@sjcrh/proteinpaint-client 2.185.0 → 2.186.0

package/dist/chunk-ST644IDH.js

@@ -1,217 +0,0 @@
-import {
-  dofetch,
-  dofetch2
-} from "./chunk-6ZCHECOT.js";
-import {
-  contigNameNoChr2
-} from "./chunk-AMYSEKPF.js";
-
-// tracks/hic/data/parseData.ts
-async function hicParseFile(hic, debugmode, errList = []) {
-  if (debugmode) window["hic"] = hic;
-  if (hic.tklst) {
-    const lst = [];
-    for (const t of hic.tklst) {
-      if (!t.type) {
-        errList.push("type missing from one of the tracks accompanying HiC");
-      } else {
-        t.iscustom = true;
-        lst.push(t);
-      }
-    }
-    if (lst.length) {
-      hic.tklst = lst;
-    } else {
-      delete hic.tklst;
-    }
-  }
-  if (hic.enzyme) {
-    if (hic.genome.hicenzymefragment) {
-      let frag = null;
-      for (const f of hic.genome.hicenzymefragment) {
-        if (f.enzyme == hic.enzyme) {
-          frag = f;
-          break;
-        }
-      }
-      if (frag) {
-        hic.enzymefile = frag.file;
-      } else {
-        errList.push("unknown enzyme: " + hic.enzyme);
-        delete hic.enzyme;
-      }
-    } else {
-      errList.push("no enzyme fragment information available for this genome");
-      delete hic.enzyme;
-    }
-  }
-  try {
-    if (hic.sv && hic.sv.file) {
-      const re = await dofetch(hic.hostURL + "/textfile", {
-        method: "POST",
-        body: JSON.stringify({ file: hic.sv.file, jwt: hic.jwt })
-      });
-      const data2 = re.json();
-      const [err2, header, items] = parseSV(data2.text);
-      if (err2) throw { message: "Error parsing SV: " + err2 };
-      hic.sv.header = header;
-      hic.sv.items = items;
-    }
-    const data = await dofetch2("hicstat?" + (hic.file ? "file=" + hic.file : "url=" + hic.url));
-    if (data.error) {
-      errList.push(data.error);
-      return;
-    }
-    const err = hicparsestat(hic, data.out);
-    if (err) throw { message: err };
-  } catch (err) {
-    errList.push(err.message || err);
-    if (err.stack) {
-      console.log(err.stack);
-    }
-  }
-  return hic;
-}
-function parseSV(txt) {
-  const lines = txt.trim().split(/\r?\n/);
-  const [err, header] = parseSVheader(lines[0]);
-  if (err) return ["header error: " + err];
-  const items = [];
-  for (let i = 1; i < lines.length; i++) {
-    const line = lines[i];
-    if (line[0] == "#") continue;
-    const [e, m] = parseSVline(line, header);
-    if (e) return ["line " + (i + 1) + " error: " + e];
-    items.push(m);
-  }
-  return [null, header, items];
-}
-function parseSVheader(line) {
-  const header = line.toLowerCase().split("	");
-  if (header.length <= 1) return "invalid file header for fusions";
-  const htry = (...lst) => {
-    for (const a of lst) {
-      const j = header.indexOf(a);
-      if (j != -1) return j;
-    }
-    return -1;
-  };
-  let i = htry("chr_a", "chr1", "chra");
-  if (i == -1) return "chr_A missing from header";
-  header[i] = "chr1";
-  i = htry("chr_b", "chr2", "chrb");
-  if (i == -1) return "chr_B missing from header";
-  header[i] = "chr2";
-  i = htry("pos_a", "position_a", "position1", "posa");
-  if (i == -1) return "pos_a missing from header";
-  header[i] = "position1";
-  i = htry("pos_b", "position_b", "position2", "posb");
-  if (i == -1) return "pos_b missing from header";
-  header[i] = "position2";
-  i = htry("strand_a", "orta", "orienta");
-  if (i == -1) return "strand_a missing from header";
-  header[i] = "strand1";
-  i = htry("strand_b", "ortb", "orientb");
-  if (i == -1) return "strand_b missing from header";
-  header[i] = "strand2";
-  i = htry("numreadsa");
-  if (i != -1) header[i] = "reads1";
-  i = htry("numreadsb");
-  if (i != -1) header[i] = "reads2";
-  return [null, header];
-}
-function parseSVline(line, header) {
-  const lst = line.split("	");
-  const m = {};
-  for (let j = 0; j < header.length; j++) {
-    m[header[j]] = lst[j];
-  }
-  if (!m.chr1) return ["missing chr1"];
-  if (m.chr1.toLowerCase().indexOf("chr") != 0) {
-    m.chr1 = "chr" + m.chr1;
-  }
-  if (!m.chr2) return ["missing chr2"];
-  if (m.chr2.toLowerCase().indexOf("chr") != 0) {
-    m.chr2 = "chr" + m.chr2;
-  }
-  if (!m.position1) return ["missing position1"];
-  let v = Number.parseInt(m.position1);
-  if (Number.isNaN(v) || v <= 0) return ["position1 invalid value"];
-  m.position1 = v;
-  if (!m.position2) return ["missing position2"];
-  v = Number.parseInt(m.position2);
-  if (Number.isNaN(v) || v <= 0) return ["position2 invalid value"];
-  m.position2 = v;
-  if (m.reads1) {
-    v = Number.parseInt(m.reads1);
-    if (Number.isNaN(v)) return ["reads1 invalid value"];
-    m.reads1 = v;
-  }
-  if (m.reads2) {
-    v = Number.parseInt(m.reads2);
-    if (Number.isNaN(v)) return ["reads2 invalid value"];
-    m.reads2 = v;
-  }
-  return [null, m];
-}
-function hicparsestat(hic, j) {
-  if (!j) return "cannot stat hic file";
-  hic.normalization = j.normalization;
-  hic.version = j.version;
-  if (!j.Chromosomes) return "Chromosomes not found in file stat";
-  if (!Array.isArray(j.chrorder)) return ".chrorder[] missing";
-  if (j.chrorder.length == 0) return ".chrorder[] empty array";
-  hic.chrorder = j.chrorder;
-  if (!j["Base pair-delimited resolutions"]) return "Base pair-delimited resolutions not found in file stat";
-  if (!Array.isArray(j["Base pair-delimited resolutions"])) return "Base pair-delimited resolutions should be array";
-  hic.bpresolution = j["Base pair-delimited resolutions"];
-  if (!j["Fragment-delimited resolutions"]) return "Fragment-delimited resolutions not found in file stat";
-  if (!Array.isArray(j["Fragment-delimited resolutions"])) return "Fragment-delimited resolutions is not array";
-  hic.fragresolution = j["Fragment-delimited resolutions"];
-  const chrlst = [];
-  for (const chr in j.Chromosomes) {
-    chrlst.push(chr);
-  }
-  const [nochrcount, haschrcount] = contigNameNoChr2(hic.genome, chrlst);
-  if (nochrcount + haschrcount == 0) return "chromosome names do not match with genome build";
-  if (nochrcount > 0) {
-    hic.nochr = true;
-    for (let i = 0; i < hic.chrorder.length; i++) hic.chrorder[i] = "chr" + hic.chrorder[i];
-  }
-  hic.chrlst = [];
-  for (const chr of hic.genome.majorchrorder) {
-    const c2 = hic.nochr ? chr.replace("chr", "") : chr;
-    if (chrlst.indexOf(c2) != -1) {
-      hic.chrlst.push(chr);
-    }
-  }
-}
-function hicparsefragdata(items) {
-  const id2coord = /* @__PURE__ */ new Map();
-  let min = null, max;
-  for (const i of items) {
-    if (!i.rest || !i.rest[0]) {
-      return ["items[].rest data problem"];
-    }
-    const id = Number.parseInt(i.rest[0]);
-    if (Number.isNaN(id)) {
-      return [i.start + "." + i.stop + " invalid fragment id: " + i.rest[0]];
-    }
-    id2coord.set(id, [i.start, i.stop]);
-    if (min == null) {
-      min = id;
-      max = id;
-    } else {
-      min = Math.min(min, id);
-      max = Math.max(max, id);
-    }
-  }
-  return [null, id2coord, min, max];
-}
-
-export {
-  hicParseFile,
-  hicparsestat,
-  hicparsefragdata
-};
-//# sourceMappingURL=chunk-ST644IDH.js.map