@sjcrh/proteinpaint-client 2.181.0 → 2.182.0

package/dist/chunk-RZ5JP44H.js.map

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