@sjcrh/proteinpaint-shared 2.187.0 → 2.188.1

package/dist/src/bulk.sv.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/bulk.sv.js"],
+  "sourcesContent": ["import * as bulk from './bulk.js'\nimport * as common from './common.js'\n\n/////////////////////////////////\n//\n// client/server shared\n//\n/////////////////////////////////\n\n// work for both sv/fusion\n// must tell if the data is fusion or sv\n\nexport function parseheader(line, flag, issv) {\n\tconst header = line.toLowerCase().split('\\t')\n\tif (header.length <= 1) return 'invalid file header for fusions'\n\tconst htry = (...lst) => {\n\t\tfor (const a of lst) {\n\t\t\tconst j = header.indexOf(a)\n\t\t\tif (j != -1) return j\n\t\t}\n\t\treturn -1\n\t}\n\tlet i = htry('gene_a', 'gene1', 'genea')\n\tif (i == -1) return 'gene_a missing from header'\n\theader[i] = 'gene1'\n\ti = htry('gene_b', 'gene2', 'geneb')\n\tif (i == -1) return 'gene_b missing from header'\n\theader[i] = 'gene2'\n\ti = htry('chr_a', 'chr1', 'chra')\n\tif (i == -1) return 'chr_a missing from header'\n\theader[i] = 'chr1'\n\ti = htry('chr_b', 'chr2', 'chrb')\n\tif (i == -1) return 'chr_b missing from header'\n\theader[i] = 'chr2'\n\ti = htry('pos_a', 'position_a', 'position1', 'posa')\n\tif (i == -1) return 'pos_a missing from header'\n\theader[i] = 'position1'\n\ti = htry('pos_b', 'position_b', 'position2', 'posb')\n\tif (i == -1) return 'pos_b missing from header'\n\theader[i] = 'position2'\n\ti = htry('isoform_a', 'refseq_a', 'refseq1', 'isoform1', 'sv_refseqa')\n\tif (i == -1) return 'isoform_a missing from header'\n\theader[i] = 'isoform1'\n\ti = htry('isoform_b', 'refseq_b', 'refseq2', 'isoform2', 'sv_refseqb')\n\tif (i == -1) return 'isoform_b missing from header'\n\theader[i] = 'isoform2'\n\ti = htry('strand_a', 'orta')\n\tif (i == -1) return 'strand_a missing from header'\n\theader[i] = 'strand1'\n\ti = htry('strand_b', 'ortb')\n\tif (i == -1) return 'strand_b missing from header'\n\theader[i] = 'strand2'\n\t// optional\n\ti = htry('sample', 'sample_name', 'tumor_sample_barcode')\n\tif (i != -1) header[i] = 'sample'\n\ti = htry('patient', 'donor', 'target_case_id')\n\tif (i != -1) header[i] = 'patient'\n\ti = htry('sampletype', 'sample type', 'sample_type')\n\tif (i != -1) header[i] = 'sampletype'\n\ti = htry('disease')\n\tif (i != -1) header[i] = 'disease'\n\ti = htry('origin')\n\tif (i != -1) header[i] = 'origin'\n\tif (issv) {\n\t\tflag.sv.loaded = true\n\t\tflag.sv.header = header\n\t} else {\n\t\tflag.fusion.loaded = true\n\t\tflag.fusion.header = header\n\t}\n\treturn false\n}\n\nexport function parseline(i, line, flag, issv) {\n\tif (line == '' || line[0] == '#') return\n\tconst lst = line.split('\\t')\n\tconst m = {}\n\tconst header = issv ? flag.sv.header : flag.fusion.header\n\tconst badlines = issv ? flag.sv.badlines : flag.fusion.badlines\n\n\tfor (let j = 0; j < header.length; j++) {\n\t\tm[header[j]] = lst[j]\n\t}\n\tif (!m.chr1) {\n\t\tbadlines.push([i, 'missing chr1', lst])\n\t\treturn\n\t}\n\tif (m.chr1.toLowerCase().indexOf('chr') != 0) {\n\t\tm.chr1 = 'chr' + m.chr1\n\t}\n\tif (!m.chr2) {\n\t\tbadlines.push([i, 'missing chr2', lst])\n\t\treturn\n\t}\n\tif (m.chr2.toLowerCase().indexOf('chr') != 0) {\n\t\tm.chr2 = 'chr' + m.chr2\n\t}\n\tlet v = m.position1\n\tif (!v) {\n\t\tbadlines.push([i, 'missing position1', lst])\n\t\treturn\n\t}\n\tlet v2 = Number.parseInt(v)\n\tif (Number.isNaN(v2) || v2 <= 0) {\n\t\tbadlines.push([i, 'invalid value for position1', lst])\n\t\treturn\n\t}\n\tm.position1 = v2\n\tv = m.position2\n\tif (!v) {\n\t\tbadlines.push([i, 'missing position2', lst])\n\t\treturn\n\t}\n\tv2 = Number.parseInt(v)\n\tif (Number.isNaN(v2) || v2 <= 0) {\n\t\tbadlines.push([i, 'invalid value for position2', lst])\n\t\treturn\n\t}\n\tm.position2 = v2\n\tif (bulk.parsesample(m, flag, i, lst, badlines)) {\n\t\treturn\n\t}\n\tif (m.isoform1 && m.isoform1.indexOf(',') != -1) {\n\t\tconst lst2 = m.isoform1.split(',')\n\t\tm.isoform1 = undefined\n\t\tfor (const t of lst2) {\n\t\t\tif (t != '') m.isoform1 = t\n\t\t}\n\t}\n\tif (m.isoform2 && m.isoform2.indexOf(',') != -1) {\n\t\tconst lst2 = m.isoform2.split(',')\n\t\tm.isoform2 = undefined\n\t\tfor (const t of lst2) {\n\t\t\tif (t != '') m.isoform2 = t\n\t\t}\n\t}\n\tif (!m.gene1) {\n\t\tm.isoform1 = undefined\n\t}\n\tif (!m.gene2) {\n\t\tm.isoform2 = undefined\n\t}\n\tif (m.gene1) {\n\t\t// put data under gene1\n\t\tflag.good++\n\t\tconst m2 = {\n\t\t\tdt: issv ? common.dtsv : common.dtfusionrna,\n\t\t\tclass: issv ? common.mclasssv : common.mclassfusionrna,\n\t\t\tisoform: m.isoform1,\n\t\t\tmname: m.gene2 || m.chr2,\n\t\t\tsample: m.sample,\n\t\t\tpatient: m.patient,\n\t\t\tsampletype: m.sampletype,\n\t\t\torigin: m.origin,\n\t\t\tdisease: m.disease,\n\t\t\tpairlst: [\n\t\t\t\t{\n\t\t\t\t\ta: {\n\t\t\t\t\t\tname: m.gene1,\n\t\t\t\t\t\tisoform: m.isoform1,\n\t\t\t\t\t\tstrand: m.strand1,\n\t\t\t\t\t\tchr: m.chr1,\n\t\t\t\t\t\tposition: m.position1\n\t\t\t\t\t},\n\t\t\t\t\tb: {\n\t\t\t\t\t\tname: m.gene2,\n\t\t\t\t\t\tisoform: m.isoform2,\n\t\t\t\t\t\tstrand: m.strand2,\n\t\t\t\t\t\tchr: m.chr2,\n\t\t\t\t\t\tposition: m.position2\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t}\n\t\tconst n = flag.geneToUpper ? m.gene1.toUpperCase() : m.gene1\n\t\tif (!flag.data[n]) {\n\t\t\tflag.data[n] = []\n\t\t}\n\t\tflag.data[n].push(m2)\n\t}\n\tif (m.gene2 && m.gene2 != m.gene1) {\n\t\t// put data under gene2\n\t\tflag.good++\n\t\tconst m2 = {\n\t\t\tdt: issv ? common.dtsv : common.dtfusionrna,\n\t\t\tclass: issv ? common.mclasssv : common.mclassfusionrna,\n\t\t\tisoform: m.isoform2,\n\t\t\tmname: m.gene1 || m.chr1,\n\t\t\tsample: m.sample,\n\t\t\tpatient: m.patient,\n\t\t\tsampletype: m.sampletype,\n\t\t\torigin: m.origin,\n\t\t\tdisease: m.disease,\n\t\t\tpairlst: [\n\t\t\t\t{\n\t\t\t\t\ta: {\n\t\t\t\t\t\tname: m.gene1,\n\t\t\t\t\t\tisoform: m.isoform1,\n\t\t\t\t\t\tstrand: m.strand1,\n\t\t\t\t\t\tchr: m.chr1,\n\t\t\t\t\t\tposition: m.position1\n\t\t\t\t\t},\n\t\t\t\t\tb: {\n\t\t\t\t\t\tname: m.gene2,\n\t\t\t\t\t\tisoform: m.isoform2,\n\t\t\t\t\t\tstrand: m.strand2,\n\t\t\t\t\t\tchr: m.chr2,\n\t\t\t\t\t\tposition: m.position2\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t]\n\t\t}\n\t\tconst n = flag.geneToUpper ? m.gene2.toUpperCase() : m.gene2\n\t\tif (!flag.data[n]) {\n\t\t\tflag.data[n] = []\n\t\t}\n\t\tflag.data[n].push(m2)\n\t}\n}\n\nexport function duplicate(m) {\n\tconst n = {}\n\tfor (const k in m) {\n\t\tif (k == 'pairlst') continue\n\t\tconst v = m[k]\n\t\tconst type = typeof v\n\t\tif (type == 'object') {\n\t\t\tcontinue\n\t\t}\n\t\tn[k] = v\n\t}\n\tif (m.pairlst) {\n\t\tn.pairlst = []\n\t\tfor (const pair of m.pairlst) {\n\t\t\tconst p = {}\n\t\t\tfor (const k in pair) {\n\t\t\t\tif (k == 'a' || k == 'b' || k == 'interstitial') {\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tp[k] = pair[k]\n\t\t\t}\n\t\t\tif (pair.a) {\n\t\t\t\tp.a = {}\n\t\t\t\tfor (const k in pair.a) {\n\t\t\t\t\tconst v = pair.a[k]\n\t\t\t\t\tif (typeof v == 'object') {\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tp.a[k] = v\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (pair.b) {\n\t\t\t\tp.b = {}\n\t\t\t\tfor (const k in pair.b) {\n\t\t\t\t\tconst v = pair.b[k]\n\t\t\t\t\tif (typeof v == 'object') {\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tp.b[k] = v\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (pair.interstitial) {\n\t\t\t\tp.interstitial = {}\n\t\t\t\tfor (const k in pair.interstitial) {\n\t\t\t\t\tconst v = pair.interstitial[k]\n\t\t\t\t\tif (typeof v == 'object') {\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t\tp.interstitial[k] = v\n\t\t\t\t}\n\t\t\t}\n\t\t\tn.pairlst.push(p)\n\t\t}\n\t}\n\treturn n\n}\n"],
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+  "names": []
+}

package/dist/src/bulk.svjson.js

@@ -0,0 +1,151 @@
+import * as common from "./common.js";
+import * as bulk from "./bulk.js";
+function parseheader(line, flag) {
+  const header = line.toLowerCase().split("	");
+  if (header.length <= 1) return "invalid file header for svjson";
+  const htry = (...lst) => {
+    for (const a of lst) {
+      const j = header.indexOf(a);
+      if (j != -1) return j;
+    }
+    return -1;
+  };
+  let i = htry("sample");
+  if (i != -1) header[i] = "sample";
+  i = htry("sampletype");
+  if (i != -1) header[i] = "sampletype";
+  i = htry("patient");
+  if (i != -1) header[i] = "patient";
+  i = htry("json", "jsontext");
+  if (i == -1) return ["json missing from header"];
+  header[i] = "jsontext";
+  return [null, header];
+}
+function parseline(i, line, flag, header) {
+  if (line == "" || line[0] == "#") return;
+  const lst = line.split("	");
+  const m = {};
+  const badlines = flag.svjson.badlines;
+  for (let j = 0; j < header.length; j++) {
+    m[header[j]] = lst[j];
+  }
+  if (!m.jsontext) {
+    badlines.push([i, "missing jsontext", lst]);
+    return;
+  }
+  if (bulk.parsesample(m, flag, i, lst, badlines)) {
+    return;
+  }
+  let json;
+  try {
+    json = JSON.parse(m.jsontext);
+  } catch (e) {
+    badlines.push([i, "invalid JSON text", lst]);
+    return;
+  }
+  if (Array.isArray(json)) {
+    for (const pair of json) {
+      if (pair.a && pair.a.name && pair.a.isoform) {
+        flag.good++;
+        const m2 = {
+          dt: common.dtfusionrna,
+          class: common.mclassfusionrna,
+          isoform: pair.a.isoform,
+          mname: pair.b.name
+        };
+        for (const k in m) {
+          if (k != "jsontext") m2[k] = m[k];
+        }
+        m2.pairlst = duplicate(json);
+        const n = pair.a.name.toUpperCase();
+        if (!flag.data[n]) {
+          flag.data[n] = [];
+        }
+        flag.data[n].push(m2);
+      }
+      if (pair.b && pair.b.name && pair.b.isoform) {
+        flag.good++;
+        const m2 = {
+          dt: common.dtfusionrna,
+          class: common.mclassfusionrna,
+          isoform: pair.b.isoform,
+          mname: pair.a.name
+        };
+        for (const k in m) {
+          if (k != "jsontext") m2[k] = m[k];
+        }
+        m2.pairlst = duplicate(json);
+        const n = pair.b.name.toUpperCase();
+        if (!flag.data[n]) {
+          flag.data[n] = [];
+        }
+        flag.data[n].push(m2);
+      }
+    }
+  } else {
+    json.dt = json.typecode;
+    delete json.typecode;
+    switch (json.dt) {
+      case common.dtitd:
+        json.class = common.mclassitd;
+        json.mname = "ITD";
+        break;
+      case common.dtnloss:
+        json.class = common.mclassnloss;
+        json.mname = "N-loss";
+        break;
+      case common.dtcloss:
+        json.class = common.mclasscloss;
+        json.mname = "C-loss";
+        break;
+      case common.dtdel:
+        json.class = common.mclassdel;
+        json.mname = "Del";
+        break;
+      case common.dtsv:
+        json.class = common.mclasssv;
+        json.mname = "SV";
+        break;
+      default:
+        badlines.push([i, "unknown datatype", lst]);
+        return;
+    }
+    if (!json.gene) {
+      badlines.push([i, "json.gene missing", lst]);
+      return;
+    }
+    flag.good++;
+    for (const k in m) {
+      if (k != "jsontext") {
+        json[k] = m[k];
+      }
+    }
+    const n = flag.geneToUpper ? json.gene.toUpperCase() : json.gene.toUpperCase();
+    if (!flag.data[n]) {
+      flag.data[n] = [];
+    }
+    flag.data[n].push(json);
+  }
+}
+function duplicate(lst) {
+  const d = [];
+  for (const pair of lst) {
+    const p = { a: {}, b: {} };
+    for (const k in pair) {
+      if (k != "a" && k != "b") p[k] = pair[k];
+    }
+    for (const k in pair.a) {
+      p.a[k] = pair.a[k];
+    }
+    for (const k in pair.b) {
+      p.b[k] = pair.b[k];
+    }
+    d.push(p);
+  }
+  return d;
+}
+export {
+  parseheader,
+  parseline
+};
+//# sourceMappingURL=bulk.svjson.js.map

package/dist/src/bulk.svjson.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/bulk.svjson.js"],
+  "sourcesContent": ["/////////////////////////////////\n//\n// client/server shared\n//\n/////////////////////////////////\n\nimport * as common from './common.js'\nimport * as bulk from './bulk.js'\n\n// work for both sv/fusion\n// must tell if the data is fusion or sv\n\nexport function parseheader(line, flag) {\n\tconst header = line.toLowerCase().split('\\t')\n\tif (header.length <= 1) return 'invalid file header for svjson'\n\tconst htry = (...lst) => {\n\t\tfor (const a of lst) {\n\t\t\tconst j = header.indexOf(a)\n\t\t\tif (j != -1) return j\n\t\t}\n\t\treturn -1\n\t}\n\tlet i = htry('sample')\n\tif (i != -1) header[i] = 'sample'\n\ti = htry('sampletype')\n\tif (i != -1) header[i] = 'sampletype'\n\ti = htry('patient')\n\tif (i != -1) header[i] = 'patient'\n\ti = htry('json', 'jsontext')\n\tif (i == -1) return ['json missing from header']\n\theader[i] = 'jsontext'\n\treturn [null, header]\n}\n\nexport function parseline(i, line, flag, header) {\n\tif (line == '' || line[0] == '#') return\n\tconst lst = line.split('\\t')\n\tconst m = {}\n\tconst badlines = flag.svjson.badlines\n\n\tfor (let j = 0; j < header.length; j++) {\n\t\tm[header[j]] = lst[j]\n\t}\n\tif (!m.jsontext) {\n\t\tbadlines.push([i, 'missing jsontext', lst])\n\t\treturn\n\t}\n\tif (bulk.parsesample(m, flag, i, lst, badlines)) {\n\t\treturn\n\t}\n\tlet json\n\ttry {\n\t\tjson = JSON.parse(m.jsontext)\n\t} catch (e) {\n\t\tbadlines.push([i, 'invalid JSON text', lst])\n\t\treturn\n\t}\n\t// duplicating logic in pediatric.js\n\tif (Array.isArray(json)) {\n\t\t// json is pairlst\n\t\tfor (const pair of json) {\n\t\t\tif (pair.a && pair.a.name && pair.a.isoform) {\n\t\t\t\tflag.good++\n\t\t\t\tconst m2 = {\n\t\t\t\t\tdt: common.dtfusionrna,\n\t\t\t\t\tclass: common.mclassfusionrna,\n\t\t\t\t\tisoform: pair.a.isoform,\n\t\t\t\t\tmname: pair.b.name\n\t\t\t\t}\n\t\t\t\tfor (const k in m) {\n\t\t\t\t\tif (k != 'jsontext') m2[k] = m[k]\n\t\t\t\t}\n\t\t\t\tm2.pairlst = duplicate(json)\n\t\t\t\tconst n = pair.a.name.toUpperCase()\n\t\t\t\tif (!flag.data[n]) {\n\t\t\t\t\tflag.data[n] = []\n\t\t\t\t}\n\t\t\t\tflag.data[n].push(m2)\n\t\t\t}\n\t\t\tif (pair.b && pair.b.name && pair.b.isoform) {\n\t\t\t\tflag.good++\n\t\t\t\tconst m2 = {\n\t\t\t\t\tdt: common.dtfusionrna,\n\t\t\t\t\tclass: common.mclassfusionrna,\n\t\t\t\t\tisoform: pair.b.isoform,\n\t\t\t\t\tmname: pair.a.name\n\t\t\t\t}\n\t\t\t\tfor (const k in m) {\n\t\t\t\t\tif (k != 'jsontext') m2[k] = m[k]\n\t\t\t\t}\n\t\t\t\tm2.pairlst = duplicate(json)\n\t\t\t\tconst n = pair.b.name.toUpperCase()\n\t\t\t\tif (!flag.data[n]) {\n\t\t\t\t\tflag.data[n] = []\n\t\t\t\t}\n\t\t\t\tflag.data[n].push(m2)\n\t\t\t}\n\t\t}\n\t} else {\n\t\tjson.dt = json.typecode\n\t\tdelete json.typecode\n\t\tswitch (json.dt) {\n\t\t\tcase common.dtitd:\n\t\t\t\tjson.class = common.mclassitd\n\t\t\t\tjson.mname = 'ITD'\n\t\t\t\tbreak\n\t\t\tcase common.dtnloss:\n\t\t\t\tjson.class = common.mclassnloss\n\t\t\t\tjson.mname = 'N-loss'\n\t\t\t\tbreak\n\t\t\tcase common.dtcloss:\n\t\t\t\tjson.class = common.mclasscloss\n\t\t\t\tjson.mname = 'C-loss'\n\t\t\t\tbreak\n\t\t\tcase common.dtdel:\n\t\t\t\tjson.class = common.mclassdel\n\t\t\t\tjson.mname = 'Del'\n\t\t\t\tbreak\n\t\t\tcase common.dtsv:\n\t\t\t\tjson.class = common.mclasssv\n\t\t\t\tjson.mname = 'SV'\n\t\t\t\tbreak\n\t\t\tdefault:\n\t\t\t\tbadlines.push([i, 'unknown datatype', lst])\n\t\t\t\treturn\n\t\t}\n\t\t// record only about a single gene\n\t\tif (!json.gene) {\n\t\t\tbadlines.push([i, 'json.gene missing', lst])\n\t\t\treturn\n\t\t}\n\t\tflag.good++\n\t\tfor (const k in m) {\n\t\t\tif (k != 'jsontext') {\n\t\t\t\tjson[k] = m[k]\n\t\t\t}\n\t\t}\n\t\tconst n = flag.geneToUpper ? json.gene.toUpperCase() : json.gene.toUpperCase()\n\t\tif (!flag.data[n]) {\n\t\t\tflag.data[n] = []\n\t\t}\n\t\tflag.data[n].push(json)\n\t}\n}\n\nfunction duplicate(lst) {\n\tconst d = []\n\tfor (const pair of lst) {\n\t\tconst p = { a: {}, b: {} }\n\t\tfor (const k in pair) {\n\t\t\tif (k != 'a' && k != 'b') p[k] = pair[k]\n\t\t}\n\t\tfor (const k in pair.a) {\n\t\t\tp.a[k] = pair.a[k]\n\t\t}\n\t\tfor (const k in pair.b) {\n\t\t\tp.b[k] = pair.b[k]\n\t\t}\n\t\td.push(p)\n\t}\n\treturn d\n}\n"],
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+  "names": []
+}

package/dist/src/bulk.trunc.js

@@ -0,0 +1,122 @@
+import * as common from "./common.js";
+import * as bulk from "./bulk.js";
+function parseheader(line, flag) {
+  const header = line.toLowerCase().split("	");
+  if (header.length <= 1) return "invalid header line for truncation";
+  const htry = (...lst) => {
+    for (const e of lst) {
+      const j = header.indexOf(e);
+      if (j != -1) return j;
+    }
+    return -1;
+  };
+  let i = htry("gene");
+  if (i == -1) return "gene missing from header";
+  header[i] = "gene";
+  i = htry(
+    "annovar_isoform",
+    "mrna_accession",
+    "mrna accession",
+    "refseq_mrna_id",
+    "annovar_sj_filter_isoform",
+    "refseq",
+    "isoform"
+  );
+  if (i == -1) return "isoform missing from header";
+  header[i] = "isoform";
+  let hasrnapos = false;
+  i = htry("rnaposition");
+  if (i != -1) {
+    header[i] = "rnaposition";
+    hasrnapos = true;
+  }
+  i = htry("losstype");
+  if (i == -1) return "lossType missing from header";
+  header[i] = "losstype";
+  let hasgenomic = false;
+  i = htry("chromosome", "chr");
+  if (i != -1) {
+    header[i] = "chr";
+    i = htry("start", "start_position", "wu_hg19_pos", "chr_position", "position");
+    if (i == -1) {
+      return "genomic position missing from header";
+    }
+    header[i] = "pos";
+    hasgenomic = true;
+  }
+  if (!hasrnapos && !hasgenomic) {
+    return "neither rnaposition nor genomic position is given";
+  }
+  i = htry("sample", "sample_name", "tumor_sample_barcode");
+  if (i != -1) header[i] = "sample";
+  i = htry("patient", "donor", "target_case_id");
+  if (i != -1) header[i] = "patient";
+  i = htry("disease");
+  if (i != -1) header[i] = "disease";
+  i = htry("origin");
+  if (i != -1) header[i] = "origin";
+  i = htry("sampletype", "sample type", "sample_type");
+  if (i != -1) header[i] = "sampletype";
+  flag.truncation.header = header;
+  flag.truncation.loaded = true;
+  return false;
+}
+function parseline(i, line, flag) {
+  if (line == "" || line[0] == "#") return;
+  const lst = line.split("	");
+  const m = {};
+  for (let j = 0; j < flag.truncation.header.length; j++) {
+    m[flag.truncation.header[j]] = lst[j];
+  }
+  if (!m.gene) {
+    flag.truncation.badlines.push([i, "missing gene", lst]);
+    return;
+  }
+  if (m.rnaposition) {
+    const v = Number.parseInt(m.rnaposition);
+    if (Number.isNaN(v) || v < 0) {
+      flag.truncation.badlines.push([i, "invalid rnaPosition value", lst]);
+      return;
+    }
+    m.rnaposition = v;
+  }
+  if (m.pos) {
+    const v = Number.parseInt(m.pos);
+    if (Number.isNaN(v) || v < 0) {
+      flag.truncation.badlines.push([i, "invalid genomic position", lst]);
+      return;
+    }
+    m.pos = v;
+  }
+  if (!m.losstype) {
+    flag.truncation.badlines.push([i, "missing lossType value", lst]);
+    return;
+  }
+  if (m.losstype != "n" && m.losstype != "c") {
+    flag.truncation.badlines.push([i, 'lossType value not "n" or "c"', lst]);
+    return;
+  }
+  if (bulk.parsesample(m, flag, i, lst, flag.truncation.badlines)) {
+    return;
+  }
+  if (m.losstype == "n") {
+    m.dt = common.dtnloss;
+    m.class = common.mclassnloss;
+    m.mname = "N-loss";
+  } else {
+    m.dt = common.dtcloss;
+    m.class = common.mclasscloss;
+    m.mname = "C-loss";
+  }
+  flag.good++;
+  const n = flag.geneToUpper ? m.gene.toUpperCase() : m.gene;
+  if (!(n in flag.data)) {
+    flag.data[n] = [];
+  }
+  flag.data[n].push(m);
+}
+export {
+  parseheader,
+  parseline
+};
+//# sourceMappingURL=bulk.trunc.js.map

package/dist/src/bulk.trunc.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/bulk.trunc.js"],
+  "sourcesContent": ["////////////////////////////////////\n//\n//  shared between client and server\n//\n////////////////////////////////////\n\nimport * as common from './common.js'\nimport * as bulk from './bulk.js'\n\nexport function parseheader(line, flag) {\n\tconst header = line.toLowerCase().split('\\t')\n\tif (header.length <= 1) return 'invalid header line for truncation'\n\tconst htry = (...lst) => {\n\t\tfor (const e of lst) {\n\t\t\tconst j = header.indexOf(e)\n\t\t\tif (j != -1) return j\n\t\t}\n\t\treturn -1\n\t}\n\tlet i = htry('gene')\n\tif (i == -1) return 'gene missing from header'\n\theader[i] = 'gene'\n\ti = htry(\n\t\t'annovar_isoform',\n\t\t'mrna_accession',\n\t\t'mrna accession',\n\t\t'refseq_mrna_id',\n\t\t'annovar_sj_filter_isoform',\n\t\t'refseq',\n\t\t'isoform'\n\t)\n\tif (i == -1) return 'isoform missing from header'\n\theader[i] = 'isoform'\n\tlet hasrnapos = false\n\ti = htry('rnaposition')\n\tif (i != -1) {\n\t\theader[i] = 'rnaposition'\n\t\thasrnapos = true\n\t}\n\ti = htry('losstype')\n\tif (i == -1) return 'lossType missing from header'\n\theader[i] = 'losstype'\n\tlet hasgenomic = false\n\ti = htry('chromosome', 'chr')\n\tif (i != -1) {\n\t\theader[i] = 'chr'\n\t\ti = htry('start', 'start_position', 'wu_hg19_pos', 'chr_position', 'position')\n\t\tif (i == -1) {\n\t\t\treturn 'genomic position missing from header'\n\t\t}\n\t\theader[i] = 'pos'\n\t\thasgenomic = true\n\t}\n\tif (!hasrnapos && !hasgenomic) {\n\t\treturn 'neither rnaposition nor genomic position is given'\n\t}\n\n\ti = htry('sample', 'sample_name', 'tumor_sample_barcode')\n\tif (i != -1) header[i] = 'sample'\n\ti = htry('patient', 'donor', 'target_case_id')\n\tif (i != -1) header[i] = 'patient'\n\ti = htry('disease')\n\tif (i != -1) header[i] = 'disease'\n\ti = htry('origin')\n\tif (i != -1) header[i] = 'origin'\n\ti = htry('sampletype', 'sample type', 'sample_type')\n\tif (i != -1) header[i] = 'sampletype'\n\tflag.truncation.header = header\n\tflag.truncation.loaded = true\n\treturn false\n}\n\nexport function parseline(i, line, flag) {\n\tif (line == '' || line[0] == '#') return\n\tconst lst = line.split('\\t')\n\tconst m = {}\n\tfor (let j = 0; j < flag.truncation.header.length; j++) {\n\t\tm[flag.truncation.header[j]] = lst[j]\n\t}\n\tif (!m.gene) {\n\t\tflag.truncation.badlines.push([i, 'missing gene', lst])\n\t\treturn\n\t}\n\tif (m.rnaposition) {\n\t\tconst v = Number.parseInt(m.rnaposition)\n\t\tif (Number.isNaN(v) || v < 0) {\n\t\t\tflag.truncation.badlines.push([i, 'invalid rnaPosition value', lst])\n\t\t\treturn\n\t\t}\n\t\tm.rnaposition = v\n\t}\n\tif (m.pos) {\n\t\tconst v = Number.parseInt(m.pos)\n\t\tif (Number.isNaN(v) || v < 0) {\n\t\t\tflag.truncation.badlines.push([i, 'invalid genomic position', lst])\n\t\t\treturn\n\t\t}\n\t\tm.pos = v\n\t}\n\tif (!m.losstype) {\n\t\tflag.truncation.badlines.push([i, 'missing lossType value', lst])\n\t\treturn\n\t}\n\tif (m.losstype != 'n' && m.losstype != 'c') {\n\t\tflag.truncation.badlines.push([i, 'lossType value not \"n\" or \"c\"', lst])\n\t\treturn\n\t}\n\tif (bulk.parsesample(m, flag, i, lst, flag.truncation.badlines)) {\n\t\treturn\n\t}\n\tif (m.losstype == 'n') {\n\t\tm.dt = common.dtnloss\n\t\tm.class = common.mclassnloss\n\t\tm.mname = 'N-loss'\n\t} else {\n\t\tm.dt = common.dtcloss\n\t\tm.class = common.mclasscloss\n\t\tm.mname = 'C-loss'\n\t}\n\tflag.good++\n\tconst n = flag.geneToUpper ? m.gene.toUpperCase() : m.gene\n\tif (!(n in flag.data)) {\n\t\tflag.data[n] = []\n\t}\n\tflag.data[n].push(m)\n}\n"],
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+  "names": []
+}

package/dist/src/clustering.js

@@ -0,0 +1,71 @@
+const clusterMethodLst = [
+  {
+    label: "Average",
+    value: "average",
+    title: `Cluster by average value`
+  },
+  {
+    label: `Complete`,
+    value: "complete",
+    title: `Use the complete clustering method`
+  },
+  {
+    label: `Single`,
+    value: "single",
+    title: `Use the single clustering method`
+  },
+  {
+    label: `Ward.D`,
+    value: "ward.D",
+    title: `Use the ward.D clustering method`
+  },
+  {
+    label: `Ward.D2`,
+    value: "ward.D2",
+    title: `Use the ward.D2 clustering method`
+  },
+  {
+    label: `Mcquitty`,
+    value: "mcquitty",
+    title: `Use the Mcquity clustering method`
+  }
+  /* These methods are currently disabled because the dendrogram lines tend to cross one another.
+  {
+  	label: `Centroid`,
+  	value: 'centroid',
+  	title: `Use the centroid clustering method`
+  },
+     	{
+  	label: `Median`,
+  	value: 'median',
+  	title: `Use the median clustering method`
+  }
+         */
+];
+const distanceMethodLst = [
+  {
+    label: "Euclidean",
+    value: "euclidean",
+    title: `Calculate distance using euclidean method`
+  },
+  {
+    label: "Maximum",
+    value: "maximum",
+    title: `Maximum distance between two components of x and y`
+  },
+  {
+    label: "Manhattan",
+    value: "manhattan",
+    title: `Calculate distance using the absolute distance between the two vectors`
+  },
+  {
+    label: "Canberra",
+    value: "canberra",
+    title: `Calculate distance using Canberra method`
+  }
+];
+export {
+  clusterMethodLst,
+  distanceMethodLst
+};
+//# sourceMappingURL=clustering.js.map

package/dist/src/clustering.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/clustering.js"],
+  "sourcesContent": ["export const clusterMethodLst = [\n\t{\n\t\tlabel: 'Average',\n\t\tvalue: 'average',\n\t\ttitle: `Cluster by average value`\n\t},\n\t{\n\t\tlabel: `Complete`,\n\t\tvalue: 'complete',\n\t\ttitle: `Use the complete clustering method`\n\t},\n\t{\n\t\tlabel: `Single`,\n\t\tvalue: 'single',\n\t\ttitle: `Use the single clustering method`\n\t},\n\t{\n\t\tlabel: `Ward.D`,\n\t\tvalue: 'ward.D',\n\t\ttitle: `Use the ward.D clustering method`\n\t},\n\t{\n\t\tlabel: `Ward.D2`,\n\t\tvalue: 'ward.D2',\n\t\ttitle: `Use the ward.D2 clustering method`\n\t},\n\t{\n\t\tlabel: `Mcquitty`,\n\t\tvalue: 'mcquitty',\n\t\ttitle: `Use the Mcquity clustering method`\n\t}\n\t/* These methods are currently disabled because the dendrogram lines tend to cross one another.\n\t{\n\t\tlabel: `Centroid`,\n\t\tvalue: 'centroid',\n\t\ttitle: `Use the centroid clustering method`\n\t},\n    \t{\n\t\tlabel: `Median`,\n\t\tvalue: 'median',\n\t\ttitle: `Use the median clustering method`\n\t}\n        */\n]\nexport const distanceMethodLst = [\n\t{\n\t\tlabel: 'Euclidean',\n\t\tvalue: 'euclidean',\n\t\ttitle: `Calculate distance using euclidean method`\n\t},\n\t{\n\t\tlabel: 'Maximum',\n\t\tvalue: 'maximum',\n\t\ttitle: `Maximum distance between two components of x and y`\n\t},\n\t{\n\t\tlabel: 'Manhattan',\n\t\tvalue: 'manhattan',\n\t\ttitle: `Calculate distance using the absolute distance between the two vectors`\n\t},\n\t{\n\t\tlabel: 'Canberra',\n\t\tvalue: 'canberra',\n\t\ttitle: `Calculate distance using Canberra method`\n\t}\n]\n"],
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+  "names": []
+}