@sjcrh/proteinpaint-shared 2.187.0 → 2.188.1

package/dist/src/bulk.js

@@ -0,0 +1,183 @@
+import * as common from "./common.js";
+var bulk_default = {};
+function init_bulk_flag(genome) {
+  if (!genome) {
+    return null;
+  }
+  const mclasslabel2key = {};
+  for (const n in common.mclass) {
+    mclasslabel2key[common.mclass[n].label.toUpperCase()] = n;
+  }
+  return {
+    genome,
+    mclasslabel2key,
+    data: {},
+    sample2disease: {},
+    // (proof) k: sample, v: disease
+    // will only record this when origin is used
+    patient2st: {},
+    // k: patient, v: { k: sampletype, v: sample }
+    // new sample names always override old
+    good: 0,
+    geneToUpper: true,
+    // option to not force uppercase on gene names
+    snv: {
+      loaded: false,
+      header: null,
+      badlines: [],
+      // jinghui: based on missense/silent ratio of entire dataset to decide whether to include silent when importing...
+      // hard-coded class codes
+      missense: 0,
+      silent: 0
+    },
+    svjson: {
+      loaded: false,
+      header: null,
+      badlines: []
+    },
+    fusion: {
+      loaded: false,
+      header: null,
+      badlines: [],
+      original: []
+    },
+    sv: {
+      loaded: false,
+      header: null,
+      badlines: [],
+      original: []
+    },
+    cnv: {
+      loaded: false,
+      header: null,
+      badlines: []
+    },
+    itd: {
+      loaded: false,
+      header: null,
+      badlines: []
+    },
+    del: {
+      loaded: false,
+      header: null,
+      badlines: []
+    },
+    truncation: {
+      loaded: false,
+      header: null,
+      badlines: []
+    }
+  };
+}
+function parsesample(m, flag, i, lst, badline) {
+  let variantorigin = common.moriginsomatic;
+  if (m.sampletype) {
+    const s = m.sampletype.toLowerCase();
+    switch (s) {
+      case "relapse":
+        variantorigin = common.moriginrelapse;
+        break;
+      case "germline":
+        variantorigin = common.morigingermline;
+        break;
+      case "somatic":
+      case "diagnosis":
+        break;
+    }
+    if (m.sample) {
+      if (m.patient) {
+      } else {
+        m.patient = m.sample + " " + m.sampletype;
+      }
+    } else {
+      if (m.patient) {
+        m.sample = m.patient + " " + m.sampletype;
+      } else {
+      }
+    }
+  } else {
+    if (m.patient) {
+      if (m.sample) {
+        m.sampletype = m.sample;
+      } else {
+        m.sample = m.sampletype = m.patient;
+      }
+    } else {
+      if (m.sample) {
+        m.sampletype = m.sample;
+      } else {
+      }
+    }
+  }
+  if (m.origin) {
+    const s = m.origin.toLowerCase();
+    switch (s) {
+      case "r":
+      case "relapse":
+        variantorigin = common.moriginrelapse;
+        m.isrim2 = true;
+        break;
+      case "g":
+      case "germline":
+        variantorigin = common.morigingermline;
+        m.isrim1 = true;
+        break;
+      case "gp":
+      case "germline pathogenic":
+        variantorigin = common.morigingermlinepathogenic;
+        m.isrim1 = true;
+        break;
+      case "gnp":
+      case "germline nonpathogenic":
+      case "germline non-pathogenic":
+        variantorigin = common.morigingermlinenonpathogenic;
+        m.isrim1 = true;
+        break;
+      case "s":
+      case "somatic":
+      case "diagnosis":
+        variantorigin = common.moriginsomatic;
+        break;
+    }
+  }
+  m.origin = variantorigin;
+  if (!m.sample && !m.patient) {
+    return;
+  }
+  const nopatientname = "no patient/individual name";
+  let p;
+  if (m.patient) {
+    if (!flag.patient2st[m.patient]) {
+      flag.patient2st[m.patient] = {};
+    }
+    flag.patient2st[m.patient][m.sampletype] = m.sample;
+  } else {
+    if (!flag.patient2st[nopatientname]) {
+      flag.patient2st[nopatientname] = {};
+    }
+    flag.patient2st[nopatientname][m.sampletype] = m.sample;
+  }
+  if (m.sample) {
+    if (m.disease) {
+      if (m.sample in flag.sample2disease) {
+        if (m.disease != flag.sample2disease[m.sample]) {
+          flag.snv.badlines.push([
+            i,
+            'conflict of disease types for sample "' + m.sample + '": ' + m.disease + ", " + flag.sample2disease[m.sample],
+            lst
+          ]);
+          return true;
+        }
+      } else {
+        flag.sample2disease[m.sample] = m.disease;
+      }
+    }
+  }
+  return false;
+}
+export {
+  bulk_default as default,
+  init_bulk_flag,
+  parsesample
+};
+//# sourceMappingURL=bulk.js.map

package/dist/src/bulk.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/bulk.js"],
+  "sourcesContent": ["////////////////////////////////////\n//\n//  shared between client and server\n//\n////////////////////////////////////\n\nimport * as common from './common.js'\n\nexport default {}\n\nexport function init_bulk_flag(genome) {\n\tif (!genome) {\n\t\treturn null\n\t}\n\tconst mclasslabel2key = {}\n\tfor (const n in common.mclass) {\n\t\tmclasslabel2key[common.mclass[n].label.toUpperCase()] = n\n\t}\n\treturn {\n\t\tgenome: genome,\n\t\tmclasslabel2key: mclasslabel2key,\n\t\tdata: {},\n\t\tsample2disease: {}, // (proof) k: sample, v: disease\n\t\t// will only record this when origin is used\n\t\tpatient2st: {},\n\t\t// k: patient, v: { k: sampletype, v: sample }\n\t\t// new sample names always override old\n\t\tgood: 0,\n\t\tgeneToUpper: true, // option to not force uppercase on gene names\n\t\tsnv: {\n\t\t\tloaded: false,\n\t\t\theader: null,\n\t\t\tbadlines: [],\n\t\t\t// jinghui: based on missense/silent ratio of entire dataset to decide whether to include silent when importing...\n\t\t\t// hard-coded class codes\n\t\t\tmissense: 0,\n\t\t\tsilent: 0\n\t\t},\n\t\tsvjson: {\n\t\t\tloaded: false,\n\t\t\theader: null,\n\t\t\tbadlines: []\n\t\t},\n\t\tfusion: {\n\t\t\tloaded: false,\n\t\t\theader: null,\n\t\t\tbadlines: [],\n\t\t\toriginal: []\n\t\t},\n\t\tsv: {\n\t\t\tloaded: false,\n\t\t\theader: null,\n\t\t\tbadlines: [],\n\t\t\toriginal: []\n\t\t},\n\t\tcnv: {\n\t\t\tloaded: false,\n\t\t\theader: null,\n\t\t\tbadlines: []\n\t\t},\n\t\titd: {\n\t\t\tloaded: false,\n\t\t\theader: null,\n\t\t\tbadlines: []\n\t\t},\n\t\tdel: {\n\t\t\tloaded: false,\n\t\t\theader: null,\n\t\t\tbadlines: []\n\t\t},\n\t\ttruncation: {\n\t\t\tloaded: false,\n\t\t\theader: null,\n\t\t\tbadlines: []\n\t\t}\n\t}\n}\n\nexport function parsesample(m, flag, i, lst, badline) {\n\tlet variantorigin = common.moriginsomatic\n\tif (m.sampletype) {\n\t\tconst s = m.sampletype.toLowerCase()\n\t\tswitch (s) {\n\t\t\tcase 'relapse':\n\t\t\t\tvariantorigin = common.moriginrelapse\n\t\t\t\tbreak\n\t\t\tcase 'germline':\n\t\t\t\tvariantorigin = common.morigingermline\n\t\t\t\tbreak\n\t\t\tcase 'somatic':\n\t\t\tcase 'diagnosis':\n\t\t\t\tbreak\n\t\t}\n\t\tif (m.sample) {\n\t\t\tif (m.patient) {\n\t\t\t\t// good\n\t\t\t} else {\n\t\t\t\tm.patient = m.sample + ' ' + m.sampletype\n\t\t\t}\n\t\t} else {\n\t\t\tif (m.patient) {\n\t\t\t\tm.sample = m.patient + ' ' + m.sampletype\n\t\t\t} else {\n\t\t\t\t// neither sample or patient, will quit later\n\t\t\t}\n\t\t}\n\t} else {\n\t\tif (m.patient) {\n\t\t\tif (m.sample) {\n\t\t\t\tm.sampletype = m.sample\n\t\t\t} else {\n\t\t\t\tm.sample = m.sampletype = m.patient\n\t\t\t}\n\t\t} else {\n\t\t\tif (m.sample) {\n\t\t\t\tm.sampletype = m.sample\n\t\t\t} else {\n\t\t\t\t// no patient/sample, will quit later\n\t\t\t}\n\t\t}\n\t}\n\tif (m.origin) {\n\t\t// override existing variantorigin\n\t\tconst s = m.origin.toLowerCase()\n\t\tswitch (s) {\n\t\t\tcase 'r':\n\t\t\tcase 'relapse':\n\t\t\t\tvariantorigin = common.moriginrelapse\n\t\t\t\tm.isrim2 = true\n\t\t\t\tbreak\n\t\t\tcase 'g':\n\t\t\tcase 'germline':\n\t\t\t\tvariantorigin = common.morigingermline\n\t\t\t\tm.isrim1 = true\n\t\t\t\tbreak\n\t\t\tcase 'gp':\n\t\t\tcase 'germline pathogenic':\n\t\t\t\tvariantorigin = common.morigingermlinepathogenic\n\t\t\t\tm.isrim1 = true\n\t\t\t\tbreak\n\t\t\tcase 'gnp':\n\t\t\tcase 'germline nonpathogenic':\n\t\t\tcase 'germline non-pathogenic':\n\t\t\t\tvariantorigin = common.morigingermlinenonpathogenic\n\t\t\t\tm.isrim1 = true\n\t\t\t\tbreak\n\t\t\tcase 's':\n\t\t\tcase 'somatic':\n\t\t\tcase 'diagnosis':\n\t\t\t\tvariantorigin = common.moriginsomatic\n\t\t\t\tbreak\n\t\t}\n\t}\n\tm.origin = variantorigin\n\n\tif (!m.sample && !m.patient) {\n\t\t// will not go into sample table\n\t\treturn\n\t}\n\n\tconst nopatientname = 'no patient/individual name'\n\tlet p\n\tif (m.patient) {\n\t\tif (!flag.patient2st[m.patient]) {\n\t\t\tflag.patient2st[m.patient] = {}\n\t\t}\n\t\tflag.patient2st[m.patient][m.sampletype] = m.sample\n\t} else {\n\t\tif (!flag.patient2st[nopatientname]) {\n\t\t\tflag.patient2st[nopatientname] = {}\n\t\t}\n\t\tflag.patient2st[nopatientname][m.sampletype] = m.sample\n\t}\n\n\tif (m.sample) {\n\t\tif (m.disease) {\n\t\t\tif (m.sample in flag.sample2disease) {\n\t\t\t\tif (m.disease != flag.sample2disease[m.sample]) {\n\t\t\t\t\tflag.snv.badlines.push([\n\t\t\t\t\t\ti,\n\t\t\t\t\t\t'conflict of disease types for sample \"' +\n\t\t\t\t\t\t\tm.sample +\n\t\t\t\t\t\t\t'\": ' +\n\t\t\t\t\t\t\tm.disease +\n\t\t\t\t\t\t\t', ' +\n\t\t\t\t\t\t\tflag.sample2disease[m.sample],\n\t\t\t\t\t\tlst\n\t\t\t\t\t])\n\t\t\t\t\treturn true\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tflag.sample2disease[m.sample] = m.disease\n\t\t\t}\n\t\t}\n\t}\n\treturn false\n}\n"],
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+  "names": []
+}

package/dist/src/bulk.snv.js

@@ -0,0 +1,175 @@
+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 snv/indel";
+  const htry = (...args) => {
+    for (const s of args) {
+      const i2 = header.indexOf(s);
+      if (i2 != -1) return i2;
+    }
+    return -1;
+  };
+  let i = htry("annovar_gene", "annovar_sj_gene", "gene", "genename", "gene_symbol", "hugo_symbol");
+  if (i == -1) return "gene missing from header";
+  header[i] = "gene";
+  i = htry("annovar_aachange", "amino_acid_change", "annovar_sj_aachange", "aachange", "protein_change", "variant");
+  if (i == -1) return "amino_acid_change missing from header";
+  header[i] = "mname";
+  i = htry("annovar_class", "class", "mclass", "variant_class", "variant_classification", "annovar_sj_class");
+  if (i == -1) return "variant_class missing from header";
+  header[i] = "class";
+  i = htry("chromosome", "chr");
+  if (i == -1) return "chromosome missing from header";
+  header[i] = "chr";
+  i = htry("wu_hg19_pos", "start", "start_position", "chr_position", "position");
+  if (i == -1) return "start missing from header";
+  header[i] = "pos";
+  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";
+  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("quantitative_measurements");
+  if (i != -1) header[i] = "qmset";
+  i = htry("mutant_reads_in_case", "mutant_in_tumor", "tumor_readcount_alt");
+  if (i != -1) header[i] = "maf_tumor_v1";
+  i = htry("total_reads_in_case", "total_in_tumor", "tumor_readcount_total");
+  if (i != -1) header[i] = "maf_tumor_v2";
+  i = htry("mutant_reads_in_control", "mutant_in_normal", "normal_readcount_alt");
+  if (i != -1) header[i] = "maf_normal_v1";
+  i = htry("total_reads_in_control", "total_in_normal", "normal_readcount_total");
+  if (i != -1) header[i] = "maf_normal_v2";
+  i = htry("cdna_change");
+  if (i != -1) header[i] = "cdna_change";
+  i = htry("sampletype", "sample type", "sample_type");
+  if (i != -1) header[i] = "sampletype";
+  i = htry("origin");
+  if (i != -1) header[i] = "origin";
+  i = htry("cancer", "disease", "diagnosis");
+  if (i != -1) header[i] = "disease";
+  flag.snv.header = header;
+  flag.snv.loaded = true;
+  return false;
+}
+function parseline(linei, line, flag) {
+  if (line == "" || line[0] == "#") return;
+  const lst = line.split("	");
+  const m = {};
+  for (let j = 0; j < flag.snv.header.length; j++) {
+    if (lst[j] == void 0) break;
+    m[flag.snv.header[j]] = lst[j];
+  }
+  if (!m.gene) {
+    flag.snv.badlines.push([linei, "missing gene", lst]);
+    return;
+  }
+  if (m.gene.toUpperCase() == "UNKNOWN") {
+    flag.snv.badlines.push([linei, "gene name is UNKNOWN", lst]);
+    return;
+  }
+  if (!m.isoform) {
+    flag.snv.badlines.push([linei, "missing isoform", lst]);
+    return;
+  }
+  if (!m.mname) {
+    m.mname = m.cdna_change;
+    if (!m.mname) {
+      flag.snv.badlines.push([linei, "missing amino acid change", lst]);
+      return;
+    }
+  } else {
+    if (m.mname.indexOf("p.") == 0) {
+      m.mname = m.mname.replace(/^p\./, "");
+    }
+  }
+  if (!m.class) {
+    flag.snv.badlines.push([linei, "missing mutation class", lst]);
+    return;
+  }
+  let _c = flag.mclasslabel2key[m.class.toUpperCase()];
+  if (_c) {
+    m.class = _c;
+  } else {
+    _c = common.mclasstester(m.class);
+    if (_c) {
+      m.class = _c;
+    } else {
+      flag.snv.badlines.push([linei, "wrong mutation class: " + m.class, lst]);
+      return;
+    }
+  }
+  if (bulk.parsesample(m, flag, linei, lst, flag.snv.badlines)) {
+    return;
+  }
+  if (!m.chr) {
+    flag.snv.badlines.push([linei, "missing chromosome", lst]);
+    return;
+  }
+  if (m.chr.toLowerCase().indexOf("chr") != 0) {
+    m.chr = "chr" + m.chr;
+  }
+  if (!m.pos) {
+    flag.snv.badlines.push([linei, "missing chromosome position", lst]);
+    return;
+  }
+  const v = Number.parseInt(m.pos);
+  if (Number.isNaN(v)) {
+    flag.snv.badlines.push([linei, "invalid chromosome position", lst]);
+    return;
+  }
+  m.pos = v - 1;
+  if (m.maf_tumor_v2 != void 0 && m.maf_tumor_v1 != void 0) {
+    if (m.maf_tumor_v2 == "") {
+    } else {
+      let v1 = Number.parseInt(m.maf_tumor_v1), v2 = Number.parseInt(m.maf_tumor_v2);
+      if (Number.isNaN(v1) || Number.isNaN(v2)) {
+        flag.snv.badlines.push([linei, "invalid maf_tumor mutant and/or total read count", lst]);
+        return;
+      }
+      m.maf_tumor = { f: v1 / v2, v1, v2 };
+    }
+    delete m.maf_tumor_v1;
+    delete m.maf_tumor_v2;
+  }
+  if (m.maf_normal_v1 != void 0 && m.maf_normal_v2 != void 0) {
+    if (m.maf_normal_v2 == "") {
+    } else {
+      let v1 = Number.parseInt(m.maf_normal_v1), v2 = Number.parseInt(m.maf_normal_v2);
+      if (Number.isNaN(v1) || Number.isNaN(v2)) {
+        flag.snv.badlines.push([linei, "invalid maf_normal mutant and/or total read count", lst]);
+        return;
+      }
+      m.maf_normal = { f: v1 / v2, v1, v2 };
+    }
+    delete m.maf_normal_v1;
+    delete m.maf_normal_v2;
+  }
+  flag.good++;
+  if (m.class == "M") {
+    flag.snv.missense++;
+  } else if (m.class == "S") {
+    flag.snv.silent++;
+  }
+  const n = flag.geneToUpper ? m.gene.toUpperCase() : m.gene;
+  if (!flag.data[n]) {
+    flag.data[n] = [];
+  }
+  m.dt = common.dtsnvindel;
+  flag.data[n].push(m);
+}
+export {
+  parseheader,
+  parseline
+};
+//# sourceMappingURL=bulk.snv.js.map

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

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/bulk.snv.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 file header for snv/indel'\n\tconst htry = (...args) => {\n\t\tfor (const s of args) {\n\t\t\tconst i = header.indexOf(s)\n\t\t\tif (i != -1) return i\n\t\t}\n\t\treturn -1\n\t}\n\tlet i = htry('annovar_gene', 'annovar_sj_gene', 'gene', 'genename', 'gene_symbol', 'hugo_symbol')\n\tif (i == -1) return 'gene missing from header'\n\theader[i] = 'gene'\n\ti = htry('annovar_aachange', 'amino_acid_change', 'annovar_sj_aachange', 'aachange', 'protein_change', 'variant')\n\tif (i == -1) return 'amino_acid_change missing from header'\n\theader[i] = 'mname'\n\ti = htry('annovar_class', 'class', 'mclass', 'variant_class', 'variant_classification', 'annovar_sj_class')\n\tif (i == -1) return 'variant_class missing from header'\n\theader[i] = 'class'\n\ti = htry('chromosome', 'chr')\n\tif (i == -1) return 'chromosome missing from header'\n\theader[i] = 'chr'\n\ti = htry('wu_hg19_pos', 'start', 'start_position', 'chr_position', 'position')\n\tif (i == -1) return 'start missing from header'\n\theader[i] = 'pos'\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\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('quantitative_measurements')\n\tif (i != -1) header[i] = 'qmset'\n\t// dna maf tumor\n\ti = htry('mutant_reads_in_case', 'mutant_in_tumor', 'tumor_readcount_alt')\n\tif (i != -1) header[i] = 'maf_tumor_v1'\n\ti = htry('total_reads_in_case', 'total_in_tumor', 'tumor_readcount_total')\n\tif (i != -1) header[i] = 'maf_tumor_v2'\n\t// dna maf normal\n\ti = htry('mutant_reads_in_control', 'mutant_in_normal', 'normal_readcount_alt')\n\tif (i != -1) header[i] = 'maf_normal_v1'\n\ti = htry('total_reads_in_control', 'total_in_normal', 'normal_readcount_total')\n\tif (i != -1) header[i] = 'maf_normal_v2'\n\t// rna maf\n\t// cdna\n\ti = htry('cdna_change')\n\tif (i != -1) header[i] = 'cdna_change'\n\ti = htry('sampletype', 'sample type', 'sample_type')\n\tif (i != -1) header[i] = 'sampletype'\n\ti = htry('origin')\n\tif (i != -1) header[i] = 'origin'\n\ti = htry('cancer', 'disease', 'diagnosis')\n\tif (i != -1) header[i] = 'disease'\n\tflag.snv.header = header\n\tflag.snv.loaded = true\n\treturn false\n}\n\nexport function parseline(linei, line, flag) {\n\tif (line == '' || line[0] == '#') return\n\tconst lst = line.split('\\t')\n\tconst m = {}\n\tfor (let j = 0; j < flag.snv.header.length; j++) {\n\t\tif (lst[j] == undefined) break\n\t\tm[flag.snv.header[j]] = lst[j]\n\t}\n\tif (!m.gene) {\n\t\tflag.snv.badlines.push([linei, 'missing gene', lst])\n\t\treturn\n\t}\n\tif (m.gene.toUpperCase() == 'UNKNOWN') {\n\t\tflag.snv.badlines.push([linei, 'gene name is UNKNOWN', lst])\n\t\treturn\n\t}\n\tif (!m.isoform) {\n\t\tflag.snv.badlines.push([linei, 'missing isoform', lst])\n\t\treturn\n\t}\n\tif (!m.mname) {\n\t\tm.mname = m.cdna_change\n\t\tif (!m.mname) {\n\t\t\tflag.snv.badlines.push([linei, 'missing amino acid change', lst])\n\t\t\treturn\n\t\t}\n\t} else {\n\t\tif (m.mname.indexOf('p.') == 0) {\n\t\t\tm.mname = m.mname.replace(/^p\\./, '')\n\t\t}\n\t}\n\tif (!m.class) {\n\t\tflag.snv.badlines.push([linei, 'missing mutation class', lst])\n\t\treturn\n\t}\n\tlet _c = flag.mclasslabel2key[m.class.toUpperCase()]\n\tif (_c) {\n\t\tm.class = _c\n\t} else {\n\t\t_c = common.mclasstester(m.class)\n\t\tif (_c) {\n\t\t\tm.class = _c\n\t\t} else {\n\t\t\tflag.snv.badlines.push([linei, 'wrong mutation class: ' + m.class, lst])\n\t\t\treturn\n\t\t}\n\t}\n\tif (bulk.parsesample(m, flag, linei, lst, flag.snv.badlines)) {\n\t\treturn\n\t}\n\tif (!m.chr) {\n\t\tflag.snv.badlines.push([linei, 'missing chromosome', lst])\n\t\treturn\n\t}\n\tif (m.chr.toLowerCase().indexOf('chr') != 0) {\n\t\tm.chr = 'chr' + m.chr\n\t}\n\tif (!m.pos) {\n\t\tflag.snv.badlines.push([linei, 'missing chromosome position', lst])\n\t\treturn\n\t}\n\tconst v = Number.parseInt(m.pos)\n\tif (Number.isNaN(v)) {\n\t\tflag.snv.badlines.push([linei, 'invalid chromosome position', lst])\n\t\treturn\n\t}\n\tm.pos = v - 1\n\n\tif (m.maf_tumor_v2 != undefined && m.maf_tumor_v1 != undefined) {\n\t\tif (m.maf_tumor_v2 == '') {\n\t\t\t// no value, do not parse\n\t\t} else {\n\t\t\tlet v1 = Number.parseInt(m.maf_tumor_v1),\n\t\t\t\tv2 = Number.parseInt(m.maf_tumor_v2)\n\t\t\tif (Number.isNaN(v1) || Number.isNaN(v2)) {\n\t\t\t\tflag.snv.badlines.push([linei, 'invalid maf_tumor mutant and/or total read count', lst])\n\t\t\t\treturn\n\t\t\t}\n\t\t\tm.maf_tumor = { f: v1 / v2, v1: v1, v2: v2 }\n\t\t}\n\t\tdelete m.maf_tumor_v1\n\t\tdelete m.maf_tumor_v2\n\t}\n\n\tif (m.maf_normal_v1 != undefined && m.maf_normal_v2 != undefined) {\n\t\tif (m.maf_normal_v2 == '') {\n\t\t\t// no value\n\t\t} else {\n\t\t\tlet v1 = Number.parseInt(m.maf_normal_v1),\n\t\t\t\tv2 = Number.parseInt(m.maf_normal_v2)\n\t\t\tif (Number.isNaN(v1) || Number.isNaN(v2)) {\n\t\t\t\tflag.snv.badlines.push([linei, 'invalid maf_normal mutant and/or total read count', lst])\n\t\t\t\treturn\n\t\t\t}\n\t\t\tm.maf_normal = { f: v1 / v2, v1: v1, v2: v2 }\n\t\t}\n\t\tdelete m.maf_normal_v1\n\t\tdelete m.maf_normal_v2\n\t}\n\n\t/*\n\tif(m.qmset) {\n\t\ttry{\n\t\t\tvar v=JSON.parse(m.qmset)\n\t\t} catch(e){\n\t\t\tflag.snv.badlines.push([linei,'invalid JSON for quantitative_measurements',lst])\n\t\t\tv=null\n\t\t} finally {\n\t\t\tif(v) {\n\t\t\t\tif(typeof(v)!='object') {\n\t\t\t\t\tflag.snv.badlines.push([linei,'value of quantitative_measurements must be an object',lst])\n\t\t\t\t\tdelete m.qmset\n\t\t\t\t} else {\n\t\t\t\t\tfor(var n in v) {\n\t\t\t\t\t\tif(!Array.isArray(v[n])) {\n\t\t\t\t\t\t\tflag.snv.badlines.push([linei,'quantitative_measurements: \"'+n+'\" value must be an array',lst])\n\t\t\t\t\t\t\tdelete v[n]\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tvar tmp=[]\n\t\t\t\t\t\t\tv[n].forEach(function(v2){\n\t\t\t\t\t\t\t\tif(typeof(v2)=='number') {\n\t\t\t\t\t\t\t\t\ttmp.push({v:v2})\n\t\t\t\t\t\t\t\t} else if(v2.v && typeof(v2.v)=='number') {\n\t\t\t\t\t\t\t\t\ttmp.push(v2)\n\t\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\t})\n\t\t\t\t\t\t\tif(tmp.length) {\n\t\t\t\t\t\t\t\tv[n]=tmp\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tflag.snv.badlines.push([linei,'quantitative_measurements: no valid value for \"'+n+'\"',lst])\n\t\t\t\t\t\t\t\tdelete v[n]\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\tm.qmset=v\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tdelete m.qmset\n\t\t\t}\n\t\t}\n\t}\n\t*/\n\tflag.good++\n\t// FIXME hard-coded M and S\n\tif (m.class == 'M') {\n\t\tflag.snv.missense++\n\t} else if (m.class == 'S') {\n\t\tflag.snv.silent++\n\t}\n\tconst n = flag.geneToUpper ? m.gene.toUpperCase() : m.gene\n\tif (!flag.data[n]) {\n\t\tflag.data[n] = []\n\t}\n\tm.dt = common.dtsnvindel\n\tflag.data[n].push(m)\n}\n"],
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+  "names": ["i"]
+}

package/dist/src/bulk.sv.js

@@ -0,0 +1,266 @@
+import * as bulk from "./bulk.js";
+import * as common from "./common.js";
+function parseheader(line, flag, issv) {
+  const header = line.toLowerCase().split("	");
+  if (header.length <= 1) return "invalid file header for fusions";
+  const htry = (...lst) => {
+    for (const a of lst) {
+      const j = header.indexOf(a);
+      if (j != -1) return j;
+    }
+    return -1;
+  };
+  let i = htry("gene_a", "gene1", "genea");
+  if (i == -1) return "gene_a missing from header";
+  header[i] = "gene1";
+  i = htry("gene_b", "gene2", "geneb");
+  if (i == -1) return "gene_b missing from header";
+  header[i] = "gene2";
+  i = htry("chr_a", "chr1", "chra");
+  if (i == -1) return "chr_a missing from header";
+  header[i] = "chr1";
+  i = htry("chr_b", "chr2", "chrb");
+  if (i == -1) return "chr_b missing from header";
+  header[i] = "chr2";
+  i = htry("pos_a", "position_a", "position1", "posa");
+  if (i == -1) return "pos_a missing from header";
+  header[i] = "position1";
+  i = htry("pos_b", "position_b", "position2", "posb");
+  if (i == -1) return "pos_b missing from header";
+  header[i] = "position2";
+  i = htry("isoform_a", "refseq_a", "refseq1", "isoform1", "sv_refseqa");
+  if (i == -1) return "isoform_a missing from header";
+  header[i] = "isoform1";
+  i = htry("isoform_b", "refseq_b", "refseq2", "isoform2", "sv_refseqb");
+  if (i == -1) return "isoform_b missing from header";
+  header[i] = "isoform2";
+  i = htry("strand_a", "orta");
+  if (i == -1) return "strand_a missing from header";
+  header[i] = "strand1";
+  i = htry("strand_b", "ortb");
+  if (i == -1) return "strand_b missing from header";
+  header[i] = "strand2";
+  i = htry("sample", "sample_name", "tumor_sample_barcode");
+  if (i != -1) header[i] = "sample";
+  i = htry("patient", "donor", "target_case_id");
+  if (i != -1) header[i] = "patient";
+  i = htry("sampletype", "sample type", "sample_type");
+  if (i != -1) header[i] = "sampletype";
+  i = htry("disease");
+  if (i != -1) header[i] = "disease";
+  i = htry("origin");
+  if (i != -1) header[i] = "origin";
+  if (issv) {
+    flag.sv.loaded = true;
+    flag.sv.header = header;
+  } else {
+    flag.fusion.loaded = true;
+    flag.fusion.header = header;
+  }
+  return false;
+}
+function parseline(i, line, flag, issv) {
+  if (line == "" || line[0] == "#") return;
+  const lst = line.split("	");
+  const m = {};
+  const header = issv ? flag.sv.header : flag.fusion.header;
+  const badlines = issv ? flag.sv.badlines : flag.fusion.badlines;
+  for (let j = 0; j < header.length; j++) {
+    m[header[j]] = lst[j];
+  }
+  if (!m.chr1) {
+    badlines.push([i, "missing chr1", lst]);
+    return;
+  }
+  if (m.chr1.toLowerCase().indexOf("chr") != 0) {
+    m.chr1 = "chr" + m.chr1;
+  }
+  if (!m.chr2) {
+    badlines.push([i, "missing chr2", lst]);
+    return;
+  }
+  if (m.chr2.toLowerCase().indexOf("chr") != 0) {
+    m.chr2 = "chr" + m.chr2;
+  }
+  let v = m.position1;
+  if (!v) {
+    badlines.push([i, "missing position1", lst]);
+    return;
+  }
+  let v2 = Number.parseInt(v);
+  if (Number.isNaN(v2) || v2 <= 0) {
+    badlines.push([i, "invalid value for position1", lst]);
+    return;
+  }
+  m.position1 = v2;
+  v = m.position2;
+  if (!v) {
+    badlines.push([i, "missing position2", lst]);
+    return;
+  }
+  v2 = Number.parseInt(v);
+  if (Number.isNaN(v2) || v2 <= 0) {
+    badlines.push([i, "invalid value for position2", lst]);
+    return;
+  }
+  m.position2 = v2;
+  if (bulk.parsesample(m, flag, i, lst, badlines)) {
+    return;
+  }
+  if (m.isoform1 && m.isoform1.indexOf(",") != -1) {
+    const lst2 = m.isoform1.split(",");
+    m.isoform1 = void 0;
+    for (const t of lst2) {
+      if (t != "") m.isoform1 = t;
+    }
+  }
+  if (m.isoform2 && m.isoform2.indexOf(",") != -1) {
+    const lst2 = m.isoform2.split(",");
+    m.isoform2 = void 0;
+    for (const t of lst2) {
+      if (t != "") m.isoform2 = t;
+    }
+  }
+  if (!m.gene1) {
+    m.isoform1 = void 0;
+  }
+  if (!m.gene2) {
+    m.isoform2 = void 0;
+  }
+  if (m.gene1) {
+    flag.good++;
+    const m2 = {
+      dt: issv ? common.dtsv : common.dtfusionrna,
+      class: issv ? common.mclasssv : common.mclassfusionrna,
+      isoform: m.isoform1,
+      mname: m.gene2 || m.chr2,
+      sample: m.sample,
+      patient: m.patient,
+      sampletype: m.sampletype,
+      origin: m.origin,
+      disease: m.disease,
+      pairlst: [
+        {
+          a: {
+            name: m.gene1,
+            isoform: m.isoform1,
+            strand: m.strand1,
+            chr: m.chr1,
+            position: m.position1
+          },
+          b: {
+            name: m.gene2,
+            isoform: m.isoform2,
+            strand: m.strand2,
+            chr: m.chr2,
+            position: m.position2
+          }
+        }
+      ]
+    };
+    const n = flag.geneToUpper ? m.gene1.toUpperCase() : m.gene1;
+    if (!flag.data[n]) {
+      flag.data[n] = [];
+    }
+    flag.data[n].push(m2);
+  }
+  if (m.gene2 && m.gene2 != m.gene1) {
+    flag.good++;
+    const m2 = {
+      dt: issv ? common.dtsv : common.dtfusionrna,
+      class: issv ? common.mclasssv : common.mclassfusionrna,
+      isoform: m.isoform2,
+      mname: m.gene1 || m.chr1,
+      sample: m.sample,
+      patient: m.patient,
+      sampletype: m.sampletype,
+      origin: m.origin,
+      disease: m.disease,
+      pairlst: [
+        {
+          a: {
+            name: m.gene1,
+            isoform: m.isoform1,
+            strand: m.strand1,
+            chr: m.chr1,
+            position: m.position1
+          },
+          b: {
+            name: m.gene2,
+            isoform: m.isoform2,
+            strand: m.strand2,
+            chr: m.chr2,
+            position: m.position2
+          }
+        }
+      ]
+    };
+    const n = flag.geneToUpper ? m.gene2.toUpperCase() : m.gene2;
+    if (!flag.data[n]) {
+      flag.data[n] = [];
+    }
+    flag.data[n].push(m2);
+  }
+}
+function duplicate(m) {
+  const n = {};
+  for (const k in m) {
+    if (k == "pairlst") continue;
+    const v = m[k];
+    const type = typeof v;
+    if (type == "object") {
+      continue;
+    }
+    n[k] = v;
+  }
+  if (m.pairlst) {
+    n.pairlst = [];
+    for (const pair of m.pairlst) {
+      const p = {};
+      for (const k in pair) {
+        if (k == "a" || k == "b" || k == "interstitial") {
+          continue;
+        }
+        p[k] = pair[k];
+      }
+      if (pair.a) {
+        p.a = {};
+        for (const k in pair.a) {
+          const v = pair.a[k];
+          if (typeof v == "object") {
+            continue;
+          }
+          p.a[k] = v;
+        }
+      }
+      if (pair.b) {
+        p.b = {};
+        for (const k in pair.b) {
+          const v = pair.b[k];
+          if (typeof v == "object") {
+            continue;
+          }
+          p.b[k] = v;
+        }
+      }
+      if (pair.interstitial) {
+        p.interstitial = {};
+        for (const k in pair.interstitial) {
+          const v = pair.interstitial[k];
+          if (typeof v == "object") {
+            continue;
+          }
+          p.interstitial[k] = v;
+        }
+      }
+      n.pairlst.push(p);
+    }
+  }
+  return n;
+}
+export {
+  duplicate,
+  parseheader,
+  parseline
+};
+//# sourceMappingURL=bulk.sv.js.map