", 0.5).style("font-size", ".8em").style("margin-bottom", "2px").text("SET EFFECT ALLELE AS");
-  const select_alleleType = div.append("select");
-  select_alleleType.append("option").text("Minor allele");
-  select_alleleType.append("option").text("Alternative allele");
-  if (termtype !== "snplocus") {
-    select_alleleType.append("option").text("Custom allele");
-  }
-  div.append("div").attr("class", "sjpp-allele-type-hint").style("display", "inline-block").style("margin-left", "15px").style("opacity", 0.5).style("font-size", ".7em").style("font-style", "italic").text(getAlleleTypeHint(select_alleleType));
-  select_alleleType.on("change", async () => {
-    div.select(".sjpp-allele-type-hint").text(getAlleleTypeHint(select_alleleType));
-    self.q.alleleType = select_alleleType.property("selectedIndex");
-    if (termtype !== "snplocus") {
-      if (!self.term.snps) throw `Missing term.snps [snplst.ts makeSnpSelect()]`;
-      for (const snp of self.term.snps) {
-        snp.effectAllele = false;
-      }
-      await makeSampleSummary(self);
-      renderSnpEditTable(self, select_alleleType);
-    }
-  });
-  div.append("div").style("margin-top", "15px").style("margin-bottom", "2px").style("opacity", 0.5).style("font-size", ".8em").text("GENETIC MODEL");
-  const select_geneticModel = div.append("select");
-  select_geneticModel.append("option").text("Additive: EE=2, EN=1, NN=0");
-  select_geneticModel.append("option").text("Dominant: EE=1, EN=1, NN=0");
-  select_geneticModel.append("option").text("Recessive: EE=1, EN=0, NN=0");
-  select_geneticModel.append("option").text("By genotype: EE and EN compared to NN");
-  div.append("div").style("display", "inline-block").style("margin-left", "15px").style("opacity", 0.5).style("font-size", ".7em").style("font-style", "italic").html("E = effect allele; N = non-effect allele");
-  const missingGenotypeLabel = div.append("div").style("margin-top", "15px").style("opacity", 0.5).style("font-size", ".7em");
-  if (termtype == "snplocus") {
-    missingGenotypeLabel.text("Samples with missing genotypes are dropped.");
-  } else {
-    missingGenotypeLabel.text("MISSING GENOTYPE").style("font-size", ".8em").style("margin-bottom", "2px");
-    select_missingGenotype = div.append("select");
-    select_missingGenotype.append("option").text("Impute as homozygous for non-effect allele");
-    select_missingGenotype.append("option").text("Drop sample");
-  }
-  if (Number.isInteger(self.q?.alleleType)) select_alleleType.property("selectedIndex", self.q.alleleType);
-  if (Number.isFinite(self.q?.AFcutoff)) input_AFcutoff.property("value", self.q.AFcutoff);
-  if (Number.isInteger(self.q?.geneticModel)) select_geneticModel.property("selectedIndex", self.q.geneticModel);
-  if (select_missingGenotype && Number.isInteger(self.q?.missingGenotype))
-    select_missingGenotype.property("selectedIndex", self.q.missingGenotype);
-  return [input_AFcutoff, select_alleleType, select_geneticModel, select_missingGenotype];
-}
-async function mayRestrictAncestry(self, holder) {
-  if (self.q?.doNotRestrictAncestry) return;
-  const tdbcfg = await self.vocabApi.getTermdbConfig();
-  if (!tdbcfg.restrictAncestries) return;
-  const row = holder.append("div").style("margin-bottom", "15px");
-  self.dom.restrictAncestriesRow = row;
-  row.append("span").text("Restrict analysis to").style("margin-right", "5px").style("opacity", 0.5);
-  const select = row.append("select");
-  for (const ancestry of tdbcfg.restrictAncestries) {
-    const opt = select.append("option").text(ancestry.name);
-    opt.node().__ancestry_obj = ancestry;
-  }
-  if (self.q && self.q.restrictAncestry) {
-    const i = tdbcfg.restrictAncestries.findIndex((i2) => i2.name == self.q.restrictAncestry.name);
-    if (i == -1) throw "unknown restrictAncestry: " + self.q.restrictAncestry.name;
-    select.property("selectedIndex", i);
-  }
-  return select;
-}
-function getAlleleTypeHint(select_alleleType) {
-  let hint;
-  const i = select_alleleType.property("selectedIndex");
-  if (i == 0) {
-    hint = "For multi-allelic variants, the second most common allele is used as the effect allele";
-  } else if (i == 1) {
-    hint = "For multi-allelic variants, the most common alternative allele is used as the effect allele";
-  } else {
-    hint = "";
-  }
-  return hint;
-}
-
-export {
-  getHandler,
-  fillTW,
-  makeSnpSelect,
-  mayRestrictAncestry
-};
-//# sourceMappingURL=chunk-HKR5R5YR.js.map

package/dist/chunk-HULTLO4D.js

@@ -1,217 +0,0 @@
-import {
-  dofetch,
-  dofetch2
-} from "./chunk-6V7ITU5F.js";
-import {
-  contigNameNoChr2
-} from "./chunk-2N345NXD.js";
-
-// tracks/hic/data/parseData.ts
-async function hicParseFile(hic, debugmode, errList = []) {
-  if (debugmode) window["hic"] = hic;
-  if (hic.tklst) {
-    const lst = [];
-    for (const t of hic.tklst) {
-      if (!t.type) {
-        errList.push("type missing from one of the tracks accompanying HiC");
-      } else {
-        t.iscustom = true;
-        lst.push(t);
-      }
-    }
-    if (lst.length) {
-      hic.tklst = lst;
-    } else {
-      delete hic.tklst;
-    }
-  }
-  if (hic.enzyme) {
-    if (hic.genome.hicenzymefragment) {
-      let frag = null;
-      for (const f of hic.genome.hicenzymefragment) {
-        if (f.enzyme == hic.enzyme) {
-          frag = f;
-          break;
-        }
-      }
-      if (frag) {
-        hic.enzymefile = frag.file;
-      } else {
-        errList.push("unknown enzyme: " + hic.enzyme);
-        delete hic.enzyme;
-      }
-    } else {
-      errList.push("no enzyme fragment information available for this genome");
-      delete hic.enzyme;
-    }
-  }
-  try {
-    if (hic.sv && hic.sv.file) {
-      const re = await dofetch(hic.hostURL + "/textfile", {
-        method: "POST",
-        body: JSON.stringify({ file: hic.sv.file, jwt: hic.jwt })
-      });
-      const data2 = re.json();
-      const [err2, header, items] = parseSV(data2.text);
-      if (err2) throw { message: "Error parsing SV: " + err2 };
-      hic.sv.header = header;
-      hic.sv.items = items;
-    }
-    const data = await dofetch2("hicstat?" + (hic.file ? "file=" + hic.file : "url=" + hic.url));
-    if (data.error) {
-      errList.push(data.error);
-      return;
-    }
-    const err = hicparsestat(hic, data.out);
-    if (err) throw { message: err };
-  } catch (err) {
-    errList.push(err.message || err);
-    if (err.stack) {
-      console.log(err.stack);
-    }
-  }
-  return hic;
-}
-function parseSV(txt) {
-  const lines = txt.trim().split(/\r?\n/);
-  const [err, header] = parseSVheader(lines[0]);
-  if (err) return ["header error: " + err];
-  const items = [];
-  for (let i = 1; i < lines.length; i++) {
-    const line = lines[i];
-    if (line[0] == "#") continue;
-    const [e, m] = parseSVline(line, header);
-    if (e) return ["line " + (i + 1) + " error: " + e];
-    items.push(m);
-  }
-  return [null, header, items];
-}
-function parseSVheader(line) {
-  const header = line.toLowerCase().split("	");
-  if (header.length <= 1) return "invalid file header for fusions";
-  const htry = (...lst) => {
-    for (const a of lst) {
-      const j = header.indexOf(a);
-      if (j != -1) return j;
-    }
-    return -1;
-  };
-  let i = htry("chr_a", "chr1", "chra");
-  if (i == -1) return "chr_A missing from header";
-  header[i] = "chr1";
-  i = htry("chr_b", "chr2", "chrb");
-  if (i == -1) return "chr_B missing from header";
-  header[i] = "chr2";
-  i = htry("pos_a", "position_a", "position1", "posa");
-  if (i == -1) return "pos_a missing from header";
-  header[i] = "position1";
-  i = htry("pos_b", "position_b", "position2", "posb");
-  if (i == -1) return "pos_b missing from header";
-  header[i] = "position2";
-  i = htry("strand_a", "orta", "orienta");
-  if (i == -1) return "strand_a missing from header";
-  header[i] = "strand1";
-  i = htry("strand_b", "ortb", "orientb");
-  if (i == -1) return "strand_b missing from header";
-  header[i] = "strand2";
-  i = htry("numreadsa");
-  if (i != -1) header[i] = "reads1";
-  i = htry("numreadsb");
-  if (i != -1) header[i] = "reads2";
-  return [null, header];
-}
-function parseSVline(line, header) {
-  const lst = line.split("	");
-  const m = {};
-  for (let j = 0; j < header.length; j++) {
-    m[header[j]] = lst[j];
-  }
-  if (!m.chr1) return ["missing chr1"];
-  if (m.chr1.toLowerCase().indexOf("chr") != 0) {
-    m.chr1 = "chr" + m.chr1;
-  }
-  if (!m.chr2) return ["missing chr2"];
-  if (m.chr2.toLowerCase().indexOf("chr") != 0) {
-    m.chr2 = "chr" + m.chr2;
-  }
-  if (!m.position1) return ["missing position1"];
-  let v = Number.parseInt(m.position1);
-  if (Number.isNaN(v) || v <= 0) return ["position1 invalid value"];
-  m.position1 = v;
-  if (!m.position2) return ["missing position2"];
-  v = Number.parseInt(m.position2);
-  if (Number.isNaN(v) || v <= 0) return ["position2 invalid value"];
-  m.position2 = v;
-  if (m.reads1) {
-    v = Number.parseInt(m.reads1);
-    if (Number.isNaN(v)) return ["reads1 invalid value"];
-    m.reads1 = v;
-  }
-  if (m.reads2) {
-    v = Number.parseInt(m.reads2);
-    if (Number.isNaN(v)) return ["reads2 invalid value"];
-    m.reads2 = v;
-  }
-  return [null, m];
-}
-function hicparsestat(hic, j) {
-  if (!j) return "cannot stat hic file";
-  hic.normalization = j.normalization;
-  hic.version = j.version;
-  if (!j.Chromosomes) return "Chromosomes not found in file stat";
-  if (!Array.isArray(j.chrorder)) return ".chrorder[] missing";
-  if (j.chrorder.length == 0) return ".chrorder[] empty array";
-  hic.chrorder = j.chrorder;
-  if (!j["Base pair-delimited resolutions"]) return "Base pair-delimited resolutions not found in file stat";
-  if (!Array.isArray(j["Base pair-delimited resolutions"])) return "Base pair-delimited resolutions should be array";
-  hic.bpresolution = j["Base pair-delimited resolutions"];
-  if (!j["Fragment-delimited resolutions"]) return "Fragment-delimited resolutions not found in file stat";
-  if (!Array.isArray(j["Fragment-delimited resolutions"])) return "Fragment-delimited resolutions is not array";
-  hic.fragresolution = j["Fragment-delimited resolutions"];
-  const chrlst = [];
-  for (const chr in j.Chromosomes) {
-    chrlst.push(chr);
-  }
-  const [nochrcount, haschrcount] = contigNameNoChr2(hic.genome, chrlst);
-  if (nochrcount + haschrcount == 0) return "chromosome names do not match with genome build";
-  if (nochrcount > 0) {
-    hic.nochr = true;
-    for (let i = 0; i < hic.chrorder.length; i++) hic.chrorder[i] = "chr" + hic.chrorder[i];
-  }
-  hic.chrlst = [];
-  for (const chr of hic.genome.majorchrorder) {
-    const c2 = hic.nochr ? chr.replace("chr", "") : chr;
-    if (chrlst.indexOf(c2) != -1) {
-      hic.chrlst.push(chr);
-    }
-  }
-}
-function hicparsefragdata(items) {
-  const id2coord = /* @__PURE__ */ new Map();
-  let min = null, max;
-  for (const i of items) {
-    if (!i.rest || !i.rest[0]) {
-      return ["items[].rest data problem"];
-    }
-    const id = Number.parseInt(i.rest[0]);
-    if (Number.isNaN(id)) {
-      return [i.start + "." + i.stop + " invalid fragment id: " + i.rest[0]];
-    }
-    id2coord.set(id, [i.start, i.stop]);
-    if (min == null) {
-      min = id;
-      max = id;
-    } else {
-      min = Math.min(min, id);
-      max = Math.max(max, id);
-    }
-  }
-  return [null, id2coord, min, max];
-}
-
-export {
-  hicParseFile,
-  hicparsestat,
-  hicparsefragdata
-};
-//# sourceMappingURL=chunk-HULTLO4D.js.map