@sjcrh/proteinpaint-client 2.225.0 → 2.226.0

package/dist/svmr-6BDEZAS6.js

@@ -0,0 +1,3834 @@
+import {
+  appear2 as appear,
+  axisstyle,
+  bulk_badline,
+  colorbgleft,
+  colorbgright,
+  colorctx,
+  colorinframe,
+  coloroutframe,
+  disappear2 as disappear,
+  export_data,
+  font,
+  make_table_2col,
+  newpane,
+  sayerror
+} from "./chunk-DPWSIN62.js";
+import {
+  genomic2gm
+} from "./chunk-HJ6L54YS.js";
+import "./chunk-KZ54E2FU.js";
+import {
+  Menu
+} from "./chunk-CNFTQSNE.js";
+import "./chunk-DOC3HBOV.js";
+import "./chunk-TVJOSRCH.js";
+import "./chunk-3CIL7KH7.js";
+import "./chunk-T4XPCSLP.js";
+import "./chunk-6V7ITU5F.js";
+import "./chunk-W5J3LTYS.js";
+import "./chunk-KUOXZIH4.js";
+import "./chunk-T2W4JHWJ.js";
+import {
+  axisTop,
+  bplen,
+  dtcloss,
+  dtfusionrna,
+  dtitd,
+  dtnloss,
+  mclasscloss,
+  mclassfusionrna,
+  mclassitd,
+  mclassnloss
+} from "./chunk-2N345NXD.js";
+import "./chunk-HBNB5TRH.js";
+import "./chunk-PF4DSFDR.js";
+import {
+  linear
+} from "./chunk-4OLM3KSB.js";
+import "./chunk-PWYMHUXY.js";
+import "./chunk-TLT4YIG3.js";
+import "./chunk-5R63Q5KH.js";
+import {
+  select_default
+} from "./chunk-I6Y4O3RR.js";
+import "./chunk-Q5RDQNIT.js";
+import "./chunk-HS5PO5ZQ.js";
+
+// src/svmr.unload.js
+function svmr_export_json(svmr, hqonly) {
+  var rows = [];
+  for (const sample of svmr.samples) {
+    for (const egg of sample.egglst) {
+      for (const eg of egg.lst) {
+        if (eg.ismsg) {
+          const lst = eg.lst.map((evt) => evt.lst[0]);
+          if (hqonly) {
+            let hashq = false;
+            for (const i of lst) {
+              if (i.rating == "Major") hashq = true;
+            }
+            if (hashq) {
+              rows.push(lst);
+            }
+          } else {
+            rows.push(lst);
+          }
+        } else {
+          for (const evt of eg.lst) {
+            for (const p of evt.lst) {
+              if (hqonly) {
+                if (p.rating == "Major") rows.push([p]);
+              } else {
+                rows.push([p]);
+              }
+            }
+          }
+        }
+      }
+    }
+  }
+  const lines = [], e_itd = [], e_nloss = [], e_closs = [];
+  for (const row of rows) {
+    if (row.length == 1 && row[0].usepair) {
+      const p = row[0];
+      if (p.isitd) {
+        const u = p.usepair;
+        const gm = svmr.genome.isoformmatch(u.a.isoform, p.chrA, p.posA);
+        if (!gm) {
+          e_itd.push(p.sample + " " + p.geneA + " ITD (" + p.rating + "): no gene model found for " + u.a.isoform);
+          continue;
+        }
+        const exonbp1 = genomic2gm(p.posA, gm).rnapos;
+        const exonbp2 = genomic2gm(p.posB, gm).rnapos;
+        if (exonbp1 <= exonbp2) {
+          e_itd.push(p.sample + " " + p.geneA + " ITD (" + p.rating + "): negative duplication length");
+          continue;
+        }
+        const itd = {
+          typecode: dtitd,
+          gene: p.geneA,
+          isoform: u.a.isoform,
+          rating: p.rating,
+          score: p.score,
+          functioneffect: p.functioneffect,
+          rnaposition: exonbp2,
+          rnaduplength: exonbp1 - exonbp2 + 1,
+          a: {
+            chr: p.chrA,
+            position: p.posA,
+            strand: p.ortA,
+            ratio: p.ratioA,
+            chimericreads: p.readsA,
+            totalreads: p.totalreadsA,
+            match: p.matchA,
+            repeat: p.repeatA
+          },
+          b: {
+            chr: p.chrB,
+            position: p.posB,
+            strand: p.ortB,
+            ratio: p.ratioB,
+            chimericreads: p.readsB,
+            totalreads: p.totalreadsB,
+            match: p.matchB,
+            repeat: p.repeatB
+          }
+        };
+        let aalen = 0, bplen2 = 0;
+        if (u.a.contigaa && u.b.contigaa) {
+          aalen = u.b.contigaa - u.a.contigaa - 1;
+        }
+        if (u.a.contigbp && u.b.contigbp) {
+          bplen2 = u.b.contigbp - u.a.contigbp - 1;
+        }
+        if (aalen > 0) {
+          itd.interstitial = { aalen };
+        }
+        if (bplen2 > 0) {
+          if (!itd.interstitial) itd.interstitial = {};
+          itd.interstitial.bplen = bplen2;
+        }
+        lines.push([p.sample, p.geneA, p.usepair.a.isoform, JSON.stringify(itd)]);
+        continue;
+      }
+      if (p.isnloss) {
+        const p2 = p.usepair.b;
+        if (!p2.isoform) {
+          e_nloss.push(p.sample + " " + p.geneB + " NLoss (" + p.rating + "): no isoform");
+          continue;
+        }
+        const gm = svmr.genome.isoformmatch(p2.isoform, p.chrB, p.posB);
+        if (!gm) {
+          e_nloss.push(p.sample + " " + p.geneB + " NLoss (" + p.rating + "): no gene model found for " + p2.isoform);
+          continue;
+        }
+        const exonbp = genomic2gm(p.posB, gm).rnapos;
+        const pp = {
+          typecode: dtnloss,
+          gene: p.geneB,
+          isoform: p2.isoform,
+          rating: p.rating,
+          score: p.score,
+          functioneffect: p.functioneffect,
+          rnaposition: exonbp,
+          chr: p.chrB,
+          position: p.posB,
+          strand: p.ortB,
+          ratio: p.ratioB,
+          chimericreads: p.readsB,
+          match: p.matchB,
+          repeat: p.repeatB,
+          partner: {
+            chr: p.chrA,
+            position: p.posA,
+            strand: p.ortA,
+            ratio: p.ratioA,
+            chimericreads: p.readsA,
+            match: p.matchA,
+            repeat: p.repeatA
+          }
+        };
+        if (p.geneA) {
+          pp.partner.gene = p.geneA;
+        }
+        if (p.usepair.a.isoform) {
+          pp.partner.isoform = p.usepair.a.isoform;
+        }
+        lines.push([p.sample, p.geneB, p2.isoform, JSON.stringify(pp)]);
+        continue;
+      }
+      if (p.iscloss) {
+        const p2 = p.usepair.a;
+        if (!p2.isoform) {
+          e_nloss.push(p.sample + " " + p.geneA + " CLoss (" + p.rating + "): no isoform");
+          continue;
+        }
+        const gm = svmr.genome.isoformmatch(p2.isoform, p.chrA, p.posA);
+        if (!gm) {
+          e_nloss.push(p.sample + " " + p.geneA + " CLoss (" + p.rating + "): no gene model found by " + p2.isoform);
+          continue;
+        }
+        const exonbp = genomic2gm(p.posA, gm).rnapos;
+        const pp = {
+          typecode: dtcloss,
+          gene: p.geneA,
+          isoform: p2.isoform,
+          rating: p.rating,
+          score: p.score,
+          functioneffect: p.functioneffect,
+          rnaposition: exonbp,
+          chr: p.chrA,
+          position: p.posA,
+          strand: p.ortA,
+          ratio: p.ratioA,
+          chimericreads: p.readsA,
+          match: p.matchA,
+          repeat: p.repeatA,
+          partner: {
+            chr: p.chrB,
+            position: p.posB,
+            strand: p.ortB,
+            ratio: p.ratioB,
+            chimericreads: p.readsB,
+            match: p.matchB,
+            repeat: p.repeatB
+          }
+        };
+        if (p.geneB) {
+          pp.partner.gene = p.geneB;
+        }
+        if (p.usepair.b.isoform) {
+          pp.partner.isoform = p.usepair.b.isoform;
+        }
+        lines.push([p.sample, p.geneA, p2.isoform, JSON.stringify(pp)]);
+        continue;
+      }
+    }
+    const genes = /* @__PURE__ */ new Set(), isoforms = /* @__PURE__ */ new Set(), cleanup = [];
+    for (const p of row) {
+      if (p.geneA) genes.add(p.geneA);
+      if (p.geneB) genes.add(p.geneB);
+      if (p.usepair) {
+        if (p.usepair.a.isoform) isoforms.add(p.usepair.a.isoform);
+        if (p.usepair.b.isoform) isoforms.add(p.usepair.b.isoform);
+      }
+      const clean = {
+        type: p.type,
+        type2: p.type2,
+        rating: p.rating,
+        score: p.score,
+        functioneffect: p.functioneffect,
+        a: {
+          name: p.geneA,
+          chr: p.chrA,
+          position: p.posA,
+          strand: p.ortA,
+          ratio: p.ratioA,
+          feature: p.featureA,
+          chimericreads: p.readsA,
+          contiglen: p.matchA,
+          repeatscore: p.repeatA
+        },
+        b: {
+          name: p.geneB,
+          chr: p.chrB,
+          position: p.posB,
+          strand: p.ortB,
+          ratio: p.ratioB,
+          feature: p.featureB,
+          chimericreads: p.readsB,
+          contiglen: p.matchB,
+          repeatscore: p.repeatB
+        }
+      };
+      if (p.usepair) {
+        const u = p.usepair;
+        clean.frame = u.frame;
+        if (u.a.isoform) {
+          clean.a.isoform = u.a.isoform;
+        }
+        if (u.b.isoform) {
+          clean.b.isoform = u.b.isoform;
+        }
+        let aalen = 0, bplen2 = 0;
+        if (u.a.contigaa && u.b.contigaa) {
+          aalen = u.b.contigaa - u.a.contigaa - 1;
+        }
+        if (u.a.contigbp && u.b.contigbp) {
+          bplen2 = u.b.contigbp - u.a.contigbp - 1;
+        }
+        if (aalen > 0) {
+          clean.interstitial = { aalen };
+        }
+        if (bplen2 > 0) {
+          if (!clean.interstitial) clean.interstitial = {};
+          clean.interstitial.bplen = bplen2;
+        }
+      }
+      cleanup.push(clean);
+    }
+    const genenames = [...genes];
+    const isoformnames = [...isoforms];
+    lines.push([
+      row[0].sample,
+      genenames.length ? genenames.join(",") : "none",
+      isoformnames.length ? isoformnames.join(",") : "none",
+      JSON.stringify(cleanup)
+    ]);
+  }
+  if (e_itd.length) {
+    svmr.err(e_itd.join("<br>"));
+  }
+  if (e_nloss.length) {
+    svmr.err(e_nloss.join("<br>"));
+  }
+  if (e_closs.length) {
+    svmr.err(e_closs.join("<br>"));
+  }
+  export_data("Fusion data from " + svmr.filename, [{ text: lines.map((i) => i.join("	")).join("\n") }]);
+}
+function svmr_2pp(svmr, hqonly) {
+  const rows = [];
+  for (const sample of svmr.samples) {
+    for (const egg of sample.egglst) {
+      for (const eg of egg.lst) {
+        if (eg.ismsg) {
+          const lst = eg.lst.map((evt) => evt.lst[0]);
+          if (hqonly) {
+            let hashq = false;
+            for (const i of lst) {
+              if (i.rating == "Major") hashq = true;
+            }
+            if (hashq) {
+              rows.push(lst);
+            }
+          } else {
+            rows.push(lst);
+          }
+        } else {
+          for (const evt of eg.lst) {
+            for (const p of evt.lst) {
+              if (hqonly) {
+                if (p.rating == "Major") rows.push([p]);
+              } else {
+                rows.push([p]);
+              }
+            }
+          }
+        }
+      }
+    }
+  }
+  const genes = {}, e_itd = [], e_nloss = [], e_closs = [];
+  for (const row of rows) {
+    if (row.length == 1 && row[0].usepair) {
+      const p = row[0];
+      if (p.isitd) {
+        if (!p.geneA) {
+          e_itd.push(p.sample + " ITD (" + p.rating + "): no gene name??");
+          continue;
+        }
+        const u = p.usepair;
+        const gm = svmr.genome.isoformmatch(u.a.isoform, p.chrA, p.posA);
+        if (!gm) {
+          e_itd.push(p.sample + " " + p.geneA + " ITD (" + p.rating + "): no gene model found for " + u.a.isoform);
+          continue;
+        }
+        const exonbp1 = genomic2gm(p.posA, gm).rnapos;
+        const exonbp2 = genomic2gm(p.posB, gm).rnapos;
+        if (exonbp1 <= exonbp2) {
+          e_itd.push(p.sample + " " + p.geneA + " ITD (" + p.rating + "): negative duplication length");
+          continue;
+        }
+        const itd = {
+          dt: dtitd,
+          class: mclassitd,
+          mname: "ITD",
+          gene: p.geneA,
+          sample: p.sample,
+          isoform: u.a.isoform,
+          rating: p.rating,
+          score: p.score,
+          functioneffect: p.functioneffect,
+          rnaposition: exonbp2,
+          rnaduplength: exonbp1 - exonbp2 + 1,
+          a: {
+            chr: p.chrA,
+            position: p.posA,
+            strand: p.ortA,
+            ratio: p.ratioA,
+            chimericreads: p.readsA,
+            totalreads: p.totalreadsA,
+            match: p.matchA,
+            repeat: p.repeatA
+          },
+          b: {
+            chr: p.chrB,
+            position: p.posB,
+            strand: p.ortB,
+            ratio: p.ratioB,
+            chimericreads: p.readsB,
+            totalreads: p.totalreadsB,
+            match: p.matchB,
+            repeat: p.repeatB
+          }
+        };
+        let aalen = 0, bplen2 = 0;
+        if (u.a.contigaa && u.b.contigaa) {
+          aalen = u.b.contigaa - u.a.contigaa - 1;
+        }
+        if (u.a.contigbp && u.b.contigbp) {
+          bplen2 = u.b.contigbp - u.a.contigbp - 1;
+        }
+        if (aalen > 0) {
+          itd.interstitial = { aalen };
+        }
+        if (bplen2 > 0) {
+          if (!itd.interstitial) itd.interstitial = {};
+          itd.interstitial.bplen = bplen2;
+        }
+        if (!(p.geneA in genes)) {
+          genes[p.geneA] = [];
+        }
+        genes[p.geneA].push(itd);
+        continue;
+      }
+      if (p.isnloss) {
+        if (!p.geneB) {
+          e_nloss.push(p.sample + " NLoss (" + p.rating + "): no geneB");
+          continue;
+        }
+        const p2 = p.usepair.b;
+        if (!p2.isoform) {
+          e_nloss.push(p.sample + " " + p.geneB + " NLoss (" + p.rating + "): no isoform");
+          continue;
+        }
+        const gm = svmr.genome.isoformmatch(p2.isoform, p.chrB, p.posB);
+        if (!gm) {
+          e_nloss.push(p.sample + " " + p.geneB + " NLoss (" + p.rating + "): no gene model found for " + p2.isoform);
+          continue;
+        }
+        const exonbp = genomic2gm(p.posB, gm).rnapos;
+        const pp = {
+          dt: dtnloss,
+          class: mclassnloss,
+          mname: "N-loss",
+          gene: p.geneB,
+          sample: p.sample,
+          isoform: p2.isoform,
+          rating: p.rating,
+          score: p.score,
+          functioneffect: p.functioneffect,
+          rnaposition: exonbp,
+          chr: p.chrB,
+          position: p.posB,
+          strand: p.ortB,
+          ratio: p.ratioB,
+          chimericreads: p.readsB,
+          match: p.matchB,
+          repeat: p.repeatB,
+          partner: {
+            chr: p.chrA,
+            position: p.posA,
+            strand: p.ortA,
+            ratio: p.ratioA,
+            chimericreads: p.readsA,
+            match: p.matchA,
+            repeat: p.repeatA
+          }
+        };
+        if (p.geneA) {
+          pp.partner.gene = p.geneA;
+        }
+        if (p.usepair.a.isoform) {
+          pp.partner.isoform = p.usepair.a.isoform;
+        }
+        if (!(p.geneB in genes)) {
+          genes[p.geneB] = [];
+        }
+        genes[p.geneB].push(pp);
+        continue;
+      }
+      if (p.iscloss) {
+        if (!p.geneA) {
+          e_closs.push(p.sample + " CLoss (" + p.rating + "): no geneA");
+          continue;
+        }
+        const p2 = p.usepair.a;
+        if (!p2.isoform) {
+          e_closs.push(p.sample + " " + p.geneA + " CLoss (" + p.rating + "): no isoform");
+          continue;
+        }
+        const gm = svmr.genome.isoformmatch(p2.isoform, p.chrA, p.posA);
+        if (!gm) {
+          e_closs.push(p.sample + " " + p.geneA + " CLoss (" + p.rating + "): no gene model found by " + p2.isoform);
+          continue;
+        }
+        const exonbp = genomic2gm(p.posA, gm).rnapos;
+        const pp = {
+          dt: dtcloss,
+          class: mclasscloss,
+          mname: "C-loss",
+          gene: p.geneA,
+          sample: p.sample,
+          isoform: p2.isoform,
+          rating: p.rating,
+          score: p.score,
+          functioneffect: p.functioneffect,
+          rnaposition: exonbp,
+          chr: p.chrA,
+          position: p.posA,
+          strand: p.ortA,
+          ratio: p.ratioA,
+          chimericreads: p.readsA,
+          match: p.matchA,
+          repeat: p.repeatA,
+          partner: {
+            chr: p.chrB,
+            position: p.posB,
+            strand: p.ortB,
+            ratio: p.ratioB,
+            chimericreads: p.readsB,
+            match: p.matchB,
+            repeat: p.repeatB
+          }
+        };
+        if (p.geneB) {
+          pp.partner.gene = p.geneB;
+        }
+        if (p.usepair.b.isoform) {
+          pp.partner.isoform = p.usepair.b.isoform;
+        }
+        if (!(p.geneA in genes)) {
+          genes[p.geneA] = [];
+        }
+        genes[p.geneA].push(pp);
+        continue;
+      }
+    }
+    const gene2isoform = /* @__PURE__ */ new Map();
+    const cleanup = [];
+    for (const p of row) {
+      if (p.geneA) {
+        if (!gene2isoform.has(p.geneA)) gene2isoform.set(p.geneA, /* @__PURE__ */ new Set());
+        if (p.usepair) {
+          if (p.usepair.a.isoform) gene2isoform.get(p.geneA).add(p.usepair.a.isoform);
+        }
+      }
+      if (p.geneB) {
+        if (!gene2isoform.has(p.geneB)) gene2isoform.set(p.geneB, /* @__PURE__ */ new Set());
+        if (p.usepair) {
+          if (p.usepair.b.isoform) gene2isoform.get(p.geneB).add(p.usepair.b.isoform);
+        }
+      }
+      const clean = {
+        type: p.type,
+        type2: p.type2,
+        rating: p.rating,
+        score: p.score,
+        functioneffect: p.functioneffect,
+        a: {
+          name: p.geneA,
+          chr: p.chrA,
+          position: p.posA,
+          strand: p.ortA,
+          ratio: p.ratioA,
+          feature: p.featureA,
+          chimericreads: p.readsA,
+          contiglen: p.matchA,
+          repeatscore: p.repeatA
+        },
+        b: {
+          name: p.geneB,
+          chr: p.chrB,
+          position: p.posB,
+          strand: p.ortB,
+          ratio: p.ratioB,
+          feature: p.featureB,
+          chimericreads: p.readsB,
+          contiglen: p.matchB,
+          repeatscore: p.repeatB
+        }
+      };
+      if (p.usepair) {
+        const u = p.usepair;
+        clean.frame = u.frame;
+        if (u.a.isoform) {
+          clean.a.isoform = u.a.isoform;
+        }
+        if (u.b.isoform) {
+          clean.b.isoform = u.b.isoform;
+        }
+        let aalen = 0, bplen2 = 0;
+        if (u.a.contigaa && u.b.contigaa) {
+          aalen = u.b.contigaa - u.a.contigaa - 1;
+        }
+        if (u.a.contigbp && u.b.contigbp) {
+          bplen2 = u.b.contigbp - u.a.contigbp - 1;
+        }
+        if (aalen > 0) {
+          clean.interstitial = { aalen };
+        }
+        if (bplen2 > 0) {
+          if (!clean.interstitial) clean.interstitial = {};
+          clean.interstitial.bplen = bplen2;
+        }
+      }
+      cleanup.push(clean);
+    }
+    for (const [genename, iset] of gene2isoform) {
+      for (const isoform of iset) {
+        if (!(genename in genes)) {
+          genes[genename] = [];
+        }
+        const pp = {
+          dt: dtfusionrna,
+          class: mclassfusionrna,
+          sample: row[0].sample,
+          isoform,
+          pairlst: duplicate(cleanup)
+        };
+        for (const i of cleanup) {
+          if (i.functioneffect) {
+            pp.functioneffect = i.functioneffect;
+          }
+        }
+        genes[genename].push(pp);
+      }
+    }
+  }
+  if (e_itd.length) {
+    svmr.err(e_itd.join("<br>"));
+  }
+  if (e_nloss.length) {
+    svmr.err(e_nloss.join("<br>"));
+  }
+  if (e_closs.length) {
+    svmr.err(e_closs.join("<br>"));
+  }
+  let genecount = 0, genesup = {};
+  for (const k in genes) {
+    genecount++;
+    genesup[k.toUpperCase()] = genes[k];
+  }
+  if (genecount == 0) {
+    alert("No data can be added.");
+    return;
+  }
+  let ds = null;
+  for (const n in svmr.genome.datasets) {
+    if (svmr.genome.datasets[n].svmrid == svmr.id) {
+      ds = svmr.genome.datasets[n];
+      break;
+    }
+  }
+  if (ds) {
+    ds.bulkdata = genesup;
+  } else {
+    ds = {
+      label: svmr.filename,
+      svmrid: svmr.id,
+      bulkdata: genesup
+    };
+    svmr.genome.datasets[svmr.filename] = ds;
+  }
+  if (svmr.cohort) {
+    svmr.cohortpane.pane.remove();
+  } else {
+    svmr.cohort = {
+      name: svmr.filename,
+      genome: svmr.genome,
+      show_genetable: 1,
+      jwt: svmr.jwt,
+      dsset: {}
+    };
+    svmr.cohort.dsset[svmr.filename] = ds;
+  }
+  const pane = newpane({ x: 200, y: 200 });
+  import("./tp.ui-M4TZVT53.js").then((p) => {
+    p.default(svmr.cohort, pane.body, svmr.hostURL);
+    svmr.cohortpane = pane;
+  });
+}
+function svmr_export_text(svmr, hqonly) {
+  const rows = [];
+  const headerlst = svmr.atlst.map((i) => i.label);
+  headerlst.push("transcript_nbr");
+  headerlst.push("breakpoint_nbr");
+  headerlst.push("functionalClass");
+  for (const sample of svmr.samples) {
+    const whole = [];
+    for (const egg of sample.egglst) {
+      for (const eg of egg.lst) {
+        if (eg.ismsg) {
+          const lst = eg.lst.map((evt) => evt.lst[0]);
+          if (hqonly) {
+            let hashq = false;
+            for (const i of lst) {
+              if (i.rating == "Major") hashq = true;
+            }
+            if (hashq) {
+              whole.push(lst);
+            }
+          } else {
+            whole.push(lst);
+          }
+        } else {
+          for (const evt of eg.lst) {
+            for (const p of evt.lst) {
+              if (hqonly) {
+                if (p.rating == "Major") whole.push([p]);
+              } else {
+                whole.push([p]);
+              }
+            }
+          }
+        }
+      }
+    }
+    for (let gid = 0; gid < whole.length; gid++) {
+      for (let prodid = 0; prodid < whole[gid].length; prodid++) {
+        let prod = whole[gid][prodid];
+        const frame = [], a_isoform = [], a_codon = [], a_exon = [], a_anchor = [], a_contigaa = [], a_contigbp = [], b_isoform = [], b_codon = [], b_exon = [], b_anchor = [], b_contigaa = [], b_contigbp = [];
+        for (const p of prod.pairs) {
+          frame.push(p.frame);
+          a_isoform.push(p.a.isoform);
+          b_isoform.push(p.b.isoform);
+          let v = p.a.codon;
+          a_codon.push(Number.isNaN(v) ? "" : v);
+          v = p.b.codon;
+          b_codon.push(Number.isNaN(v) ? "" : v);
+          v = p.a.exon;
+          a_exon.push(Number.isNaN(v) ? "" : v);
+          v = p.b.exon;
+          b_exon.push(Number.isNaN(v) ? "" : v);
+          a_anchor.push(p.a.anchor ? p.a.anchor : "");
+          b_anchor.push(p.b.anchor ? p.b.anchor : "");
+          v = p.a.contigaa;
+          a_contigaa.push(v == void 0 ? "" : v);
+          v = p.b.contigaa;
+          b_contigaa.push(v == void 0 ? "" : v);
+          v = p.a.contigbp;
+          a_contigbp.push(v == void 0 ? "" : v);
+          v = p.b.contigbp;
+          b_contigbp.push(v == void 0 ? "" : v);
+        }
+        const row = [];
+        for (const i of svmr.atlst) {
+          switch (i.key) {
+            case "lstframe":
+              row.push(frame.join(","));
+              break;
+            // A
+            case "lstisoforma":
+              row.push(a_isoform.join(","));
+              break;
+            case "lstisoformacodon":
+              row.push(a_codon.join(","));
+              break;
+            case "lstisoformaexon":
+              row.push(a_exon.join(","));
+              break;
+            case "lstisoformaanchor":
+              row.push(a_anchor.join(","));
+              break;
+            case "lstcontigaaA":
+              row.push(a_contigaa.join(","));
+              break;
+            case "lstcontigbpA":
+              row.push(a_contigbp.join(","));
+              break;
+            // B
+            case "lstisoformb":
+              row.push(b_isoform.join(","));
+              break;
+            case "lstisoformbcodon":
+              row.push(b_codon.join(","));
+              break;
+            case "lstisoformbexon":
+              row.push(b_exon.join(","));
+              break;
+            case "lstisoformbanchor":
+              row.push(b_anchor.join(","));
+              break;
+            case "lstcontigaaB":
+              row.push(b_contigaa.join(","));
+              break;
+            case "lstcontigbpB":
+              row.push(b_contigbp.join(","));
+              break;
+            default:
+              row.push(prod[i.key]);
+          }
+        }
+        row.push(gid + 1);
+        row.push(prodid + 1);
+        row.push(prod.functioneffect ? prod.functioneffect : "");
+        rows.push(row);
+      }
+    }
+  }
+  export_data("Fusion data from " + svmr.filename, [{ text: headerlst.join("	") + "\n" + rows.join("\n") }]);
+}
+function duplicate(i) {
+  const lst = [];
+  for (const j of i) {
+    const k = {};
+    for (const n in j) k[n] = j[n];
+    k.a = {};
+    for (const n in j.a) k.a[n] = j.a[n];
+    k.b = {};
+    for (const n in j.b) k.b[n] = j.b[n];
+    if (j.interstitial) {
+      k.interstitial = {};
+      for (const n in j.interstitial) k.interstitial[n] = j.interstitial[n];
+    }
+    lst.push(k);
+  }
+  return lst;
+}
+
+// src/svmr.c.js
+var genomelimit = 1e4;
+var knownprod_c = "#A702C4";
+var tip = new Menu();
+var svmr_c_default = class {
+  constructor(genome, atlst, items, filename, holder, hostURL, jwt) {
+    window.svmr = this;
+    this.hostURL = hostURL;
+    this.jwt = jwt;
+    this.id = Math.random();
+    this.items = items;
+    this.genome = genome;
+    this.filename = filename;
+    this.atlst = atlst;
+    this.cf_repeat = 0.7, this.cf_reads = 2;
+    this.cf_match = 40;
+    this.cf_ratio = 0.01;
+    this.expression = {};
+    this.samples = [];
+    this.genelst = [];
+    this.elab2sample = {};
+    if (!holder) {
+      const pane = newpane({ x: 100, y: 100, toshrink: true });
+      pane.header.append("span").style("color", "#858585").style("font-size", ".7em").html("Fusion Editor&nbsp;");
+      pane.header.append("span").text(filename);
+      holder = pane.body;
+    }
+    this.holder = holder;
+    this.errdiv = holder.append("div").style("width", "500px").style("margin", "10px");
+    const butrow = holder.append("div").style("margin", "20px").style("padding", "0px");
+    this.buttgene = butrow.append("button").text("Loading genes").on("click", () => {
+      if (genediv.style("display") == "none") {
+        appear(genediv);
+      } else {
+        disappear(genediv);
+      }
+    });
+    this.buttsample = butrow.append("button").text("Loading samples").on("click", () => {
+      if (this.ul.style("display") == "none") {
+        appear(this.ul);
+      } else {
+        disappear(this.ul);
+      }
+    });
+    butrow.append("button").text("Gene expression").on("click", () => {
+      if (this.expression.div.style("display") == "none") {
+        appear(this.expression.div);
+      } else {
+        disappear(this.expression.div);
+      }
+    });
+    butrow.append("button").text("Parameter cutoff").on("click", () => {
+      if (cutoffdiv.style("display") == "none") {
+        appear(cutoffdiv);
+      } else {
+        disappear(cutoffdiv);
+      }
+    });
+    butrow.append("button").text("Legend").on("click", () => {
+      if (legenddiv.style("display") == "none") {
+        appear(legenddiv);
+      } else {
+        disappear(legenddiv);
+      }
+    });
+    butrow.append("button").style("margin-right", "20px").text("Export data").on("click", (event) => {
+      let single_hq = 0, multi_hq = 0, single_nhq = 0, multi_nhq = 0, itd_hq = 0, itd_nhq = 0, trunc_hq = 0, trunc_nhq = 0;
+      for (const sample of this.samples) {
+        for (const egg of sample.egglst) {
+          for (const eg of egg.lst) {
+            if (eg.ismsg) {
+              let hashq = false;
+              for (const i of eg.lst) {
+                if (i.rating == "Major") hashq = true;
+              }
+              if (hashq) multi_hq++;
+              else multi_nhq++;
+            } else {
+              for (const evt of eg.lst) {
+                for (const p of evt.lst) {
+                  if (p.rating == "Major") {
+                    if (p.isitd) itd_hq++;
+                    else if (p.iscloss || p.isnloss) trunc_hq++;
+                    else single_hq++;
+                  } else {
+                    if (p.isitd) itd_nhq++;
+                    else if (p.iscloss || p.isnloss) trunc_nhq++;
+                    else single_nhq++;
+                  }
+                }
+              }
+            }
+          }
+        }
+      }
+      const d02 = tip.clear().showunder(event.target).d.append("div");
+      const table = d02.append("table").style("border-spacing", "10px").style("border-collapse", "separate");
+      let tr = table.append("tr").style("color", "#858585");
+      tr.append("td");
+      tr.append("td").text("2-gene fusion");
+      tr.append("td").text("Multi-gene fusion");
+      tr.append("td").text("ITD");
+      tr.append("td").text("Truncation");
+      tr = table.append("tr");
+      tr.append("td").text("Major").style("color", "#858585").style("text-align", "right");
+      tr.append("td").text(single_hq);
+      tr.append("td").text(multi_hq);
+      tr.append("td").text(itd_hq);
+      tr.append("td").text(trunc_hq);
+      tr = table.append("tr");
+      tr.append("td").text("not Major").style("color", "#858585").style("text-align", "right");
+      tr.append("td").text(single_nhq);
+      tr.append("td").text(multi_nhq);
+      tr.append("td").text(itd_nhq);
+      tr.append("td").text(trunc_nhq);
+      let dd = d02.append("div").style("margin", "10px").text('Export fusions labeled as "Major"');
+      dd.append("button").style("margin", "10px").text("Tabular format").on("click", () => svmr_export_text(this, true));
+      dd.append("button").style("margin", "10px").text("JSON format").on("click", () => svmr_export_json(this, true));
+      dd.append("button").style("margin", "10px").text("View in ProteinPaint").on("click", () => svmr_2pp(this, true));
+      dd = d02.append("div").style("margin", "10px").text("Export all fusions");
+      dd.append("button").style("margin", "10px").text("Tabular format").on("click", () => svmr_export_text(this, false));
+      dd.append("button").style("margin", "10px").text("JSON format").on("click", () => svmr_export_json(this, false));
+      dd.append("button").style("margin", "10px").text("View in ProteinPaint").on("click", () => svmr_2pp(this, false));
+    });
+    butrow.append("a").attr("target", "_blank").attr("href", "https://docs.google.com/document/d/1DRVzE_WenG490eRYB7VGFOygtSqtF5L97rhK0HOUCNY/edit?usp=sharing").text("Help");
+    this.expression.div = holder.append("div").style("display", "none").style("margin", "20px").style("padding", "20px").style("border", "dashed 1px #bbb");
+    this.expression.prediv = this.expression.div.append("div");
+    this.expression.prediv.append("div").style("margin", "5px").text("Load a file that includes gene expression data for current samples.");
+    this.expression.prediv.append("div").style("margin", "5px 5px 10px 5px").style("font-size", "80%").text("The first 3 columns of the file should be: 1) gene name, 2) expression value, 3) sample name");
+    this.expression.input = this.expression.prediv.append("input").attr("type", "file").on("change", (event) => {
+      loadexpression(this, event.target.files[0]);
+    });
+    this.expression.presays = this.expression.prediv.append("span").style("padding-left", "20px");
+    this.expression.afterdiv = this.expression.div.append("div").style("display", "none");
+    const genediv = holder.append("div").style("display", "none").style("margin", "20px");
+    let d0 = genediv.append("div").style("display", "inline-block").style("border", "dashed 1px #bbb");
+    this.genefilter = d0.append("div").style("background-color", "#ededed").style("padding", "10px 20px");
+    let d01 = d0.append("div").style("padding", "10px 20px").style("overflow-y", "scroll").style("resize", "vertical").style("height", "300px");
+    d01.append("div").style("margin", "10px").style("font-size", "70%").text("Not included: read-through and intergenic events (including one or both sides).");
+    this.genetable = d01.append("table");
+    const cutoffdiv = holder.append("div").style("display", "none").style("margin", "20px");
+    d0 = cutoffdiv.append("div").style("display", "inline-block").style("padding", "20px").style("border", "solid 1px #ededed");
+    d0.append("span").style("padding", "0px 10px").text("Alert if:");
+    d01 = d0.append("span").style("padding", "0px 10px");
+    d01.append("span").html("chimeric reads &le;&nbsp;");
+    d01.append("input").attr("size", 3).property("value", this.cf_reads).on("change", (event) => {
+      const v = Number.parseInt(event.target.value);
+      if (Number.isNaN(v)) {
+        return;
+      }
+      this.cf_reads = v;
+    });
+    d01 = d0.append("span").style("padding", "0px 10px");
+    d01.append("span").html("repeat score &ge;&nbsp;");
+    d01.append("input").attr("size", 3).property("value", this.cf_repeat).on("change", (event) => {
+      const v = Number.parseFloat(event.target.value);
+      if (Number.isNaN(v)) {
+        return;
+      }
+      this.cf_repeat = v;
+    });
+    d01 = d0.append("span").style("padding", "0px 10px");
+    d01.append("span").html("contig bp length &le;&nbsp;");
+    d01.append("input").attr("size", 3).property("value", this.cf_match).on("change", (event) => {
+      const v = Number.parseInt(event.target.value);
+      if (Number.isNaN(v)) {
+        return;
+      }
+      this.cf_match = v;
+    });
+    d01 = d0.append("span").style("padding", "0px 10px");
+    d01.append("span").html("ratio &le;&nbsp;");
+    d01.append("input").attr("size", 3).property("value", this.cf_ratio).on("change", (event) => {
+      const v = Number.parseFloat(event.target.value);
+      if (Number.isNaN(v)) {
+        return;
+      }
+      this.cf_ratio = v;
+    });
+    const legenddiv = holder.append("div").style("display", "none").style("margin", "20px");
+    var h = 16;
+    legenddiv.append("div").style("display", "inline-block").style("padding", "10px").style("border", "solid 1px #ededed").html(
+      '<table style="margin:20px"><tr><td><div style="display:inline-block;font-size:80%;color:white;background-color:' + colorinframe + ';padding:2px 5px">IN</div></td><td>In-frame fusion</td></tr><tr><td><div style="display:inline-block;font-size:80%;color:white;background-color:' + coloroutframe + ';padding:2px 5px">O</div></td><td>Out-of-frame fusion</td></tr><tr><td><div style="display:inline-block;font-size:80%;color:black;border:solid 1px black;padding:1px 3px">?</div></td><td>Intergenic fusion, or gene isoform not specified</td></tr></table><table style="margin:20px"><tr><td>chr5 <span style="border:solid 1px black;padding:0px 10px;"></span>-<span style="border:solid 1px black;padding:0px 10px;"></span> chr5</td><td>Intra-chromosomal breakpoints</td></tr><tr><td><span style="color:red">chr5</span> <span style="border:solid 1px black;padding:0px 10px;"></span>-<span style="border:solid 1px black;padding:0px 10px;"></span> <span style="color:red">chr10</span></td><td>Inter-chromosomal breakpoints</td></tr></tr></table><table style="margin:20px"><tr><td><div style="display:inline-block;border:solid 1px black;padding:2px 10px;font-size:70%">geneA</div>-<div style="display:inline-block;border:solid 1px black;padding:2px 10px;font-size:70%">geneB</div></td><td>Neither geneA nor geneB is known fusion partner</td></tr><tr><td><div style="display:inline-block;border:solid 1px black;padding:2px 10px;font-size:70%;font-weight:bold;">geneA</div>-<div style="display:inline-block;border:solid 1px black;padding:2px 10px;font-size:70%">geneB</div></td><td>GeneA is a known fusion partner</td></tr><tr><td><div style="display:inline-block;border:solid 1px black;padding:2px 10px;font-size:70%;font-weight:bold;">geneA</div>-<div style="display:inline-block;border:solid 1px black;padding:2px 10px;font-size:70%;font-weight:bold;">geneB</div></td><td>Both genes are known fusion partners, but they do not make a known fusion product.</td></tr><tr><td><div style="display:inline-block;border:solid 1px black;padding:2px 10px;font-size:70%;font-weight:bold;color:' + knownprod_c + '">geneA</div>-<div style="display:inline-block;border:solid 1px black;padding:2px 10px;font-size:70%;font-weight:bold;color:' + knownprod_c + '">geneB</div></td><td>A known fusion product</td></tr></table><table style="margin:20px"><tr><td><div style="width:40px;height:16px;position:relative;"><div style="position:absolute;right:0px;top:0px;width:20px;height:16px;background-color:' + colorbgleft + '"></div><div style="position:absolute;border:solid 1px black;width:100%;height:15px"></div></div></td><td>ratioA: for geneA, the ratio of chimeric reads over total reads</td></tr><tr><td><div style="width:40px;height:16px;position:relative;"><div style="position:absolute;left:0px;top:0px;width:20px;height:16px;background-color:' + colorbgright + '"></div><div style="position:absolute;border:solid 1px black;width:100%;height:15px"></div></div></td><td>ratioB: for geneB, the ratio of chimeric reads over total reads</td></tr><tr><td><div style="width:40px;height:16px;border:solid 1px red;"></div></td><td>Antisense (reported strand is on the opposite of gene strand)</td></tr></table>'
+    );
+    this.ul = holder.append("ul");
+    this.step_isoform(items);
+  }
+  // end of constructor
+  err(m) {
+    sayerror(this.errdiv, m);
+  }
+  step_isoform(items) {
+    const newset = /* @__PURE__ */ new Set();
+    for (const item of items) {
+      for (const i of item.pairs) {
+        let n = i.a.isoform;
+        if (n && !this.genome.isoformcache.has(n.toUpperCase())) {
+          newset.add(n);
+        }
+        n = i.b.isoform;
+        if (n && !this.genome.isoformcache.has(n.toUpperCase())) {
+          newset.add(n);
+        }
+      }
+    }
+    if (newset.size == 0) {
+      this.step_eat(items);
+      return;
+    }
+    const newisoform = [];
+    for (const n of newset) {
+      newisoform.push(n);
+    }
+    const wait = this.holder.append("div").style("margin", "20px").text("Loading " + newset.size + " isoforms ...");
+    fetch(
+      new Request(this.hostURL + "/isoformlst", {
+        method: "POST",
+        headers: { "content-type": "application/json" },
+        body: JSON.stringify({ genome: this.genome.name, lst: newisoform, jwt: this.jwt })
+      })
+    ).then((data) => {
+      return data.json();
+    }).then((data) => {
+      if (data.error) throw { message: "Cannot load isoforms: " + data.error };
+      wait.remove();
+      for (const ilst of data.lst) {
+        if (ilst[0]) {
+          this.genome.isoformcache.set(ilst[0].isoform, ilst);
+        }
+      }
+      const isoformErr = [];
+      for (const k of newset) {
+        if (!this.genome.isoformcache.has(k.toUpperCase())) {
+          isoformErr.push(k);
+        }
+      }
+      if (isoformErr.length) {
+        this.err(
+          isoformErr.length + " invalid isoform" + (isoformErr.length > 1 ? "s" : "") + ": " + isoformErr.join(", ")
+        );
+      }
+      this.step_eat(items);
+    }).catch((err) => {
+      this.err(err.message);
+      if (err.stack) console.log(err.stack);
+    });
+  }
+  step_eat(items) {
+    for (const prod of items) {
+      prod.hook = {};
+      let use = null;
+      for (const p of prod.pairs) {
+        let gm = this.genome.isoformmatch(p.a.isoform, prod.chrA, prod.posA);
+        if (gm) {
+          prod.geneA = gm.name;
+          p.a.isdefault = gm.isdefault;
+          if (Number.isNaN(p.a.codon) || p.a.codon < 0) {
+            p.a.codon = void 0;
+            const a = genomic2gm(prod.posA, gm);
+            if (a.atupstream) {
+              p.a.atupstream = a.atupstream;
+            } else if (a.atdownstream) {
+              p.a.atdownstream = a.atdownstream;
+            } else if (a.atutr3) {
+              p.a.atutr3 = a.atutr3;
+            } else if (a.atutr5) {
+              p.a.atutr5 = a.atutr5;
+            } else {
+              p.a.codon = a.codon;
+            }
+          }
+        }
+        gm = this.genome.isoformmatch(p.b.isoform, prod.chrB, prod.posB);
+        if (gm) {
+          prod.geneB = gm.name;
+          p.b.isdefault = gm.isdefault;
+          if (Number.isNaN(p.b.codon) || p.b.codon < 0) {
+            p.b.codon = void 0;
+            const a = genomic2gm(prod.posB, gm);
+            if (a.atupstream) {
+              p.b.atupstream = a.atupstream;
+            } else if (a.atdownstream) {
+              p.b.atdownstream = a.atdownstream;
+            } else if (a.atutr3) {
+              p.b.atutr3 = a.atutr3;
+            } else if (a.atutr5) {
+              p.b.atutr5 = a.atutr5;
+            } else {
+              p.b.codon = a.codon;
+            }
+          }
+        }
+        if (p.a.isdefault && p.b.isdefault) {
+          if (!use) {
+            use = p;
+          }
+          if (p.inframe) {
+            use = p;
+          }
+        }
+      }
+      if (use) {
+        prod.usepair = use;
+      } else {
+        prod.notes.push("No preferred isoform pair");
+        prod.usepair = prod.pairs[0];
+      }
+      if (prod.usepair) {
+        prod.usepair.inuse = true;
+      }
+      prod.eventlabel = (prod.geneA ? prod.geneA : prod.chrA) + "-" + (prod.geneB ? prod.geneB : prod.chrB);
+    }
+    const tmp = /* @__PURE__ */ Object.create(null);
+    const sampleless = /* @__PURE__ */ Object.create(null);
+    let hassampleless = false;
+    for (const prod of items) {
+      let n = prod.sample;
+      if (n) {
+        if (!(n in tmp)) {
+          tmp[n] = {};
+        }
+        if (!(prod.eventlabel in tmp[n])) {
+          tmp[n][prod.eventlabel] = [];
+        }
+        tmp[n][prod.eventlabel].push(prod);
+      } else {
+        hassampleless = true;
+        if (!(prod.eventlabel in sampleless)) {
+          sampleless[prod.eventlabel] = [];
+        }
+        sampleless[prod.eventlabel].push(prod);
+      }
+    }
+    for (const sn in tmp) {
+      this.samples.push({
+        name: sn,
+        events: tmp[sn]
+      });
+    }
+    if (hassampleless) {
+      this.samples.push({
+        name: "No name",
+        events: sampleless
+      });
+    }
+    this.buttsample.text(this.samples.length + " sample" + (this.samples.length > 1 ? "s" : ""));
+    for (const sample of this.samples) {
+      for (const elab in sample.events) {
+        if (!(elab in this.elab2sample)) {
+          this.elab2sample[elab] = [];
+        }
+        this.elab2sample[elab].push(sample);
+      }
+    }
+    for (const sample of this.samples) {
+      sample.gene2events = {};
+      for (const elab in sample.events) {
+        for (const prod of sample.events[elab]) {
+          const a = prod.geneA;
+          if (a) {
+            if (!(a in sample.gene2events)) {
+              sample.gene2events[a] = {};
+            }
+            sample.gene2events[a][elab] = 1;
+          }
+          const b = prod.geneB;
+          if (b) {
+            if (!(b in sample.gene2events)) {
+              sample.gene2events[b] = {};
+            }
+            sample.gene2events[b][elab] = 1;
+          }
+        }
+      }
+    }
+    for (const sample of this.samples) {
+      const newholder = [];
+      for (const elab in sample.events) {
+        for (const prod of sample.events[elab]) {
+          if (prod.rating == "HQ") msjoin(prod, newholder);
+        }
+      }
+      for (const elab in sample.events) {
+        for (const prod of sample.events[elab]) {
+          if (prod.rating == "LQ") msjoin(prod, newholder);
+        }
+      }
+      for (const elab in sample.events) {
+        for (const prod of sample.events[elab]) {
+          if (prod.rating == "RT") msjoin(prod, newholder);
+        }
+      }
+      for (const elab in sample.events) {
+        for (const prod of sample.events[elab]) {
+          if (prod.rating == "bad") msjoin(prod, newholder);
+        }
+      }
+      let msgid = 0;
+      const msglst = [];
+      for (const lst of newholder) {
+        if (lst.length > 1) {
+          for (const prod of lst) {
+            prod.msgid = msgid;
+          }
+          msgid++;
+          msglst.push(lst);
+        }
+      }
+      const hqin = [], hqt = [], hqo = [], lqin = [], lqt = [], lqo = [], rtin = [], rtt = [], rto = [], badin = [], badt = [], bado = [];
+      for (const msg of msglst) {
+        const thisset = [];
+        let hqin3 = false, hqt3 = false, hqo3 = false, lqin3 = false, lqt3 = false, lqo3 = false, rtin3 = false, rtt3 = false, rto3 = false, badin3 = false, badt3 = false, bado3 = false;
+        for (const prod of msg) {
+          thisset.push({ label: prod.eventlabel, lst: [prod] });
+          const pair2 = prod.usepair;
+          if (prod.rating == "HQ") {
+            if (pair2) {
+              if (pair2.inframe) hqin3 = true;
+              else hqt3 = true;
+            } else if (prod.isnloss || prod.iscloss) {
+              hqt3 = true;
+            } else {
+              hqo3 = true;
+            }
+          } else if (prod.rating == "LQ") {
+            if (pair2) {
+              if (pair2.inframe) lqin3 = true;
+              else lqt3 = true;
+            } else if (prod.isnloss || prod.iscloss) {
+              lqt3 = true;
+            } else {
+              lqo3 = true;
+            }
+          } else if (prod.rating == "RT") {
+            if (pair2) {
+              if (pair2.inframe) rtin3 = true;
+              else rtt3 = true;
+            } else if (prod.isnloss || prod.iscloss) {
+              rtt3 = true;
+            } else {
+              rto3 = true;
+            }
+          } else {
+            if (pair2) {
+              if (pair2.inframe) badin3 = true;
+              else badt3 = true;
+            } else if (prod.isnloss || prod.iscloss) {
+              badt3 = true;
+            } else {
+              bado3 = true;
+            }
+          }
+        }
+        if (hqin3) {
+          hqin.push({ label: "", lst: thisset, ismsg: true });
+        } else if (hqt3) {
+          hqt.push({ label: "", lst: thisset, ismsg: true });
+        } else if (hqo3) {
+          hqo.push({ label: "", lst: thisset, ismsg: true });
+        } else if (lqin3) {
+          lqin.push({ label: "", lst: thisset, ismsg: true });
+        } else if (lqt3) {
+          lqt.push({ label: "", lst: thisset, ismsg: true });
+        } else if (lqo3) {
+          lqo.push({ label: "", lst: thisset, ismsg: true });
+        } else if (rtin3) {
+          rtin.push({ label: "", lst: thisset, ismsg: true });
+        } else if (rtt3) {
+          rtt.push({ label: "", lst: thisset, ismsg: true });
+        } else if (rto3) {
+          rto.push({ label: "", lst: thisset, ismsg: true });
+        } else if (badin3) {
+          badin.push({ label: "", lst: thisset, ismsg: true });
+        } else if (badt3) {
+          badt.push({ label: "", lst: thisset, ismsg: true });
+        } else if (bado3) {
+          bado.push({ label: "", lst: thisset, ismsg: true });
+        } else {
+          console.log("multi-seg group unclassfied? " + key);
+        }
+      }
+      const genepairs = {};
+      for (const elab in sample.events) {
+        const hqin2 = [], hqt2 = [], hqo2 = [], lqin2 = [], lqt2 = [], lqo2 = [], rtin2 = [], rtt2 = [], rto2 = [], badin2 = [], badt2 = [], bado2 = [];
+        for (const prod of sample.events[elab]) {
+          if (prod.msgid != void 0) {
+            continue;
+          }
+          if (prod.geneA && prod.geneB) {
+            const key2 = prod.geneA + "-" + prod.geneB;
+            let hash = genepairs[key2];
+            if (!hash) {
+              const key22 = prod.geneB + "-" + prod.geneA;
+              hash = genepairs[key22];
+            }
+            if (hash) {
+              if (!(key2 in hash)) {
+                hash[key2] = [];
+              }
+              hash[key2].push(prod);
+            } else {
+              genepairs[key2] = {};
+              genepairs[key2][key2] = [prod];
+            }
+            continue;
+          }
+          var pair = prod.usepair;
+          if (prod.rating == "HQ") {
+            if (pair) {
+              if (pair.inframe) hqin2.push(prod);
+              else hqt2.push(prod);
+            } else if (prod.isnloss || prod.iscloss) {
+              hqt2.push(prod);
+            } else {
+              hqo2.push(prod);
+            }
+          } else if (prod.rating == "LQ") {
+            if (pair) {
+              if (pair.inframe) lqin2.push(prod);
+              else lqt2.push(prod);
+            } else if (prod.isnloss || prod.iscloss) {
+              lqt2.push(prod);
+            } else {
+              lqo2.push(prod);
+            }
+          } else if (prod.rating == "RT") {
+            if (pair) {
+              if (pair.inframe) rtin2.push(prod);
+              else rtt2.push(prod);
+            } else if (prod.isnloss || prod.iscloss) {
+              rtt2.push(prod);
+            } else {
+              rto2.push(prod);
+            }
+          } else {
+            if (pair) {
+              if (pair.inframe) badin2.push(prod);
+              else badt2.push(prod);
+            } else if (prod.isnloss || prod.iscloss) {
+              badt2.push(prod);
+            } else {
+              bado2.push(prod);
+            }
+          }
+        }
+        if (hqin2.length > 0) {
+          hqin.push({ label: elab, lst: [{ label: elab, lst: hqin2 }] });
+        } else if (hqt2.length > 0) {
+          hqt.push({ label: elab, lst: [{ label: elab, lst: hqt2 }] });
+        } else if (hqo2.length > 0) {
+          hqo.push({ label: elab, lst: [{ label: elab, lst: hqo2 }] });
+        } else if (lqin2.length > 0) {
+          lqin.push({ label: elab, lst: [{ label: elab, lst: lqin2 }] });
+        } else if (lqt2.length > 0) {
+          lqt.push({ label: elab, lst: [{ label: elab, lst: lqt2 }] });
+        } else if (lqo2.length > 0) {
+          lqo.push({ label: elab, lst: [{ label: elab, lst: lqo2 }] });
+        } else if (rtin2.length > 0) {
+          rtin.push({ label: elab, lst: [{ label: elab, lst: rtin2 }] });
+        } else if (rtt2.length > 0) {
+          rtt.push({ label: elab, lst: [{ label: elab, lst: rtt2 }] });
+        } else if (rto2.length > 0) {
+          rto.push({ label: elab, lst: [{ label: elab, lst: rto2 }] });
+        } else if (badin2.length > 0) {
+          badin.push({ label: elab, lst: [{ label: elab, lst: badin2 }] });
+        } else if (badt2.length > 0) {
+          badt.push({ label: elab, lst: [{ label: elab, lst: badt2 }] });
+        } else if (bado2.length > 0) {
+          bado.push({ label: elab, lst: [{ label: elab, lst: bado2 }] });
+        }
+      }
+      for (const key2 in genepairs) {
+        let hqin3 = false, hqt3 = false, hqo3 = false, lqin3 = false, lqt3 = false, lqo3 = false, rtin3 = false, rtt3 = false, rto3 = false, badin3 = false, badt3 = false, bado3 = false;
+        const thisset = [];
+        for (const elab in genepairs[key2]) {
+          const prodlst = genepairs[key2][elab];
+          if (prodlst.length == 1) {
+            if (prodlst[0].msgid != void 0) {
+              continue;
+            }
+          }
+          thisset.push({ label: elab, lst: prodlst });
+          for (const prod of prodlst) {
+            const pair2 = prod.usepair;
+            if (prod.rating == "HQ") {
+              if (pair2) {
+                if (pair2.inframe) hqin3 = true;
+                else hqt3 = true;
+              } else if (prod.isnloss || prod.iscloss) {
+                hqt3 = true;
+              } else {
+                hqo3 = true;
+              }
+            } else if (prod.rating == "LQ") {
+              if (pair2) {
+                if (pair2.inframe) lqin3 = true;
+                else lqt3 = true;
+              } else if (prod.isnloss || prod.iscloss) {
+                lqt3 = true;
+              } else {
+                lqo3 = true;
+              }
+            } else if (prod.rating == "RT") {
+              if (pair2) {
+                if (pair2.inframe) rtin3 = true;
+                else rtt3 = true;
+              } else if (prod.isnloss || prod.iscloss) {
+                rtt3 = true;
+              } else {
+                rto3 = true;
+              }
+            } else {
+              if (pair2) {
+                if (pair2.inframe) badin3 = true;
+                else badt3 = true;
+              } else if (prod.isnloss || prod.iscloss) {
+                badt3 = true;
+              } else {
+                bado3 = true;
+              }
+            }
+          }
+        }
+        if (hqin3) {
+          hqin.push({ label: key2, lst: thisset });
+        } else if (hqt3) {
+          hqt.push({ label: key2, lst: thisset });
+        } else if (hqo3) {
+          hqo.push({ label: key2, lst: thisset });
+        } else if (lqin3) {
+          lqin.push({ label: key2, lst: thisset });
+        } else if (lqt3) {
+          lqt.push({ label: key2, lst: thisset });
+        } else if (lqo3) {
+          lqo.push({ label: key2, lst: thisset });
+        } else if (rtin3) {
+          rtin.push({ label: key2, lst: thisset });
+        } else if (rtt3) {
+          rtt.push({ label: key2, lst: thisset });
+        } else if (rto3) {
+          rto.push({ label: key2, lst: thisset });
+        } else if (badin3) {
+          badin.push({ label: key2, lst: thisset });
+        } else if (badt3) {
+          badt.push({ label: key2, lst: thisset });
+        } else if (bado3) {
+          bado.push({ label: key2, lst: thisset });
+        }
+      }
+      sample.egglst = [];
+      sample.hqincount = 0;
+      sample.lqincount = 0;
+      if (hqin.length) {
+        sample.egglst.push({
+          htmlab: 'HQ&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color:' + colorinframe + ';color:white;padding:1px 3px;font-size:80%;">in-frame&nbsp;&nbsp;</span>',
+          lst: hqin
+        });
+        sample.hqincount = hqin.reduce((i, j) => i + j.lst.length, 0);
+      }
+      if (hqt.length) {
+        sample.egglst.push({
+          htmlab: 'HQ&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color:#E3C3C8;padding:1px 3px;font-size:80%;">truncation</span>',
+          lst: hqt
+        });
+      }
+      if (hqo.length) {
+        sample.egglst.push({
+          htmlab: 'HQ&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color:#ccc;padding:1px 3px;font-size:80%;">others&nbsp;&nbsp;&nbsp;&nbsp;</span>',
+          lst: hqo
+        });
+      }
+      if (lqin.length) {
+        sample.egglst.push({
+          htmlab: 'LQ&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color:' + colorinframe + ';color:white;padding:1px 3px;font-size:80%;">in-frame&nbsp;&nbsp;</span>',
+          lst: lqin
+        });
+        sample.lqincount = lqin.reduce((i, j) => i + j, 0);
+      }
+      if (lqt.length) {
+        sample.egglst.push({
+          htmlab: 'LQ&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color:#E3C3C8;padding:1px 3px;font-size:80%;">truncation</span>',
+          lst: lqt
+        });
+      }
+      if (lqo.length) {
+        sample.egglst.push({
+          htmlab: 'LQ&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color:#ccc;padding:1px 3px;font-size:80%;">others&nbsp;&nbsp;&nbsp;&nbsp;</span>',
+          lst: lqo
+        });
+      }
+      if (rtin.length) {
+        sample.egglst.push({
+          htmlab: 'Read-through <span style="background-color:' + colorinframe + ';color:white;padding:1px 3px;font-size:80%;">in-frame&nbsp;&nbsp;</span>',
+          lst: rtin
+        });
+      }
+      if (rtt.length) {
+        sample.egglst.push({
+          htmlab: 'Read-through <span style="background-color:#E3C3C8;padding:1px 3px;font-size:80%;">truncation</span>',
+          lst: rtt
+        });
+      }
+      if (rto.length) {
+        sample.egglst.push({
+          htmlab: 'Read-through <span style="background-color:#ccc;padding:1px 3px;font-size:80%;">others&nbsp;&nbsp;&nbsp;&nbsp;</span>',
+          lst: rto
+        });
+      }
+      if (badin.length) {
+        sample.egglst.push({
+          htmlab: 'Bad&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color:' + colorinframe + ';color:white;padding:1px 3px;font-size:80%;">in-frame</span>',
+          lst: badin
+        });
+      }
+      if (badt.length) {
+        sample.egglst.push({
+          htmlab: 'Bad&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color:#E3C3C8;padding:1px 3px;font-size:80%;">truncation</span>',
+          lst: badt
+        });
+      }
+      if (bado.length) {
+        sample.egglst.push({
+          htmlab: 'Bad&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<span style="background-color:#ccc;padding:1px 3px;font-size:80%;">others&nbsp;&nbsp;&nbsp;&nbsp;</span>',
+          lst: bado
+        });
+      }
+    }
+    this.samples.sort((a, b) => {
+      if (a.hqincount == b.hqincount) {
+        return b.lqincount - a.lqincount;
+      }
+      return b.hqincount - a.hqincount;
+    });
+    for (const sample of this.samples) {
+      for (const egg of sample.egglst) {
+        for (const eg of egg.lst) {
+          for (const evt of eg.lst) {
+            evt.lst.sort((a, b) => {
+              const pa = a.usepair, pb = b.usepair;
+              if (pa) {
+                if (pb) {
+                  if (pa.inframe) {
+                    if (!pb.inframe) {
+                      return -1;
+                    }
+                  } else {
+                    if (pb.inframe) {
+                      return 1;
+                    }
+                  }
+                } else {
+                  return -1;
+                }
+              } else {
+                if (pb) {
+                  return 1;
+                }
+              }
+              return b.score - a.score;
+            });
+          }
+        }
+        egg.lst.sort((a, b) => {
+          if (a.lst.length != b.lst.length) {
+            return b.lst.length - a.lst.length;
+          }
+          let scorea = 0;
+          for (const evta of a.lst) {
+            for (const prod of evta.lst) {
+              scorea = Math.max(scorea, prod.score);
+            }
+          }
+          let scoreb = 0;
+          for (const evtb of b.lst) {
+            for (const prod of evtb.lst) {
+              scoreb = Math.max(scoreb, prod.score);
+            }
+          }
+          return scoreb - scorea;
+        });
+      }
+      let prodid = 1;
+      for (const egg of sample.egglst) {
+        for (const eg of egg.lst) {
+          for (const evt of eg.lst) {
+            for (const prod of evt.lst) {
+              prod.prodid = prodid++;
+            }
+          }
+        }
+      }
+    }
+    this.step_gene();
+    this.step_table();
+  }
+  dogenefilter() {
+    let va = this.gui.inputa.property("value");
+    let vb = this.gui.inputb.property("value");
+    if (va.length + vb.length == 0) {
+      this.gui.says.text(
+        "Showing " + (this.genelst.length > 100 ? 100 : "all") + " of " + this.genelst.length + " pairs"
+      );
+      this.geneshow(this.genelst.length > 100 ? this.genelst.slice(0, 100) : this.genelst);
+      return;
+    }
+    va = va.length == 0 ? null : va.toLowerCase();
+    vb = vb.length == 0 ? null : vb.toLowerCase();
+    const uselst = [];
+    for (const g of this.genelst) {
+      if (va) {
+        if (!g.a) continue;
+        if (g.a.toLowerCase().indexOf(va) == -1) continue;
+      }
+      if (vb) {
+        if (!g.b) continue;
+        if (g.b.toLowerCase().indexOf(vb) == -1) continue;
+      }
+      uselst.push(g);
+    }
+    this.gui.says.text("Showing " + Math.min(100, uselst.length) + " of " + this.genelst.length + " pairs");
+    this.geneshow(uselst.length > 100 ? uselst.slice(0, 100) : uselst);
+  }
+  geneshow(lst) {
+    this.genetable.selectAll("*").remove();
+    const tr = this.genetable.append("tr").style("background-color", "#ededed").style("font-size", ".8em");
+    tr.append("td").text("gene A");
+    tr.append("td").text("gene B");
+    tr.append("td").text("# sample");
+    tr.append("td").text("rating");
+    for (const evt of lst) {
+      let color1 = "black", color2 = "black", weight1, weight2;
+      if (evt.ainter) {
+        color1 = "#aaa";
+        weight1 = "normal";
+      } else {
+        const a = evt.samples[0].prodlst[0].hlgene;
+        if (a == 1 || a == 3 || a == 4) weight1 = "bold";
+        if (a == 4) color1 = knownprod_c;
+      }
+      if (evt.binter) {
+        color2 = "#aaa";
+        weight2 = "normal";
+      } else {
+        const a = evt.samples[0].prodlst[0].hlgene;
+        if (a == 2 || a == 3 || a == 4) weight2 = "bold";
+        if (a == 4) color2 = knownprod_c;
+      }
+      const tr2 = this.genetable.append("tr").attr("class", "sja_clb");
+      tr2.append("td").text(evt.a).style("color", color1).style("font-weight", weight1);
+      tr2.append("td").text(evt.b).style("color", color2).style("font-weight", weight2);
+      const td = tr2.append("td").text(evt.samples.length);
+      tr2.on("click", () => {
+        const p = tr2.node().getBoundingClientRect();
+        const pane2 = newpane({ x: p.left + p.width + 10, y: p.top });
+        pane2.header.text(evt.a + " - " + evt.b);
+        const table = pane2.body.append("table");
+        for (const sample of evt.samples) {
+          const tr3 = table.append("tr");
+          tr3.append("td").style("vertical-align", "top").style("padding-top", "5px").text(sample.name);
+          const td2 = tr3.append("td");
+          for (const prod of sample.prodlst) {
+            const logo = this.eventlogo([prod], td2);
+            logo.style("position", "relative");
+            logo.append("div").style("position", "absolute").style("width", "100%").style("height", "100%").style("top", "0px").style("left", "0px").on("mouseover", (event) => {
+              const p2 = event.target.getBoundingClientRect();
+              tip.clear().show(p2.left + p2.width - 2, p2.top - 30);
+              this.showsvpairs({
+                prodlst: [prod],
+                holder: tip.d.append("div"),
+                nodetail: true,
+                sample,
+                eglst: null,
+                showothersample: false
+              });
+            }).on("click", (event) => {
+              const p2 = event.target.getBoundingClientRect();
+              const pane = newpane({ x: p2.left + p2.width + 40, y: p2.top - 60 });
+              pane.header.text(sample.name);
+              this.showsvpairs({
+                prodlst: [prod],
+                holder: pane.body
+              });
+            });
+          }
+        }
+      });
+      const hash = {};
+      for (const smp of evt.samples) {
+        const hash2 = {};
+        for (const p of smp.prodlst) {
+          hash2[p.rating] = 1;
+        }
+        for (var n in hash2) {
+          if (!(n in hash)) {
+            hash[n] = 0;
+          }
+          hash[n]++;
+        }
+      }
+      const lst2 = [];
+      for (const smp of ["HQ", "LQ", "RT", "bad"]) {
+        if (hash[smp]) {
+          lst2.push(
+            '<span style="border-radius:6px;background-color:#ededed;padding:1px 6px;font-size:80%">' + smp + (hash[smp] > 1 ? ' <span style="font-size:80%">' + hash[smp] + "</span>" : "") + "</span>"
+          );
+        }
+      }
+      tr2.append("td").html(lst2.join(" "));
+    }
+  }
+  step_gene() {
+    this.gui = {};
+    this.genefilter.append("span").text("Filter:");
+    this.gui.inputa = this.genefilter.append("input").attr("size", 7).attr("placeholder", "gene A").style("margin-left", "10px").on("keyup", () => this.dogenefilter());
+    this.gui.inputb = this.genefilter.append("input").attr("size", 7).attr("placeholder", "gene B").style("margin-left", "10px").on("keyup", () => this.dogenefilter());
+    this.genefilter.append("button").style("margin-left", "10px").text("Reset").on("click", () => {
+      this.gui.inputa.property("value", "");
+      this.gui.inputb.property("value", "");
+      this.dogenefilter();
+    });
+    this.gui.says = this.genefilter.append("span").style("padding-left", "20px");
+    const events = {};
+    const genes = /* @__PURE__ */ new Set();
+    for (const sample of this.samples) {
+      for (const k in sample.events) {
+        for (const prod of sample.events[k]) {
+          if (!prod.geneA || !prod.geneB) continue;
+          if (prod.rating == "RT") continue;
+          if (prod.geneA) {
+            genes.add(prod.geneA);
+          }
+          if (prod.geneB) {
+            genes.add(prod.geneB);
+          }
+          const n = (prod.geneA ? prod.geneA : "<" + prod.chrA) + " - " + (prod.geneB ? prod.geneB : "<" + prod.chrB);
+          if (!(n in events)) {
+            events[n] = /* @__PURE__ */ Object.create(null);
+          }
+          if (!(sample.name in events[n])) {
+            events[n][sample.name] = [];
+          }
+          events[n][sample.name].push(prod);
+        }
+      }
+    }
+    this.buttgene.text(genes.size + " gene" + (genes.size > 1 ? "s" : ""));
+    for (const k in events) {
+      const tmp = k.split(" - ");
+      const evt = { samples: [] };
+      if (tmp[0][0] == "<") {
+        evt.a = tmp[0].slice(1, tmp[0].length);
+        evt.ainter = true;
+      } else {
+        evt.a = tmp[0];
+      }
+      if (tmp[1][0] == "<") {
+        evt.b = tmp[1].slice(1, tmp[1].length);
+        evt.binter = true;
+      } else {
+        evt.b = tmp[1];
+      }
+      for (const sn in events[k]) {
+        evt.samples.push({ name: sn, prodlst: events[k][sn] });
+      }
+      this.genelst.push(evt);
+    }
+    this.genelst.sort((a, b) => {
+      let ca = 0;
+      for (const s of a.samples) {
+        for (const p of s.prodlst) {
+          if (p.rating == "HQ") ca++;
+        }
+      }
+      let cb = 0;
+      for (const s of b.samples) {
+        for (const p of s.prodlst) {
+          if (p.rating == "HQ") cb++;
+        }
+      }
+      return cb - ca;
+    });
+    this.dogenefilter();
+  }
+  step_table() {
+    this.eggbar = [];
+    this.ul.selectAll("*").remove();
+    for (const sample of this.samples) {
+      this.ul.append("li").style("font-weight", "bold").style("color", "#545454").text(sample.name);
+      sample.ul = this.ul.append("ul").style("margin-bottom", "10px");
+      this.showsample(sample);
+    }
+  }
+  showsample(sample) {
+    sample.ul.selectAll("*").remove();
+    for (const egg of sample.egglst) {
+      const evtnum = egg.lst.reduce((i, j) => i + j.lst.length, 0);
+      const li = sample.ul.append("li");
+      const bar = li.append("div").attr("class", "sja_clb2").html(egg.htmlab + " " + evtnum);
+      bar.on("click", () => {
+        for (const bar0 of this.eggbar) {
+          bar0.style("background-color", "");
+        }
+        bar.style("background-color", "yellow");
+        const next = select_default(li.node().nextSibling);
+        if (next.style("display") == "none") {
+          appear(next);
+          egg.isopen = true;
+        } else {
+          disappear(next);
+          egg.isopen = false;
+        }
+      });
+      this.eggbar.push(bar);
+      const div = sample.ul.append("div").style("margin", "10px");
+      this.showevents(sample, egg.lst, div);
+    }
+  }
+  showevents(sample, eglst, holder) {
+    const svg = holder.append("svg");
+    let rowh = 22, rowh2 = 15, rows = 13, fontsize = rowh - 3, fontsizeframe = 14, fontsizefeature = 10, hpad0 = 20, hpad = 10, vpad = 10, gvpad = 10, chrAw = 60, chrBw = 60, s1 = 10, s2 = 10, s3 = 10, s4 = 10, s5 = 5, s6 = 15, s7 = 13, eventlogow = 0, etw = 25, genesp = 12, geneAw = 0, geneBw = 0, recurw = 0, graphheight = 0;
+    for (const eg of eglst) {
+      graphheight += rows;
+      if (eg.lst.length == 1) {
+        graphheight += rowh;
+      } else {
+        graphheight += vpad * 2 + (rowh + rows) * eg.lst.length + (rowh2 + rows) * (eg.lst.length - 1) + gvpad;
+      }
+      for (const evt of eg.lst) {
+        evt.svg = {};
+        const prodlst = evt.lst;
+        const prod = prodlst[0];
+        let labA, labB;
+        if (prod.geneA) {
+          const t = prod.geneA.split(",");
+          if (t.length > 2) {
+            labA = t[0] + "," + t[1] + "...";
+          } else {
+            labA = prod.geneA;
+          }
+        } else {
+          labA = "";
+        }
+        if (prod.geneB) {
+          const t = prod.geneB.split(",");
+          if (t.length > 2) {
+            labB = t[0] + "," + t[1] + "...";
+          } else {
+            labB = prod.geneB;
+          }
+        } else {
+          labB = "";
+        }
+        svg.append("text").text(labA).attr("font-size", fontsize).attr("font-family", "Courier").each(function() {
+          geneAw = Math.max(geneAw, this.getBBox().width);
+        }).remove();
+        svg.append("text").text(labB).attr("font-size", fontsize).attr("font-family", "Courier").each(function() {
+          geneBw = Math.max(geneBw, this.getBBox().width);
+        }).remove();
+        svg.append("text").text(prod.rating).attr("font-size", fontsize).attr("font-family", "Courier").each(function() {
+          evt.svg.ratingw = this.getBBox().width;
+        }).remove();
+        evt.svg.framew = 22;
+        evt.svg.typew = 60;
+        if (prod.usepair) {
+          evt.svg.frameword = prod.usepair.inframe ? "IN" : "O";
+        } else {
+          evt.svg.frameword = "?";
+        }
+        svg.append("text").text(prod.featureA).attr("font-size", fontsizefeature).attr("font-family", font).each(function() {
+          evt.svg.featurew = this.getBBox().width;
+        }).remove();
+        svg.append("text").text(prod.featureB).attr("font-size", fontsizefeature).attr("font-family", font).each(function() {
+          evt.svg.featurew = Math.max(evt.svg.featurew, this.getBBox().width);
+        }).remove();
+        svg.append("text").text(Math.floor(prod.score)).attr("font-size", fontsize).attr("font-family", font).each(function() {
+          evt.svg.scorew = this.getBBox().width;
+        }).remove();
+        evt.svg.logow = evt.svg.ratingw + evt.svg.framew + evt.svg.typew + evt.svg.featurew + evt.svg.scorew + s5 * 6;
+        eventlogow = Math.max(eventlogow, evt.svg.logow + (prodlst.length > 1 ? s4 + etw : 0));
+        if (prod.geneA && prod.geneB) {
+          const slst = this.elab2sample[evt.label];
+          if (!slst) {
+            evt.svg.recurtext = "Recurrence check error";
+            evt.svg.recurtextcolor = "red";
+          } else if (slst.length == 1) {
+            evt.svg.recurtext = "No recurrence";
+            evt.svg.recurtextcolor = "#aaaaaa";
+          } else {
+            evt.svg.hasrecurrence = true;
+            evt.svg.recurtext = "In " + slst.length + " samples";
+            evt.svg.recurtextcolor = "black";
+          }
+        } else {
+          evt.svg.recurtext = "Unknown recurrence";
+          evt.svg.recurtextcolor = "#aaaaaa";
+        }
+        svg.append("text").text(evt.svg.recurtext).attr("font-size", fontsize - 4).attr("font-family", font).each(function() {
+          evt.svg.recurw = this.getBBox().width;
+        }).remove();
+        recurw = Math.max(recurw, evt.svg.recurw);
+      }
+    }
+    geneAw += 10;
+    geneBw += 10;
+    graphheight += rows;
+    let ghandlew = 100;
+    let roww = chrAw + s1 + rowh + s7 + geneAw + genesp + s2 + genesp + geneBw + s7 + rowh + s1 + chrBw + s3 + eventlogow + s6 + recurw;
+    svg.attr("width", hpad0 * 2 + hpad * 2 + roww + ghandlew).attr("height", graphheight);
+    const g = svg.append("g").attr("transform", "translate(" + hpad0 + ",0)");
+    let y = 0;
+    for (const eg of eglst) {
+      y += rows;
+      const g_eg = g.append("g").attr("transform", "translate(0," + y + ")");
+      const groupheight = (rowh + rows) * eg.lst.length - rows + (eg.lst.length > 1 ? vpad * 2 : 0) + (eg.lst.length > 1 ? (rowh2 + rows) * (eg.lst.length - 1) : 0);
+      if (eg.lst.length > 1) {
+        g_eg.append("rect").attr("stroke", "black").attr("stroke-dasharray", eg.ismsg ? "none" : "2,3").attr("fill", "none").attr("width", roww + hpad * 2).attr("height", groupheight).attr("shape-rendering", "crispEdges");
+        if (eg.ismsg) {
+          const g2 = g_eg.append("g").attr("transform", "translate(" + (roww + hpad * 2) + ",0)");
+          g2.append("rect").attr("width", ghandlew).attr("height", rowh).attr("fill", "#858585").attr("shape-rendering", "crispEdges");
+          g2.append("text").text("multi-seg").attr("x", 10).attr("y", rowh / 2).attr("font-size", rowh - 6).attr("font-family", font).attr("fill", "white").attr("dominant-baseline", "middle");
+          g2.append("rect").attr("width", ghandlew).attr("height", rowh).attr("fill", "white").attr("fill-opacity", 0).on("click", (event) => {
+            const joinlst = [];
+            const idlst = [];
+            for (const evt of eg.lst) {
+              const prod = evt.lst[0];
+              idlst.push(prod.prodid);
+              const p2 = {
+                a: {
+                  chr: prod.chrA,
+                  position: prod.posA,
+                  strand: prod.ortA,
+                  name: prod.geneA ? prod.geneA : prod.chrA,
+                  ratio: prod.ratioA.toFixed(2),
+                  feature: prod.featureA,
+                  contiglen: prod.matchA,
+                  chimericreads: prod.readsA,
+                  repeatscore: prod.repeatA
+                },
+                b: {
+                  chr: prod.chrB,
+                  position: prod.posB,
+                  strand: prod.ortB,
+                  name: prod.geneB ? prod.geneB : prod.chrB,
+                  ratio: prod.ratioB.toFixed(2),
+                  feature: prod.featureB,
+                  contiglen: prod.matchB,
+                  chimericreads: prod.readsB,
+                  repeatscore: prod.repeatB
+                },
+                rating: prod.rating,
+                score: Math.ceil(prod.score)
+              };
+              if (prod.usepair) {
+                p2.inframe = prod.usepair.inframe;
+                const x = prod.usepair.a;
+                p2.a.gm = this.genome.isoformmatch(x.isoform, p2.a.chr, p2.a.position);
+                p2.a.codon = x.codon;
+                p2.a.exon = x.exon;
+                p2.a.atupstream = x.atupstream;
+                p2.a.atdownstream = x.atdownstream;
+                p2.a.atutr5 = x.atutr5;
+                p2.a.atutr3 = x.atutr3;
+                const y2 = prod.usepair.b;
+                p2.b.gm = this.genome.isoformmatch(y2.isoform, p2.b.chr, p2.b.position);
+                p2.b.codon = y2.codon;
+                p2.b.exon = y2.exon;
+                p2.b.atupstream = y2.atupstream;
+                p2.b.atdownstream = y2.atdownstream;
+                p2.b.atutr5 = y2.atutr5;
+                p2.b.atutr3 = y2.atutr3;
+                let aalen = 0, bplen2 = 0;
+                if (x.contigaa && y2.contigaa) {
+                  aalen = y2.contigaa - x.contigaa - 1;
+                }
+                if (x.contigbp && y2.contigbp) {
+                  bplen2 = y2.contigbp - x.contigbp - 1;
+                }
+                if (aalen) {
+                  p2.interstitial = { aalen };
+                }
+                if (bplen2) {
+                  if (!p2.interstitial) p2.interstitial = {};
+                  p2.interstitial.bplen = bplen2;
+                }
+              }
+              joinlst.push(p2);
+            }
+            const p = event.target.getBoundingClientRect();
+            const pane = newpane({ x: p.left + 10, y: p.top + p.height + 10 });
+            const div = pane.body.append("div").style("margin", "10px");
+            div.append("span").style("padding-right", "20px").text("Product id: " + idlst.join(", "));
+            div.append("button").style("margin-right", "10px").text("Break").on("click", () => {
+              const eg2id = eg.lst.map((j) => j.lst[0].prodid);
+              let idx = 0;
+              for (; idx < eglst.length; idx++) {
+                const eg2 = eglst[idx];
+                if (eg2.ismsg) {
+                  const eg22id = eg2.lst.map((j) => j.lst[0].prodid);
+                  if (eg22id.join(",") == eg2id.join(",")) {
+                    break;
+                  }
+                }
+              }
+              delete eg.ismsg;
+              const oldlst = eg.lst;
+              eg.lst = [eg.lst[0]];
+              for (let j = 1; j < oldlst.length; j++) {
+                eglst.splice(idx, 0, {
+                  label: "",
+                  lst: [oldlst[j]]
+                });
+              }
+              svg.remove();
+              this.showevents(sample, eglst, holder);
+              pane.pane.remove();
+            });
+            div.append("button").text("Edit").on("click", (event2) => {
+              const inputdom = document.createElement("input");
+              div.node().insertBefore(inputdom, event2.target);
+              const buttdom = document.createElement("button");
+              div.node().insertBefore(buttdom, event2.target);
+              div.node().removeChild(event2.target);
+              inputdom.focus();
+              const input = select_default(inputdom);
+              const butt = select_default(buttdom);
+              input.attr("size", 10).style("margin", "0px 10px").property("value", idlst.join(","));
+              butt.text("Apply").on("click", () => {
+                const lst0 = inputdom.value.trim().split(",");
+                const goodid = [];
+                for (const s of lst0) {
+                  if (!s) continue;
+                  const j = Number.parseInt(s);
+                  if (Number.isNaN(j)) return alert("invalid id: " + s);
+                  if (this.prodidisinvalid(j, sample)) return alert("invalid id " + j);
+                  goodid.push(j);
+                }
+                if (goodid.length <= 1) return alert("must be at least 2 products");
+                const newevtlst = [];
+                for (const id of goodid) {
+                  const lookprod = this.extractprod(id, sample);
+                  if (lookprod) {
+                    newevtlst.push({ label: lookprod.eventlabel, lst: [lookprod] });
+                  } else {
+                    return alert("unknown product id " + id);
+                  }
+                }
+                if (newevtlst.length <= 1) return alert("less than 2 products cannot make a group");
+                eglst.unshift({ lst: newevtlst, ismsg: true });
+                this.showsample(sample);
+                pane.pane.remove();
+              });
+            });
+            svtable({
+              samplelst: [
+                {
+                  pairlst: joinlst
+                }
+              ],
+              nosample: true,
+              holder: pane.body
+            });
+            const par = {
+              pairlst: joinlst,
+              genome: this.genome,
+              holder: pane.body,
+              hostURL: this.hostURL,
+              jwt: this.jwt
+            };
+            import("./svgraph-VJLB7BBN.js").then((p2) => {
+              p2.default(par);
+            });
+          });
+        }
+      }
+      const g_rows = g_eg.append("g").attr("transform", "translate(" + hpad + "," + (eg.lst.length > 1 ? vpad : 0) + ")");
+      let y1 = 0;
+      let evtid = 0;
+      const bgcolor = "#ededed";
+      const elabhash = {};
+      for (const e of eg.lst) {
+        elabhash[e.label] = 1;
+      }
+      const showngenenotip = {};
+      for (const evt of eg.lst) {
+        const prodlst = evt.lst;
+        const prod = prodlst[0];
+        const thispair = prod.usepair;
+        if (eg.lst.length > 1 && evtid > 0) {
+          const g_row2 = g_rows.append("g").attr("transform", "translate(" + (chrAw + s1 + rowh + s7 + geneAw + genesp + s2 / 2) + "," + y1 + ")");
+          const text2 = g_row2.append("text").attr("fill", "#858585").attr("font-size", rowh2).attr("text-anchor", "middle").attr("font-family", font).attr("y", rowh2 / 2).attr("dominant-baseline", "middle");
+          if (eg.ismsg) {
+            text2.text(prod.mswhat ? prod.mswhat : "No connection detail");
+          } else {
+            text2.text("Reciprocal");
+          }
+          y1 += rowh2 + rows;
+        }
+        const textcolor = prod.chrA == prod.chrB ? "black" : colorctx;
+        const g_row = g_rows.append("g").attr("transform", "translate(0," + y1 + ")");
+        g_row.append("text").text(prod.chrA).attr("x", chrAw).attr("y", rowh / 2).attr("font-size", fontsize - 4).attr("text-anchor", "end").attr("dominant-baseline", "middle").attr("fill", textcolor);
+        const extevt = { a: null, b: null };
+        if (prod.geneA) {
+          if (prod.geneA in showngenenotip) {
+            showngenenotip[prod.geneA] = 1;
+          } else {
+            const lst = [];
+            for (const elab in sample.gene2events[prod.geneA]) {
+              if (!(elab in elabhash)) {
+                lst.push(elab);
+              }
+            }
+            if (lst.length > 0) {
+              extevt.a = { lst };
+              extevt.a.circle = g_row.append("circle").attr("fill", "white").attr("stroke", "black").attr("cx", chrAw + s1 + rowh / 2).attr("cy", rowh / 2).attr("r", rowh / 2);
+              if (lst.length > 1) {
+                extevt.a.text = g_row.append("text").text(lst.length).attr("x", chrAw + s1 + rowh / 2).attr("y", rowh / 2).attr("text-anchor", "middle").attr("font-size", rowh2).attr("dominant-baseline", "middle").attr("fill", "black");
+              }
+              g_row.append("line").attr("x1", chrAw + s1 + rowh).attr("x2", chrAw + s1 + rowh + s7).attr("y1", rowh / 2).attr("y2", rowh / 2).attr("stroke", "black").attr("shape-rendering", "crispEdges");
+            }
+          }
+        }
+        g_row.append("rect").attr("fill", colorbgleft).attr("x", chrAw + s1 + rowh + s7 + (geneAw + genesp) * (1 - prod.ratioA)).attr("width", (geneAw + genesp) * prod.ratioA).attr("height", rowh).attr("shape-rendering", "crispEdges");
+        let antisense = false;
+        if (thispair) {
+          const thisn = thispair.a.isoform;
+          if (thisn) {
+            const _gm = this.genome.isoformmatch(thisn, prod.chrA, prod.posA);
+            if (_gm && _gm.strand != prod.ortA) {
+              antisense = true;
+            }
+          }
+        }
+        const boxa = g_row.append("rect").attr("fill", "none").attr("stroke", antisense ? "red" : "black").attr("shape-rendering", "crispEdges").attr("x", chrAw + s1 + rowh + s7).attr("width", geneAw + genesp).attr("height", rowh);
+        let labA;
+        if (prod.geneA) {
+          const t = prod.geneA.split(",");
+          if (t.length > 2) {
+            labA = t[0] + "," + t[1] + "...";
+          } else {
+            labA = prod.geneA;
+          }
+        } else {
+          labA = "";
+        }
+        g_row.append("text").text(labA).attr("x", chrAw + s1 + rowh + s7 + geneAw).attr("y", rowh / 2).attr("font-size", fontsize).attr("font-family", "Courier").attr(
+          "font-weight",
+          prod.hlgene ? prod.hlgene == 1 || prod.hlgene == 3 || prod.hlgene == 4 ? "bold" : "normal" : "normal"
+        ).attr("fill", prod.hlgene ? prod.hlgene == 4 ? knownprod_c : "#545454" : "#545454").attr("text-anchor", "end").attr("dominant-baseline", "central");
+        g_row.append("line").attr("x1", chrAw + s1 + rowh + s7 + geneAw + genesp).attr("x2", chrAw + s1 + rowh + s7 + geneAw + genesp + s2).attr("y1", rowh / 2).attr("y2", rowh / 2).attr("shape-rendering", "crispEdges").attr("stroke", "black");
+        g_row.append("rect").attr("fill", colorbgright).attr("x", chrAw + s1 + rowh + s7 + geneAw + genesp + s2).attr("width", (genesp + geneBw) * prod.ratioB).attr("height", rowh).attr("shape-rendering", "crispEdges");
+        antisense = false;
+        if (thispair) {
+          const thisn = thispair.b.isoform;
+          if (thisn) {
+            const _gm = this.genome.isoformmatch(thisn, prod.chrB, prod.posB);
+            if (_gm && _gm.strand != prod.ortB) {
+              antisense = true;
+            }
+          }
+        }
+        const boxb = g_row.append("rect").attr("fill", "none").attr("stroke", antisense ? "red" : "black").attr("shape-rendering", "crispEdges").attr("x", chrAw + s1 + rowh + s7 + geneAw + genesp + s2).attr("width", geneBw + genesp).attr("height", rowh);
+        let labB;
+        if (prod.geneB) {
+          let t = prod.geneB.split(",");
+          if (t.length > 2) {
+            labB = t[0] + "," + t[1] + "...";
+          } else {
+            labB = prod.geneB;
+          }
+        } else {
+          labB = "";
+        }
+        g_row.append("text").text(labB).attr("x", chrAw + s1 + rowh + s7 + geneAw + genesp + s2 + genesp).attr("y", rowh / 2).attr("font-size", fontsize).attr("font-family", "Courier").attr(
+          "font-weight",
+          prod.hlgene ? prod.hlgene == 2 || prod.hlgene == 3 || prod.hlgene == 4 ? "bold" : "normal" : "normal"
+        ).attr("fill", prod.hlgene ? prod.hlgene == 4 ? knownprod_c : "#545454" : "#545454").attr("dominant-baseline", "central");
+        if (prod.geneB) {
+          if (prod.geneB in showngenenotip) {
+          } else {
+            showngenenotip[prod.geneB] = 1;
+            const lst = [];
+            for (const elab in sample.gene2events[prod.geneB]) {
+              if (!(elab in elabhash)) {
+                lst.push(elab);
+              }
+            }
+            if (lst.length > 0) {
+              extevt.b = { lst };
+              extevt.b.circle = g_row.append("circle").attr("fill", "white").attr("stroke", "black").attr("cx", chrAw + s1 + rowh + s7 + geneAw + genesp + s2 + genesp + geneBw + s7 + rowh / 2).attr("cy", rowh / 2).attr("r", rowh / 2);
+              if (lst.length > 1) {
+                extevt.b.text = g_row.append("text").text(lst.length).attr("x", chrAw + s1 + rowh + s7 + geneAw + genesp + s2 + genesp + geneBw + s7 + rowh / 2).attr("y", rowh / 2).attr("text-anchor", "middle").attr("font-size", rowh2).attr("dominant-baseline", "middle").attr("fill", "black");
+              }
+              g_row.append("line").attr("x1", chrAw + s1 + rowh + s7 + geneAw + genesp + s2 + genesp + geneBw).attr("x2", chrAw + s1 + rowh + s7 + geneAw + genesp + s2 + genesp + geneBw + s7).attr("y1", rowh / 2).attr("y2", rowh / 2).attr("stroke", "black").attr("shape-rendering", "crispEdges");
+            }
+          }
+        }
+        g_row.append("text").text(prod.chrB).attr("x", chrAw + s1 + rowh + s7 + geneAw + genesp + s2 + genesp + geneBw + s7 + rowh + s1).attr("y", rowh / 2).attr("font-size", fontsize - 4).attr("dominant-baseline", "middle").attr("fill", textcolor);
+        let x = chrAw + s1 + rowh + s7 + geneAw + genesp + s2 + genesp + geneBw + s7 + rowh + s1 + chrBw + s3;
+        const x0 = x;
+        const logobg = g_row.append("rect").attr("fill", "white").attr("stroke", "#858585").attr("x", x).attr("y", -1.5).attr("width", evt.svg.logow).attr("height", rowh + 2).attr("rx", 5).attr("ry", 5);
+        x += s5;
+        prod.hook.mainRating = g_row.append("text").text(prod.rating).attr("font-size", fontsize).attr("font-family", font).attr("fill", "#858585").attr("x", x).attr("y", rowh / 2).attr("dominant-baseline", "middle");
+        x += evt.svg.ratingw + s5;
+        prod.hook.mainFrame = {};
+        prod.hook.mainFrame.bg = g_row.append("rect").attr("x", x + 1).attr("y", 3).attr("width", evt.svg.framew).attr("height", rowh - 7).attr("shape-rendering", "crispEdges");
+        if (prod.usepair) {
+          prod.hook.mainFrame.bg.attr("fill", prod.usepair.inframe ? colorinframe : coloroutframe);
+        } else {
+          prod.hook.mainFrame.bg.attr("fill", "none").attr("stroke", "black");
+        }
+        prod.hook.mainFrame.text = g_row.append("text").text(evt.svg.frameword).attr("font-size", fontsizeframe).attr("font-family", font).attr("fill", prod.usepair ? "white" : "black").attr("x", x + 1 + evt.svg.framew / 2).attr("text-anchor", "middle").attr("y", rowh / 2).attr("dominant-baseline", "middle");
+        x += evt.svg.framew + s5;
+        prod.hook.mainType = g_row.append("text").text(prod.type2).attr("font-size", fontsize).attr("font-family", font).attr("fill", "#858585").attr("x", x).attr("y", rowh / 2).attr("dominant-baseline", "middle");
+        x += evt.svg.typew + s5;
+        g_row.append("text").text(prod.featureA).attr("font-size", fontsizefeature).attr("font-family", font).attr("fill", "black").attr("x", x).attr("y", rowh / 4).attr("dominant-baseline", "middle");
+        g_row.append("text").text(prod.featureB).attr("font-size", fontsizefeature).attr("font-family", font).attr("fill", "black").attr("x", x).attr("y", rowh * 3 / 4).attr("dominant-baseline", "middle");
+        x += evt.svg.featurew + s5;
+        g_row.append("text").text(Math.floor(prod.score)).attr("font-size", fontsize).attr("font-family", font).attr("fill", "#858585").attr("x", x).attr("y", rowh / 2).attr("dominant-baseline", "middle");
+        x += evt.svg.scorew + s5 + s4;
+        g_row.append("rect").attr("fill", "white").attr("fill-opacity", 0).attr("stroke", "none").attr("x", x0).attr("y", -1.5).attr("width", evt.svg.logow).attr("height", rowh + 2).on("mouseover", () => {
+          logobg.attr("stroke-width", "2");
+          const d = tip.clear().showunder(logobg.node()).d.append("div");
+          this.prodstat(prod, d);
+        }).on("mouseout", () => {
+          logobg.attr("stroke-width", "1");
+          tip.hide();
+        });
+        if (prodlst.length > 1) {
+          const logobg2 = g_row.append("rect").attr("fill", "none").attr("stroke", "#858585").attr("x", x).attr("y", 3.5).attr("width", etw).attr("height", rowh - 4).attr("rx", 5).attr("ry", 5);
+          g_row.append("text").text(prodlst.length - 1).attr("fill", "black").attr("font-size", fontsizefeature).attr("font-family", font).attr("x", x + etw / 2).attr("y", 3.5 + (rowh - 3.5) / 2).attr("text-anchor", "middle").attr("dominant-baseline", "middle");
+          g_row.append("rect").attr("fill", "white").attr("fill-opacity", 0).attr("x", x).attr("y", 3.5).attr("width", etw).attr("height", rowh - 4).on("mouseover", (event) => {
+            logobg2.attr("stroke-width", "2");
+            const table = tip.clear().showunder(event.target).d.append("table").style("border-spacing", "10px").style("border-collapse", "separate");
+            const tr1 = table.append("tr");
+            const tr2 = table.append("tr");
+            for (var k = 1; k < prodlst.length; k++) {
+              this.eventlogo([prodlst[k]], tr1.append("td"));
+              this.prodstat(prodlst[k], tr2.append("td"));
+            }
+          }).on("mouseout", () => {
+            logobg2.attr("stroke-width", "1");
+            tip.hide();
+          });
+        }
+        x = chrAw + s1 + rowh + s7 + geneAw + genesp + s2 + genesp + geneBw + s7 + rowh + s1 + chrBw + s3 + eventlogow + s6;
+        const text = g_row.append("text").text(evt.svg.recurtext).attr("font-size", fontsize - 4).attr("font-family", font).attr("fill", evt.svg.recurtextcolor).attr("x", x).attr("y", rowh / 2).attr("dominant-baseline", "middle");
+        if (evt.svg.hasrecurrence) {
+          text.attr("class", "sja_svgtext2").on("mouseover", (event) => {
+            const p = event.target.getBoundingClientRect();
+            tip.clear().show(p.left + p.width + 10, p.top - 15);
+            const slst = this.elab2sample[evt.label];
+            const dd = tip.d;
+            dd.append("div").style("margin", "10px").style("color", "#aaa").text("This fusion is recurrent in other samples:");
+            const table = dd.append("table").style("border-spacing", "10px").style("border-collapse", "separate");
+            for (const s of slst) {
+              if (s.name == sample.name) {
+                continue;
+              }
+              const tr = table.append("tr");
+              tr.append("td").style("font-weight", "bold").style("color", "#858585").text(s.name);
+              this.eventlogo(s.events[evt.label], tr.append("td"));
+            }
+          }).on("mouseout", () => tip.hide());
+        }
+        g_row.append("rect").attr("x", chrAw + s1 + rowh + s7).attr("width", geneAw + genesp + s2 + genesp + geneBw).attr("height", rowh).attr("fill", "white").attr("fill-opacity", 0).on("mouseover", (event) => {
+          boxa.attr("stroke-width", 2);
+          boxb.attr("stroke-width", 2);
+          const p = event.target.getBoundingClientRect();
+          tip.clear().show(p.left + p.width + s7 / 2, p.top - 30);
+          this.showsvpairs({
+            prodlst: evt.lst,
+            holder: tip.d,
+            nodetail: true,
+            sample,
+            eglst,
+            showothersample: true
+          });
+        }).on("mouseout", () => {
+          tip.hide();
+          boxa.attr("stroke-width", 1);
+          boxb.attr("stroke-width", 1);
+        }).on("click", (event) => {
+          if (evt.inclick) {
+            return;
+          }
+          evt.inclick = true;
+          const p = event.target.getBoundingClientRect();
+          const pane3 = newpane({
+            x: p.left + p.width + s7 + rowh + s1 + chrBw + s3 + eventlogow + s6 + recurw + 5,
+            y: p.top - 100,
+            close: function() {
+              evt.inclick = false;
+              pane3.pane.remove();
+            }
+          });
+          const prod2 = evt.lst[0];
+          pane3.header.html(
+            '<span style="padding:2px 4px;background-color:' + colorbgleft + ';">' + (prod2.geneA ? prod2.geneA : prod2.chrA) + '</span><span style="padding:2px 4px;background-color:' + colorbgright + ';">' + (prod2.geneB ? prod2.geneB : prod2.chrB) + "</span>"
+          );
+          this.showsvpairs({
+            prodlst: evt.lst,
+            holder: pane3.body
+          });
+        });
+        if (extevt.a) {
+          g_row.append("circle").attr("cx", chrAw + s1 + rowh / 2).attr("cy", rowh / 2).attr("r", rowh / 2).attr("fill", "white").attr("fill-opacity", 0).on("mouseover", (event) => this.extevt_mover(extevt.a, event.target, sample)).on("mouseout", () => {
+            this.extevt_mo(extevt.a);
+            tip.hide();
+          }).on("click", (event) => {
+            this.extevt_c(extevt.a, event.target, sample);
+          });
+        }
+        if (extevt.b) {
+          g_row.append("circle").attr("cx", chrAw + s1 + rowh + s7 + geneAw + genesp + s2 + genesp + geneBw + s7 + rowh / 2).attr("cy", rowh / 2).attr("r", rowh / 2).attr("fill", "white").attr("fill-opacity", 0).on("mouseover", (event) => this.extevt_mover(extevt.b, event.target, sample)).on("mouseout", () => {
+            this.extevt_mo(extevt.b);
+            tip.hide();
+          }).on("click", (event) => this.extevt_c(extevt.b, event.target, sample));
+        }
+        y1 += rowh + rows;
+        evtid++;
+      }
+      y += groupheight + (eg.lst.length > 1 ? gvpad : 0);
+    }
+    holder.style("display", "none");
+  }
+  extevt_mover(ext, dom, sample) {
+    ext.circle.attr("fill", "#858585");
+    if (ext.text) {
+      ext.text.attr("fill", "white");
+    }
+    tip.clear().showunder(dom);
+    tip.d.append("div").style("margin", "10px").style("color", "#aaa").text("Associated fusions from this sample:");
+    this.extevt_table(ext.lst, tip.d, sample);
+  }
+  extevt_mo(ext) {
+    ext.circle.attr("fill", "white");
+    if (ext.text) {
+      ext.text.attr("fill", "black");
+    }
+  }
+  extevt_c(ext, dom, sample) {
+    const p = dom.getBoundingClientRect();
+    const pane = newpane({ x: p.left, y: p.top + p.height + 10 });
+    this.extevt_table(ext.lst, pane.body, sample);
+  }
+  extevt_table(lst, holder, sample) {
+    const table = holder.append("table").style("border-spacing", "10px").style("border-collapse", "separate");
+    for (const elab of lst) {
+      const tr = table.append("tr");
+      const prodlst = sample.events[elab];
+      if (!prodlst) {
+        tr.append('<td colspan=2 style="color:red">No products found for ' + elab + "</td>");
+        continue;
+      }
+      const prod = prodlst[0];
+      tr.append("td").style("text-align", "right").text(prod.geneA ? prod.geneA : prod.chrA);
+      tr.append("td").text(prod.geneB ? prod.geneB : prod.chrB);
+      this.eventlogo(prodlst, tr.append("td"));
+    }
+  }
+  eventlogo(prodlst, holder) {
+    const d = holder.append("div");
+    if (!prodlst || prodlst.length == 0) {
+      d.style("color", "red").text("No products");
+    } else {
+      const p = prodlst[0];
+      d.append("div").style("display", "inline-block").style("padding", "2px 4px").style("border", "solid 1px #858585").style("border-radius", "5px").html(
+        p.rating + '&nbsp;<span style="font-size:70%;vertical-align:2px;' + (p.usepair ? p.usepair.inframe ? "padding:2px 4px;background-color:" + colorinframe + ';color:white;">IN' : "padding:2px 4px;background-color:" + coloroutframe + ';color:white;">O' : 'padding:1px 3px;border:solid 1px black;background-color:white;color:black;">?') + '</span>&nbsp;<span style="color:#858585">' + p.type2 + '</span>&nbsp;<div style="display:inline-block;font-size:70%;line-height:.9">' + p.featureA + "<br>" + p.featureB + "</div>&nbsp;" + Math.floor(p.score)
+      );
+      if (prodlst.length > 1) {
+        d.append("div").style("display", "inline-block").style("margin-left", "10px").style("padding", "2px 4px").style("font-size", ".7em").style("border", "solid 1px #858585").style("border-radius", 5).text(prodlst.length - 1);
+      }
+    }
+    return d;
+  }
+  prodstat(prod, holder) {
+    holder.append("p").text("Product id: " + prod.prodid);
+    const alertcolor = "#FFb3b3", bg = "#f1f1f1";
+    const table = holder.append("table").style("border-spacing", "8px").style("border-collapse", "separate");
+    let tr = table.append("tr");
+    tr.append("td");
+    tr.append("td").style("background-color", bg).text(prod.geneA ? prod.geneA : prod.chrA);
+    tr.append("td").style("background-color", bg).text(prod.geneB ? prod.geneB : prod.chrB);
+    tr = table.append("tr");
+    tr.append("td").style("font-size", "80%").style("background-color", bg).text("chimeric reads");
+    tr.append("td").style("padding", "5px").style("background-color", prod.readsA <= this.cf_reads ? alertcolor : "").text(prod.readsA);
+    tr.append("td").style("padding", "5px").style("background-color", prod.readsB <= this.cf_reads ? alertcolor : "").text(prod.readsB);
+    tr = table.append("tr");
+    tr.append("td").style("font-size", "80%").style("background-color", bg).text("ratio");
+    tr.append("td").style("padding", "5px").style("background-color", prod.ratioA <= this.cf_ratio ? alertcolor : "").text(Math.ceil(prod.ratioA * 100) + "%");
+    tr.append("td").style("padding", "5px").style("background-color", prod.ratioB <= this.cf_ratio ? alertcolor : "").text(Math.ceil(prod.ratioB * 100) + "%");
+    tr = table.append("tr");
+    tr.append("td").style("font-size", "80%").style("background-color", bg).text("contig length");
+    tr.append("td").style("padding", "5px").style("background-color", prod.matchA <= this.cf_match ? alertcolor : "").text(prod.matchA + " bp");
+    tr.append("td").style("padding", "5px").style("background-color", prod.matchB <= this.cf_match ? alertcolor : "").text(prod.matchB + " bp");
+    tr = table.append("tr");
+    tr.append("td").style("font-size", "80%").style("background-color", bg).text("repeat score");
+    tr.append("td").style("padding", "5px").style("background-color", prod.repeatA >= this.cf_repeat ? alertcolor : "").text(prod.repeatA);
+    tr.append("td").style("padding", "5px").style("background-color", prod.repeatB >= this.cf_repeat ? alertcolor : "").text(prod.repeatB);
+  }
+  showsvpairs(arg) {
+    const table = arg.holder.append("table").style("border-spacing", "10px").style("border-collapse", "separate");
+    const tr = table.append("tr");
+    const _tr = table.append("tr");
+    const expressiontd = _tr.append("td").attr("colspan", arg.prodlst.length);
+    const tr2 = table.append("tr");
+    const geneset = /* @__PURE__ */ new Set();
+    for (const prod of arg.prodlst) {
+      if (prod.geneA) {
+        geneset.add(prod.geneA);
+      }
+      if (prod.geneB) {
+        geneset.add(prod.geneB);
+      }
+      const td = tr.append("td").style("vertical-align", "top");
+      if (arg.nodetail) {
+        const div = td.append("div");
+        div.append("span").style("padding-right", "20px").text("Product id: " + prod.prodid);
+        const ratingsl = div.append("select").style("margin-right", "5px").on("change", (event) => {
+          const sl = event.target;
+          const newv = sl.options[sl.selectedIndex].innerHTML;
+          prod.rating = newv;
+          if (prod.hook.mainRating) {
+            prod.hook.mainRating.text(newv);
+          }
+          if (prod.hook.lessRating) {
+            prod.hook.lessRating.text(newv);
+          }
+        });
+        const framesl = div.append("select").style("margin-right", "5px").on("change", (event) => {
+          const sl = event.target;
+          const inframe = sl.options[sl.selectedIndex].innerHTML == "in-frame";
+          prod.usepair.inframe = inframe;
+          if (prod.hook.mainFrame) {
+            prod.hook.mainFrame.text.text(inframe ? "IN" : "O");
+            prod.hook.mainFrame.bg.attr("fill", inframe ? colorinframe : coloroutframe);
+          }
+          if (prod.hook.lessFrame) {
+            prod.hook.lessFrame.html(
+              inframe ? '<span style="background-color:' + colorinframe + ';color:white;padding:2px 3px;font-size:80%;white-space:nowrap">In frame</span>' : '<span style="background-color:' + coloroutframe + ';color:white;padding:2px 3px;font-size:80%;white-space:nowrap">Out of frame</span>'
+            );
+          }
+        });
+        const typesl = div.append("select").style("margin-right", "5px").on("change", (event) => {
+          const sl = event.target;
+          const i = sl.selectedIndex;
+          const newv = sl.options[i].innerHTML;
+          prod.type2 = newv;
+          if (prod.hook.mainType) {
+            prod.hook.mainType.text(newv);
+          }
+          prod.iscloss = i == 0;
+          prod.isnloss = i == 1;
+          prod.isfusion = i == 2;
+          prod.isitd = i == 3;
+          prod.isuptss = i == 4;
+          prod.isother = i == 5;
+        });
+        const effectsl = div.append("select").style("margin-right", "5px").on("change", (event) => {
+          const sl = event.target;
+          const newv = sl.options[sl.selectedIndex].innerHTML;
+          prod.functioneffect = newv;
+        });
+        div.append("button").text("Create group").on("click", (event) => {
+          let dnew = document.createElement("div");
+          div.node().insertBefore(dnew, event.target);
+          select_default(event.target).remove();
+          dnew = select_default(dnew);
+          dnew.style("display", "inline-block");
+          if (!arg.eglst) {
+            dnew.text("Cannot do it here: please go to sample " + arg.sample.name);
+            return;
+          }
+          dnew.append("input").attr("size", 10).property("value", prod.prodid + ",");
+          dnew.append("button").style("margin", "0px 10px").text("Apply").on("click", (event2) => {
+            const lst0 = event2.target.previousSibling.value.trim().split(",");
+            const goodid = [];
+            for (const i of lst0) {
+              const j = Number.parseInt(i);
+              if (Number.isNaN(j)) return alert("invalid id " + i);
+              if (this.prodidisinvalid(j, arg.sample)) return alert("invalid id " + j);
+              goodid.push(j);
+            }
+            if (goodid.length <= 1) return alert("need at least 2 id");
+            const newevtlst = [];
+            for (const i of goodid) {
+              const thisprod = this.extractprod(i, arg.sample);
+              if (thisprod) {
+                newevtlst.push({ label: thisprod.eventlabel, lst: [thisprod] });
+              } else {
+                return alert("invalid id " + i);
+              }
+            }
+            if (newevtlst.length <= 1) return alert("less than 2 products cannot make a group");
+            arg.eglst.unshift({ lst: newevtlst, ismsg: true });
+            this.showsample(arg.sample);
+            tip.hide();
+          });
+        });
+        ratingsl.append("option").text("HQ");
+        ratingsl.append("option").text("LQ");
+        ratingsl.append("option").text("RT");
+        ratingsl.append("option").text("bad");
+        ratingsl.append("option").text("Major");
+        switch (prod.rating) {
+          case "HQ":
+            ratingsl.property("selectedindex", 0);
+            break;
+          case "LQ":
+            ratingsl.property("selectedIndex", 1);
+            break;
+          case "RT":
+            ratingsl.property("selectedIndex", 2);
+            break;
+          case "bad":
+            ratingsl.property("selectedIndex", 3);
+            break;
+          case "Major":
+            ratingsl.property("selectedIndex", 4);
+            break;
+          default:
+            alert("unknown rating: " + prod.rating);
+        }
+        framesl.append("option").text("in-frame");
+        framesl.append("option").text("out-of-frame");
+        if (!prod.usepair) {
+          framesl.attr("disabled", 1);
+        } else {
+          framesl.property("selectedIndex", prod.usepair.inframe ? 0 : 1);
+        }
+        typesl.append("option").text("CLoss");
+        typesl.append("option").text("NLoss");
+        typesl.append("option").text("Fusion");
+        typesl.append("option").text("ITD");
+        typesl.append("option").text("upTSS");
+        typesl.append("option").text("other");
+        if (prod.iscloss) {
+          typesl.property("selectedIndex", 0);
+        } else if (prod.isnloss) {
+          typesl.property("selectedIndex", 1);
+        } else if (prod.isfusion) {
+          typesl.property("selectedIndex", 2);
+        } else if (prod.isitd) {
+          typesl.property("selectedIndex", 3);
+        } else if (prod.isuptss) {
+          typesl.property("selectedIndex", 4);
+        } else if (prod.isother) {
+          typesl.property("selectedIndex", 5);
+        } else {
+          alert("unknown type2: " + prod.type2);
+        }
+        effectsl.append("option").text("unknown effect");
+        effectsl.append("option").text("fusion gene");
+        effectsl.append("option").text("truncation, activated oncogene");
+        effectsl.append("option").text("truncation, loss-of-function");
+        effectsl.append("option").text("truncation, no consequence");
+        effectsl.append("option").text("ITD");
+        switch (prod.functioneffect) {
+          case void 0:
+            effectsl.property("selectedIndex", 0);
+            break;
+          case "fusion gene":
+            effectsl.property("selectedIndex", 1);
+            break;
+          case "truncation, activated oncogene":
+            effectsl.property("selectedIndex", 2);
+            break;
+          case "truncation, loss-of-function":
+            effectsl.property("selectedIndex", 3);
+            break;
+          case "truncation, no consequence":
+            effectsl.property("selectedIndex", 4);
+            break;
+          case "ITD":
+            effectsl.property("selectedIndex", 5);
+            break;
+        }
+      }
+      const p = {
+        a: {
+          chr: prod.chrA,
+          position: prod.posA,
+          strand: prod.ortA,
+          name: prod.geneA ? prod.geneA : prod.chrA,
+          ratio: prod.ratioA.toFixed(2),
+          feature: prod.featureA,
+          contiglen: prod.matchA,
+          chimericreads: prod.readsA,
+          repeatscore: prod.repeatA
+        },
+        b: {
+          chr: prod.chrB,
+          position: prod.posB,
+          strand: prod.ortB,
+          name: prod.geneB ? prod.geneB : prod.chrB,
+          ratio: prod.ratioB.toFixed(2),
+          feature: prod.featureB,
+          contiglen: prod.matchB,
+          chimericreads: prod.readsB,
+          repeatscore: prod.repeatB
+        },
+        rating: prod.rating,
+        score: Math.ceil(prod.score),
+        originalprod: prod
+      };
+      if (prod.usepair) {
+        p.inframe = prod.usepair.inframe;
+        const x = prod.usepair.a;
+        p.a.gm = this.genome.isoformmatch(x.isoform, prod.chrA, prod.posA);
+        p.a.codon = x.codon;
+        p.a.exon = x.exon;
+        p.a.atupstream = x.atupstream;
+        p.a.atdownstream = x.atdownstream;
+        p.a.atutr5 = x.atutr5;
+        p.a.atutr3 = x.atutr3;
+        const y = prod.usepair.b;
+        p.b.gm = this.genome.isoformmatch(y.isoform, prod.chrB, prod.posB);
+        p.b.codon = y.codon;
+        p.b.exon = y.exon;
+        p.b.atupstream = y.atupstream;
+        p.b.atdownstream = y.atdownstream;
+        p.b.atutr5 = y.atutr5;
+        p.b.atutr3 = y.atutr3;
+        let aalen = 0, bplen2 = 0;
+        if (x.contigaa && y.contigaa) {
+          aalen = y.contigaa - x.contigaa - 1;
+        }
+        if (x.contigbp && y.contigbp) {
+          bplen2 = y.contigbp - x.contigbp - 1;
+        }
+        if (aalen) {
+          p.interstitial = { aalen };
+        }
+        if (bplen2) {
+          if (!p.interstitial) p.interstitial = {};
+          p.interstitial.bplen = bplen2;
+        }
+      }
+      svtable({
+        samplelst: [
+          {
+            pairlst: [p]
+          }
+        ],
+        nosample: true,
+        holder: td
+      });
+      const par = {
+        pairlst: [p],
+        genome: this.genome,
+        holder: td,
+        quiet: true,
+        hostURL: this.hostURL,
+        jwt: this.jwt
+      };
+      import("./svgraph-VJLB7BBN.js").then((p2) => {
+        p2.default(par);
+      });
+      if (!arg.nodetail) {
+        const td2 = tr2.append("td").style("font-size", ".8em").style("vertical-align", "top");
+        const lst = [];
+        for (const at of this.atlst) {
+          if (!at.custom) continue;
+          const v = prod[at.key];
+          lst.push({
+            k: at.label,
+            v: v == void 0 ? "" : v
+          });
+        }
+        make_table_2col(td2, lst, 25);
+        prod.pairs.sort((a, b) => {
+          if (a.inuse) return -1;
+          if (b.inuse) return 1;
+          return 0;
+        });
+        const table0 = td2.append("table");
+        for (const pair of prod.pairs) {
+          const tr3 = table0.append("tr");
+          tr3.append("td").html(
+            (pair.inframe ? "in-frame" : "out-of-frame") + '<div style="font-size:70%">frame code: ' + pair.frame + "</div>"
+          );
+          const td3 = tr3.append("td");
+          const table2 = td3.append("table").style("margin-bottom", "20px").style("border", pair.inuse ? "solid 1px black" : "").style("border-spacing", "10px").style("border-collapse", "separate");
+          let _tr2 = table2.append("tr").style("color", "#858585").style("font-size", ".7em");
+          _tr2.append("td").text("gene");
+          _tr2.append("td").text("isoform");
+          _tr2.append("td").text("gene position");
+          _tr2.append("td").text("exon");
+          _tr2.append("td").text("anchor");
+          _tr2.append("td").text("contig AA");
+          _tr2.append("td").text("contig bp");
+          const tr1 = table2.append("tr");
+          const tr22 = table2.append("tr");
+          tr1.append("td").text(prod.geneA ? prod.geneA : prod.chrA);
+          tr22.append("td").text(prod.geneB ? prod.geneB : prod.chrB);
+          tr1.append("td").text(pair.a.isoform ? pair.a.isoform : "");
+          tr22.append("td").text(pair.b.isoform ? pair.b.isoform : "");
+          tr1.append("td").text(
+            pair.a.isoform ? pair.a.codon != void 0 ? "codon: " + pair.a.codon : pair.a.atutr5 ? "5' UTR" : pair.a.atutr3 ? "3' UTR" : pair.a.atupstream ? "upstream" : "downstream" : ""
+          );
+          tr22.append("td").text(
+            pair.b.isoform ? pair.b.codon != void 0 ? "codon: " + pair.b.codon : pair.b.atutr5 ? "5' UTR" : pair.b.atutr3 ? "3' UTR" : pair.b.atupstream ? "upstream" : "downstream" : ""
+          );
+          tr1.append("td").text(pair.a.exon ? pair.a.exon : "");
+          tr22.append("td").text(pair.b.exon ? pair.b.exon : "");
+          tr1.append("td").text(pair.a.anchor ? pair.a.anchor : "");
+          tr22.append("td").text(pair.b.anchor ? pair.b.anchor : "");
+          tr1.append("td").html(pair.a.contigaa ? '<span style="color:#858585;font-size:70%">ends at</span> ' + pair.a.contigaa : "?");
+          tr22.append("td").html(
+            pair.b.contigaa ? '<span style="color:#858585;font-size:70%">starts at</span> ' + pair.b.contigaa : "?"
+          );
+          tr1.append("td").html(pair.a.contigbp ? '<span style="color:#858585;font-size:70%">ends at</span> ' + pair.a.contigbp : "?");
+          tr22.append("td").html(
+            pair.b.contigbp ? '<span style="color:#858585;font-size:70%">starts at</span> ' + pair.b.contigbp : "?"
+          );
+        }
+      }
+    }
+    if (!arg.sample) {
+      return;
+    }
+    const thislab = arg.prodlst[0].eventlabel;
+    const samplelst = this.elab2sample[thislab];
+    const othersample = [];
+    if (samplelst) {
+      for (const s of samplelst) {
+        if (s.name != arg.sample.name) othersample.push(s);
+      }
+    }
+    if (arg.showothersample && othersample.length > 0) {
+      arg.holder.append("button").style("display", "block").style("margin", "20px").text("Show in " + othersample.length + " other sample" + (othersample.length > 1 ? "s" : "")).on("click", (event) => {
+        select_default(event.target).remove();
+        for (const sample of othersample) {
+          const prodlst = sample.events[thislab];
+          if (!prodlst) {
+            arg.holder.append("div").style("margin", "20px").style("color", "red").text("Error: no products for this event in " + sample.name);
+            continue;
+          }
+          const table2 = arg.holder.append("table").style("margin-top", "20px").style("border", "solid 1px #ccc");
+          const tr3 = table2.append("tr");
+          tr3.append("td").text(sample.name);
+          const td = tr3.append("td");
+          this.showsvpairs({
+            prodlst,
+            holder: td,
+            nodetail: true,
+            sample,
+            // FIXME: eglst info is hidden somewhere in sample.egglst
+            eglst: null
+          });
+        }
+      });
+    }
+    if (this.expression.genes && geneset.size > 0) {
+      const table2 = expressiontd.append("table");
+      const tr3 = table2.append("tr");
+      for (const gene of geneset) {
+        const expd = this.expression.genes[gene];
+        if (expd) {
+          const div = tr3.append("td").style("vertical-align", "top").append("div").style("display", "inline-block").style("margin-right", "20px").style("border", "solid 1px #ccc");
+          div.append("div").style("background-color", "#ededed").style("padding", "10px").text(gene);
+          if (arg.sample) {
+            for (const v of expd) {
+              if (v.sample == arg.sample.name) {
+                v.ishighlight = true;
+                div.append("div").style("padding", "10px").style("font-size", "70%").html("Expression in " + arg.sample.name + ': <span style="font-size:150%">' + v.value + "</span>");
+              } else {
+                v.ishighlight = false;
+              }
+            }
+          }
+          showgenevalues({
+            data: this.expression.genes[gene],
+            holder: div.append("div").style("margin", "10px"),
+            width: 200,
+            height: 200,
+            namename: "sample"
+          });
+        } else {
+          tr3.append("td").style("vertical-align", "top").text("No expression data for " + gene + "</td>");
+        }
+      }
+    }
+  }
+  prodidisinvalid(id, sample) {
+    for (const egg of sample.egglst) {
+      for (const eg of egg.lst) {
+        for (const e of eg.lst) {
+          for (const p of e.lst) {
+            if (p.prodid == id) return false;
+          }
+        }
+      }
+    }
+    return true;
+  }
+  extractprod(id, sample) {
+    let prod = null;
+    for (let n = 0; n < sample.egglst.length; n++) {
+      const _egg = sample.egglst[n];
+      for (let j = 0; j < _egg.lst.length; j++) {
+        const _eg = _egg.lst[j];
+        for (let k = 0; k < _eg.lst.length; k++) {
+          const _evt = _eg.lst[k];
+          for (let p = 0; p < _evt.lst.length; p++) {
+            const p2 = _evt.lst[p];
+            if (p2.prodid == id) {
+              prod = p2;
+              _evt.lst.splice(p, 1);
+              break;
+            }
+          }
+          if (prod) {
+            if (_evt.lst.length == 0) {
+              _eg.lst.splice(k, 1);
+            }
+            break;
+          }
+        }
+        if (prod) {
+          if (_eg.lst.length == 0) {
+            _egg.lst.splice(j, 1);
+          } else {
+            if (_eg.ismsg && _eg.lst.length == 1) {
+              delete _eg.ismsg;
+            }
+          }
+          break;
+        }
+      }
+      if (prod) {
+        if (_egg.lst.length == 0) {
+          sample.egglst.splice(n, 1);
+        }
+        break;
+      }
+    }
+    return prod;
+  }
+  // end of class
+};
+function msjoin(prod, newholder) {
+  if (prod.isitd) return;
+  if (prod.sv_ort == "?") return;
+  var single = true;
+  var thispair = prod.usepair;
+  for (var i = 0; i < newholder.length; i++) {
+    var tmplst = newholder[i];
+    var prod2 = tmplst[0];
+    if (prod.chrB == prod2.chrA && prod.ortB == prod2.ortA) {
+      if (testreadcount(prod, prod2)) {
+        var thatpair = prod2.usepair;
+        if (thispair && thatpair && thispair.b.isoform && thispair.b.isoform == thatpair.a.isoform) {
+          var p1 = thispair.b;
+          var p2 = thatpair.a;
+          var ahead = false;
+          if (p1.atutr5) {
+            if (p2.codon != void 0) {
+              ahead = true;
+              prod2.mswhat = "5' UTR to coding region";
+            } else if (p2.atutr3) {
+              ahead = true;
+              prod2.mswhat = "5' UTR to 3' UTR";
+            } else if (p2.atutr5 && p1.atutr5.off < p2.atutr5.off) {
+              ahead = true;
+              prod2.mswhat = p2.atutr5.off - p1.atutr5.off + " bp apart in 5' UTR";
+            }
+          } else if (p1.atutr3) {
+            if (p2.atutr3 && p1.atutr3.off < p2.atutr3.off) {
+              ahead = true;
+              prod2.mswhat = p2.atutr3.off - p1.atutr3.off + " bp apart in 3' UTR";
+            }
+          } else if (p1.codon != void 0) {
+            if (p2.codon != void 0 && p2.codon > p1.codon) {
+              ahead = true;
+              prod2.mswhat = p2.codon - p1.codon + " aa apart in protein";
+            } else if (p2.atutr3) {
+              ahead = true;
+              prod2.mswhat = "coding region to 3' UTR";
+            }
+          }
+          if (ahead) {
+            tmplst.unshift(prod);
+            single = false;
+            break;
+          }
+        }
+        var dst = prod2.posA - prod.posB;
+        if (prod.ortB == "+" && dst > 0 && dst < genomelimit || prod.ortB == "-" && dst < 0 && -dst < genomelimit) {
+          prod2.mswhat = Math.abs(dst) + " bp apart on genome";
+          tmplst.unshift(prod);
+          single = false;
+          break;
+        }
+      }
+    }
+    prod2 = tmplst[tmplst.length - 1];
+    if (prod.chrA == prod2.chrB && prod.ortA == prod2.ortB) {
+      if (testreadcount(prod2, prod)) {
+        var thatpair = prod2.usepair;
+        if (thispair && thatpair && thispair.a.isoform && thispair.a.isoform == thatpair.b.isoform) {
+          var p1 = thatpair.b;
+          var p2 = thispair.a;
+          var behind = false;
+          if (p1.atutr5) {
+            if (p2.codon != void 0) {
+              behind = true;
+              prod.mswhat = "5' UTR to coding region";
+            } else if (p2.atutr3) {
+              behind = true;
+              prod.mswhat = "5' UTR to 3' UTR";
+            } else if (p2.atutr5 && p1.atutr5.off < p2.atutr5.off) {
+              behind = true;
+              prod.mswhat = p2.atutr5.off - p1.atutr5.off + " bp apart in 5' UTR";
+            }
+          } else if (p1.atutr3) {
+            if (p2.atutr3 && p1.atutr3.off < p2.atutr3.off) {
+              behind = true;
+              prod.mswhat = p2.atutr3.off - p1.atutr3.off + " bp apart in 3' UTR";
+            }
+          } else if (p1.codon != void 0) {
+            if (p2.codon != void 0 && p2.codon > p1.codon) {
+              behind = true;
+              prod.mswhat = p2.codon - p1.codon + " aa apart in protein";
+            } else if (p2.atutr3) {
+              behind = true;
+              prod.mswhat = "coding region to 3' UTR";
+            }
+          }
+          if (behind) {
+            tmplst.push(prod);
+            single = false;
+            break;
+          }
+        }
+        var dst = prod.posA - prod2.posB;
+        if (prod.ortA == "+" && dst > 0 && dst < genomelimit && prod.ortA == "-" && dst < 0 && -dst < genomelimit) {
+          prod.mswhat = Math.abs(dst) + " bp apart on genome";
+          tmplst.push(prod);
+          single = false;
+          break;
+        }
+      }
+    }
+  }
+  if (single) {
+    newholder.push([prod]);
+  }
+  function testreadcount(p12, p22) {
+    if (!p12.usepair || !p12.usepair.inframe) return false;
+    if (!p22.usepair || !p22.usepair.inframe) return false;
+    if (p12.readsB == 0 || p22.readsA == 0) return false;
+    var fold = p12.readsB / p22.readsA;
+    return fold >= 0.2 && fold <= 5;
+  }
+}
+function svtable(arg) {
+  const table = arg.holder.append("table").style("border-spacing", "10px").style("border-collapse", "separate");
+  const htr = table.append("tr").style("font-size", "70%").style("color", "#858585");
+  const fields = [
+    { label: "Feature", hide: true, get: (a) => a.feature },
+    { label: "Ratio", hide: true, get: (a) => Math.ceil(a.ratio * 100) + "%" },
+    { label: "Chimeric<br>reads", hide: true, get: (a) => a.chimericreads },
+    { label: "Contig<br>length", hide: true, get: (a) => a.contiglen },
+    { label: "Repeat<br>score", hide: true, get: (a) => a.repeatscore },
+    { label: "Cicero<br>score", hide: true, atpair: true, get: (a) => a.score },
+    { label: "Cicero<br>rating", israting: true, hide: true, atpair: true, get: (a) => a.rating }
+  ];
+  for (const sample of arg.samplelst) {
+    for (const p of sample.pairlst) {
+      if (p.a.feature || p.b.feature) fields[0].hide = false;
+      if (typeof p.a.ratio == "number" || typeof (p.b.ratio == "number")) fields[1].hide = false;
+      if (typeof p.a.chimericreads == "number" || typeof p.b.chimericreads == "number") fields[2].hide = false;
+      if (typeof p.a.contiglen == "number" || typeof p.b.contiglen == "number") fields[3].hide = false;
+      if (typeof p.a.repeatscore == "number" || typeof p.b.repeatscore == "number") fields[4].hide = false;
+      if (typeof p.score == "number") fields[5].hide = false;
+      if (p.rating) fields[6].hide = false;
+    }
+  }
+  if (!arg.nosample) {
+    htr.append("td");
+  }
+  htr.append("td");
+  htr.append("td");
+  htr.append("td").html("Genomic<br>position");
+  htr.append("td").html("Genomic<br>dist.");
+  for (const f of fields) {
+    if (f.hide) return;
+    htr.append("td").html(f.label);
+  }
+  for (const sample of arg.samplelst) {
+    let tr = table.append("tr");
+    if (!arg.nosample) {
+      const td = tr.append("td").text(sample.sample);
+      if (sample.pairlst.length > 1) {
+        td.attr("rowspan", sample.pairlst.length);
+      }
+    }
+    for (let i = 0; i < sample.pairlst.length; i++) {
+      if (i > 0) {
+        tr = table.append("tr");
+      }
+      const pair = sample.pairlst[i];
+      tr.append("td").style("text-align", "right").html(
+        '<span style="background-color:' + colorbgleft + ';padding:2px 3px;font-size:80%">' + pair.a.name + '</span><span style="background-color:' + colorbgright + ';padding:2px 3px;font-size:80%">' + pair.b.name + "</span>"
+      );
+      const td = tr.append("td");
+      if (pair.originalprod && pair.originalprod.hook.lessFrame) {
+        pair.originalprod.hook.lessFrame = td;
+      }
+      if (pair.inframe) {
+        td.html(
+          '<span style="background-color:' + colorinframe + ';color:white;padding:2px 3px;font-size:80%;white-space:nowrap">In frame</span>'
+        );
+      } else {
+        if (pair.a.gm || pair.b.gm) {
+          td.html(
+            '<span style="background-color:#858585;color:white;padding:2px 3px;font-size:80%;white-space:nowrap">Out of frame</span>'
+          );
+        } else {
+          td.html(
+            '<span style="border:solid 1px #858585;color:#858585;padding:1px 2px;font-size:80%;white-space:nowrap">no gene ?</span>'
+          );
+        }
+      }
+      tr.append("td").html(
+        '<div style="background-color:' + colorbgleft + ';padding:1px 3px;font-size:70%;white-space:nowrap">' + pair.a.chr + ":" + pair.a.position + " " + pair.a.strand + '</div><div style="background-color:' + colorbgright + ';padding:1px 3px;font-size:70%;white-space:nowrap">' + pair.b.chr + ":" + pair.b.position + " " + pair.b.strand + "</div>"
+      );
+      tr.append("td").html(
+        pair.a.chr == pair.b.chr ? bplen(Math.abs(pair.a.position - pair.b.position)) : '<span style="color:' + colorctx + '">CTX</span>'
+      );
+      for (const f of fields) {
+        if (f.hide) continue;
+        const td2 = tr.append("td");
+        if (f.israting && pair.originalprod && pair.originalprod.hook.lessRating) {
+          pair.originalprod.hook.lessRating = td2;
+        }
+        if (f.atpair) {
+          td2.text(f.get(pair));
+        } else {
+          td2.html(
+            '<span style="background-color:' + colorbgleft + ';padding:2px 3px;font-size:80%">' + f.get(pair.a) + '</span><span style="background-color:' + colorbgright + ';padding:2px 3px;font-size:80%">' + f.get(pair.b) + "</span>"
+          );
+        }
+      }
+    }
+  }
+}
+function loadexpression(svmr, file) {
+  const genes = {};
+  const ep = svmr.expression;
+  ep.genes = genes;
+  const reader = new FileReader();
+  const chunksize = 4096;
+  let chunks = [];
+  let offset = 0;
+  reader.onloadend = (e) => {
+    if (e.target.readyState != FileReader.DONE) return;
+    const chunk = e.target.result;
+    chunks.push(chunk);
+    const isend = offset >= file.size;
+    process(isend);
+    if (isend) {
+      done();
+    } else {
+      offset += chunksize;
+      ep.presays.text("Reading file: " + Math.ceil(offset / file.size * 100) + "%");
+      reader.readAsText(file.slice(offset, offset + chunksize));
+    }
+  };
+  reader.readAsText(file.slice(0, chunksize));
+  const hg = {}, hs = {};
+  let good = 0, bad = 0;
+  function process(isend) {
+    const lines = chunks.join("").split("\n");
+    for (let i = 0; i < lines.length - 1 - (isend ? 0 : 1); i++) {
+      const l = lines[i].split("	");
+      if (l.length == 3) {
+        const v = Number.parseFloat(l[1]);
+        if (Number.isNaN(v)) {
+          bad++;
+        } else {
+          good++;
+          hg[l[0]] = 1;
+          hs[l[2]] = 1;
+          if (!(l[0] in genes)) {
+            genes[l[0]] = [];
+          }
+          genes[l[0]].push({
+            sample: l[2],
+            value: v
+          });
+        }
+      } else {
+        bad++;
+      }
+    }
+    if (!isend) {
+      chunks = [lines[lines.length - 1]];
+    }
+  }
+  function done() {
+    let genec = 0;
+    for (const n in hg) genec++;
+    let samplec = 0;
+    for (const n in hs) samplec++;
+    disappear(ep.prediv);
+    appear(ep.afterdiv);
+    ep.afterdiv.selectAll("*").remove();
+    ep.afterdiv.append("div").text(
+      "Expression data loaded for " + genec + " genes, " + samplec + " samples, " + good + " data points" + (bad > 0 ? ", " + bad + " bad lines" : "")
+    );
+    ep.afterdiv.append("button").text("Delete").style("margin", "20px").on("click", () => {
+      delete ep.genes;
+      ep.prediv.node().removeChild(ep.input.node());
+      ep.input = ep.prediv.append("input").attr("type", "file").on("change", (event) => {
+        loadexpression(svmr, event.target.files[0]);
+      });
+      ep.presays.text("");
+      disappear(ep.afterdiv);
+      appear(ep.prediv);
+    });
+  }
+}
+function showgenevalues(arg) {
+  const hlcolor = "red";
+  arg.data.sort((a, b) => {
+    return b.value - a.value;
+  });
+  let width = arg.width ? arg.width : 400, height = arg.height ? arg.height : 400;
+  let maxv = 0;
+  for (const v of arg.data) {
+    maxv = Math.max(maxv, v.value);
+  }
+  let dotr;
+  const xscale = linear().domain([0, maxv]);
+  const svg = arg.holder.append("svg");
+  const axisg = svg.append("g");
+  const dotg = svg.append("g");
+  const dotset = dotg.selectAll().data(arg.data).enter().append("g");
+  const dotcir = dotset.append("circle").attr("fill", "white").attr("fill-opacity", 0).attr("stroke", (d) => d.ishighlight ? hlcolor : "black").attr("stroke-opacity", (d) => d.ishighlight ? 0.7 : 0.2).on("mouseover", (event, d) => {
+    event.target.setAttribute("transform", "scale(1.5)");
+    drag.text((d.sample ? d.sample : d.patient + " " + d.sampletype) + " " + d.value).attr("fill", d.ishighlight ? hlcolor : "black");
+  }).on("mouseout", (event, d) => {
+    event.target.setAttribute("transform", "scale(1)");
+    drag.text("drag to resize").attr("fill", "black");
+  });
+  const drag = svg.append("text").text("drag to resize").attr("font-size", 12).attr("class", "sja_svgtext").attr("font-family", font).attr("text-anchor", "end").on("mousedown", (event) => {
+    event.preventDefault();
+    const x0 = event.clientX, y0 = event.clientY, width0 = width, height0 = height;
+    const b = select_default(document.body);
+    b.on("mousemove", () => {
+      width = width0 + event.clientX - x0;
+      height = height0 + event.clientY - y0;
+      sizing();
+    }).on("mouseup", () => {
+      b.on("mousemove", null).on("mouseup", null);
+    });
+  });
+  function sizing() {
+    dotr = Math.max(5, Math.min(width, height) / 40);
+    const fontsize = Math.min(18, Math.max(12, dotr * 2)), ticksize = 5, axish = fontsize + ticksize + 5, axispad = dotr + 5, width2 = dotr * 3;
+    xscale.range([0, width]);
+    svg.attr("width", dotr * 2 + width + width2).attr("height", axish + axispad + height + dotr * 2);
+    axisstyle({
+      axis: axisg.attr("transform", "translate(" + dotr * 2 + "," + axish + ")").call(
+        axisTop().scale(xscale).ticks(Math.min(10, Math.ceil(width / 50)))
+      ),
+      fontsize,
+      color: "black",
+      showline: true
+    });
+    dotg.attr("transform", "translate(" + dotr * 2 + "," + (axish + axispad) + ")");
+    dotset.attr("transform", (d, i) => {
+      return "translate(" + xscale(d.value) + "," + height * i / arg.data.length + ")";
+    });
+    dotcir.attr("r", (d) => {
+      return dotr * (d.ishighlight ? 1.5 : 1);
+    });
+    drag.attr("font-size", fontsize).attr("x", dotr * 2 + width + width2 - 5).attr("y", axish + axispad + height + dotr * 2 - 5);
+  }
+  sizing();
+  return this;
+}
+
+// src/svmr.js
+function svmrparseinput(arg, sayerror2, genome, holder, hostURL, jwt) {
+  if (!arg.dataname) {
+    arg.dataname = "Unnamed dataset";
+  }
+  if (arg.input) {
+    const [e, header, items] = svmrparseraw(arg.input, genome);
+    if (e) {
+      sayerror2("Fusion Editor input error: " + e);
+      return;
+    }
+    svmrlaunch(genome, header, items, arg.dataname, holder, hostURL, jwt);
+    return;
+  }
+  if (!arg.urls) {
+    sayerror2('neither .input:"" or .urls:[] is provided for Fusion Editor');
+    return;
+  }
+  if (!Array.isArray(arg.urls)) {
+    sayerror2("fusioneditor.urls[] should be an array of URL strings");
+    return;
+  }
+  if (arg.urls.length == 0) {
+    sayerror2("fusioneditor.urls[] is empty");
+    return;
+  }
+  const wait = holder.append("div").style("margin", "20px").style("color", "#aaa").style("font-size", "1.5em").text("Loading fusion gene data ...");
+  const tasks = [];
+  arg.urls.forEach((url) => {
+    tasks.push(
+      fetch(
+        new Request(hostURL + "/urltextfile", {
+          method: "POST",
+          headers: { "content-type": "application/json" },
+          body: JSON.stringify({ url, jwt })
+        })
+      ).then((data) => {
+        return data.json();
+      }).then((data) => {
+        if (data.error) throw { message: "Error with " + url + ": " + data.error };
+        return { data: data.text, url };
+      })
+    );
+  });
+  Promise.all(tasks).then((data) => {
+    wait.remove();
+    if (data.length == 0) {
+      sayerror2("No data retrieved from fusioneditor.urls");
+      return;
+    }
+    const [e, header, items] = svmrparseraw(data[0].data, genome);
+    if (e) {
+      sayerror2("Error parsing fusion gene data in file " + data[0].url);
+      return;
+    }
+    for (let i = 1; i < data.length; i++) {
+      const [e2, header2, items2] = svmrparseraw(data[i].data, genome);
+      if (e2) {
+        sayerror2("Error parsing fusion gene data in file " + data[i].url);
+        return;
+      }
+      for (const j of items2) {
+        items.push(j);
+      }
+      for (const h of header2) {
+        let notfound = true;
+        for (const h2 of header) {
+          if (h2.key == h.key) {
+            notfound = false;
+            break;
+          }
+        }
+        if (notfound) {
+          header.push(h);
+        }
+      }
+    }
+    if (items.length == 0) {
+      sayerror2("No fusion genes parsed from fusioneditor");
+      return;
+    }
+    svmrlaunch(genome, header, items, arg.dataname, holder, hostURL, jwt);
+  }).catch((err) => {
+    wait.remove();
+    sayerror2(err.message);
+    if (err.stack) console.log(err.stack);
+  });
+}
+function svmrui(dlst, genomes, hostURL, jwt) {
+  const [pane, inputdiv, gselect, filediv, saydiv, visualdiv] = dlst;
+  inputdiv.append("div").style("margin-top", "20px").html(
+    "<p>Please upload CICERO output as a text file. See <a href=https://docs.google.com/document/d/1jkVYRPIJpkWvA9vqtahRlNn63Hk5DehjHbF_BH9k7Rs/edit?usp=sharing target=_blank>file format</a>.</p><p>See <a href=https://docs.google.com/document/d/1DRVzE_WenG490eRYB7VGFOygtSqtF5L97rhK0HOUCNY/edit?usp=sharing target=_blank>function usage</a>.</p>"
+  );
+  inputdiv.append("p").html("<a href=https://proteinpaint.stjude.org/ppdemo/hg19/fusion/cicero.output target=_blank>Example file</a>");
+  function cmt(t, red) {
+    saydiv.style("color", red ? "red" : "black").text(t);
+  }
+  const fileui = () => {
+    filediv.selectAll("*").remove();
+    const input = filediv.append("input").attr("type", "file").on("change", (event) => {
+      const file = event.target.files[0];
+      if (!file) {
+        fileui();
+        return;
+      }
+      if (!file.size) {
+        cmt("Invalid file " + file.name);
+        fileui();
+        return;
+      }
+      const reader = new FileReader();
+      reader.onload = (event2) => {
+        const usegenome = gselect.options[gselect.selectedIndex].innerHTML;
+        const genomeobj = genomes[usegenome];
+        const [err, header, items] = svmrparseraw(event2.target.result, genomeobj);
+        if (err) {
+          cmt(err, 1);
+          fileui();
+          return;
+        }
+        svmrlaunch(genomeobj, header, items, file.name, visualdiv, hostURL, jwt);
+        filediv.remove();
+        inputdiv.remove();
+      };
+      reader.onerror = function() {
+        cmt("Error reading file " + file.name, 1);
+        fileui();
+        return;
+      };
+      reader.readAsText(file, "utf8");
+    });
+    setTimeout(() => input.node().focus(), 1100);
+  };
+  fileui();
+}
+function svmrlaunch(genome, header, items, filename, holder, hostURL, jwt) {
+  new svmr_c_default(genome, header, items, filename, holder, hostURL, jwt);
+}
+function svmrparseraw(raw, genome) {
+  const lines = raw.trim().split("\n");
+  const [err, header] = parseheader(lines[0]);
+  if (err) {
+    return ["File header error: " + err];
+  }
+  const skipword = lines[0].split("	")[0];
+  const items = [];
+  const badlines = [];
+  for (let i = 1; i < lines.length; i++) {
+    const line = lines[i];
+    if (line == "") continue;
+    if (line[0] == "#") continue;
+    const lst = line.trim().split("	");
+    if (lst[0] == skipword) continue;
+    const m = {
+      notes: []
+      // collect notes
+    };
+    for (let j = 0; j < header.length; j++) {
+      if (lst[j] !== void 0 && lst[j].includes('"'))
+        return ['Input file has  invalid character " e.g. "NM_001007565"'];
+      m[header[j].key] = lst[j];
+    }
+    if (!m.rating) {
+      badlines.push([i, "rating unspecified", lst]);
+      continue;
+    }
+    let s = m.rating;
+    if (s.toLowerCase() == "major") {
+      m.rating = "HQ";
+      s = "HQ";
+    }
+    if (s != "HQ" && s != "LQ" && s != "RT" && s != "bad") {
+      badlines.push([i, "invalid rating: " + m.rating, lst]);
+      continue;
+    }
+    if (!m.chrA) {
+      badlines.push([i, "missing chrA", lst]);
+      continue;
+    }
+    if (!genome.chrlookup[m.chrA.toUpperCase()]) {
+      badlines.push([i, "invalid chrA: " + m.chrA, lst]);
+      continue;
+    }
+    if (!m.chrB) {
+      badlines.push([i, "missing chrB", lst]);
+      continue;
+    }
+    if (!genome.chrlookup[m.chrB.toUpperCase()]) {
+      badlines.push([i, "invalid chrB: " + m.chrB, lst]);
+      continue;
+    }
+    s = m.posA;
+    if (!s) {
+      badlines.push([i, "missing posA", lst]);
+      continue;
+    }
+    let v = Number.parseInt(s);
+    if (Number.isNaN(v)) {
+      badlines.push([i, "invalid posA: " + s, lst]);
+      continue;
+    }
+    if (v < 0 || v >= genome.chrlookup[m.chrA.toUpperCase()]) {
+      badlines.push([i, "invalid posA: " + s, lst]);
+      continue;
+    }
+    m.posA = v;
+    s = m.posB;
+    if (!s) {
+      badlines.push([i, "missing posB", lst]);
+      continue;
+    }
+    v = Number.parseInt(s);
+    if (isNaN(v)) {
+      badlines.push([i, "invalid posB: " + s, lst]);
+      continue;
+    }
+    if (v < 0 || v >= genome.chrlookup[m.chrB.toUpperCase()]) {
+      badlines.push([i, "invalid posB: " + s, lst]);
+      continue;
+    }
+    m.posB = v;
+    if (!m.ratioA) {
+      badlines.push([i, "missing ratioA", lst]);
+      continue;
+    }
+    v = Number.parseFloat(m.ratioA);
+    if (Number.isNaN(v)) {
+      badlines.push([i, "invalid value for ratioA", lst]);
+      continue;
+    }
+    if (v > 1) {
+      badlines.push([i, "ratioA > 100%", lst]);
+      v = 1;
+    }
+    m.ratioA = v;
+    if (!m.ratioB) {
+      badlines.push([i, "missing ratioB", lst]);
+      continue;
+    }
+    v = Number.parseFloat(m.ratioB);
+    if (Number.isNaN(v)) {
+      badlines.push([i, "invalid value for ratioB", lst]);
+      continue;
+    }
+    if (v > 1) {
+      badlines.push([i, "ratioB > 100%", lst]);
+      v = 1;
+    }
+    m.ratioB = v;
+    if (!m.score) {
+      badlines.push([i, "missing score", lst]);
+      continue;
+    }
+    v = Number.parseFloat(m.score);
+    if (Number.isNaN(v)) {
+      badlines.push([i, "invalid value for score", lst]);
+      continue;
+    }
+    m.score = v;
+    if (!m.readsA) {
+      badlines.push([i, "readsA missing", lst]);
+      continue;
+    }
+    v = Number.parseInt(m.readsA);
+    if (Number.isNaN(v)) {
+      badlines.push([i, "invalid value for readsA", lst]);
+      continue;
+    }
+    m.readsA = v;
+    if (!m.readsB) {
+      badlines.push([i, "readsB missing", lst]);
+      continue;
+    }
+    v = Number.parseInt(m.readsB);
+    if (Number.isNaN(v)) {
+      badlines.push([i, "invalid value for readsB", lst]);
+      continue;
+    }
+    m.readsB = v;
+    if (!m.matchA) {
+      badlines.push([i, "matchA missing", lst]);
+      continue;
+    }
+    v = Number.parseInt(m.matchA);
+    if (Number.isNaN(v)) {
+      badlines.push([i, "invalid value for matchA", lst]);
+      continue;
+    }
+    m.matchA = v;
+    if (!m.matchB) {
+      badlines.push([i, "matchB missing", lst]);
+      continue;
+    }
+    v = Number.parseInt(m.matchB);
+    if (Number.isNaN(v)) {
+      badlines.push([i, "invalid value for matchB", lst]);
+      continue;
+    }
+    m.matchB = v;
+    if (!m.repeatA) {
+      badlines.push([i, "repeatA missing", lst]);
+      continue;
+    }
+    v = Number.parseFloat(m.repeatA);
+    if (Number.isNaN(v)) {
+      badlines.push([i, "invalid value for repeatA", lst]);
+      continue;
+    }
+    m.repeatA = v;
+    if (!m.repeatB) {
+      badlines.push([i, "repeatB missing", lst]);
+      continue;
+    }
+    v = Number.parseFloat(m.repeatB);
+    if (Number.isNaN(v)) {
+      badlines.push([i, "invalid value for repeatB", lst]);
+      continue;
+    }
+    m.repeatB = v;
+    if (m.type2) {
+      switch (m.type2.toLowerCase()) {
+        case "closs":
+          m.iscloss = true;
+          break;
+        case "nloss":
+          m.isnloss = true;
+          break;
+        case "fusion":
+          m.isfusion = true;
+          break;
+        case "itd":
+          m.isitd = true;
+          break;
+        case "other":
+          m.isother = true;
+          break;
+        case "uptss":
+          m.isuptss = true;
+          break;
+        default:
+          badlines.push([i, "unknown type2: " + m.type2, lst]);
+          continue;
+      }
+    }
+    if (m.geneA == "" || m.geneA == "NA") {
+      m.geneA = null;
+    }
+    if (m.geneB == "" || m.geneB == "NA") {
+      m.geneB = null;
+    }
+    if (m.featureA == "intergenic") m.geneA = null;
+    if (m.featureB == "intergenic") m.geneB = null;
+    const isoforma = m.lstisoforma ? m.lstisoforma.toUpperCase().split(",") : [], isoformb = m.lstisoformb ? m.lstisoformb.toUpperCase().split(",") : [], codona = m.lstisoformacodon ? m.lstisoformacodon.split(",") : [], codonb = m.lstisoformbcodon ? m.lstisoformbcodon.split(",") : [], frame = m.lstframe ? m.lstframe.split(",") : [];
+    let exona = null, exonb = null, anchora = null, anchorb = null, contigaaA = null, contigaaB = null, contigbpA = null, contigbpB = null;
+    if (m.lstisoformaexon) exona = m.lstisoformaexon.split(",");
+    if (m.lstisoformbexon) exonb = m.lstisoformbexon.split(",");
+    if (m.lstisoformaanchor) anchora = m.lstisoformaanchor.split(",");
+    if (m.lstisoformbanchor) anchorb = m.lstisoformbanchor.split(",");
+    if (m.lstcontigaaA) contigaaA = m.lstcontigaaA.split(",");
+    if (m.lstcontigaaB) contigaaB = m.lstcontigaaB.split(",");
+    if (m.lstcontigbpA) contigbpA = m.lstcontigbpA.split(",");
+    if (m.lstcontigbpB) contigbpB = m.lstcontigbpB.split(",");
+    const paircount = Math.max(isoforma.length, isoformb.length, codona.length, codonb.length, frame.length);
+    m.pairs = [];
+    for (let j = 0; j < paircount; j++) {
+      const pair = {
+        a: {
+          isoform: isoforma[j] && isoforma[j].length > 0 ? isoforma[j] : null,
+          exon: exona ? Number.parseInt(exona[j]) : NaN,
+          codon: codona[j] ? Number.parseInt(codona[j]) : NaN,
+          anchor: anchora ? anchora[j] : void 0
+        },
+        b: {
+          isoform: isoformb[j] && isoformb[j].length > 0 ? isoformb[j] : null,
+          exon: exonb ? Number.parseInt(exonb[j]) : NaN,
+          codon: codonb[j] ? Number.parseInt(codonb[j]) : NaN,
+          anchor: anchorb ? anchorb[j] : void 0
+        },
+        frame: frame[j],
+        inframe: frame[j] == "1" || frame[j] == "2"
+      };
+      if (m.isuptss) {
+        pair.inframe = true;
+      }
+      let aaa = NaN, aab = NaN, bpa = NaN, bpb = NaN;
+      if (contigaaA && contigaaA[j]) aaa = Number.parseInt(contigaaA[j]);
+      if (contigaaB && contigaaB[j]) aab = Number.parseInt(contigaaB[j]);
+      if (contigbpA && contigbpA[j]) bpa = Number.parseInt(contigbpA[j]);
+      if (contigbpB && contigbpB[j]) bpb = Number.parseInt(contigbpB[j]);
+      if (!Number.isNaN(aaa) && !Number.isNaN(aab)) {
+        pair.a.contigaa = aaa;
+        pair.b.contigaa = aab;
+      }
+      if (!Number.isNaN(bpa) && !Number.isNaN(bpb)) {
+        pair.a.contigbp = bpa;
+        pair.b.contigbp = bpb;
+      }
+      m.pairs.push(pair);
+    }
+    if (m.exception) {
+      m.notes.push(m.exception);
+    }
+    if (m.hlgene) {
+      const v2 = Number.parseInt(m.hlgene);
+      if (Number.isNaN(v2) || v2 != 0 && v2 != 1 && v2 != 2 && v2 != 3 && v2 != 4) {
+        badlines.push([i, "invalid value for highlight gene flag: " + m.hlgene, lst]);
+        delete m.hlgene;
+      } else {
+        m.hlgene = v2;
+      }
+    }
+    items.push(m);
+  }
+  if (badlines.length > 0) {
+    const hlst = header.map((i) => i.key);
+    bulk_badline(hlst, badlines);
+  }
+  if (items.length == 0) {
+    return ["No data loaded"];
+  }
+  return [null, header, items];
+}
+function parseheader(line) {
+  const original = line.trim().split("	");
+  if (original.length <= 1) return ["invalid file header"];
+  const header = [];
+  const lower = [];
+  for (const i2 of original) {
+    lower.push(i2.toLowerCase());
+    header.push({
+      label: i2,
+      key: i2.toLowerCase(),
+      custom: true
+    });
+  }
+  const htry = (...arg) => {
+    for (const s of arg) {
+      const i2 = lower.indexOf(s);
+      if (i2 != -1) return i2;
+    }
+    return -1;
+  };
+  let i = htry("genea");
+  if (i == -1) return ["geneA missing"];
+  header[i].key = "geneA";
+  delete header[i].custom;
+  i = htry("chra");
+  if (i == -1) return ["chrA missing"];
+  header[i].key = "chrA";
+  delete header[i].custom;
+  i = htry("posa");
+  if (i == -1) return ["posA missing"];
+  header[i].key = "posA";
+  delete header[i].custom;
+  i = htry("orta");
+  if (i == -1) return ["ortA missing"];
+  header[i].key = "ortA";
+  delete header[i].custom;
+  i = htry("featurea");
+  if (i == -1) return ["featureA missing"];
+  header[i].key = "featureA";
+  delete header[i].custom;
+  i = htry("ratioa");
+  if (i == -1) return ["ratioA missing"];
+  header[i].key = "ratioA";
+  delete header[i].custom;
+  i = htry("readsa");
+  if (i == -1) return ["readsA missing"];
+  header[i].key = "readsA";
+  delete header[i].custom;
+  i = htry("sv_refseqa_aa_index");
+  if (i != -1) {
+    header[i].key = "lstcontigaaA";
+    delete header[i].custom;
+  }
+  i = htry("sv_refseqa_contig_index");
+  if (i != -1) {
+    header[i].key = "lstcontigbpA";
+    delete header[i].custom;
+  }
+  i = htry("total_readsa");
+  if (i != -1) {
+    header[i].key = "totalreadsA";
+    delete header[i].custom;
+  }
+  i = htry("geneb");
+  if (i == -1) return ["geneB missing"];
+  header[i].key = "geneB";
+  delete header[i].custom;
+  i = htry("chrb");
+  if (i == -1) return ["chrB missing"];
+  header[i].key = "chrB";
+  delete header[i].custom;
+  i = htry("posb");
+  if (i == -1) return ["posB missing"];
+  header[i].key = "posB";
+  delete header[i].custom;
+  i = htry("ortb");
+  if (i == -1) return ["ortB missing"];
+  header[i].key = "ortB";
+  delete header[i].custom;
+  i = htry("featureb");
+  if (i == -1) return ["featureB missing"];
+  header[i].key = "featureB";
+  delete header[i].custom;
+  i = htry("ratiob");
+  if (i == -1) return ["ratioB missing"];
+  header[i].key = "ratioB";
+  delete header[i].custom;
+  i = htry("readsb");
+  if (i == -1) return ["readsB missing"];
+  header[i].key = "readsB";
+  delete header[i].custom;
+  i = htry("sv_refseqb_aa_index");
+  if (i != -1) {
+    header[i].key = "lstcontigaaB";
+    delete header[i].custom;
+  }
+  i = htry("sv_refseqb_contig_index");
+  if (i != -1) {
+    header[i].key = "lstcontigbpB";
+    delete header[i].custom;
+  }
+  i = htry("total_readsb");
+  if (i != -1) {
+    header[i].key = "totalreadsB";
+    delete header[i].custom;
+  }
+  i = htry("sv_inframe", "frame");
+  if (i == -1) return ["sv_inframe missing"];
+  header[i].key = "lstframe";
+  delete header[i].custom;
+  i = htry("sv_refseqa");
+  if (i == -1) return ["sv_refseqA missing"];
+  header[i].key = "lstisoforma";
+  delete header[i].custom;
+  i = htry("sv_refseqa_codon");
+  if (i != -1) {
+    header[i].key = "lstisoformacodon";
+  }
+  i = htry("sv_refseqb_codon");
+  if (i != -1) {
+    header[i].key = "lstisoformbcodon";
+  }
+  i = htry("score");
+  if (i == -1) return ["score missing"];
+  header[i].key = "score";
+  delete header[i].custom;
+  i = htry("sv_refseqb");
+  if (i == -1) return ["sv_refseqB missing"];
+  header[i].key = "lstisoformb";
+  delete header[i].custom;
+  i = htry("rating");
+  if (i == -1) return ["rating missing"];
+  header[i].key = "rating";
+  delete header[i].custom;
+  i = htry("matcha");
+  if (i == -1) return ["matchA missing"];
+  header[i].key = "matchA";
+  delete header[i].custom;
+  i = htry("matchb");
+  if (i == -1) return ["matchB missing"];
+  header[i].key = "matchB";
+  delete header[i].custom;
+  i = htry("repeata");
+  if (i == -1) return ["repeatA missing"];
+  header[i].key = "repeatA";
+  delete header[i].custom;
+  i = htry("repeatb");
+  if (i == -1) return ["repeatB missing"];
+  header[i].key = "repeatB";
+  delete header[i].custom;
+  i = htry("functional effect");
+  if (i == -1) return ["functional effect missing"];
+  header[i].key = "type2";
+  delete header[i].custom;
+  i = htry("sample");
+  if (i != -1) {
+    header[i].key = "sample";
+    delete header[i].custom;
+  }
+  i = htry("sv_processing_exception");
+  if (i != -1) {
+    header[i].key = "exception";
+  }
+  i = htry("medal");
+  if (i != -1) {
+    header[i].key = "hlgene";
+  }
+  i = htry("sv_refseqa_exon");
+  if (i != -1) {
+    header[i].key = "lstisoformaexon";
+    delete header[i].custom;
+  }
+  i = htry("sv_refseqb_exon");
+  if (i != -1) {
+    header[i].key = "lstisoformbexon";
+    delete header[i].custom;
+  }
+  i = htry("sv_refseqa_anchor_type");
+  if (i != -1) {
+    header[i].key = "lstisoformaanchor";
+    delete header[i].custom;
+  }
+  i = htry("sv_refseqb_anchor_type");
+  if (i != -1) {
+    header[i].key = "lstisoformbanchor";
+    delete header[i].custom;
+  }
+  return [null, header];
+}
+export {
+  svmrlaunch,
+  svmrparseinput,
+  svmrparseraw,
+  svmrui
+};
+//# sourceMappingURL=svmr-6BDEZAS6.js.map