@sjcrh/proteinpaint-client 2.190.2 → 2.191.0

package/dist/chunk-IYOGX7A4.js

@@ -0,0 +1,158 @@
+import {
+  NumericDensity
+} from "./chunk-WHI6466S.js";
+import {
+  HandlerBase
+} from "./chunk-LSEFWW72.js";
+import {
+  Tabs
+} from "./chunk-HBW42TDT.js";
+
+// termsetting/handlers/NumericHandler.ts
+var NumericHandler = class extends HandlerBase {
+  constructor(opts) {
+    super(opts);
+    this.tabs = [];
+    this.handlerByMode = {};
+    this.dom = {};
+    this.opts = opts;
+    this.termsetting = opts.termsetting;
+    this.tw = opts.termsetting.tw;
+    this.tabs = this.setTabData();
+    this.density = new NumericDensity(opts);
+  }
+  getPillStatus() {
+    this.tw = this.termsetting.tw;
+    return this.tw.getStatus(this.termsetting.usecase, this.termsetting.data);
+  }
+  setTabData() {
+    const self = this.termsetting;
+    const tabs = [];
+    const callback = async (event, tabData) => {
+      if (event) event.stopPropagation();
+      try {
+        await this.setEditHandler(tabData);
+        await this.editHandler.showEditMenu(tabData.contentHolder);
+      } catch (e) {
+        this.dom.errdiv.style("display", "").text(e);
+      }
+    };
+    const numTabs = self.opts.numericEditMenuVersion.length;
+    if (self.opts.numericEditMenuVersion.includes("continuous")) {
+      tabs.push({
+        mode: "continuous",
+        label: self.term.type == "survival" ? "Time to Event" : "Continuous",
+        callback,
+        active: this.tw.q.mode === "continuous" || numTabs === 1
+      });
+    }
+    if (self.opts.numericEditMenuVersion.includes("discrete")) {
+      tabs.push({
+        mode: "discrete",
+        label: self.term.type == "survival" ? "Exit code" : "Discrete",
+        callback,
+        active: this.tw.q.mode === "discrete" || numTabs === 1
+      });
+    }
+    if (self.opts.numericEditMenuVersion.includes("spline")) {
+      tabs.push({
+        mode: "spline",
+        label: "Cubic spline",
+        callback,
+        active: this.tw.q.mode === "spline" || numTabs === 1
+      });
+    }
+    if (self.opts.numericEditMenuVersion.includes("binary")) {
+      tabs.push({
+        mode: "binary",
+        label: "Binary",
+        callback,
+        active: this.tw.q.mode === "binary" || numTabs === 1
+      });
+    }
+    return tabs;
+  }
+  async setEditHandler(tabData) {
+    if (!this.handlerByMode[tabData.mode]) {
+      switch (tabData.mode) {
+        case "continuous": {
+          const { NumContEditor } = await import("./NumContEditor-Y4CDFJM2.js");
+          this.handlerByMode.continuous = new NumContEditor(this.opts, this);
+          break;
+        }
+        case "discrete": {
+          const { NumDiscreteEditor } = await import("./NumDiscreteEditor-RXXL3AQ4.js");
+          this.handlerByMode.discrete = new NumDiscreteEditor(this.opts, this);
+          break;
+        }
+        case "binary": {
+          const { NumBinaryEditor } = await import("./NumBinaryEditor-ENHACYTK.js");
+          this.handlerByMode.binary = new NumBinaryEditor(this.opts, this);
+          break;
+        }
+        case "spline": {
+          const { NumSplineEditor } = await import("./NumSplineEditor-33SUCGNJ.js");
+          this.handlerByMode.spline = new NumSplineEditor(this.opts, this);
+          break;
+        }
+        default:
+          throw `unexpected numeric tabData.mode='${tabData.mode}'`;
+          break;
+      }
+    }
+    this.editHandler = this.handlerByMode[tabData.mode];
+  }
+  async showEditMenu(div) {
+    try {
+      this.showLoading(div);
+      this.dom.errdiv = div.append("div").attr("class", "sja_errorbar").style("display", "none");
+      this.tw = this.termsetting.tw;
+      const self = this.tw;
+      for (const t of this.tabs) {
+        t.active = this.tabs.length === 1 || self.q.mode == t.mode || t.mode == "continuous" && !self.q.mode;
+      }
+      this.density_data = await this.density.setData();
+      await this.setEditHandler(this.tabs.find((t) => t.active));
+      this.dom.editDiv = div.append("div").attr("data-testid", "sjpp-num-ts-edit-div");
+      this.dom.btnDiv = div.append("div");
+      this.renderButtons(this.dom.btnDiv);
+      if (this.tabs.length > 1) {
+        this.dom.topBar = this.dom.editDiv.append("div").style("padding", "10px");
+        this.dom.topBar.append("span").html("Use as ");
+        new Tabs({
+          holder: this.dom.topBar.append("div").style("display", "inline-block"),
+          contentHolder: this.dom.editDiv.append("div"),
+          noTopContentStyle: true,
+          tabs: this.tabs
+        }).main();
+      } else {
+        await this.editHandler.showEditMenu(this.dom.editDiv);
+      }
+      this.dom.loadingDiv.style("display", "none");
+    } catch (e) {
+      this.hideLoading();
+      this.dom.errdiv.style("display", "").text(typeof e == "object" ? e.message || e.error || e : e);
+    }
+  }
+  renderButtons(btnDiv) {
+    btnDiv.append("button").style("margin", "5px").attr("data-testId", "sjpp_numeric_edit_apply").html("Apply").on("click", () => {
+      this.termsetting.q = this.editHandler.getEditedQ();
+      this.termsetting.dom.tip.hide();
+      this.termsetting.api.runCallback();
+    });
+    btnDiv.append("button").style("margin", "5px").attr("data-testId", "sjpp_numeric_edit_reset").html("Reset").on("click", () => {
+      this.editHandler.undoEdits();
+    });
+  }
+  destroy() {
+    for (const s of Object.values(this.dom)) {
+      if (typeof s.remove == "function") s.remove();
+    }
+    this.density.destroy();
+  }
+};
+
+export {
+  NumericHandler
+};
+//# sourceMappingURL=chunk-IYOGX7A4.js.map

package/dist/chunk-IYOGX7A4.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../termsetting/handlers/NumericHandler.ts"],
+  "sourcesContent": ["import { HandlerBase } from '../HandlerBase.ts'\nimport type { Handler } from '../index.ts'\nimport type { NumRegularBin, NumCustomBins, NumCont, NumSpline } from '#tw'\nimport { Tabs } from '#dom'\nimport { NumericDensity } from './NumericDensity.ts'\nimport type { NumContEditor } from './NumContEditor'\nimport type { NumDiscreteEditor } from './NumDiscreteEditor'\nimport type { NumBinaryEditor } from './NumBinaryEditor'\nimport type { NumSplineEditor } from './NumSplineEditor'\n\ntype NumericTabCallback = (event: PointerEvent, tab: TabData) => void\n\ntype TabData = {\n\tmode: 'continuous' | 'discrete' | 'binary' | 'spline'\n\tlabel: string\n\tcallback: NumericTabCallback\n\tcontentHolder?: any //\n\tactive?: boolean\n}\n\n/*\n\tNumericHandler \n\t- NumericDensity\n\t- NumericDiscrete\n\t\t - NumRegularBinEditor\n\t\t - NumCustomBinEditor\n*/\n\ntype EditHandler = NumContEditor | NumDiscreteEditor | NumBinaryEditor | NumSplineEditor\n\nexport class NumericHandler extends HandlerBase implements Handler {\n\topts: any // TODO\n\ttw: NumRegularBin | NumCustomBins | NumCont | NumSpline\n\ttabs: TabData[] = []\n\thandlerByMode: {\n\t\t[twType: string]: EditHandler\n\t} = {}\n\teditHandler!: EditHandler\n\ttoggleBtns!: Tabs\n\n\tdom: {\n\t\t[name: string]: any\n\t} = {}\n\n\tdensity: NumericDensity\n\tdensity_data!: any\n\n\tconstructor(opts) {\n\t\tsuper(opts)\n\t\tthis.opts = opts\n\t\tthis.termsetting = opts.termsetting\n\t\tthis.tw = opts.termsetting.tw\n\t\tthis.tabs = this.setTabData()\n\t\tthis.density = new NumericDensity(opts)\n\t}\n\n\tgetPillStatus() {\n\t\tthis.tw = this.termsetting.tw as NumRegularBin | NumCustomBins | NumCont | NumSpline // TODO: do not force type\n\t\treturn this.tw.getStatus(this.termsetting.usecase, this.termsetting.data)\n\t}\n\n\tsetTabData() {\n\t\tconst self = this.termsetting\n\t\tconst tabs: TabData[] = []\n\t\tconst callback = async (event, tabData) => {\n\t\t\tif (event) event.stopPropagation()\n\t\t\ttry {\n\t\t\t\tawait this.setEditHandler(tabData)\n\t\t\t\t//this.dom.editDiv.selectAll('*').remove()\n\t\t\t\tawait this.editHandler.showEditMenu(tabData.contentHolder) //this.dom.editDiv)\n\t\t\t} catch (e) {\n\t\t\t\tthis.dom.errdiv.style('display', '').text(e)\n\t\t\t}\n\t\t}\n\n\t\tconst numTabs = self.opts.numericEditMenuVersion.length\n\t\tif (self.opts.numericEditMenuVersion.includes('continuous')) {\n\t\t\ttabs.push({\n\t\t\t\tmode: 'continuous',\n\t\t\t\tlabel: self.term.type == 'survival' ? 'Time to Event' : 'Continuous',\n\t\t\t\tcallback,\n\t\t\t\tactive: this.tw.q.mode === 'continuous' || numTabs === 1\n\t\t\t})\n\t\t}\n\n\t\tif (self.opts.numericEditMenuVersion.includes('discrete')) {\n\t\t\ttabs.push({\n\t\t\t\tmode: 'discrete',\n\t\t\t\tlabel: self.term.type == 'survival' ? 'Exit code' : 'Discrete',\n\t\t\t\tcallback,\n\t\t\t\tactive: this.tw.q.mode === 'discrete' || numTabs === 1\n\t\t\t})\n\t\t}\n\n\t\tif (self.opts.numericEditMenuVersion.includes('spline')) {\n\t\t\ttabs.push({\n\t\t\t\tmode: 'spline',\n\t\t\t\tlabel: 'Cubic spline',\n\t\t\t\tcallback,\n\t\t\t\tactive: this.tw.q.mode === 'spline' || numTabs === 1\n\t\t\t})\n\t\t}\n\n\t\tif (self.opts.numericEditMenuVersion.includes('binary')) {\n\t\t\ttabs.push({\n\t\t\t\tmode: 'binary',\n\t\t\t\tlabel: 'Binary',\n\t\t\t\tcallback,\n\t\t\t\tactive: this.tw.q.mode === 'binary' || numTabs === 1\n\t\t\t})\n\t\t}\n\n\t\treturn tabs\n\t}\n\n\tasync setEditHandler(tabData) {\n\t\tif (!this.handlerByMode[tabData.mode]) {\n\t\t\tswitch (tabData.mode) {\n\t\t\t\tcase 'continuous': {\n\t\t\t\t\tconst { NumContEditor } = await import('./NumContEditor.ts')\n\t\t\t\t\tthis.handlerByMode.continuous = new NumContEditor(this.opts, this)\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t\tcase 'discrete': {\n\t\t\t\t\tconst { NumDiscreteEditor } = await import('./NumDiscreteEditor.ts')\n\t\t\t\t\tthis.handlerByMode.discrete = new NumDiscreteEditor(this.opts, this)\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t\tcase 'binary': {\n\t\t\t\t\tconst { NumBinaryEditor } = await import('./NumBinaryEditor.ts')\n\t\t\t\t\tthis.handlerByMode.binary = new NumBinaryEditor(this.opts, this)\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t\tcase 'spline': {\n\t\t\t\t\tconst { NumSplineEditor } = await import('./NumSplineEditor.ts')\n\t\t\t\t\tthis.handlerByMode.spline = new NumSplineEditor(this.opts, this)\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t\tdefault:\n\t\t\t\t\tthrow `unexpected numeric tabData.mode='${tabData.mode}'`\n\t\t\t\t\tbreak\n\t\t\t}\n\t\t}\n\t\tthis.editHandler = this.handlerByMode[tabData.mode]\n\t}\n\n\tasync showEditMenu(div) {\n\t\ttry {\n\t\t\tthis.showLoading(div)\n\t\t\tthis.dom.errdiv = div.append('div').attr('class', 'sja_errorbar').style('display', 'none')\n\t\t\tthis.tw = this.termsetting.tw as NumRegularBin | NumCustomBins | NumCont | NumSpline // TODO: do not force type\n\n\t\t\tconst self = this.tw\n\t\t\tfor (const t of this.tabs) {\n\t\t\t\tt.active = this.tabs.length === 1 || self.q.mode == t.mode || (t.mode == 'continuous' && !self.q.mode)\n\t\t\t}\n\n\t\t\tthis.density_data = await this.density.setData()\n\t\t\tawait this.setEditHandler(this.tabs.find(t => t.active))\n\t\t\tthis.dom.editDiv = div.append('div').attr('data-testid', 'sjpp-num-ts-edit-div')\n\t\t\tthis.dom.btnDiv = div.append('div')\n\t\t\tthis.renderButtons(this.dom.btnDiv)\n\n\t\t\tif (this.tabs.length > 1) {\n\t\t\t\tthis.dom.topBar = this.dom.editDiv.append('div').style('padding', '10px')\n\t\t\t\tthis.dom.topBar.append('span').html('Use as ')\n\t\t\t\tnew Tabs({\n\t\t\t\t\tholder: this.dom.topBar.append('div').style('display', 'inline-block'),\n\t\t\t\t\tcontentHolder: this.dom.editDiv.append('div'),\n\t\t\t\t\tnoTopContentStyle: true,\n\t\t\t\t\ttabs: this.tabs\n\t\t\t\t}).main()\n\t\t\t} else {\n\t\t\t\tawait this.editHandler.showEditMenu(this.dom.editDiv)\n\t\t\t}\n\n\t\t\tthis.dom.loadingDiv.style('display', 'none')\n\t\t} catch (e: any) {\n\t\t\tthis.hideLoading()\n\t\t\tthis.dom.errdiv.style('display', '').text(typeof e == 'object' ? e.message || e.error || e : e)\n\t\t}\n\t}\n\n\trenderButtons(btnDiv) {\n\t\tbtnDiv\n\t\t\t.append('button')\n\t\t\t.style('margin', '5px')\n\t\t\t.attr('data-testId', 'sjpp_numeric_edit_apply')\n\t\t\t.html('Apply')\n\t\t\t.on('click', () => {\n\t\t\t\tthis.termsetting.q = this.editHandler.getEditedQ()\n\t\t\t\tthis.termsetting.dom.tip.hide()\n\t\t\t\tthis.termsetting.api.runCallback()\n\t\t\t})\n\n\t\tbtnDiv\n\t\t\t.append('button')\n\t\t\t.style('margin', '5px')\n\t\t\t.attr('data-testId', 'sjpp_numeric_edit_reset')\n\t\t\t.html('Reset')\n\t\t\t.on('click', () => {\n\t\t\t\tthis.editHandler.undoEdits()\n\t\t\t})\n\t}\n\n\tdestroy() {\n\t\tfor (const s of Object.values(this.dom)) {\n\t\t\tif (typeof s.remove == 'function') s.remove()\n\t\t}\n\t\tthis.density.destroy()\n\t}\n}\n"],
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+  "names": []
+}

package/dist/chunk-J5SV3MFB.js

@@ -0,0 +1,217 @@
+import {
+  dofetch,
+  dofetch2
+} from "./chunk-H5BIGL3W.js";
+import {
+  contigNameNoChr2
+} from "./chunk-EBKERML3.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-J5SV3MFB.js.map

package/dist/chunk-J7X5JRRI.js

@@ -0,0 +1,276 @@
+import {
+  parsesample
+} from "./chunk-H5BIGL3W.js";
+import {
+  dtfusionrna,
+  dtsv,
+  mclassfusionrna,
+  mclasssv
+} from "./chunk-EBKERML3.js";
+
+// ../shared/utils/dist/src/bulk.sv.js
+function parseheader(line, flag, issv) {
+  const header = line.toLowerCase().split("	");
+  if (header.length <= 1) return "invalid file header for fusions";
+  const htry = (...lst) => {
+    for (const a of lst) {
+      const j = header.indexOf(a);
+      if (j != -1) return j;
+    }
+    return -1;
+  };
+  let i = htry("gene_a", "gene1", "genea");
+  if (i == -1) return "gene_a missing from header";
+  header[i] = "gene1";
+  i = htry("gene_b", "gene2", "geneb");
+  if (i == -1) return "gene_b missing from header";
+  header[i] = "gene2";
+  i = htry("chr_a", "chr1", "chra");
+  if (i == -1) return "chr_a missing from header";
+  header[i] = "chr1";
+  i = htry("chr_b", "chr2", "chrb");
+  if (i == -1) return "chr_b missing from header";
+  header[i] = "chr2";
+  i = htry("pos_a", "position_a", "position1", "posa");
+  if (i == -1) return "pos_a missing from header";
+  header[i] = "position1";
+  i = htry("pos_b", "position_b", "position2", "posb");
+  if (i == -1) return "pos_b missing from header";
+  header[i] = "position2";
+  i = htry("isoform_a", "refseq_a", "refseq1", "isoform1", "sv_refseqa");
+  if (i == -1) return "isoform_a missing from header";
+  header[i] = "isoform1";
+  i = htry("isoform_b", "refseq_b", "refseq2", "isoform2", "sv_refseqb");
+  if (i == -1) return "isoform_b missing from header";
+  header[i] = "isoform2";
+  i = htry("strand_a", "orta");
+  if (i == -1) return "strand_a missing from header";
+  header[i] = "strand1";
+  i = htry("strand_b", "ortb");
+  if (i == -1) return "strand_b missing from header";
+  header[i] = "strand2";
+  i = htry("sample", "sample_name", "tumor_sample_barcode");
+  if (i != -1) header[i] = "sample";
+  i = htry("patient", "donor", "target_case_id");
+  if (i != -1) header[i] = "patient";
+  i = htry("sampletype", "sample type", "sample_type");
+  if (i != -1) header[i] = "sampletype";
+  i = htry("disease");
+  if (i != -1) header[i] = "disease";
+  i = htry("origin");
+  if (i != -1) header[i] = "origin";
+  if (issv) {
+    flag.sv.loaded = true;
+    flag.sv.header = header;
+  } else {
+    flag.fusion.loaded = true;
+    flag.fusion.header = header;
+  }
+  return false;
+}
+function parseline(i, line, flag, issv) {
+  if (line == "" || line[0] == "#") return;
+  const lst = line.split("	");
+  const m = {};
+  const header = issv ? flag.sv.header : flag.fusion.header;
+  const badlines = issv ? flag.sv.badlines : flag.fusion.badlines;
+  for (let j = 0; j < header.length; j++) {
+    m[header[j]] = lst[j];
+  }
+  if (!m.chr1) {
+    badlines.push([i, "missing chr1", lst]);
+    return;
+  }
+  if (m.chr1.toLowerCase().indexOf("chr") != 0) {
+    m.chr1 = "chr" + m.chr1;
+  }
+  if (!m.chr2) {
+    badlines.push([i, "missing chr2", lst]);
+    return;
+  }
+  if (m.chr2.toLowerCase().indexOf("chr") != 0) {
+    m.chr2 = "chr" + m.chr2;
+  }
+  let v = m.position1;
+  if (!v) {
+    badlines.push([i, "missing position1", lst]);
+    return;
+  }
+  let v2 = Number.parseInt(v);
+  if (Number.isNaN(v2) || v2 <= 0) {
+    badlines.push([i, "invalid value for position1", lst]);
+    return;
+  }
+  m.position1 = v2;
+  v = m.position2;
+  if (!v) {
+    badlines.push([i, "missing position2", lst]);
+    return;
+  }
+  v2 = Number.parseInt(v);
+  if (Number.isNaN(v2) || v2 <= 0) {
+    badlines.push([i, "invalid value for position2", lst]);
+    return;
+  }
+  m.position2 = v2;
+  if (parsesample(m, flag, i, lst)) {
+    return;
+  }
+  if (m.isoform1 && m.isoform1.indexOf(",") != -1) {
+    const lst2 = m.isoform1.split(",");
+    m.isoform1 = void 0;
+    for (const t of lst2) {
+      if (t != "") m.isoform1 = t;
+    }
+  }
+  if (m.isoform2 && m.isoform2.indexOf(",") != -1) {
+    const lst2 = m.isoform2.split(",");
+    m.isoform2 = void 0;
+    for (const t of lst2) {
+      if (t != "") m.isoform2 = t;
+    }
+  }
+  if (!m.gene1) {
+    m.isoform1 = void 0;
+  }
+  if (!m.gene2) {
+    m.isoform2 = void 0;
+  }
+  if (m.gene1) {
+    flag.good++;
+    const m2 = {
+      dt: issv ? dtsv : dtfusionrna,
+      class: issv ? mclasssv : mclassfusionrna,
+      isoform: m.isoform1,
+      mname: m.gene2 || m.chr2,
+      sample: m.sample,
+      patient: m.patient,
+      sampletype: m.sampletype,
+      origin: m.origin,
+      disease: m.disease,
+      pairlst: [
+        {
+          a: {
+            name: m.gene1,
+            isoform: m.isoform1,
+            strand: m.strand1,
+            chr: m.chr1,
+            position: m.position1
+          },
+          b: {
+            name: m.gene2,
+            isoform: m.isoform2,
+            strand: m.strand2,
+            chr: m.chr2,
+            position: m.position2
+          }
+        }
+      ]
+    };
+    const n = flag.geneToUpper ? m.gene1.toUpperCase() : m.gene1;
+    if (!flag.data[n]) {
+      flag.data[n] = [];
+    }
+    flag.data[n].push(m2);
+  }
+  if (m.gene2 && m.gene2 != m.gene1) {
+    flag.good++;
+    const m2 = {
+      dt: issv ? dtsv : dtfusionrna,
+      class: issv ? mclasssv : mclassfusionrna,
+      isoform: m.isoform2,
+      mname: m.gene1 || m.chr1,
+      sample: m.sample,
+      patient: m.patient,
+      sampletype: m.sampletype,
+      origin: m.origin,
+      disease: m.disease,
+      pairlst: [
+        {
+          a: {
+            name: m.gene1,
+            isoform: m.isoform1,
+            strand: m.strand1,
+            chr: m.chr1,
+            position: m.position1
+          },
+          b: {
+            name: m.gene2,
+            isoform: m.isoform2,
+            strand: m.strand2,
+            chr: m.chr2,
+            position: m.position2
+          }
+        }
+      ]
+    };
+    const n = flag.geneToUpper ? m.gene2.toUpperCase() : m.gene2;
+    if (!flag.data[n]) {
+      flag.data[n] = [];
+    }
+    flag.data[n].push(m2);
+  }
+}
+function duplicate(m) {
+  const n = {};
+  for (const k in m) {
+    if (k == "pairlst") continue;
+    const v = m[k];
+    const type = typeof v;
+    if (type == "object") {
+      continue;
+    }
+    n[k] = v;
+  }
+  if (m.pairlst) {
+    n.pairlst = [];
+    for (const pair of m.pairlst) {
+      const p = {};
+      for (const k in pair) {
+        if (k == "a" || k == "b" || k == "interstitial") {
+          continue;
+        }
+        p[k] = pair[k];
+      }
+      if (pair.a) {
+        p.a = {};
+        for (const k in pair.a) {
+          const v = pair.a[k];
+          if (typeof v == "object") {
+            continue;
+          }
+          p.a[k] = v;
+        }
+      }
+      if (pair.b) {
+        p.b = {};
+        for (const k in pair.b) {
+          const v = pair.b[k];
+          if (typeof v == "object") {
+            continue;
+          }
+          p.b[k] = v;
+        }
+      }
+      if (pair.interstitial) {
+        p.interstitial = {};
+        for (const k in pair.interstitial) {
+          const v = pair.interstitial[k];
+          if (typeof v == "object") {
+            continue;
+          }
+          p.interstitial[k] = v;
+        }
+      }
+      n.pairlst.push(p);
+    }
+  }
+  return n;
+}
+
+export {
+  parseheader,
+  parseline,
+  duplicate
+};
+//# sourceMappingURL=chunk-J7X5JRRI.js.map