@sjcrh/proteinpaint-shared 2.188.1 → 2.189.0

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

@@ -1,7 +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"],
-  "mappings": "AAAA,YAAY,UAAU;AACtB,YAAY,YAAY;AAWjB,SAAS,YAAY,MAAM,MAAM,MAAM;AAC7C,QAAM,SAAS,KAAK,YAAY,EAAE,MAAM,GAAI;AAC5C,MAAI,OAAO,UAAU,EAAG,QAAO;AAC/B,QAAM,OAAO,IAAI,QAAQ;AACxB,eAAW,KAAK,KAAK;AACpB,YAAM,IAAI,OAAO,QAAQ,CAAC;AAC1B,UAAI,KAAK,GAAI,QAAO;AAAA,IACrB;AACA,WAAO;AAAA,EACR;AACA,MAAI,IAAI,KAAK,UAAU,SAAS,OAAO;AACvC,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,UAAU,SAAS,OAAO;AACnC,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,SAAS,QAAQ,MAAM;AAChC,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,SAAS,QAAQ,MAAM;AAChC,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,SAAS,cAAc,aAAa,MAAM;AACnD,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,SAAS,cAAc,aAAa,MAAM;AACnD,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,aAAa,YAAY,WAAW,YAAY,YAAY;AACrE,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,aAAa,YAAY,WAAW,YAAY,YAAY;AACrE,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,YAAY,MAAM;AAC3B,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,YAAY,MAAM;AAC3B,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AAEZ,MAAI,KAAK,UAAU,eAAe,sBAAsB;AACxD,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,WAAW,SAAS,gBAAgB;AAC7C,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,cAAc,eAAe,aAAa;AACnD,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,SAAS;AAClB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,QAAQ;AACjB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,MAAM;AACT,SAAK,GAAG,SAAS;AACjB,SAAK,GAAG,SAAS;AAAA,EAClB,OAAO;AACN,SAAK,OAAO,SAAS;AACrB,SAAK,OAAO,SAAS;AAAA,EACtB;AACA,SAAO;AACR;AAEO,SAAS,UAAU,GAAG,MAAM,MAAM,MAAM;AAC9C,MAAI,QAAQ,MAAM,KAAK,CAAC,KAAK,IAAK;AAClC,QAAM,MAAM,KAAK,MAAM,GAAI;AAC3B,QAAM,IAAI,CAAC;AACX,QAAM,SAAS,OAAO,KAAK,GAAG,SAAS,KAAK,OAAO;AACnD,QAAM,WAAW,OAAO,KAAK,GAAG,WAAW,KAAK,OAAO;AAEvD,WAAS,IAAI,GAAG,IAAI,OAAO,QAAQ,KAAK;AACvC,MAAE,OAAO,CAAC,CAAC,IAAI,IAAI,CAAC;AAAA,EACrB;AACA,MAAI,CAAC,EAAE,MAAM;AACZ,aAAS,KAAK,CAAC,GAAG,gBAAgB,GAAG,CAAC;AACtC;AAAA,EACD;AACA,MAAI,EAAE,KAAK,YAAY,EAAE,QAAQ,KAAK,KAAK,GAAG;AAC7C,MAAE,OAAO,QAAQ,EAAE;AAAA,EACpB;AACA,MAAI,CAAC,EAAE,MAAM;AACZ,aAAS,KAAK,CAAC,GAAG,gBAAgB,GAAG,CAAC;AACtC;AAAA,EACD;AACA,MAAI,EAAE,KAAK,YAAY,EAAE,QAAQ,KAAK,KAAK,GAAG;AAC7C,MAAE,OAAO,QAAQ,EAAE;AAAA,EACpB;AACA,MAAI,IAAI,EAAE;AACV,MAAI,CAAC,GAAG;AACP,aAAS,KAAK,CAAC,GAAG,qBAAqB,GAAG,CAAC;AAC3C;AAAA,EACD;AACA,MAAI,KAAK,OAAO,SAAS,CAAC;AAC1B,MAAI,OAAO,MAAM,EAAE,KAAK,MAAM,GAAG;AAChC,aAAS,KAAK,CAAC,GAAG,+BAA+B,GAAG,CAAC;AACrD;AAAA,EACD;AACA,IAAE,YAAY;AACd,MAAI,EAAE;AACN,MAAI,CAAC,GAAG;AACP,aAAS,KAAK,CAAC,GAAG,qBAAqB,GAAG,CAAC;AAC3C;AAAA,EACD;AACA,OAAK,OAAO,SAAS,CAAC;AACtB,MAAI,OAAO,MAAM,EAAE,KAAK,MAAM,GAAG;AAChC,aAAS,KAAK,CAAC,GAAG,+BAA+B,GAAG,CAAC;AACrD;AAAA,EACD;AACA,IAAE,YAAY;AACd,MAAI,KAAK,YAAY,GAAG,MAAM,GAAG,KAAK,QAAQ,GAAG;AAChD;AAAA,EACD;AACA,MAAI,EAAE,YAAY,EAAE,SAAS,QAAQ,GAAG,KAAK,IAAI;AAChD,UAAM,OAAO,EAAE,SAAS,MAAM,GAAG;AACjC,MAAE,WAAW;AACb,eAAW,KAAK,MAAM;AACrB,UAAI,KAAK,GAAI,GAAE,WAAW;AAAA,IAC3B;AAAA,EACD;AACA,MAAI,EAAE,YAAY,EAAE,SAAS,QAAQ,GAAG,KAAK,IAAI;AAChD,UAAM,OAAO,EAAE,SAAS,MAAM,GAAG;AACjC,MAAE,WAAW;AACb,eAAW,KAAK,MAAM;AACrB,UAAI,KAAK,GAAI,GAAE,WAAW;AAAA,IAC3B;AAAA,EACD;AACA,MAAI,CAAC,EAAE,OAAO;AACb,MAAE,WAAW;AAAA,EACd;AACA,MAAI,CAAC,EAAE,OAAO;AACb,MAAE,WAAW;AAAA,EACd;AACA,MAAI,EAAE,OAAO;AAEZ,SAAK;AACL,UAAM,KAAK;AAAA,MACV,IAAI,OAAO,OAAO,OAAO,OAAO;AAAA,MAChC,OAAO,OAAO,OAAO,WAAW,OAAO;AAAA,MACvC,SAAS,EAAE;AAAA,MACX,OAAO,EAAE,SAAS,EAAE;AAAA,MACpB,QAAQ,EAAE;AAAA,MACV,SAAS,EAAE;AAAA,MACX,YAAY,EAAE;AAAA,MACd,QAAQ,EAAE;AAAA,MACV,SAAS,EAAE;AAAA,MACX,SAAS;AAAA,QACR;AAAA,UACC,GAAG;AAAA,YACF,MAAM,EAAE;AAAA,YACR,SAAS,EAAE;AAAA,YACX,QAAQ,EAAE;AAAA,YACV,KAAK,EAAE;AAAA,YACP,UAAU,EAAE;AAAA,UACb;AAAA,UACA,GAAG;AAAA,YACF,MAAM,EAAE;AAAA,YACR,SAAS,EAAE;AAAA,YACX,QAAQ,EAAE;AAAA,YACV,KAAK,EAAE;AAAA,YACP,UAAU,EAAE;AAAA,UACb;AAAA,QACD;AAAA,MACD;AAAA,IACD;AACA,UAAM,IAAI,KAAK,cAAc,EAAE,MAAM,YAAY,IAAI,EAAE;AACvD,QAAI,CAAC,KAAK,KAAK,CAAC,GAAG;AAClB,WAAK,KAAK,CAAC,IAAI,CAAC;AAAA,IACjB;AACA,SAAK,KAAK,CAAC,EAAE,KAAK,EAAE;AAAA,EACrB;AACA,MAAI,EAAE,SAAS,EAAE,SAAS,EAAE,OAAO;AAElC,SAAK;AACL,UAAM,KAAK;AAAA,MACV,IAAI,OAAO,OAAO,OAAO,OAAO;AAAA,MAChC,OAAO,OAAO,OAAO,WAAW,OAAO;AAAA,MACvC,SAAS,EAAE;AAAA,MACX,OAAO,EAAE,SAAS,EAAE;AAAA,MACpB,QAAQ,EAAE;AAAA,MACV,SAAS,EAAE;AAAA,MACX,YAAY,EAAE;AAAA,MACd,QAAQ,EAAE;AAAA,MACV,SAAS,EAAE;AAAA,MACX,SAAS;AAAA,QACR;AAAA,UACC,GAAG;AAAA,YACF,MAAM,EAAE;AAAA,YACR,SAAS,EAAE;AAAA,YACX,QAAQ,EAAE;AAAA,YACV,KAAK,EAAE;AAAA,YACP,UAAU,EAAE;AAAA,UACb;AAAA,UACA,GAAG;AAAA,YACF,MAAM,EAAE;AAAA,YACR,SAAS,EAAE;AAAA,YACX,QAAQ,EAAE;AAAA,YACV,KAAK,EAAE;AAAA,YACP,UAAU,EAAE;AAAA,UACb;AAAA,QACD;AAAA,MACD;AAAA,IACD;AACA,UAAM,IAAI,KAAK,cAAc,EAAE,MAAM,YAAY,IAAI,EAAE;AACvD,QAAI,CAAC,KAAK,KAAK,CAAC,GAAG;AAClB,WAAK,KAAK,CAAC,IAAI,CAAC;AAAA,IACjB;AACA,SAAK,KAAK,CAAC,EAAE,KAAK,EAAE;AAAA,EACrB;AACD;AAEO,SAAS,UAAU,GAAG;AAC5B,QAAM,IAAI,CAAC;AACX,aAAW,KAAK,GAAG;AAClB,QAAI,KAAK,UAAW;AACpB,UAAM,IAAI,EAAE,CAAC;AACb,UAAM,OAAO,OAAO;AACpB,QAAI,QAAQ,UAAU;AACrB;AAAA,IACD;AACA,MAAE,CAAC,IAAI;AAAA,EACR;AACA,MAAI,EAAE,SAAS;AACd,MAAE,UAAU,CAAC;AACb,eAAW,QAAQ,EAAE,SAAS;AAC7B,YAAM,IAAI,CAAC;AACX,iBAAW,KAAK,MAAM;AACrB,YAAI,KAAK,OAAO,KAAK,OAAO,KAAK,gBAAgB;AAChD;AAAA,QACD;AACA,UAAE,CAAC,IAAI,KAAK,CAAC;AAAA,MACd;AACA,UAAI,KAAK,GAAG;AACX,UAAE,IAAI,CAAC;AACP,mBAAW,KAAK,KAAK,GAAG;AACvB,gBAAM,IAAI,KAAK,EAAE,CAAC;AAClB,cAAI,OAAO,KAAK,UAAU;AACzB;AAAA,UACD;AACA,YAAE,EAAE,CAAC,IAAI;AAAA,QACV;AAAA,MACD;AACA,UAAI,KAAK,GAAG;AACX,UAAE,IAAI,CAAC;AACP,mBAAW,KAAK,KAAK,GAAG;AACvB,gBAAM,IAAI,KAAK,EAAE,CAAC;AAClB,cAAI,OAAO,KAAK,UAAU;AACzB;AAAA,UACD;AACA,YAAE,EAAE,CAAC,IAAI;AAAA,QACV;AAAA,MACD;AACA,UAAI,KAAK,cAAc;AACtB,UAAE,eAAe,CAAC;AAClB,mBAAW,KAAK,KAAK,cAAc;AAClC,gBAAM,IAAI,KAAK,aAAa,CAAC;AAC7B,cAAI,OAAO,KAAK,UAAU;AACzB;AAAA,UACD;AACA,YAAE,aAAa,CAAC,IAAI;AAAA,QACrB;AAAA,MACD;AACA,QAAE,QAAQ,KAAK,CAAC;AAAA,IACjB;AAAA,EACD;AACA,SAAO;AACR;",
+  "sources": ["../../src/bulk.sv.ts"],
+  "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: Record<string, any> = {}\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)) {\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: Record<string, any> = {}\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: Record<string, any> = {}\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"],
+  "mappings": "AAAA,YAAY,UAAU;AACtB,YAAY,YAAY;AAWjB,SAAS,YAAY,MAAM,MAAM,MAAM;AAC7C,QAAM,SAAS,KAAK,YAAY,EAAE,MAAM,GAAI;AAC5C,MAAI,OAAO,UAAU,EAAG,QAAO;AAC/B,QAAM,OAAO,IAAI,QAAQ;AACxB,eAAW,KAAK,KAAK;AACpB,YAAM,IAAI,OAAO,QAAQ,CAAC;AAC1B,UAAI,KAAK,GAAI,QAAO;AAAA,IACrB;AACA,WAAO;AAAA,EACR;AACA,MAAI,IAAI,KAAK,UAAU,SAAS,OAAO;AACvC,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,UAAU,SAAS,OAAO;AACnC,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,SAAS,QAAQ,MAAM;AAChC,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,SAAS,QAAQ,MAAM;AAChC,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,SAAS,cAAc,aAAa,MAAM;AACnD,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,SAAS,cAAc,aAAa,MAAM;AACnD,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,aAAa,YAAY,WAAW,YAAY,YAAY;AACrE,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,aAAa,YAAY,WAAW,YAAY,YAAY;AACrE,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,YAAY,MAAM;AAC3B,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,KAAK,YAAY,MAAM;AAC3B,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AAEZ,MAAI,KAAK,UAAU,eAAe,sBAAsB;AACxD,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,WAAW,SAAS,gBAAgB;AAC7C,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,cAAc,eAAe,aAAa;AACnD,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,SAAS;AAClB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,QAAQ;AACjB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,MAAM;AACT,SAAK,GAAG,SAAS;AACjB,SAAK,GAAG,SAAS;AAAA,EAClB,OAAO;AACN,SAAK,OAAO,SAAS;AACrB,SAAK,OAAO,SAAS;AAAA,EACtB;AACA,SAAO;AACR;AAEO,SAAS,UAAU,GAAG,MAAM,MAAM,MAAM;AAC9C,MAAI,QAAQ,MAAM,KAAK,CAAC,KAAK,IAAK;AAClC,QAAM,MAAM,KAAK,MAAM,GAAI;AAC3B,QAAM,IAAyB,CAAC;AAChC,QAAM,SAAS,OAAO,KAAK,GAAG,SAAS,KAAK,OAAO;AACnD,QAAM,WAAW,OAAO,KAAK,GAAG,WAAW,KAAK,OAAO;AAEvD,WAAS,IAAI,GAAG,IAAI,OAAO,QAAQ,KAAK;AACvC,MAAE,OAAO,CAAC,CAAC,IAAI,IAAI,CAAC;AAAA,EACrB;AACA,MAAI,CAAC,EAAE,MAAM;AACZ,aAAS,KAAK,CAAC,GAAG,gBAAgB,GAAG,CAAC;AACtC;AAAA,EACD;AACA,MAAI,EAAE,KAAK,YAAY,EAAE,QAAQ,KAAK,KAAK,GAAG;AAC7C,MAAE,OAAO,QAAQ,EAAE;AAAA,EACpB;AACA,MAAI,CAAC,EAAE,MAAM;AACZ,aAAS,KAAK,CAAC,GAAG,gBAAgB,GAAG,CAAC;AACtC;AAAA,EACD;AACA,MAAI,EAAE,KAAK,YAAY,EAAE,QAAQ,KAAK,KAAK,GAAG;AAC7C,MAAE,OAAO,QAAQ,EAAE;AAAA,EACpB;AACA,MAAI,IAAI,EAAE;AACV,MAAI,CAAC,GAAG;AACP,aAAS,KAAK,CAAC,GAAG,qBAAqB,GAAG,CAAC;AAC3C;AAAA,EACD;AACA,MAAI,KAAK,OAAO,SAAS,CAAC;AAC1B,MAAI,OAAO,MAAM,EAAE,KAAK,MAAM,GAAG;AAChC,aAAS,KAAK,CAAC,GAAG,+BAA+B,GAAG,CAAC;AACrD;AAAA,EACD;AACA,IAAE,YAAY;AACd,MAAI,EAAE;AACN,MAAI,CAAC,GAAG;AACP,aAAS,KAAK,CAAC,GAAG,qBAAqB,GAAG,CAAC;AAC3C;AAAA,EACD;AACA,OAAK,OAAO,SAAS,CAAC;AACtB,MAAI,OAAO,MAAM,EAAE,KAAK,MAAM,GAAG;AAChC,aAAS,KAAK,CAAC,GAAG,+BAA+B,GAAG,CAAC;AACrD;AAAA,EACD;AACA,IAAE,YAAY;AACd,MAAI,KAAK,YAAY,GAAG,MAAM,GAAG,GAAG,GAAG;AACtC;AAAA,EACD;AACA,MAAI,EAAE,YAAY,EAAE,SAAS,QAAQ,GAAG,KAAK,IAAI;AAChD,UAAM,OAAO,EAAE,SAAS,MAAM,GAAG;AACjC,MAAE,WAAW;AACb,eAAW,KAAK,MAAM;AACrB,UAAI,KAAK,GAAI,GAAE,WAAW;AAAA,IAC3B;AAAA,EACD;AACA,MAAI,EAAE,YAAY,EAAE,SAAS,QAAQ,GAAG,KAAK,IAAI;AAChD,UAAM,OAAO,EAAE,SAAS,MAAM,GAAG;AACjC,MAAE,WAAW;AACb,eAAW,KAAK,MAAM;AACrB,UAAI,KAAK,GAAI,GAAE,WAAW;AAAA,IAC3B;AAAA,EACD;AACA,MAAI,CAAC,EAAE,OAAO;AACb,MAAE,WAAW;AAAA,EACd;AACA,MAAI,CAAC,EAAE,OAAO;AACb,MAAE,WAAW;AAAA,EACd;AACA,MAAI,EAAE,OAAO;AAEZ,SAAK;AACL,UAAM,KAAK;AAAA,MACV,IAAI,OAAO,OAAO,OAAO,OAAO;AAAA,MAChC,OAAO,OAAO,OAAO,WAAW,OAAO;AAAA,MACvC,SAAS,EAAE;AAAA,MACX,OAAO,EAAE,SAAS,EAAE;AAAA,MACpB,QAAQ,EAAE;AAAA,MACV,SAAS,EAAE;AAAA,MACX,YAAY,EAAE;AAAA,MACd,QAAQ,EAAE;AAAA,MACV,SAAS,EAAE;AAAA,MACX,SAAS;AAAA,QACR;AAAA,UACC,GAAG;AAAA,YACF,MAAM,EAAE;AAAA,YACR,SAAS,EAAE;AAAA,YACX,QAAQ,EAAE;AAAA,YACV,KAAK,EAAE;AAAA,YACP,UAAU,EAAE;AAAA,UACb;AAAA,UACA,GAAG;AAAA,YACF,MAAM,EAAE;AAAA,YACR,SAAS,EAAE;AAAA,YACX,QAAQ,EAAE;AAAA,YACV,KAAK,EAAE;AAAA,YACP,UAAU,EAAE;AAAA,UACb;AAAA,QACD;AAAA,MACD;AAAA,IACD;AACA,UAAM,IAAI,KAAK,cAAc,EAAE,MAAM,YAAY,IAAI,EAAE;AACvD,QAAI,CAAC,KAAK,KAAK,CAAC,GAAG;AAClB,WAAK,KAAK,CAAC,IAAI,CAAC;AAAA,IACjB;AACA,SAAK,KAAK,CAAC,EAAE,KAAK,EAAE;AAAA,EACrB;AACA,MAAI,EAAE,SAAS,EAAE,SAAS,EAAE,OAAO;AAElC,SAAK;AACL,UAAM,KAAK;AAAA,MACV,IAAI,OAAO,OAAO,OAAO,OAAO;AAAA,MAChC,OAAO,OAAO,OAAO,WAAW,OAAO;AAAA,MACvC,SAAS,EAAE;AAAA,MACX,OAAO,EAAE,SAAS,EAAE;AAAA,MACpB,QAAQ,EAAE;AAAA,MACV,SAAS,EAAE;AAAA,MACX,YAAY,EAAE;AAAA,MACd,QAAQ,EAAE;AAAA,MACV,SAAS,EAAE;AAAA,MACX,SAAS;AAAA,QACR;AAAA,UACC,GAAG;AAAA,YACF,MAAM,EAAE;AAAA,YACR,SAAS,EAAE;AAAA,YACX,QAAQ,EAAE;AAAA,YACV,KAAK,EAAE;AAAA,YACP,UAAU,EAAE;AAAA,UACb;AAAA,UACA,GAAG;AAAA,YACF,MAAM,EAAE;AAAA,YACR,SAAS,EAAE;AAAA,YACX,QAAQ,EAAE;AAAA,YACV,KAAK,EAAE;AAAA,YACP,UAAU,EAAE;AAAA,UACb;AAAA,QACD;AAAA,MACD;AAAA,IACD;AACA,UAAM,IAAI,KAAK,cAAc,EAAE,MAAM,YAAY,IAAI,EAAE;AACvD,QAAI,CAAC,KAAK,KAAK,CAAC,GAAG;AAClB,WAAK,KAAK,CAAC,IAAI,CAAC;AAAA,IACjB;AACA,SAAK,KAAK,CAAC,EAAE,KAAK,EAAE;AAAA,EACrB;AACD;AAEO,SAAS,UAAU,GAAG;AAC5B,QAAM,IAAyB,CAAC;AAChC,aAAW,KAAK,GAAG;AAClB,QAAI,KAAK,UAAW;AACpB,UAAM,IAAI,EAAE,CAAC;AACb,UAAM,OAAO,OAAO;AACpB,QAAI,QAAQ,UAAU;AACrB;AAAA,IACD;AACA,MAAE,CAAC,IAAI;AAAA,EACR;AACA,MAAI,EAAE,SAAS;AACd,MAAE,UAAU,CAAC;AACb,eAAW,QAAQ,EAAE,SAAS;AAC7B,YAAM,IAAyB,CAAC;AAChC,iBAAW,KAAK,MAAM;AACrB,YAAI,KAAK,OAAO,KAAK,OAAO,KAAK,gBAAgB;AAChD;AAAA,QACD;AACA,UAAE,CAAC,IAAI,KAAK,CAAC;AAAA,MACd;AACA,UAAI,KAAK,GAAG;AACX,UAAE,IAAI,CAAC;AACP,mBAAW,KAAK,KAAK,GAAG;AACvB,gBAAM,IAAI,KAAK,EAAE,CAAC;AAClB,cAAI,OAAO,KAAK,UAAU;AACzB;AAAA,UACD;AACA,YAAE,EAAE,CAAC,IAAI;AAAA,QACV;AAAA,MACD;AACA,UAAI,KAAK,GAAG;AACX,UAAE,IAAI,CAAC;AACP,mBAAW,KAAK,KAAK,GAAG;AACvB,gBAAM,IAAI,KAAK,EAAE,CAAC;AAClB,cAAI,OAAO,KAAK,UAAU;AACzB;AAAA,UACD;AACA,YAAE,EAAE,CAAC,IAAI;AAAA,QACV;AAAA,MACD;AACA,UAAI,KAAK,cAAc;AACtB,UAAE,eAAe,CAAC;AAClB,mBAAW,KAAK,KAAK,cAAc;AAClC,gBAAM,IAAI,KAAK,aAAa,CAAC;AAC7B,cAAI,OAAO,KAAK,UAAU;AACzB;AAAA,UACD;AACA,YAAE,aAAa,CAAC,IAAI;AAAA,QACrB;AAAA,MACD;AACA,QAAE,QAAQ,KAAK,CAAC;AAAA,IACjB;AAAA,EACD;AACA,SAAO;AACR;",
   "names": []
 }

package/dist/src/bulk.svjson.d.ts

@@ -0,0 +1,2 @@
+export declare function parseheader(line: any): any[] | "invalid file header for svjson";
+export declare function parseline(i: any, line: any, flag: any, header: any): void;

package/dist/src/bulk.svjson.js

@@ -1,6 +1,6 @@
 import * as common from "./common.js";
 import * as bulk from "./bulk.js";
-function parseheader(line, flag) {
+function parseheader(line) {
   const header = line.toLowerCase().split("	");
   if (header.length <= 1) return "invalid file header for svjson";
   const htry = (...lst) => {
@@ -33,13 +33,13 @@ function parseline(i, line, flag, header) {
     badlines.push([i, "missing jsontext", lst]);
     return;
   }
-  if (bulk.parsesample(m, flag, i, lst, badlines)) {
+  if (bulk.parsesample(m, flag, i, lst)) {
     return;
   }
   let json;
   try {
     json = JSON.parse(m.jsontext);
-  } catch (e) {
+  } catch (_) {
     badlines.push([i, "invalid JSON text", lst]);
     return;
   }

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

@@ -1,7 +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"],
-  "mappings": "AAMA,YAAY,YAAY;AACxB,YAAY,UAAU;AAKf,SAAS,YAAY,MAAM,MAAM;AACvC,QAAM,SAAS,KAAK,YAAY,EAAE,MAAM,GAAI;AAC5C,MAAI,OAAO,UAAU,EAAG,QAAO;AAC/B,QAAM,OAAO,IAAI,QAAQ;AACxB,eAAW,KAAK,KAAK;AACpB,YAAM,IAAI,OAAO,QAAQ,CAAC;AAC1B,UAAI,KAAK,GAAI,QAAO;AAAA,IACrB;AACA,WAAO;AAAA,EACR;AACA,MAAI,IAAI,KAAK,QAAQ;AACrB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,YAAY;AACrB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,SAAS;AAClB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,QAAQ,UAAU;AAC3B,MAAI,KAAK,GAAI,QAAO,CAAC,0BAA0B;AAC/C,SAAO,CAAC,IAAI;AACZ,SAAO,CAAC,MAAM,MAAM;AACrB;AAEO,SAAS,UAAU,GAAG,MAAM,MAAM,QAAQ;AAChD,MAAI,QAAQ,MAAM,KAAK,CAAC,KAAK,IAAK;AAClC,QAAM,MAAM,KAAK,MAAM,GAAI;AAC3B,QAAM,IAAI,CAAC;AACX,QAAM,WAAW,KAAK,OAAO;AAE7B,WAAS,IAAI,GAAG,IAAI,OAAO,QAAQ,KAAK;AACvC,MAAE,OAAO,CAAC,CAAC,IAAI,IAAI,CAAC;AAAA,EACrB;AACA,MAAI,CAAC,EAAE,UAAU;AAChB,aAAS,KAAK,CAAC,GAAG,oBAAoB,GAAG,CAAC;AAC1C;AAAA,EACD;AACA,MAAI,KAAK,YAAY,GAAG,MAAM,GAAG,KAAK,QAAQ,GAAG;AAChD;AAAA,EACD;AACA,MAAI;AACJ,MAAI;AACH,WAAO,KAAK,MAAM,EAAE,QAAQ;AAAA,EAC7B,SAAS,GAAG;AACX,aAAS,KAAK,CAAC,GAAG,qBAAqB,GAAG,CAAC;AAC3C;AAAA,EACD;AAEA,MAAI,MAAM,QAAQ,IAAI,GAAG;AAExB,eAAW,QAAQ,MAAM;AACxB,UAAI,KAAK,KAAK,KAAK,EAAE,QAAQ,KAAK,EAAE,SAAS;AAC5C,aAAK;AACL,cAAM,KAAK;AAAA,UACV,IAAI,OAAO;AAAA,UACX,OAAO,OAAO;AAAA,UACd,SAAS,KAAK,EAAE;AAAA,UAChB,OAAO,KAAK,EAAE;AAAA,QACf;AACA,mBAAW,KAAK,GAAG;AAClB,cAAI,KAAK,WAAY,IAAG,CAAC,IAAI,EAAE,CAAC;AAAA,QACjC;AACA,WAAG,UAAU,UAAU,IAAI;AAC3B,cAAM,IAAI,KAAK,EAAE,KAAK,YAAY;AAClC,YAAI,CAAC,KAAK,KAAK,CAAC,GAAG;AAClB,eAAK,KAAK,CAAC,IAAI,CAAC;AAAA,QACjB;AACA,aAAK,KAAK,CAAC,EAAE,KAAK,EAAE;AAAA,MACrB;AACA,UAAI,KAAK,KAAK,KAAK,EAAE,QAAQ,KAAK,EAAE,SAAS;AAC5C,aAAK;AACL,cAAM,KAAK;AAAA,UACV,IAAI,OAAO;AAAA,UACX,OAAO,OAAO;AAAA,UACd,SAAS,KAAK,EAAE;AAAA,UAChB,OAAO,KAAK,EAAE;AAAA,QACf;AACA,mBAAW,KAAK,GAAG;AAClB,cAAI,KAAK,WAAY,IAAG,CAAC,IAAI,EAAE,CAAC;AAAA,QACjC;AACA,WAAG,UAAU,UAAU,IAAI;AAC3B,cAAM,IAAI,KAAK,EAAE,KAAK,YAAY;AAClC,YAAI,CAAC,KAAK,KAAK,CAAC,GAAG;AAClB,eAAK,KAAK,CAAC,IAAI,CAAC;AAAA,QACjB;AACA,aAAK,KAAK,CAAC,EAAE,KAAK,EAAE;AAAA,MACrB;AAAA,IACD;AAAA,EACD,OAAO;AACN,SAAK,KAAK,KAAK;AACf,WAAO,KAAK;AACZ,YAAQ,KAAK,IAAI;AAAA,MAChB,KAAK,OAAO;AACX,aAAK,QAAQ,OAAO;AACpB,aAAK,QAAQ;AACb;AAAA,MACD,KAAK,OAAO;AACX,aAAK,QAAQ,OAAO;AACpB,aAAK,QAAQ;AACb;AAAA,MACD,KAAK,OAAO;AACX,aAAK,QAAQ,OAAO;AACpB,aAAK,QAAQ;AACb;AAAA,MACD,KAAK,OAAO;AACX,aAAK,QAAQ,OAAO;AACpB,aAAK,QAAQ;AACb;AAAA,MACD,KAAK,OAAO;AACX,aAAK,QAAQ,OAAO;AACpB,aAAK,QAAQ;AACb;AAAA,MACD;AACC,iBAAS,KAAK,CAAC,GAAG,oBAAoB,GAAG,CAAC;AAC1C;AAAA,IACF;AAEA,QAAI,CAAC,KAAK,MAAM;AACf,eAAS,KAAK,CAAC,GAAG,qBAAqB,GAAG,CAAC;AAC3C;AAAA,IACD;AACA,SAAK;AACL,eAAW,KAAK,GAAG;AAClB,UAAI,KAAK,YAAY;AACpB,aAAK,CAAC,IAAI,EAAE,CAAC;AAAA,MACd;AAAA,IACD;AACA,UAAM,IAAI,KAAK,cAAc,KAAK,KAAK,YAAY,IAAI,KAAK,KAAK,YAAY;AAC7E,QAAI,CAAC,KAAK,KAAK,CAAC,GAAG;AAClB,WAAK,KAAK,CAAC,IAAI,CAAC;AAAA,IACjB;AACA,SAAK,KAAK,CAAC,EAAE,KAAK,IAAI;AAAA,EACvB;AACD;AAEA,SAAS,UAAU,KAAK;AACvB,QAAM,IAAI,CAAC;AACX,aAAW,QAAQ,KAAK;AACvB,UAAM,IAAI,EAAE,GAAG,CAAC,GAAG,GAAG,CAAC,EAAE;AACzB,eAAW,KAAK,MAAM;AACrB,UAAI,KAAK,OAAO,KAAK,IAAK,GAAE,CAAC,IAAI,KAAK,CAAC;AAAA,IACxC;AACA,eAAW,KAAK,KAAK,GAAG;AACvB,QAAE,EAAE,CAAC,IAAI,KAAK,EAAE,CAAC;AAAA,IAClB;AACA,eAAW,KAAK,KAAK,GAAG;AACvB,QAAE,EAAE,CAAC,IAAI,KAAK,EAAE,CAAC;AAAA,IAClB;AACA,MAAE,KAAK,CAAC;AAAA,EACT;AACA,SAAO;AACR;",
+  "sources": ["../../src/bulk.svjson.ts"],
+  "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) {\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: Record<string, any> = {}\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)) {\n\t\treturn\n\t}\n\tlet json\n\ttry {\n\t\tjson = JSON.parse(m.jsontext)\n\t} catch (_) {\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: Record<string, any> = {\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: Record<string, any> = {\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: any[] = []\n\tfor (const pair of lst) {\n\t\tconst p: Record<string, any> = { 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"],
+  "mappings": "AAMA,YAAY,YAAY;AACxB,YAAY,UAAU;AAKf,SAAS,YAAY,MAAM;AACjC,QAAM,SAAS,KAAK,YAAY,EAAE,MAAM,GAAI;AAC5C,MAAI,OAAO,UAAU,EAAG,QAAO;AAC/B,QAAM,OAAO,IAAI,QAAQ;AACxB,eAAW,KAAK,KAAK;AACpB,YAAM,IAAI,OAAO,QAAQ,CAAC;AAC1B,UAAI,KAAK,GAAI,QAAO;AAAA,IACrB;AACA,WAAO;AAAA,EACR;AACA,MAAI,IAAI,KAAK,QAAQ;AACrB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,YAAY;AACrB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,SAAS;AAClB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,QAAQ,UAAU;AAC3B,MAAI,KAAK,GAAI,QAAO,CAAC,0BAA0B;AAC/C,SAAO,CAAC,IAAI;AACZ,SAAO,CAAC,MAAM,MAAM;AACrB;AAEO,SAAS,UAAU,GAAG,MAAM,MAAM,QAAQ;AAChD,MAAI,QAAQ,MAAM,KAAK,CAAC,KAAK,IAAK;AAClC,QAAM,MAAM,KAAK,MAAM,GAAI;AAC3B,QAAM,IAAyB,CAAC;AAChC,QAAM,WAAW,KAAK,OAAO;AAE7B,WAAS,IAAI,GAAG,IAAI,OAAO,QAAQ,KAAK;AACvC,MAAE,OAAO,CAAC,CAAC,IAAI,IAAI,CAAC;AAAA,EACrB;AACA,MAAI,CAAC,EAAE,UAAU;AAChB,aAAS,KAAK,CAAC,GAAG,oBAAoB,GAAG,CAAC;AAC1C;AAAA,EACD;AACA,MAAI,KAAK,YAAY,GAAG,MAAM,GAAG,GAAG,GAAG;AACtC;AAAA,EACD;AACA,MAAI;AACJ,MAAI;AACH,WAAO,KAAK,MAAM,EAAE,QAAQ;AAAA,EAC7B,SAAS,GAAG;AACX,aAAS,KAAK,CAAC,GAAG,qBAAqB,GAAG,CAAC;AAC3C;AAAA,EACD;AAEA,MAAI,MAAM,QAAQ,IAAI,GAAG;AAExB,eAAW,QAAQ,MAAM;AACxB,UAAI,KAAK,KAAK,KAAK,EAAE,QAAQ,KAAK,EAAE,SAAS;AAC5C,aAAK;AACL,cAAM,KAA0B;AAAA,UAC/B,IAAI,OAAO;AAAA,UACX,OAAO,OAAO;AAAA,UACd,SAAS,KAAK,EAAE;AAAA,UAChB,OAAO,KAAK,EAAE;AAAA,QACf;AACA,mBAAW,KAAK,GAAG;AAClB,cAAI,KAAK,WAAY,IAAG,CAAC,IAAI,EAAE,CAAC;AAAA,QACjC;AACA,WAAG,UAAU,UAAU,IAAI;AAC3B,cAAM,IAAI,KAAK,EAAE,KAAK,YAAY;AAClC,YAAI,CAAC,KAAK,KAAK,CAAC,GAAG;AAClB,eAAK,KAAK,CAAC,IAAI,CAAC;AAAA,QACjB;AACA,aAAK,KAAK,CAAC,EAAE,KAAK,EAAE;AAAA,MACrB;AACA,UAAI,KAAK,KAAK,KAAK,EAAE,QAAQ,KAAK,EAAE,SAAS;AAC5C,aAAK;AACL,cAAM,KAA0B;AAAA,UAC/B,IAAI,OAAO;AAAA,UACX,OAAO,OAAO;AAAA,UACd,SAAS,KAAK,EAAE;AAAA,UAChB,OAAO,KAAK,EAAE;AAAA,QACf;AACA,mBAAW,KAAK,GAAG;AAClB,cAAI,KAAK,WAAY,IAAG,CAAC,IAAI,EAAE,CAAC;AAAA,QACjC;AACA,WAAG,UAAU,UAAU,IAAI;AAC3B,cAAM,IAAI,KAAK,EAAE,KAAK,YAAY;AAClC,YAAI,CAAC,KAAK,KAAK,CAAC,GAAG;AAClB,eAAK,KAAK,CAAC,IAAI,CAAC;AAAA,QACjB;AACA,aAAK,KAAK,CAAC,EAAE,KAAK,EAAE;AAAA,MACrB;AAAA,IACD;AAAA,EACD,OAAO;AACN,SAAK,KAAK,KAAK;AACf,WAAO,KAAK;AACZ,YAAQ,KAAK,IAAI;AAAA,MAChB,KAAK,OAAO;AACX,aAAK,QAAQ,OAAO;AACpB,aAAK,QAAQ;AACb;AAAA,MACD,KAAK,OAAO;AACX,aAAK,QAAQ,OAAO;AACpB,aAAK,QAAQ;AACb;AAAA,MACD,KAAK,OAAO;AACX,aAAK,QAAQ,OAAO;AACpB,aAAK,QAAQ;AACb;AAAA,MACD,KAAK,OAAO;AACX,aAAK,QAAQ,OAAO;AACpB,aAAK,QAAQ;AACb;AAAA,MACD,KAAK,OAAO;AACX,aAAK,QAAQ,OAAO;AACpB,aAAK,QAAQ;AACb;AAAA,MACD;AACC,iBAAS,KAAK,CAAC,GAAG,oBAAoB,GAAG,CAAC;AAC1C;AAAA,IACF;AAEA,QAAI,CAAC,KAAK,MAAM;AACf,eAAS,KAAK,CAAC,GAAG,qBAAqB,GAAG,CAAC;AAC3C;AAAA,IACD;AACA,SAAK;AACL,eAAW,KAAK,GAAG;AAClB,UAAI,KAAK,YAAY;AACpB,aAAK,CAAC,IAAI,EAAE,CAAC;AAAA,MACd;AAAA,IACD;AACA,UAAM,IAAI,KAAK,cAAc,KAAK,KAAK,YAAY,IAAI,KAAK,KAAK,YAAY;AAC7E,QAAI,CAAC,KAAK,KAAK,CAAC,GAAG;AAClB,WAAK,KAAK,CAAC,IAAI,CAAC;AAAA,IACjB;AACA,SAAK,KAAK,CAAC,EAAE,KAAK,IAAI;AAAA,EACvB;AACD;AAEA,SAAS,UAAU,KAAK;AACvB,QAAM,IAAW,CAAC;AAClB,aAAW,QAAQ,KAAK;AACvB,UAAM,IAAyB,EAAE,GAAG,CAAC,GAAG,GAAG,CAAC,EAAE;AAC9C,eAAW,KAAK,MAAM;AACrB,UAAI,KAAK,OAAO,KAAK,IAAK,GAAE,CAAC,IAAI,KAAK,CAAC;AAAA,IACxC;AACA,eAAW,KAAK,KAAK,GAAG;AACvB,QAAE,EAAE,CAAC,IAAI,KAAK,EAAE,CAAC;AAAA,IAClB;AACA,eAAW,KAAK,KAAK,GAAG;AACvB,QAAE,EAAE,CAAC,IAAI,KAAK,EAAE,CAAC;AAAA,IAClB;AACA,MAAE,KAAK,CAAC;AAAA,EACT;AACA,SAAO;AACR;",
   "names": []
 }

package/dist/src/bulk.trunc.d.ts

@@ -0,0 +1,2 @@
+export declare function parseheader(line: any, flag: any): false | "gene missing from header" | "isoform missing from header" | "invalid header line for truncation" | "lossType missing from header" | "genomic position missing from header" | "neither rnaposition nor genomic position is given";
+export declare function parseline(i: any, line: any, flag: any): void;

package/dist/src/bulk.trunc.js

@@ -96,7 +96,7 @@ function parseline(i, line, flag) {
     flag.truncation.badlines.push([i, 'lossType value not "n" or "c"', lst]);
     return;
   }
-  if (bulk.parsesample(m, flag, i, lst, flag.truncation.badlines)) {
+  if (bulk.parsesample(m, flag, i, lst)) {
     return;
   }
   if (m.losstype == "n") {

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

@@ -1,7 +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"],
-  "mappings": "AAMA,YAAY,YAAY;AACxB,YAAY,UAAU;AAEf,SAAS,YAAY,MAAM,MAAM;AACvC,QAAM,SAAS,KAAK,YAAY,EAAE,MAAM,GAAI;AAC5C,MAAI,OAAO,UAAU,EAAG,QAAO;AAC/B,QAAM,OAAO,IAAI,QAAQ;AACxB,eAAW,KAAK,KAAK;AACpB,YAAM,IAAI,OAAO,QAAQ,CAAC;AAC1B,UAAI,KAAK,GAAI,QAAO;AAAA,IACrB;AACA,WAAO;AAAA,EACR;AACA,MAAI,IAAI,KAAK,MAAM;AACnB,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI;AAAA,IACH;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,EACD;AACA,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,YAAY;AAChB,MAAI,KAAK,aAAa;AACtB,MAAI,KAAK,IAAI;AACZ,WAAO,CAAC,IAAI;AACZ,gBAAY;AAAA,EACb;AACA,MAAI,KAAK,UAAU;AACnB,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,aAAa;AACjB,MAAI,KAAK,cAAc,KAAK;AAC5B,MAAI,KAAK,IAAI;AACZ,WAAO,CAAC,IAAI;AACZ,QAAI,KAAK,SAAS,kBAAkB,eAAe,gBAAgB,UAAU;AAC7E,QAAI,KAAK,IAAI;AACZ,aAAO;AAAA,IACR;AACA,WAAO,CAAC,IAAI;AACZ,iBAAa;AAAA,EACd;AACA,MAAI,CAAC,aAAa,CAAC,YAAY;AAC9B,WAAO;AAAA,EACR;AAEA,MAAI,KAAK,UAAU,eAAe,sBAAsB;AACxD,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,WAAW,SAAS,gBAAgB;AAC7C,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,SAAS;AAClB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,QAAQ;AACjB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,cAAc,eAAe,aAAa;AACnD,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,OAAK,WAAW,SAAS;AACzB,OAAK,WAAW,SAAS;AACzB,SAAO;AACR;AAEO,SAAS,UAAU,GAAG,MAAM,MAAM;AACxC,MAAI,QAAQ,MAAM,KAAK,CAAC,KAAK,IAAK;AAClC,QAAM,MAAM,KAAK,MAAM,GAAI;AAC3B,QAAM,IAAI,CAAC;AACX,WAAS,IAAI,GAAG,IAAI,KAAK,WAAW,OAAO,QAAQ,KAAK;AACvD,MAAE,KAAK,WAAW,OAAO,CAAC,CAAC,IAAI,IAAI,CAAC;AAAA,EACrC;AACA,MAAI,CAAC,EAAE,MAAM;AACZ,SAAK,WAAW,SAAS,KAAK,CAAC,GAAG,gBAAgB,GAAG,CAAC;AACtD;AAAA,EACD;AACA,MAAI,EAAE,aAAa;AAClB,UAAM,IAAI,OAAO,SAAS,EAAE,WAAW;AACvC,QAAI,OAAO,MAAM,CAAC,KAAK,IAAI,GAAG;AAC7B,WAAK,WAAW,SAAS,KAAK,CAAC,GAAG,6BAA6B,GAAG,CAAC;AACnE;AAAA,IACD;AACA,MAAE,cAAc;AAAA,EACjB;AACA,MAAI,EAAE,KAAK;AACV,UAAM,IAAI,OAAO,SAAS,EAAE,GAAG;AAC/B,QAAI,OAAO,MAAM,CAAC,KAAK,IAAI,GAAG;AAC7B,WAAK,WAAW,SAAS,KAAK,CAAC,GAAG,4BAA4B,GAAG,CAAC;AAClE;AAAA,IACD;AACA,MAAE,MAAM;AAAA,EACT;AACA,MAAI,CAAC,EAAE,UAAU;AAChB,SAAK,WAAW,SAAS,KAAK,CAAC,GAAG,0BAA0B,GAAG,CAAC;AAChE;AAAA,EACD;AACA,MAAI,EAAE,YAAY,OAAO,EAAE,YAAY,KAAK;AAC3C,SAAK,WAAW,SAAS,KAAK,CAAC,GAAG,iCAAiC,GAAG,CAAC;AACvE;AAAA,EACD;AACA,MAAI,KAAK,YAAY,GAAG,MAAM,GAAG,KAAK,KAAK,WAAW,QAAQ,GAAG;AAChE;AAAA,EACD;AACA,MAAI,EAAE,YAAY,KAAK;AACtB,MAAE,KAAK,OAAO;AACd,MAAE,QAAQ,OAAO;AACjB,MAAE,QAAQ;AAAA,EACX,OAAO;AACN,MAAE,KAAK,OAAO;AACd,MAAE,QAAQ,OAAO;AACjB,MAAE,QAAQ;AAAA,EACX;AACA,OAAK;AACL,QAAM,IAAI,KAAK,cAAc,EAAE,KAAK,YAAY,IAAI,EAAE;AACtD,MAAI,EAAE,KAAK,KAAK,OAAO;AACtB,SAAK,KAAK,CAAC,IAAI,CAAC;AAAA,EACjB;AACA,OAAK,KAAK,CAAC,EAAE,KAAK,CAAC;AACpB;",
+  "sources": ["../../src/bulk.trunc.ts"],
+  "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: Record<string, any> = {}\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)) {\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"],
+  "mappings": "AAMA,YAAY,YAAY;AACxB,YAAY,UAAU;AAEf,SAAS,YAAY,MAAM,MAAM;AACvC,QAAM,SAAS,KAAK,YAAY,EAAE,MAAM,GAAI;AAC5C,MAAI,OAAO,UAAU,EAAG,QAAO;AAC/B,QAAM,OAAO,IAAI,QAAQ;AACxB,eAAW,KAAK,KAAK;AACpB,YAAM,IAAI,OAAO,QAAQ,CAAC;AAC1B,UAAI,KAAK,GAAI,QAAO;AAAA,IACrB;AACA,WAAO;AAAA,EACR;AACA,MAAI,IAAI,KAAK,MAAM;AACnB,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI;AAAA,IACH;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,IACA;AAAA,EACD;AACA,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,YAAY;AAChB,MAAI,KAAK,aAAa;AACtB,MAAI,KAAK,IAAI;AACZ,WAAO,CAAC,IAAI;AACZ,gBAAY;AAAA,EACb;AACA,MAAI,KAAK,UAAU;AACnB,MAAI,KAAK,GAAI,QAAO;AACpB,SAAO,CAAC,IAAI;AACZ,MAAI,aAAa;AACjB,MAAI,KAAK,cAAc,KAAK;AAC5B,MAAI,KAAK,IAAI;AACZ,WAAO,CAAC,IAAI;AACZ,QAAI,KAAK,SAAS,kBAAkB,eAAe,gBAAgB,UAAU;AAC7E,QAAI,KAAK,IAAI;AACZ,aAAO;AAAA,IACR;AACA,WAAO,CAAC,IAAI;AACZ,iBAAa;AAAA,EACd;AACA,MAAI,CAAC,aAAa,CAAC,YAAY;AAC9B,WAAO;AAAA,EACR;AAEA,MAAI,KAAK,UAAU,eAAe,sBAAsB;AACxD,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,WAAW,SAAS,gBAAgB;AAC7C,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,SAAS;AAClB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,QAAQ;AACjB,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,MAAI,KAAK,cAAc,eAAe,aAAa;AACnD,MAAI,KAAK,GAAI,QAAO,CAAC,IAAI;AACzB,OAAK,WAAW,SAAS;AACzB,OAAK,WAAW,SAAS;AACzB,SAAO;AACR;AAEO,SAAS,UAAU,GAAG,MAAM,MAAM;AACxC,MAAI,QAAQ,MAAM,KAAK,CAAC,KAAK,IAAK;AAClC,QAAM,MAAM,KAAK,MAAM,GAAI;AAC3B,QAAM,IAAyB,CAAC;AAChC,WAAS,IAAI,GAAG,IAAI,KAAK,WAAW,OAAO,QAAQ,KAAK;AACvD,MAAE,KAAK,WAAW,OAAO,CAAC,CAAC,IAAI,IAAI,CAAC;AAAA,EACrC;AACA,MAAI,CAAC,EAAE,MAAM;AACZ,SAAK,WAAW,SAAS,KAAK,CAAC,GAAG,gBAAgB,GAAG,CAAC;AACtD;AAAA,EACD;AACA,MAAI,EAAE,aAAa;AAClB,UAAM,IAAI,OAAO,SAAS,EAAE,WAAW;AACvC,QAAI,OAAO,MAAM,CAAC,KAAK,IAAI,GAAG;AAC7B,WAAK,WAAW,SAAS,KAAK,CAAC,GAAG,6BAA6B,GAAG,CAAC;AACnE;AAAA,IACD;AACA,MAAE,cAAc;AAAA,EACjB;AACA,MAAI,EAAE,KAAK;AACV,UAAM,IAAI,OAAO,SAAS,EAAE,GAAG;AAC/B,QAAI,OAAO,MAAM,CAAC,KAAK,IAAI,GAAG;AAC7B,WAAK,WAAW,SAAS,KAAK,CAAC,GAAG,4BAA4B,GAAG,CAAC;AAClE;AAAA,IACD;AACA,MAAE,MAAM;AAAA,EACT;AACA,MAAI,CAAC,EAAE,UAAU;AAChB,SAAK,WAAW,SAAS,KAAK,CAAC,GAAG,0BAA0B,GAAG,CAAC;AAChE;AAAA,EACD;AACA,MAAI,EAAE,YAAY,OAAO,EAAE,YAAY,KAAK;AAC3C,SAAK,WAAW,SAAS,KAAK,CAAC,GAAG,iCAAiC,GAAG,CAAC;AACvE;AAAA,EACD;AACA,MAAI,KAAK,YAAY,GAAG,MAAM,GAAG,GAAG,GAAG;AACtC;AAAA,EACD;AACA,MAAI,EAAE,YAAY,KAAK;AACtB,MAAE,KAAK,OAAO;AACd,MAAE,QAAQ,OAAO;AACjB,MAAE,QAAQ;AAAA,EACX,OAAO;AACN,MAAE,KAAK,OAAO;AACd,MAAE,QAAQ,OAAO;AACjB,MAAE,QAAQ;AAAA,EACX;AACA,OAAK;AACL,QAAM,IAAI,KAAK,cAAc,EAAE,KAAK,YAAY,IAAI,EAAE;AACtD,MAAI,EAAE,KAAK,KAAK,OAAO;AACtB,SAAK,KAAK,CAAC,IAAI,CAAC;AAAA,EACjB;AACA,OAAK,KAAK,CAAC,EAAE,KAAK,CAAC;AACpB;",
   "names": []
 }

package/dist/src/clustering.d.ts

@@ -0,0 +1,10 @@
+export declare const clusterMethodLst: {
+    label: string;
+    value: string;
+    title: string;
+}[];
+export declare const distanceMethodLst: {
+    label: string;
+    value: string;
+    title: string;
+}[];

package/dist/src/clustering.js.map

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../src/clustering.js"],
+  "sources": ["../../src/clustering.ts"],
   "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"],
   "mappings": "AAAO,MAAM,mBAAmB;AAAA,EAC/B;AAAA,IACC,OAAO;AAAA,IACP,OAAO;AAAA,IACP,OAAO;AAAA,EACR;AAAA,EACA;AAAA,IACC,OAAO;AAAA,IACP,OAAO;AAAA,IACP,OAAO;AAAA,EACR;AAAA,EACA;AAAA,IACC,OAAO;AAAA,IACP,OAAO;AAAA,IACP,OAAO;AAAA,EACR;AAAA,EACA;AAAA,IACC,OAAO;AAAA,IACP,OAAO;AAAA,IACP,OAAO;AAAA,EACR;AAAA,EACA;AAAA,IACC,OAAO;AAAA,IACP,OAAO;AAAA,IACP,OAAO;AAAA,EACR;AAAA,EACA;AAAA,IACC,OAAO;AAAA,IACP,OAAO;AAAA,IACP,OAAO;AAAA,EACR;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAAA;AAaD;AACO,MAAM,oBAAoB;AAAA,EAChC;AAAA,IACC,OAAO;AAAA,IACP,OAAO;AAAA,IACP,OAAO;AAAA,EACR;AAAA,EACA;AAAA,IACC,OAAO;AAAA,IACP,OAAO;AAAA,IACP,OAAO;AAAA,EACR;AAAA,EACA;AAAA,IACC,OAAO;AAAA,IACP,OAAO;AAAA,IACP,OAAO;AAAA,EACR;AAAA,EACA;AAAA,IACC,OAAO;AAAA,IACP,OAAO;AAAA,IACP,OAAO;AAAA,EACR;AACD;",
   "names": []

package/dist/src/common.d.ts

@@ -0,0 +1,431 @@
+import * as d3scale from 'd3-scale';
+import * as d3 from 'd3';
+export declare class TermTypeGroups {
+    static DICTIONARY_VARIABLES: string;
+    static DNA_METHYLATION: string;
+    static GENE_DEPENDENCY: string;
+    static GENE_EXPRESSION: string;
+    static ISOFORM_EXPRESSION: string;
+    static GSEA: string;
+    static METABOLITE_INTENSITY: string;
+    static PROTEOME_ABUNDANCE: string;
+    static MUTATION_CNV_FUSION: string;
+    static MUTATION_SIGNATURE: string;
+    static PROTEIN_EXPRESSION: string;
+    static SINGLECELL_CELLTYPE: string;
+    static SINGLECELL_GENE_EXPRESSION: string;
+    static SNP: string;
+    static SNP_LIST: string;
+    static SNP_LOCUS: string;
+    static SPLICE_JUNCTION: string;
+    static SSGSEA: string;
+    static TERM_COLLECTION: string;
+    static VARIANT_GENOTYPE: string;
+}
+export declare const defaultcolor: d3.RGBColor;
+export declare const default_text_color: d3.RGBColor;
+export declare const exoncolor = "#4F8053";
+export declare const plotColor = "#ce768e";
+export declare const IN_frame = true;
+export declare const OUT_frame = false;
+/********************************
+*        on dt usage            *
+*********************************
+- once a dt value is decided and used with actual dataset,
+  the value must not be altered, since dataset file may hardcode such value and reassigning to a new integer will break!
+- never test dt value by range e.g. if(dt>10), it breaks! only test equality!
+- in code import variable from here and DO NOT use literal values, to make code tractable
+*/
+export declare const dtsnvindel = 1;
+export declare const dtfusionrna = 2;
+export declare const dtgeneexpression = 3;
+export declare const dtcnv = 4;
+export declare const dtsv = 5;
+export declare const dtitd = 6;
+export declare const dtdel = 7;
+export declare const dtnloss = 8;
+export declare const dtcloss = 9;
+export declare const dtloh = 10;
+export declare const dtmetaboliteintensity = 11;
+export declare const dtssgsea = 12;
+export declare const dtdnamethylation = 13;
+export declare const dtproteomeabundance = 14;
+export declare const dt2label: {
+    1: string;
+    2: string;
+    4: string;
+    5: string;
+    6: string;
+    7: string;
+    8: string;
+    9: string;
+    10: string;
+    3: string;
+    11: string;
+    14: string;
+};
+export declare const dt2lesion: {
+    1: {
+        uilabel: string;
+        lesionTypes: {
+            name: string;
+            lesionType: string;
+            color: string;
+        }[];
+    };
+    4: {
+        uilabel: string;
+        lesionTypes: {
+            name: string;
+            lesionType: string;
+            color: string;
+        }[];
+    };
+    5: {
+        uilabel: string;
+        lesionTypes: {
+            name: string;
+            lesionType: string;
+            color: string;
+        }[];
+    };
+    2: {
+        uilabel: string;
+        lesionTypes: {
+            name: string;
+            lesionType: string;
+            color: string;
+        }[];
+    };
+};
+export declare const optionToDt: {
+    snvindelOptions: number;
+    cnvOptions: number;
+    fusionOptions: number;
+    svOptions: number;
+};
+export declare const mclass: {
+    M: {
+        label: string;
+        color: string;
+        dt: number;
+        desc: string;
+        key: string;
+    };
+    E: {
+        label: string;
+        color: string;
+        dt: number;
+        desc: string;
+        key: string;
+    };
+    F: {
+        label: string;
+        color: string;
+        dt: number;
+        desc: string;
+        key: string;
+    };
+    N: {
+        label: string;
+        color: string;
+        dt: number;
+        desc: string;
+        key: string;
+    };
+    S: {
+        label: string;
+        color: string;
+        dt: number;
+        desc: string;
+        key: string;
+    };
+    D: {
+        label: string;
+        color: string;
+        dt: number;
+        desc: string;
+        key: string;
+    };
+    I: {
+        label: string;
+        color: string;
+        dt: number;
+        desc: string;
+        key: string;
+    };
+    ProteinAltering: {
+        label: string;
+        color: string;
+        dt: number;
+        desc: string;
+        key: string;
+    };
+    P: {
+        label: string;
+        color: string;
+        dt: number;
+        desc: string;
+        key: string;
+    };
+    L: {
+        label: string;
+        color: string;
+        dt: number;
+        desc: string;
+        key: string;
+    };
+    Intron: {
+        label: string;
+        color: string;
+        dt: number;
+        desc: string;
+        key: string;
+    };
+    StopLost: {
+        label: string;
+        color: string;
+        dt: number;
+        desc: string;
+        key: string;
+    };
+    StartLost: {
+        label: string;
+        color: string;
+        dt: number;
+        desc: string;
+        key: string;
+    };
+    Blank: {
+        label: string;
+        color: string;
+        dt: number;
+        desc: string;
+        key: string;
+    };
+    WT: {
+        label: string;
+        color: string;
+        dt: number;
+        desc: string;
+        key: string;
+    };
+};
+export declare const mclassitd = "ITD";
+export declare const mclassdel = "DEL";
+export declare const mclassnloss = "NLOSS";
+export declare const mclasscloss = "CLOSS";
+export declare const mclassutr3 = "Utr3";
+export declare const mclassutr5 = "Utr5";
+export declare const mclassnonstandard = "X";
+export declare const mclassnoncoding = "noncoding";
+export declare const class2SOterm: Map<any, any>;
+export declare const SOterm2class: Map<any, any>;
+export declare function mclasstester(s: any): "M" | "F" | "N" | "S" | "D" | "I" | "ProteinAltering" | "P" | "L" | "Blank" | "Utr3" | "Utr5" | "X" | "noncoding" | null;
+export declare const mclassfusionrna = "Fuserna";
+export declare const mclasssv = "SV";
+export declare const mclasscnvgain = "CNV_amp";
+export declare const mclasscnvloss = "CNV_loss";
+export declare const mclasscnvAmp = "CNV_amplification";
+export declare const mclasscnvHomozygousDel = "CNV_homozygous_deletion";
+export declare const mclasscnvloh = "CNV_loh";
+export declare const mclasssnv = "snv";
+export declare const mclassmnv = "mnv";
+export declare const mclassinsertion = "insertion";
+export declare const mclassdeletion = "deletion";
+export declare function mds3tkMclass(k: any): any;
+export declare const dt2color: {
+    1: string;
+};
+export declare function applyOverrides(overrides?: Record<string, any>): void;
+export declare const vepinfo: (s: any) => (string | number)[];
+export declare const germlinelegend = "<circle cx=\"7\" cy=\"12\" r=\"7\" fill=\"#b1b1b1\"></circle><path d=\"M6.735557395310443e-16,-11A11,11 0 0,1 11,0L9,0A9,9 0 0,0 5.51091059616309e-16,-9Z\" transform=\"translate(7,12)\" fill=\"#858585\" stroke=\"none\"></path>";
+export declare const morigin: Record<string, any>;
+export declare const moriginsomatic = "S";
+export declare const morigingermline = "G";
+export declare const moriginrelapse = "R";
+export declare const morigingermlinepathogenic = "GP";
+export declare const morigingermlinenonpathogenic = "GNP";
+export declare const tkt: {
+    usegm: string;
+    ds: string;
+    bigwig: string;
+    bigwigstranded: string;
+    junction: string;
+    mdsjunction: string;
+    mdssvcnv: string;
+    mdsexpressionrank: string;
+    mdsvcf: string;
+    bedj: string;
+    pgv: string;
+    bampile: string;
+    hicstraw: string;
+    expressionrank: string;
+    aicheck: string;
+    ase: string;
+    mds3: string;
+    bedgraphdot: string;
+    bam: string;
+    ld: string;
+};
+export declare function validtkt(what: any): boolean;
+export declare const mdsvcftype: {
+    vcf: string;
+};
+export declare const custommdstktype: {
+    vcf: string;
+    svcnvitd: string;
+    geneexpression: string;
+};
+export declare const codon: {
+    GCT: string;
+    GCC: string;
+    GCA: string;
+    GCG: string;
+    CGT: string;
+    CGC: string;
+    CGA: string;
+    CGG: string;
+    AGA: string;
+    AGG: string;
+    AAT: string;
+    AAC: string;
+    GAT: string;
+    GAC: string;
+    TGT: string;
+    TGC: string;
+    CAA: string;
+    CAG: string;
+    GAA: string;
+    GAG: string;
+    GGT: string;
+    GGC: string;
+    GGA: string;
+    GGG: string;
+    CAT: string;
+    CAC: string;
+    ATT: string;
+    ATC: string;
+    ATA: string;
+    TTA: string;
+    TTG: string;
+    CTT: string;
+    CTC: string;
+    CTA: string;
+    CTG: string;
+    AAA: string;
+    AAG: string;
+    ATG: string;
+    TTT: string;
+    TTC: string;
+    CCT: string;
+    CCC: string;
+    CCA: string;
+    CCG: string;
+    TCT: string;
+    TCC: string;
+    TCA: string;
+    TCG: string;
+    AGT: string;
+    AGC: string;
+    ACT: string;
+    ACC: string;
+    ACA: string;
+    ACG: string;
+    TGG: string;
+    TAT: string;
+    TAC: string;
+    GTT: string;
+    GTC: string;
+    GTA: string;
+    GTG: string;
+};
+export declare const codon_stop = "*";
+export declare function nt2aa(gm: any): string | undefined;
+export declare function bplen(len: any, isfile?: boolean): string;
+export declare const basecolor: {
+    A: string;
+    T: string;
+    C: string;
+    G: string;
+};
+export declare function basecompliment(nt: any): any;
+export declare function reversecompliment(s: any): string;
+export declare function spliceeventchangegmexon(gm: any, evt: any): {
+    chr: any;
+    start: any;
+    stop: any;
+    strand: any;
+    coding: number[][];
+};
+export declare function fasta2gmframecheck(gm: any, str: any): boolean;
+export declare function validate_vcfinfofilter(obj: any): string | undefined;
+export declare function contigNameNoChr(genome: any, chrlst: any): boolean;
+export declare function contigNameNoChr2(genome: any, chrlst: any): number[];
+export declare function getMax_byiqr(lst: any, novaluemax: any): any;
+export declare function alleleInGenotypeStr(genotype: any, allele: any): boolean;
+export declare const gmmode: {
+    genomic: string;
+    splicingrna: string;
+    exononly: string;
+    protein: string;
+    gmsum: string;
+};
+export declare function vcfcopymclass(m: any, block: any): void;
+export declare const not_annotated = "Unannotated";
+export declare function kernelDensityEstimator(kernel: any, X: any): (V: any) => any;
+export declare function kernelEpanechnikov(k: any): (v: any) => number;
+export declare const schemeCategory20: string[];
+export declare const schemeCategory2: string[];
+export declare function getColorScheme(number: any): readonly string[];
+export declare function getColors(number: any): d3scale.ScaleOrdinal<string, string, never>;
+export declare function proteinDomainColorScale(): d3scale.ScaleOrdinal<string, unknown, never>;
+export declare const truncatingMutations: string[];
+export declare const proteinChangingMutations: string[];
+export declare const synonymousMutations: string[];
+export declare const mutationClasses: string[];
+export declare const CNVClasses: string[];
+export declare const dtTerms: any[];
+export declare const colorScaleMap: {
+    blueWhiteRed: {
+        domain: number[];
+        range: string[];
+    };
+    greenWhiteRed: {
+        domain: number[];
+        range: string[];
+    };
+    blueYellowRed: {
+        domain: number[];
+        range: string[];
+    };
+    greenBlackRed: {
+        domain: number[];
+        range: string[];
+    };
+    blueBlackYellow: {
+        domain: number[];
+        range: string[];
+    };
+    whiteRed: {
+        domain: number[];
+        range: string[];
+    };
+};
+export declare function invalidcoord(thisgenome: any, chrom: any, start: any, stop: any): string | false;
+export declare function string2pos(s: any, genome: any, donotextend: any): {
+    chr: any;
+    chrlen: any;
+    start: number;
+    stop: number;
+    actualposition?: undefined;
+} | {
+    chr: any;
+    chrlen: any;
+    start: number;
+    stop: number;
+    actualposition: {
+        position: number;
+        len: number;
+    };
+} | null;