@sjcrh/proteinpaint-client 2.181.0 → 2.182.0

package/dist/chunk-RTC4U4PH.js.map

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../shared/utils/src/bulk.snv.js", "../../shared/utils/src/bulk.svjson.js", "../../shared/utils/src/bulk.cnv.js", "../../shared/utils/src/bulk.itd.js", "../../shared/utils/src/bulk.del.js", "../../shared/utils/src/bulk.trunc.js", "../src/bulk.project.js", "../src/bulk.ui.js", "../src/tp.init.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", "/////////////////////////////////\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", "////////////////////////////////////\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 CNV'\n\tconst htry = (...lst) => {\n\t\tfor (const i of lst) {\n\t\t\tconst j = header.indexOf(i)\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('cnv')\n\tif (i == -1) return 'CNV missing from header'\n\theader[i] = 'cnv'\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.cnv.header = header\n\tflag.cnv.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.cnv.header.length; j++) {\n\t\tm[flag.cnv.header[j]] = lst[j]\n\t}\n\tif (!m.gene) {\n\t\tflag.cnv.badlines.push([i, 'missing gene', lst])\n\t\treturn\n\t}\n\tif (!m.cnv) {\n\t\tflag.cnv.badlines.push([i, 'missing cnv value', lst])\n\t\treturn\n\t}\n\tconst value = m.cnv.toLowerCase()\n\tswitch (value) {\n\t\tcase 'amplification':\n\t\tcase 'gain':\n\t\t\tm.class = common.mclasscnvgain\n\t\t\tbreak\n\t\tcase 'deletion':\n\t\tcase 'loss':\n\t\t\tm.class = common.mclasscnvloss\n\t\t\tbreak\n\t\tcase 'loh':\n\t\t\tm.class = common.mclasscnvloh\n\t\t\tbreak\n\t\tdefault:\n\t\t\tflag.cnv.badlines.push([i, 'invalid cnv value: ' + m.cnv, lst])\n\t\t\tm.class = null\n\t}\n\tif (!m.class) {\n\t\treturn\n\t}\n\tif (bulk.parsesample(m, flag, i, lst, flag.cnv.badlines)) {\n\t\treturn\n\t}\n\tm.dt = common.dtcnv\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", "////////////////////////////////////\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 ITD'\n\tconst htry = (...lst) => {\n\t\tfor (const i of lst) {\n\t\t\tconst j = header.indexOf(i)\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\ti = htry('rnaposition')\n\tif (i != -1) {\n\t\theader[i] = 'rnaposition'\n\t\ti = htry('rnaduplength')\n\t\tif (i == -1) return 'rnaduplength is required when rnaposition is present'\n\t\theader[i] = 'rnaduplength'\n\t}\n\ti = htry('chromosome', 'chr')\n\tif (i != -1) {\n\t\theader[i] = 'chr'\n\t\ti = htry('chr_start')\n\t\tif (i == -1) return 'chr_start is required when chr is present'\n\t\theader[i] = 'chrpos1'\n\t\ti = htry('chr_stop')\n\t\tif (i == -1) return 'chr_stop is required when chr is present'\n\t\theader[i] = 'chrpos2'\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.itd.header = header\n\tflag.itd.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.itd.header.length; j++) {\n\t\tif (lst[j] == undefined) break\n\t\tm[flag.itd.header[j]] = lst[j]\n\t}\n\tif (!m.gene) {\n\t\tflag.itd.badlines.push([i, 'missing gene', lst])\n\t\treturn\n\t}\n\tif (m.rnaposition) {\n\t\tlet v = Number.parseInt(m.rnaposition)\n\t\tif (Number.isNaN(v) || v < 0) {\n\t\t\tflag.itd.badlines.push([i, 'invalid rnaPosition value', lst])\n\t\t\treturn\n\t\t}\n\t\tm.rnaposition = v\n\t\tif (!m.rnaduplength) {\n\t\t\tflag.itd.badlines.push([i, 'missing rnaDuplength value', lst])\n\t\t\treturn\n\t\t}\n\t\tv = Number.parseInt(m.rnaduplength)\n\t\tif (Number.isNaN(v) || v < 0) {\n\t\t\tflag.itd.badlines.push([i, 'invalid rnaDuplength value', lst])\n\t\t\treturn\n\t\t}\n\t\tm.rnaduplength = v\n\t}\n\tif (m.chr) {\n\t\tlet v = Number.parseInt(m.chrpos1)\n\t\tif (Number.isNaN(v) || v < 0) {\n\t\t\tflag.itd.badlines.push([i, 'invalid chr_start value', lst])\n\t\t\treturn\n\t\t}\n\t\tm.chrpos1 = v\n\t\tv = Number.parseInt(m.chrpos2)\n\t\tif (Number.isNaN(v) || v < 0) {\n\t\t\tflag.itd.badlines.push([i, 'invalid chr_stop value', lst])\n\t\t\treturn\n\t\t}\n\t\tm.chrpos2 = v\n\t}\n\tif (bulk.parsesample(m, flag, i, lst, flag.itd.badlines)) {\n\t\treturn\n\t}\n\tm.dt = common.dtitd\n\tm.class = common.mclassitd\n\tm.mname = 'ITD'\n\tflag.good++\n\tvar 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", "////////////////////////////////////\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 intragenic deletion'\n\tconst htry = (...lst) => {\n\t\tfor (const i of lst) {\n\t\t\tconst j = header.indexOf(i)\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\ti = htry('rnaposition')\n\tif (i != -1) {\n\t\theader[i] = 'rnaposition'\n\t\ti = htry('rnadellength')\n\t\tif (i == -1) return 'rnadellength is required when rnaPosition is used'\n\t\theader[i] = 'rnadellength'\n\t}\n\ti = htry('chromosome', 'chr')\n\tif (i != -1) {\n\t\theader[i] = 'chr'\n\t\ti = htry('chr_start')\n\t\tif (i == -1) return 'chr_start is required when chr is used'\n\t\theader[i] = 'chrpos1'\n\t\ti = htry('chr_stop')\n\t\tif (i == -1) return 'chr_stop is required when chr is used'\n\t\theader[i] = 'chrpos2'\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.del.header = header\n\tflag.del.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.del.header.length; j++) {\n\t\tif (lst[j] == undefined) break\n\t\tm[flag.del.header[j]] = lst[j]\n\t}\n\tif (!m.gene) {\n\t\tflag.del.badlines.push([i, 'missing gene', lst])\n\t\treturn\n\t}\n\tif (m.rnaposition) {\n\t\tlet v = Number.parseInt(m.rnaposition)\n\t\tif (Number.isNaN(v) || v < 0) {\n\t\t\tflag.del.badlines.push([i, 'invalid rnaPosition value', lst])\n\t\t\treturn\n\t\t}\n\t\tm.rnaposition = v\n\t\tif (!m.rnadellength) {\n\t\t\tflag.del.badlines.push([i, 'missing rnaDellength value', lst])\n\t\t\treturn\n\t\t}\n\t\tv = Number.parseInt(m.rnadellength)\n\t\tif (Number.isNaN(v) || v < 0) {\n\t\t\tflag.del.badlines.push([i, 'invalid rnaDellength value', lst])\n\t\t\treturn\n\t\t}\n\t\tm.rnadellength = v\n\t}\n\tif (m.chr) {\n\t\tlet v = Number.parseInt(m.chrpos1)\n\t\tif (Number.isNaN(v) || v < 0) {\n\t\t\tflag.del.badlines.push([i, 'invalid chr_start value', lst])\n\t\t\treturn\n\t\t}\n\t\tm.chrpos1 = v\n\t\tv = Number.parseInt(m.chrpos2)\n\t\tif (Number.isNaN(v) || v < 0) {\n\t\t\tflag.del.badlines.push([i, 'invalid chr_stop value', lst])\n\t\t\treturn\n\t\t}\n\t\tm.chrpos2 = v\n\t}\n\n\tif (bulk.parsesample(m, flag, i, lst, flag.del.badlines)) {\n\t\treturn\n\t}\n\tm.dt = common.dtdel\n\tm.class = common.mclassdel\n\tm.mname = 'DEL'\n\tflag.good++\n\tvar 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", "////////////////////////////////////\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", "import { select as d3select } from 'd3-selection'\nimport * as client from './client'\n\n// allowed schema names\nconst schemaNames = ['heatmapJSON', 'piebarJSON', 'survivalJSON', 'discoJSON', 'riverJSON']\n\n// mapping of mutation type name to numeric index,\n// as specified in client.js filetypeselect()\nconst typeIndex = {\n\tsnvindel: 0,\n\tsi: 0,\n\tsv: 1,\n\tfusion: 2,\n\titd: 3,\n\tdeletion: 4,\n\ttruncation: 5,\n\tcnv: 6\n}\n\nlet urlProjectLoaded = false\n\n/*\n\tEasily upload multiple data files\n*/\nexport class ProjectHandler {\n\t/*\n\t\tCreate a handler for multiple uploaded or fetched\n\t\tfiles in a project\n\n\t\tbt = {\n\t\t\tflag: closured flag inside bulkui.bulkui,\n\t\t\tbulkin: bulkui.bulkin,\n\t\t\tcontent2flag: bulkui.content2flag,\n\t\t\tflag2tp: closured flat2tp,\n\t\t\tfilediv: (optional) d3-wrapped container for file-input\n\t\t}\n\t*/\n\tconstructor(bt) {\n\t\tthis.bt = bt\n\t\tthis.err = this.errHandler()\n\n\t\t// autoload a project if specified via URL parameter\n\t\t// happens only once, right after the first instance of\n\t\t// projectHandler is created\n\t\tif (!urlProjectLoaded) {\n\t\t\tconst params = getParams()\n\t\t\tif (params.project) {\n\t\t\t\tthis.getData(params.project)\n\t\t\t\turlProjectLoaded = true\n\t\t\t}\n\t\t}\n\n\t\tif (bt.filediv) {\n\t\t\tthis.projectByInput(bt.filediv)\n\t\t}\n\t}\n\n\t/*\n\t\tProcess data files sequentially for rendering\n\t\tinto a TP div\n\n\t\tdata = {\n\t\t\tschemas: object {\n\t\t\t\theatmapJSON (optional),\n\t\t\t\tpiebarJSON (optional),\n\t\t\t\tsurvivalJSON (optional)\n\t\t\t},\n\t\t\tfiles: [] array of {\n\t\t\t\tname: string\n\t\t\t\ttypeL one of the typeIndex values \n\t\t\t\tcontent: string\n\t\t\t}\n\t\t}\n\t*/\n\n\tprocessData(data) {\n\t\tconst file = data.files.pop()\n\t\tconst i = data.expectedFileNames.indexOf(file.name)\n\t\tif (i == -1) {\n\t\t\tif (data.files.length)\n\t\t\t\tsetTimeout(() => {\n\t\t\t\t\tthis.processData(data)\n\t\t\t\t}, 1)\n\t\t\treturn // ignore files that are not listed in the reference file\n\t\t}\n\t\tdata.expectedFileNames.splice(i, 1)\n\t\tthis.cohort = {\n\t\t\tname: 'project',\n\t\t\tgenome: this.bt.genomes[this.bt.gselect.options[this.bt.gselect.selectedIndex].innerHTML]\n\t\t}\n\n\t\tif (!this.flag) {\n\t\t\tthis.flag = this.bt.init_bulk_flag(this.cohort.genome)\n\t\t}\n\n\t\tconst error = this.bt.content2flag(file.content, file.type, this.flag)\n\n\t\tif (error) {\n\t\t\tthis.err(error)\n\t\t\tthis.processData(data)\n\t\t} else if (!data.files.length) {\n\t\t\tif (data.expectedFileNames.length) {\n\t\t\t\tthis.err('These referenced files were not found: \"' + data.expectedFileNames.join('\", \"') + '\".')\n\t\t\t}\n\t\t\tthis.bt.flag2tp(this.flag, { name: 'project' }, Object.assign(this.cohort, data.schema), this.ds)\n\t\t\treturn\n\t\t} else {\n\t\t\t//if (this.cohort.dsset) console.log(Object.keys(this.cohort.dsset))\n\t\t\tif (!this.ds) {\n\t\t\t\tfor (const k in this.cohort.dsset) {\n\t\t\t\t\tthis.ds = this.cohort.dsset[k]\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t}\n\n\t\t\t// flag2thisds tells the data in flag will be appended to the given ds\n\t\t\tconst error1 = this.bt.bulkin(\n\t\t\t\t{\n\t\t\t\t\tflag: this.flag,\n\t\t\t\t\tcohort: this.cohort,\n\t\t\t\t\tflag2thisds: this.ds,\n\t\t\t\t\tfilename: 'project'\n\t\t\t\t},\n\t\t\t\t() => {\n\t\t\t\t\tthis.processData(data)\n\t\t\t\t}\n\t\t\t)\n\t\t\tif (error1) {\n\t\t\t\tthis.err('Error with ' + file.name + ': ' + error1)\n\t\t\t\treturn\n\t\t\t}\n\t\t\tif (this.flag.good === 0) {\n\t\t\t\tthis.err(file.name + ': no data loaded')\n\t\t\t\treturn\n\t\t\t}\n\t\t}\n\t}\n\n\tgetData(project) {\n\t\tconst [projectname, _refname] = project.split('/')\n\t\tconst refname = _refname && _refname.trim() ? _refname.trim() : 'ref.txt'\n\n\t\tthis.gettext('/data/projects/' + projectname + '/' + refname, text => {\n\t\t\tconst fileNameToType = {}\n\t\t\tconst nameToSchemaType = {}\n\t\t\tconst data = { schema: {}, files: [], expectedFileNames: [] }\n\t\t\tlet schemaFileName = ''\n\t\t\tlet numProcessedFiles = 0\n\t\t\tlet numFiles = 0\n\n\t\t\ttext\n\t\t\t\t.trim()\n\t\t\t\t.split('\\n')\n\t\t\t\t.forEach(line => {\n\t\t\t\t\tconst [type, filename] = line.trim().split('\\t')\n\t\t\t\t\tif (schemaNames.includes(type)) {\n\t\t\t\t\t\tnameToSchemaType[filename] = type\n\t\t\t\t\t\tnumFiles += 1\n\t\t\t\t\t} else if (!typeIndex[type] && typeIndex[type] !== 0) {\n\t\t\t\t\t\tthis.err('Unrecognized type ' + type + ' for file ' + filename + ' in reference.txt.')\n\t\t\t\t\t} else {\n\t\t\t\t\t\tfileNameToType[filename] = typeIndex[type]\n\t\t\t\t\t\tnumFiles += 1\n\t\t\t\t\t}\n\t\t\t\t})\n\n\t\t\tdata.expectedFileNames = Object.keys(fileNameToType)\n\t\t\tconst tracker = this.getTracker(numFiles, () => this.processData(data))\n\n\t\t\tObject.keys(nameToSchemaType).forEach(filename => {\n\t\t\t\tthis.getjson('/data/projects/' + projectname + '/' + filename, json => {\n\t\t\t\t\tdata.schema[nameToSchemaType[filename]] = json\n\t\t\t\t\ttracker()\n\t\t\t\t})\n\t\t\t})\n\n\t\t\tObject.keys(fileNameToType).forEach(filename => {\n\t\t\t\tthis.gettext('/data/projects/' + projectname + '/' + filename, text => {\n\t\t\t\t\tdata.files.push({\n\t\t\t\t\t\tname: filename,\n\t\t\t\t\t\ttype: fileNameToType[filename],\n\t\t\t\t\t\tcontent: text\n\t\t\t\t\t})\n\t\t\t\t\ttracker()\n\t\t\t\t})\n\t\t\t})\n\t\t})\n\t}\n\n\tgettext(url, callback) {\n\t\tfetch(url)\n\t\t\t.then(response => {\n\t\t\t\tif (response.ok) return response.text()\n\t\t\t\telse this.err('File request error: ' + url)\n\t\t\t})\n\t\t\t.then(callback)\n\t\t\t.catch(error => this.err('File request error: ' + url + ' ' + error))\n\t}\n\n\tgetjson(url, callback) {\n\t\tfetch(url)\n\t\t\t.then(response => {\n\t\t\t\tif (response.ok) return response.json()\n\t\t\t\telse this.err('Network error for ' + url)\n\t\t\t})\n\t\t\t.then(callback)\n\t\t\t.catch(error => this.err('file request error: ' + url + ' ' + error))\n\t}\n\n\tgetTracker(numFiles, callback) {\n\t\tlet numProcessedFiles = 0\n\n\t\treturn function tracker() {\n\t\t\tnumProcessedFiles += 1\n\t\t\tif (numProcessedFiles == numFiles) {\n\t\t\t\tcallback()\n\t\t\t}\n\t\t}\n\t}\n\n\tprojectByInput(filediv) {\n\t\tthis.tp = null\n\n\t\tconst advancedDiv = filediv.append('div')\n\t\tadvancedDiv.append('span').html('Project: reference &nbsp;')\n\n\t\tthis.refNameInput = advancedDiv\n\t\t\t.append('input')\n\t\t\t.attr('type', 'text')\n\t\t\t.property('value', 'ref.txt')\n\t\t\t.style('margin-right', '20px')\n\t\t\t.style('padding-left', '7px')\n\n\t\tconst buttlabel = advancedDiv\n\t\t\t.append('label')\n\t\t\t.attr('for', 'sja-pp-bulk-ui-project-btn')\n\t\t\t.attr('class', 'sja_btn')\n\t\t\t.style('padding', '3px 5px')\n\t\t\t.html('Choose folder')\n\n\t\tconst butt = advancedDiv\n\t\t\t.append('input')\n\t\t\t.attr('type', 'file')\n\t\t\t.attr('id', 'sja-pp-bulk-ui-project-btn')\n\t\t\t.property('multiple', true)\n\t\t\t.property('webkitdirectory', true)\n\t\t\t.property('directory', true)\n\t\t\t// .style('width', '0') Fix to show reference `Choose Files` field in study UI. Completely hidden when width == 0\n\t\t\t.on('change', event => this.readFiles(event))\n\n\t\tadvancedDiv.append('div').style('margin', '10px 10px 10px 0')\n\t\t\t.html(`<a href=\"https://docs.google.com/document/d/1wlfGzyhxFYtWu9Fyf3FK7pgvS3rVb9_vrfYUBUOUrw4/edit?usp=sharing\" target=\"new\">Project user guide</a> | \n\t\t\t<a href='https://proteinpaint.stjude.org/ppdemo/projects/target-tall-project/ref.txt' target=_blank>Example project reference file</a>`)\n\n\t\tadvancedDiv.append('div').style('margin', '20px').style('width', '100%').html('-- OR --')\n\t}\n\n\t/* to be used as a file input (FileList) handler */\n\treadFiles(event) {\n\t\tconst self = this\n\t\tconst refFileName = self.refNameInput.property('value')\n\t\tconst files = Array.from(event.target.files)\n\t\tconst ref = files.filter(f => f.name == refFileName)[0]\n\n\t\tif (!ref) {\n\t\t\tself.err(\"Missing reference file='\" + refFileName + \"'.\")\n\t\t\treturn\n\t\t}\n\n\t\tconst fileNameToType = {}\n\t\tconst nameToSchemaType = {}\n\t\tconst data = { schema: {}, files: [], expectedFileNames: [] }\n\t\tconst reader = new FileReader()\n\t\tlet schemaFileName = ''\n\t\tlet numProcessedFiles = 0\n\n\t\treader.onload = event => {\n\t\t\t// process reference file\n\t\t\tevent.target.result\n\t\t\t\t.trim()\n\t\t\t\t.split('\\n')\n\t\t\t\t.forEach(line => {\n\t\t\t\t\tconst [type, filename] = line.trim().split('\\t')\n\t\t\t\t\tif (schemaNames.includes(type)) {\n\t\t\t\t\t\tnameToSchemaType[filename] = type\n\t\t\t\t\t} else if (!typeIndex[type] && typeIndex[type] !== 0) {\n\t\t\t\t\t\tself.err('Unrecognized type ' + type + ' for file ' + filename + ' in reference.txt.')\n\t\t\t\t\t} else {\n\t\t\t\t\t\tfileNameToType[filename] = typeIndex[type]\n\t\t\t\t\t}\n\t\t\t\t})\n\n\t\t\t// track the expected files to processed by filename\n\t\t\tdata.expectedFileNames = Object.keys(fileNameToType)\n\n\t\t\t// get schemas next\n\t\t\tconst schemaFiles = files.filter(file => file.name in nameToSchemaType)\n\t\t\tlet numProcessedSchemas = 0\n\t\t\tif (!schemaFiles.length) {\n\t\t\t\tfiles.forEach(processFile)\n\t\t\t} else {\n\t\t\t\tschemaFiles.forEach(file => {\n\t\t\t\t\tconst reader = new FileReader()\n\t\t\t\t\treader.onload = event => {\n\t\t\t\t\t\tconst schema = JSON.parse(event.target.result)\n\t\t\t\t\t\tnumProcessedSchemas += 1\n\t\t\t\t\t\tif (!schema) {\n\t\t\t\t\t\t\tself.err('Unable to parse schema file=\"' + file.name + '\".')\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\tdata.schema[nameToSchemaType[file.name]] = schema\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (numProcessedSchemas == schemaFiles.length) {\n\t\t\t\t\t\t\tfiles.forEach(processFile)\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\treader.onerror = () => {\n\t\t\t\t\t\tself.err('Error reading schema.txt.')\n\t\t\t\t\t}\n\t\t\t\t\treader.readAsText(file, 'utf8')\n\t\t\t\t})\n\t\t\t}\n\n\t\t\tfunction processFile(file) {\n\t\t\t\tif (!data.expectedFileNames.includes(file.name)) {\n\t\t\t\t\tnumProcessedFiles += 1\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tif (!file) {\n\t\t\t\t\tself.err('Error reading file.')\n\t\t\t\t\tnumProcessedFiles += 1\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tif (file.size == 0) {\n\t\t\t\t\tself.err('Wrong file: ' + file.name)\n\t\t\t\t\tnumProcessedFiles += 1\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tif (!fileNameToType[file.name] && fileNameToType[file.name] !== 0 && file.name != schemaFileName) {\n\t\t\t\t\tself.err('Missing or invalid type assigned to file ' + file.name + '.')\n\t\t\t\t\tnumProcessedFiles += 1\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tconst reader = new FileReader()\n\n\t\t\t\treader.onload = event => {\n\t\t\t\t\tnumProcessedFiles += 1\n\t\t\t\t\tdata.files.push({\n\t\t\t\t\t\tname: file.name,\n\t\t\t\t\t\ttype: fileNameToType[file.name],\n\t\t\t\t\t\tcontent: event.target.result\n\t\t\t\t\t})\n\t\t\t\t\tif (numProcessedFiles == files.length) {\n\t\t\t\t\t\tself.processData(data)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\treader.onerror = () => {\n\t\t\t\t\tnumProcessedFiles += 1\n\t\t\t\t\tself.err('Error reading file ' + file.name)\n\t\t\t\t\tif (numProcessedFiles == files.length) {\n\t\t\t\t\t\tself.processData(data)\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\treader.readAsText(file, 'utf8')\n\t\t\t}\n\t\t}\n\t\treader.onerror = () => {\n\t\t\tself.err('Error reading reference.txt.')\n\t\t}\n\t\treader.readAsText(ref, 'utf8')\n\t}\n\n\t// function to track and display accumulated error messages\n\terrHandler() {\n\t\tconst errdiv = d3select('body').append('div') //.style('display','none');\n\t\tlet mssg = ''\n\t\treturn function (m) {\n\t\t\tif (!m) return //console.log(m)\n\t\t\t//mssg+=m+'<br/>\\n'\n\t\t\tclient.sayerror(errdiv, m) //mssg);\n\t\t}\n\t}\n}\n\nfunction getParams() {\n\tconst params = {}\n\twindow.location.search\n\t\t.substr(1)\n\t\t.split('&')\n\t\t.forEach(kv => {\n\t\t\tconst [key, value] = kv.split('=')\n\t\t\tparams[key] = value\n\t\t})\n\treturn params\n}\n", "import * as client from './client'\nimport * as bulk from '#shared/bulk.js'\nimport * as bulksnv from '#shared/bulk.snv.js'\nimport * as bulksv from '#shared/bulk.sv.js'\nimport * as bulksvjson from '#shared/bulk.svjson.js'\nimport * as bulkcnv from '#shared/bulk.cnv.js'\nimport * as bulkitd from '#shared/bulk.itd.js'\nimport * as bulkdel from '#shared/bulk.del.js'\nimport * as bulktrunc from '#shared/bulk.trunc.js'\nimport { ProjectHandler } from './bulk.project'\nimport * as common from '#shared/common.js'\nimport { tpinit } from './tp.init'\nimport { renderSandboxFormDiv } from '../dom/sandbox.ts'\n\n/*\n\n\nfor generating the UI that prompts user to select file type & upload text file\n\n\nbulkui()\n\ncontent2flag()\n\nbulkin()\n\nbulkembed()\n\n\n*/\n\nexport function bulkui(x, y, genomes, hostURL, holder, header) {\n\tlet pane, inputdiv, gselect, filediv, saydiv, visualdiv\n\tif (holder !== undefined) [inputdiv, gselect, filediv, saydiv, visualdiv] = renderSandboxFormDiv(holder, genomes)\n\telse {\n\t\t;[pane, inputdiv, gselect, filediv, saydiv, visualdiv] = client.newpane3(x, y, genomes)\n\t\tpane.header.text('Load mutation from text files')\n\t}\n\tinputdiv.append('div').style('margin', '20px 0px').style('color', '#858585').html(`\n\t<p>Choose one file and upload to initiate the display panel.<br>From there you can add additional files.</p>\n\t<div>Supported data types:</div>\n\t<ul>\n\t  <li>SNV and indel</li>\n\t  <ul>\n\t    <li><a href=https://drive.google.com/open?id=1OJ9aXq2_-a3BfIQdKLYCYzrJRTpu4_9i3gephTY-Z38 target=_blank>Format</a>,\n\t        <a href=https://proteinpaint.stjude.org/ppdemo/hg19/heatmap/exampleFiles/example.snvindel.txt target=_blank>example file</a></li>\n\t  </ul>\n\t  <li>SV or fusion transcript</li>\n\t  <ul>\n\t    <li><a href=https://drive.google.com/open?id=1klDZ0MHVkQTW2-lCu_AvpRE4_FcbhdB-yI17wNdPaOM target=_blank>Tabular format</a>,\n\t        <a href=https://proteinpaint.stjude.org/ppdemo/hg19/heatmap/exampleFiles/example.svfusion.txt target=_blank>example file</a>\n\t\t</li>\n\t\t<li>JSON-format, to come</li>\n\t  </ul>\n\t  <li>CNV, gene-level</li>\n\t  <ul>\n\t    <li><a href=https://drive.google.com/open?id=1WHptqOWNf96V0bYEDpj-EsKZGYnbBNc9aQIrhzdEJaU target=_blank>Format</a>, \n\t        <a href=https://proteinpaint.stjude.org/ppdemo/hg19/heatmap/exampleFiles/example.cnv.txt target=_blank>example file</a>\n\t\t</li>\n\t  </ul>\n\t  <li>ITD</li>\n\t  <ul>\n\t  \t<li>Internal tandem duplication, in-frame</li>\n\t    <li><a href=https://drive.google.com/open?id=1Bh9awBsraoHbV8iWXv_3oDeXMsjIAHaOKHr973IJyZc target=_blank>Format</a>, \n\t        <a href=https://proteinpaint.stjude.org/ppdemo/hg19/heatmap/exampleFiles/example.itd.txt target=_blank>example file</a>\n\t\t</li>\n\t  </ul>\n\t  <li>Intragenic deletion, in-frame</li>\n\t  <ul>\n\t    <li><a href=https://drive.google.com/open?id=1tWbf3rg3BmVIZPGGPk023P0aBkDw_ry5XuZLGyGodyg target=_blank>Format</a>, \n\t        <a href=https://proteinpaint.stjude.org/ppdemo/hg19/heatmap/exampleFiles/example.deletion.txt target=_blank>example file</a>\n\t\t</li>\n\t  </ul>\n\t  <li>Truncation</li>\n\t  <ul>\n\t  \t<li>Either N-terminus loss or C-terminus loss</li>\n\t    <li><a href=https://drive.google.com/open?id=1P1g-Y8r30pSKfan1BhYZcsUtSk7wRb4plaO1S-JCJr4 target=_blank>Format</a>, \n\t        <a href=https://proteinpaint.stjude.org/ppdemo/hg19/heatmap/exampleFiles/example.truncation.txt target=_blank>example file</a>\n\t\t</li>\n\t  </ul>\n\t</ul>`)\n\n\tconst fileui = () => {\n\t\tfilediv.selectAll('*').remove()\n\n\t\t// create a separate project handler for each bulk ui pane\n\t\tnew ProjectHandler({\n\t\t\tbulkin,\n\t\t\tgenomes,\n\t\t\tgselect,\n\t\t\tcontent2flag,\n\t\t\tflag2tp,\n\t\t\tfilediv,\n\t\t\tinit_bulk_flag: bulk.init_bulk_flag\n\t\t})\n\n\t\tfilediv.append('span').html('Select data type&nbsp;')\n\t\tconst typeselect = client.filetypeselect(filediv).style('margin-right', '20px')\n\n\t\t// TODO vcf, new tabular formats\n\t\tconst butt = filediv\n\t\t\t.append('input')\n\t\t\t.attr('type', 'file')\n\t\t\t.on('change', event => {\n\t\t\t\tconst flag = bulk.init_bulk_flag(genomes[gselect.options[gselect.selectedIndex].innerHTML])\n\t\t\t\tflag.geneToUpper = geneToUpper.property('checked')\n\n\t\t\t\tsaydiv.text('')\n\t\t\t\tconst file = event.target.files[0]\n\t\t\t\tif (!file) {\n\t\t\t\t\tfileui()\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tif (file.size == 0) {\n\t\t\t\t\tsaydiv.text('Wrong file: ' + file.name)\n\t\t\t\t\tfileui()\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tconst reader = new FileReader()\n\t\t\t\treader.onload = event => {\n\t\t\t\t\tconst error = content2flag(event.target.result, typeselect.node().selectedIndex, flag)\n\n\t\t\t\t\tif (error) {\n\t\t\t\t\t\tsaydiv.text('Error: ' + error)\n\t\t\t\t\t\tfileui()\n\t\t\t\t\t\treturn\n\t\t\t\t\t}\n\n\t\t\t\t\tflag2tp(flag, file)\n\t\t\t\t}\n\t\t\t\treader.onerror = function () {\n\t\t\t\t\tsaydiv.text('Error reading file ' + file.name)\n\t\t\t\t\tfileui()\n\t\t\t\t\treturn\n\t\t\t\t}\n\t\t\t\tsaydiv.text('Parsing file ' + file.name + ' ...')\n\t\t\t\treader.readAsText(file, 'utf8')\n\t\t\t})\n\n\t\tsetTimeout(() => butt.node().focus(), 1100)\n\t}\n\tfileui()\n\n\tfilediv.append('span').html('<br/>Convert gene name to uppercase &nbsp;')\n\tconst geneToUpper = filediv.append('span').append('input').attr('type', 'checkbox').property('checked', true)\n\n\t// has to keep this function here because\n\t// of referece to x,y,hostURL,etc closured variables\n\tfunction flag2tp(flag, file, _cohort = null, ds = null) {\n\t\tif (typeof flag == 'string') {\n\t\t\tsaydiv.text(flag)\n\t\t\tfileui()\n\t\t\treturn\n\t\t}\n\t\tsaydiv.text('')\n\t\tfileui()\n\t\t// good data ready\n\n\t\tconst cohort = _cohort\n\t\t\t? _cohort\n\t\t\t: Object.assign({\n\t\t\t\t\tgenome: flag.genome,\n\t\t\t\t\tname: file.name\n\t\t\t  })\n\n\t\tconst err = bulkin({\n\t\t\tflag: flag,\n\t\t\tfilename: file.name,\n\t\t\tcohort: cohort,\n\t\t\tflag2thisds: ds\n\t\t})\n\t\tif (err) {\n\t\t\tsaydiv.text('Error with ' + file.name + ': ' + err)\n\t\t\treturn\n\t\t}\n\n\t\tif (flag.good == 0) {\n\t\t\tsaydiv.text('No mutations can be loaded')\n\t\t\treturn\n\t\t}\n\n\t\tlet visual_holder\n\t\tif (pane) {\n\t\t\tclient.disappear(pane.pane)\n\t\t\tconst pane2 = client.newpane({ x: 100, y: 100, toshrink: true })\n\t\t\tpane2.header.html('<span style=\"opacity:.5\">FILE</span> ' + file.name)\n\t\t\tvisual_holder = pane2.body\n\t\t}\n\t\t// update sandbox panel for app drawer\n\t\tif (holder !== undefined) {\n\t\t\tvisual_holder = visualdiv.append('div').html('<span style=\"opacity:.5\">FILE</span> ' + file.name) //Fix for ui in a div within sandbox, rather than consuming the entire sandbox\n\t\t}\n\n\t\tinputdiv.selectAll('*').remove()\n\t\timport('./tp.ui').then(tpui => {\n\t\t\ttpui.default(cohort, visual_holder, hostURL)\n\t\t})\n\t\treturn cohort\n\t}\n\n\treturn function content2flag2tp(file, type) {\n\t\t// testing only\n\t\t// to load text files from server public/\n\n\t\tconst error = content2flag(file.content, type, flag)\n\n\t\tif (error) {\n\t\t\tsaydiv.text('Error: ' + error)\n\t\t\tfileui()\n\t\t\treturn\n\t\t}\n\n\t\tflag2tp(flag, file)\n\t}\n}\n\nexport function content2flag(text, type, flag) {\n\t/*\n\ttext:\n\t\tentire text loaded from a file\n\ttype:\n\t\tnumeric index of options in the <select> that corresponds to data types, solely defined in bulkui()\n\tflag:\n\t\tthe old flag variable\n\n\tupon any error, return string as error message\n\t*/\n\n\tif (!flag) return 'should not happen!'\n\n\tlet err\n\tswitch (type) {\n\t\tcase 0:\n\t\t\terr = parse_snvindel(text, flag)\n\t\t\tif (err) return err\n\t\t\tbreak\n\t\tcase 1:\n\t\t\terr = parse_sv(text, flag, true)\n\t\t\tif (err) return err\n\t\t\tbreak\n\t\tcase 2:\n\t\t\terr = parse_sv(text, flag, false)\n\t\t\tif (err) return err\n\t\t\tbreak\n\t\tcase 3:\n\t\t\terr = parse_itd(text, flag)\n\t\t\tif (err) return err\n\t\t\tbreak\n\t\tcase 4:\n\t\t\terr = parse_del(text, flag)\n\t\t\tif (err) return err\n\t\t\tbreak\n\t\tcase 5:\n\t\t\terr = parse_trunc(text, flag)\n\t\t\tif (err) return err\n\t\t\tbreak\n\t\tcase 6:\n\t\t\terr = parse_cnv(text, flag)\n\t\t\tif (err) return err\n\t\t\tbreak\n\t\tdefault:\n\t\t\treturn 'unknown option array index from file type <select>: ' + type\n\t}\n}\n\nexport function bulkin(p, callback = null) {\n\t/*\n\tmust always call this for ds-to-cohort flow\n\n\tp {} keys:\n\n\tflag - flag object\n\tcohort - cohort object\n\tfilename - str\n\tflag2thisds - dataset object\n\n\tif flag2thisds is set:\n\t\tflag.data will be appended to the given ds\n\t\tds must already have data\n\t\tnew data from flag must have the same attributes with existing data, so will compare and abort upon any difference\n\telse:\n\t\tcreate a new dataset for flag.data and put in cohort\n\t*/\n\tconst flag = p.flag\n\tconst cohort = p.cohort\n\tif (!cohort.p2st) {\n\t\tcohort.p2st = {}\n\t}\n\tif (!cohort.dsset) {\n\t\tcohort.dsset = {}\n\t}\n\tif (!cohort.assaylst) {\n\t\tcohort.assaylst = []\n\t}\n\tif (flag.variantgene) {\n\t\tif (cohort.variantgene) {\n\t\t\treturn 'variantgene already set for this cohort'\n\t\t}\n\t\tcohort.variantgene = flag.variantgene\n\t}\n\n\tif (flag.snv.badlines.length > 0) {\n\t\tclient.bulk_badline(flag.snv.header, flag.snv.badlines)\n\t}\n\tif (flag.fusion.badlines.length > 0) {\n\t\tclient.bulk_badline(flag.fusion.header, flag.fusion.badlines)\n\t}\n\tif (flag.sv.badlines.length > 0) {\n\t\tclient.bulk_badline(flag.sv.header, flag.sv.badlines)\n\t}\n\tif (flag.cnv.badlines.length > 0) {\n\t\tclient.bulk_badline(flag.cnv.header, flag.cnv.badlines)\n\t}\n\tif (flag.itd.badlines.length > 0) {\n\t\tclient.bulk_badline(flag.itd.header, flag.itd.badlines)\n\t}\n\tif (flag.del.badlines.length > 0) {\n\t\tclient.bulk_badline(flag.del.header, flag.del.badlines)\n\t}\n\tif (flag.truncation.badlines.length > 0) {\n\t\tclient.bulk_badline(flag.truncation.header, flag.truncation.badlines)\n\t}\n\n\t// newdt\n\tif (flag.good == 0) {\n\t\treturn false\n\t}\n\t// registering good data\n\tconst tmp = {}\n\tlet hastumormaf = false\n\tif (flag.snv.loaded) {\n\t\tfor (const i of flag.snv.header) {\n\t\t\ttmp[i] = 1\n\t\t}\n\t\tif ('maf_tumor_v1' in tmp && 'maf_tumor_v2' in tmp) {\n\t\t\thastumormaf = true\n\t\t}\n\t}\n\tif (flag.cnv.loaded) {\n\t\tfor (const i of flag.cnv.header) {\n\t\t\ttmp[i] = 1\n\t\t}\n\t}\n\tif (flag.fusion.loaded) {\n\t\tfor (const i of flag.fusion.header) {\n\t\t\ttmp[i] = 1\n\t\t}\n\t}\n\tif (flag.sv.loaded) {\n\t\tfor (const i of flag.sv.header) {\n\t\t\ttmp[i] = 1\n\t\t}\n\t}\n\tif (flag.itd.loaded) {\n\t\tfor (const i of flag.itd.header) {\n\t\t\ttmp[i] = 1\n\t\t}\n\t}\n\tif (flag.del.loaded) {\n\t\tfor (const i of flag.del.header) {\n\t\t\ttmp[i] = 1\n\t\t}\n\t}\n\tif (flag.truncation.loaded) {\n\t\tfor (const i of flag.truncation.header) {\n\t\t\ttmp[i] = 1\n\t\t}\n\t}\n\t// newdt\n\n\t// attributes of flag.data\n\tconst hassample = 'sample' in tmp || 'patient' in tmp\n\tconst hasdisease = 'disease' in tmp\n\tconst hasst = 'sampletype' in tmp\n\n\tlet dsc\n\tif (p.flag2thisds) {\n\t\tdsc = p.flag2thisds\n\t\t// flag data to existing ds\n\t\t// compare attributes\n\t\tif (hassample && !dsc.hassample) {\n\t\t\treturn '\"sample\" column found in new data but not in existing data'\n\t\t}\n\t\tif (!hassample && dsc.hassample) {\n\t\t\treturn '\"sample\" column found in existing data but not in new data'\n\t\t}\n\t\tif (hasdisease && !dsc.hasdisease) {\n\t\t\treturn '\"disease\" column found in new data but not in existing data'\n\t\t}\n\t\tif (!hasdisease && dsc.hasdisease) {\n\t\t\treturn '\"disease\" column found in existing data but not in new data'\n\t\t}\n\t\tif (hasst && !dsc.hasst) {\n\t\t\treturn '\"sampletype\" column found in new data but not in existing data'\n\t\t}\n\t\tif (!hasst && dsc.hasst) {\n\t\t\treturn '\"sampletype\" column found in existing data but not in new data'\n\t\t}\n\n\t\tfor (const genename in flag.data) {\n\t\t\tconst lst = dsc.bulkdata[genename]\n\t\t\tif (lst) {\n\t\t\t\tdsc.bulkdata[genename] = lst.concat(flag.data[genename])\n\t\t\t} else {\n\t\t\t\tdsc.bulkdata[genename] = flag.data[genename]\n\t\t\t}\n\t\t}\n\t} else {\n\t\tlet dsname = p.filename + (flag.tpsetname ? '_' + flag.tpsetname : '')\n\t\tif (dsname in flag.genome.datasets) {\n\t\t\tlet j = 1\n\t\t\tlet n2 = dsname + ' ' + j\n\t\t\twhile (n2 in flag.genome.datasets) {\n\t\t\t\tj++\n\t\t\t\tn2 = dsname + ' ' + j\n\t\t\t}\n\t\t\tdsname = n2\n\t\t}\n\t\tdsc = {\n\t\t\tlabel: dsname,\n\t\t\tbulkdata: flag.data, // official dataset don't have this\n\t\t\thassample: hassample,\n\t\t\thasdisease: hasdisease,\n\t\t\thastumormaf: hastumormaf,\n\t\t\thasst: hasst,\n\t\t\tgenome: cohort.genome,\n\t\t\timport: {},\n\t\t\timported: {},\n\t\t\timportsilent: flag.snv.silent == 0 ? false : flag.snv.missense / flag.snv.silent >= 5 ? false : true\n\t\t}\n\t\tflag.genome.datasets[dsname] = dsc\n\t\tcohort.dsset[dsname] = dsc\n\t\tif (cohort.dbexpression) {\n\t\t\tif (cohort.dbexpression.tidy) {\n\t\t\t\ttry {\n\t\t\t\t\tcohort.dbexpression.tidy = new Function(...cohort.dbexpression.tidy)\n\t\t\t\t} catch (e) {\n\t\t\t\t\terr('invalid JavaScript for dbexpression.tidy')\n\t\t\t\t\t// disable whole thing\n\t\t\t\t\tdelete cohort.dbexpression\n\t\t\t\t}\n\t\t\t}\n\t\t\tdsc.dbexpression = cohort.dbexpression\n\t\t}\n\t\tif (hasdisease) {\n\t\t\tdsc.stratify = [\n\t\t\t\t{\n\t\t\t\t\tlabel: 'disease',\n\t\t\t\t\tattr1: { k: 'disease', label: 'disease' }\n\t\t\t\t}\n\t\t\t]\n\t\t}\n\t}\n\t// flag.data to cohort.p2st\n\t// must not use bulkdata since when appending data to ds, avoid double counting samples\n\tif (hassample) {\n\t\tfor (const gene in flag.data) {\n\t\t\tfor (const m of flag.data[gene]) {\n\t\t\t\tlet pn = m.patient\n\t\t\t\tif (!pn) {\n\t\t\t\t\tpn = m.sample\n\t\t\t\t\tif (!pn) {\n\t\t\t\t\t\tcontinue\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (!cohort.p2st[pn]) {\n\t\t\t\t\tcohort.p2st[pn] = {}\n\t\t\t\t}\n\t\t\t\tlet st = m.sampletype\n\t\t\t\tif (!st) {\n\t\t\t\t\t// note this!!!\n\t\t\t\t\tst = pn\n\t\t\t\t}\n\t\t\t\tif (!cohort.p2st[pn][st]) {\n\t\t\t\t\tcohort.p2st[pn][st] = {\n\t\t\t\t\t\tdsset: {},\n\t\t\t\t\t\ttktemplate: []\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t\tif (!cohort.p2st[pn][st].dsset[dsc.label]) {\n\t\t\t\t\tcohort.p2st[pn][st].dsset[dsc.label] = []\n\t\t\t\t}\n\t\t\t\tcohort.p2st[pn][st].dsset[dsc.label].push(m)\n\t\t\t\t// XXX for sv/fusion, each n-gene record will be created into n records in flag.data,\n\t\t\t\t// thus making duplicated data in sample.dsset\n\t\t\t\t// dealt by svpairlstset in tp.sample.js\n\t\t\t}\n\t\t}\n\t}\n\tif (callback) callback()\n\treturn false\n}\n\nexport function bulkembed(arg) {\n\t/*\n\tcalled by app.js, when there is the studyview object in the parameter\n\n\targ is the studyview object\n\t\n\tTWO ways to provide text mutation data:\n\n\t.snvindel\n\t.svjson\n\t.cnv\n\t\t-- data as text string\n\t\t-- parse into one flag\n\n\t.mutationset:[{ }]\n\t\t-- standard study config\n\t\t-- parse into one or more flags\n\n\t*/\n\n\tif (!arg.name) arg.name = 'Unnamed dataset'\n\n\tlet holder = arg.holder\n\tif (!holder) {\n\t\tconst pane = client.newpane({ x: 100, y: 100 })\n\t\tholder = pane.body\n\t}\n\n\tconst saydiv = holder.append('div')\n\n\tnew Promise((resolve, reject) => {\n\t\tconst cohort = {\n\t\t\tdsset: {}\n\t\t}\n\t\tfor (const k in arg) {\n\t\t\tif (k == 'snvindel' || k == 'svjson' || k == 'cnv' || k == 'sv' || k == 'mutationset') {\n\t\t\t\t// don't copy these to cohort\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tcohort[k] = arg[k]\n\t\t}\n\t\tresolve(cohort)\n\t})\n\n\t\t.then(cohort => {\n\t\t\tif (!arg.snvindel && !arg.svjson && !arg.cnv && !arg.sv) return cohort\n\n\t\t\t/************ parse data by lumped text string, tabular format\n\t\t\t */\n\n\t\t\tconst flag = bulk.init_bulk_flag(cohort.genome)\n\n\t\t\tif (arg.snvindel) {\n\t\t\t\tconst e = parse_snvindel(arg.snvindel, flag)\n\t\t\t\tif (e) throw { message: 'error in snvindel data: ' + e }\n\t\t\t\tdelete arg.snvindel\n\t\t\t}\n\t\t\tif (arg.svjson) {\n\t\t\t\tconst e = parse_svjson(arg.svjson, flag)\n\t\t\t\tif (e) throw { message: 'error in svjson data: ' + e }\n\t\t\t\tdelete arg.svjson\n\t\t\t}\n\t\t\tif (arg.sv) {\n\t\t\t\tconst e = parse_sv(arg.sv, flag)\n\t\t\t\tif (e) throw { message: 'error in svjson data: ' + e }\n\t\t\t\tdelete arg.sv\n\t\t\t}\n\t\t\tif (arg.cnv) {\n\t\t\t\tconst e = parse_cnv(arg.cnv, flag)\n\t\t\t\tif (e) throw { message: 'error in cnv data: ' + e }\n\t\t\t\tdelete arg.cnv\n\t\t\t}\n\n\t\t\tconst err = bulkin({\n\t\t\t\tflag: flag,\n\t\t\t\tfilename: arg.name,\n\t\t\t\tcohort: cohort\n\t\t\t})\n\t\t\tif (err) throw { message: 'Error parsing data: ' + err }\n\t\t\treturn cohort\n\t\t})\n\n\t\t.then(cohort => {\n\t\t\tif (!arg.mutationset) return cohort\n\t\t\tif (!Array.isArray(arg.mutationset)) throw { message: 'mutationset is not an array' }\n\n\t\t\t/************ load server hosted text files, in groups\n\t\t\t */\n\n\t\t\tconst tasks2 = []\n\n\t\t\tfor (const mset of arg.mutationset) {\n\t\t\t\tconst flag = bulk.init_bulk_flag(cohort.genome)\n\t\t\t\tconst tasks = []\n\n\t\t\t\tif (mset.snvindel) {\n\t\t\t\t\tconst req = new Request(arg.hostURL + '/textfile', {\n\t\t\t\t\t\tmethod: 'POST',\n\t\t\t\t\t\tbody: '{\"file\":\"' + mset.snvindel + '\"}'\n\t\t\t\t\t})\n\t\t\t\t\tconst task = fetch(req)\n\t\t\t\t\t\t.then(data => {\n\t\t\t\t\t\t\treturn data.json()\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.then(data => {\n\t\t\t\t\t\t\tif (data.error) throw { message: 'error with snvindel file: ' + data.error }\n\t\t\t\t\t\t\tconst e = parse_snvindel(data.text, flag)\n\t\t\t\t\t\t\tif (e) throw { message: 'error with snvindel file: ' + e }\n\t\t\t\t\t\t})\n\t\t\t\t\ttasks.push(task)\n\t\t\t\t}\n\t\t\t\tif (mset.snvindel_url) {\n\t\t\t\t\ttasks.push(\n\t\t\t\t\t\tclient.dofetch('urltextfile', { url: mset.snvindel_url }).then(data => {\n\t\t\t\t\t\t\tif (data.error) throw { message: 'cannot get snvindel file from url' }\n\t\t\t\t\t\t\tconst e = parse_snvindel(data.text, flag)\n\t\t\t\t\t\t\tif (e) throw { message: 'error with snvindel file: ' + e }\n\t\t\t\t\t\t})\n\t\t\t\t\t)\n\t\t\t\t}\n\n\t\t\t\tif (mset.cnv) {\n\t\t\t\t\tconst req = new Request(arg.hostURL + '/textfile', {\n\t\t\t\t\t\tmethod: 'POST',\n\t\t\t\t\t\tbody: '{\"file\":\"' + mset.cnv + '\"}'\n\t\t\t\t\t})\n\t\t\t\t\tconst task = fetch(req)\n\t\t\t\t\t\t.then(data => {\n\t\t\t\t\t\t\treturn data.json()\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.then(data => {\n\t\t\t\t\t\t\tif (data.error) throw { message: 'error with cnv file: ' + data.error }\n\t\t\t\t\t\t\tconst e = parse_cnv(data.text, flag)\n\t\t\t\t\t\t\tif (e) throw { message: 'error with cnv file: ' + e }\n\t\t\t\t\t\t})\n\t\t\t\t\ttasks.push(task)\n\t\t\t\t}\n\n\t\t\t\tif (mset.cnv_url) {\n\t\t\t\t\ttasks.push(\n\t\t\t\t\t\tclient.dofetch('urltextfile', { url: mset.cnv_url }).then(data => {\n\t\t\t\t\t\t\tif (data.error) throw { message: 'cannot get cnv file from url' }\n\t\t\t\t\t\t\tconst e = parse_cnv(data.text, flag)\n\t\t\t\t\t\t\tif (e) throw { message: 'error with cnv file: ' + e }\n\t\t\t\t\t\t})\n\t\t\t\t\t)\n\t\t\t\t}\n\n\t\t\t\tif (mset.sv) {\n\t\t\t\t\tconst req = new Request(arg.hostURL + '/textfile', {\n\t\t\t\t\t\tmethod: 'POST',\n\t\t\t\t\t\tbody: '{\"file\":\"' + mset.sv + '\"}'\n\t\t\t\t\t})\n\t\t\t\t\tconst task = fetch(req)\n\t\t\t\t\t\t.then(data => {\n\t\t\t\t\t\t\treturn data.json()\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.then(data => {\n\t\t\t\t\t\t\tif (data.error) throw { message: 'error with sv file: ' + data.error }\n\t\t\t\t\t\t\tconst e = parse_sv(data.text, flag, true)\n\t\t\t\t\t\t\tif (e) throw { message: 'error with sv file: ' + e }\n\t\t\t\t\t\t})\n\t\t\t\t\ttasks.push(task)\n\t\t\t\t}\n\n\t\t\t\tif (mset.sv_url) {\n\t\t\t\t\ttasks.push(\n\t\t\t\t\t\tclient.dofetch('urltextfile', { url: mset.sv_url }).then(data => {\n\t\t\t\t\t\t\tif (data.error) throw { message: 'cannot get sv file from url' }\n\t\t\t\t\t\t\tconst e = parse_sv(data.text, flag)\n\t\t\t\t\t\t\tif (e) throw { message: 'error with sv file: ' + e }\n\t\t\t\t\t\t})\n\t\t\t\t\t)\n\t\t\t\t}\n\n\t\t\t\tif (mset.fusion) {\n\t\t\t\t\tconst req = new Request(arg.hostURL + '/textfile', {\n\t\t\t\t\t\tmethod: 'POST',\n\t\t\t\t\t\tbody: '{\"file\":\"' + mset.fusion + '\"}'\n\t\t\t\t\t})\n\t\t\t\t\tconst task = fetch(req)\n\t\t\t\t\t\t.then(data => {\n\t\t\t\t\t\t\treturn data.json()\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.then(data => {\n\t\t\t\t\t\t\tif (data.error) throw { message: 'error with fusion file: ' + data.error }\n\t\t\t\t\t\t\tconst e = parse_sv(data.text, flag, false)\n\t\t\t\t\t\t\tif (e) throw { message: 'error with fusion file: ' + e }\n\t\t\t\t\t\t})\n\t\t\t\t\ttasks.push(task)\n\t\t\t\t}\n\t\t\t\tif (mset.svjson) {\n\t\t\t\t\tconst req = new Request(arg.hostURL + '/textfile', {\n\t\t\t\t\t\tmethod: 'POST',\n\t\t\t\t\t\tbody: '{\"file\":\"' + mset.svjson + '\"}'\n\t\t\t\t\t})\n\t\t\t\t\tconst task = fetch(req)\n\t\t\t\t\t\t.then(data => {\n\t\t\t\t\t\t\treturn data.json()\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.then(data => {\n\t\t\t\t\t\t\tif (data.error) throw { message: 'error with svjson file: ' + data.error }\n\t\t\t\t\t\t\tconst e = parse_svjson(data.text, flag, false)\n\t\t\t\t\t\t\tif (e) throw { message: 'error with svjson file: ' + e }\n\t\t\t\t\t\t})\n\t\t\t\t\ttasks.push(task)\n\t\t\t\t}\n\t\t\t\tif (mset.deletion) {\n\t\t\t\t\tconst req = new Request(arg.hostURL + '/textfile', {\n\t\t\t\t\t\tmethod: 'POST',\n\t\t\t\t\t\tbody: '{\"file\":\"' + mset.deletion + '\"}'\n\t\t\t\t\t})\n\t\t\t\t\tconst task = fetch(req)\n\t\t\t\t\t\t.then(data => {\n\t\t\t\t\t\t\treturn data.json()\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.then(data => {\n\t\t\t\t\t\t\tif (data.error) throw { message: 'error with deletion file: ' + data.error }\n\t\t\t\t\t\t\tconst e = parse_del(data.text, flag, false)\n\t\t\t\t\t\t\tif (e) throw { message: 'error with deletion file: ' + e }\n\t\t\t\t\t\t})\n\t\t\t\t\ttasks.push(task)\n\t\t\t\t}\n\n\t\t\t\tif (mset.deletion_url) {\n\t\t\t\t\ttasks.push(\n\t\t\t\t\t\tclient.dofetch('urltextfile', { url: mset.deletion_url }).then(data => {\n\t\t\t\t\t\t\tif (data.error) throw { message: 'cannot get deletion file from url' }\n\t\t\t\t\t\t\tconst e = parse_del(data.text, flag)\n\t\t\t\t\t\t\tif (e) throw { message: 'error with deletion file: ' + e }\n\t\t\t\t\t\t})\n\t\t\t\t\t)\n\t\t\t\t}\n\n\t\t\t\tif (mset.truncation) {\n\t\t\t\t\tconst req = new Request(arg.hostURL + '/textfile', {\n\t\t\t\t\t\tmethod: 'POST',\n\t\t\t\t\t\tbody: '{\"file\":\"' + mset.truncation + '\"}'\n\t\t\t\t\t})\n\t\t\t\t\tconst task = fetch(req)\n\t\t\t\t\t\t.then(data => {\n\t\t\t\t\t\t\treturn data.json()\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.then(data => {\n\t\t\t\t\t\t\tif (data.error) throw { message: 'error with truncation file: ' + data.error }\n\t\t\t\t\t\t\tconst e = parse_trunc(data.text, flag, false)\n\t\t\t\t\t\t\tif (e) throw { message: 'error with truncation file: ' + e }\n\t\t\t\t\t\t})\n\t\t\t\t\ttasks.push(task)\n\t\t\t\t}\n\n\t\t\t\tif (mset.truncation_url) {\n\t\t\t\t\ttasks.push(\n\t\t\t\t\t\tclient.dofetch('urltextfile', { url: mset.truncation_url }).then(data => {\n\t\t\t\t\t\t\tif (data.error) throw { message: 'cannot get truncation file from url' }\n\t\t\t\t\t\t\tconst e = parse_trunc(data.text, flag, false)\n\t\t\t\t\t\t\tif (e) throw { message: 'error with truncation file: ' + e }\n\t\t\t\t\t\t})\n\t\t\t\t\t)\n\t\t\t\t}\n\n\t\t\t\tif (mset.itd) {\n\t\t\t\t\tconst req = new Request(arg.hostURL + '/textfile', {\n\t\t\t\t\t\tmethod: 'POST',\n\t\t\t\t\t\tbody: '{\"file\":\"' + mset.itd + '\"}'\n\t\t\t\t\t})\n\t\t\t\t\tconst task = fetch(req)\n\t\t\t\t\t\t.then(data => {\n\t\t\t\t\t\t\treturn data.json()\n\t\t\t\t\t\t})\n\t\t\t\t\t\t.then(data => {\n\t\t\t\t\t\t\tif (data.error) throw { message: 'error with itd file: ' + data.error }\n\t\t\t\t\t\t\tconst e = parse_itd(data.text, flag, false)\n\t\t\t\t\t\t\tif (e) throw { message: 'error with itd file: ' + e }\n\t\t\t\t\t\t})\n\t\t\t\t\ttasks.push(task)\n\t\t\t\t}\n\n\t\t\t\tif (mset.itd_url) {\n\t\t\t\t\ttasks.push(\n\t\t\t\t\t\tclient.dofetch('urltextfile', { url: mset.itd_url }).then(data => {\n\t\t\t\t\t\t\tif (data.error) throw { message: 'cannot get itd file from url' }\n\t\t\t\t\t\t\tconst e = parse_itd(data.text, flag, false)\n\t\t\t\t\t\t\tif (e) throw { message: 'error with itd file: ' + e }\n\t\t\t\t\t\t})\n\t\t\t\t\t)\n\t\t\t\t}\n\n\t\t\t\tconst task2 = Promise.all(tasks).then(data => {\n\t\t\t\t\tconst err = bulkin({\n\t\t\t\t\t\tflag: flag,\n\t\t\t\t\t\tfilename: arg.name,\n\t\t\t\t\t\tcohort: cohort\n\t\t\t\t\t})\n\t\t\t\t\tif (err) throw { message: 'Error parsing data from ' + mset.name + ': ' + err }\n\t\t\t\t\t// done this mset\n\t\t\t\t})\n\t\t\t\ttasks2.push(task2)\n\t\t\t}\n\n\t\t\treturn Promise.all(tasks2).then(data => {\n\t\t\t\t// done all msets\n\t\t\t\treturn cohort\n\t\t\t})\n\t\t})\n\n\t\t.then(cohort => {\n\t\t\tconst err = tpinit(cohort)\n\t\t\tif (err) throw { message: 'Error parsing study: ' + err }\n\n\t\t\tsaydiv.text('')\n\n\t\t\timport('./tp.ui').then(p => {\n\t\t\t\tp.default(cohort, holder, arg.hostURL)\n\t\t\t})\n\t\t})\n\n\t\t.catch(err => {\n\t\t\tsaydiv.text(err.message)\n\t\t\tif (err.stack) {\n\t\t\t\tconsole.log(err.stack)\n\t\t\t}\n\t\t})\n}\n\n/********* helper functions *********\n\nof loading text data of various types of mutations from server-hosted files\nslight duplication with what's in server.js, where it handles calls from studies\n*/\n\nfunction parse_snvindel(text, flag) {\n\tconst lines = text.trim().split(/\\r?\\n/)\n\tlet headerline = lines[0]\n\tlet lineidx = 0\n\twhile (headerline[0] == '#') {\n\t\tlineidx++\n\t\theaderline = lines[lineidx]\n\t}\n\tif (!headerline) return 'no header line'\n\tconst err = bulksnv.parseheader(headerline, flag)\n\tif (err) return 'header error: ' + err\n\tfor (let i = lineidx + 1; i < lines.length; i++) {\n\t\tif (lines[i] == '') continue\n\t\tif (lines[i][0] == '#') continue\n\t\tbulksnv.parseline(i, lines[i], flag)\n\t}\n}\n\nfunction parse_svjson(text, flag) {\n\tconst lines = text.split(/\\r?\\n/)\n\tlet headerline = lines[0]\n\tlet lineidx = 0\n\twhile (headerline[0] == '#') {\n\t\tlineidx++\n\t\theaderline = lines[lineidx]\n\t}\n\tif (!headerline) return 'no header line'\n\tconst [err, header] = bulksvjson.parseheader(headerline, flag)\n\tif (err) return 'header error: ' + err\n\tfor (let i = lineidx + 1; i < lines.length; i++) {\n\t\tif (lines[i] == '') continue\n\t\tif (lines[i][0] == '#') continue\n\t\tbulksvjson.parseline(i, lines[i], flag, header)\n\t}\n}\n\nfunction parse_cnv(text, flag) {\n\tconst lines = text.split(/\\r?\\n/)\n\tlet headerline = lines[0]\n\tlet lineidx = 0\n\twhile (headerline[0] == '#') {\n\t\tlineidx++\n\t\theaderline = lines[lineidx]\n\t}\n\tif (!headerline) return 'no header line'\n\tconst err = bulkcnv.parseheader(headerline, flag)\n\tif (err) return 'header error: ' + err\n\tfor (let i = lineidx + 1; i < lines.length; i++) {\n\t\tif (lines[i] == '') continue\n\t\tif (lines[i][0] == '#') continue\n\t\tbulkcnv.parseline(i, lines[i], flag)\n\t}\n}\n\nfunction parse_itd(text, flag) {\n\tconst lines = text.split(/\\r?\\n/)\n\tlet headerline = lines[0]\n\tlet lineidx = 0\n\twhile (headerline[0] == '#') {\n\t\tlineidx++\n\t\theaderline = lines[lineidx]\n\t}\n\tif (!headerline) return 'no header line'\n\tconst err = bulkitd.parseheader(headerline, flag)\n\tif (err) return 'header error: ' + err\n\tfor (let i = lineidx + 1; i < lines.length; i++) {\n\t\tif (lines[i] == '') continue\n\t\tif (lines[i][0] == '#') continue\n\t\tbulkitd.parseline(i, lines[i], flag)\n\t}\n}\n\nfunction parse_del(text, flag) {\n\tconst lines = text.split(/\\r?\\n/)\n\tlet headerline = lines[0]\n\tlet lineidx = 0\n\twhile (headerline[0] == '#') {\n\t\tlineidx++\n\t\theaderline = lines[lineidx]\n\t}\n\tif (!headerline) return 'no header line'\n\tconst err = bulkdel.parseheader(headerline, flag)\n\tif (err) return 'header error: ' + err\n\tfor (let i = lineidx + 1; i < lines.length; i++) {\n\t\tif (lines[i] == '') continue\n\t\tif (lines[i][0] == '#') continue\n\t\tbulkdel.parseline(i, lines[i], flag)\n\t}\n}\n\nfunction parse_trunc(text, flag) {\n\tconst lines = text.split(/\\r?\\n/)\n\tlet headerline = lines[0]\n\tlet lineidx = 0\n\twhile (headerline[0] == '#') {\n\t\tlineidx++\n\t\theaderline = lines[lineidx]\n\t}\n\tif (!headerline) return 'no header line'\n\tconst err = bulktrunc.parseheader(headerline, flag)\n\tif (err) return 'header error: ' + err\n\tfor (let i = lineidx + 1; i < lines.length; i++) {\n\t\tif (lines[i] == '') continue\n\t\tif (lines[i][0] == '#') continue\n\t\tbulktrunc.parseline(i, lines[i], flag)\n\t}\n}\n\nfunction parse_sv(text, flag, isSv) {\n\t// for both sv and fusion, from tabular text file\n\tconst lines = text.split(/\\r?\\n/)\n\tlet headerline = lines[0]\n\tlet lineidx = 0\n\twhile (headerline[0] == '#') {\n\t\tlineidx++\n\t\theaderline = lines[lineidx]\n\t}\n\tif (!headerline) return 'no header line'\n\tconst err = bulksv.parseheader(headerline, flag, isSv)\n\tif (err) return 'header error: ' + err\n\tfor (let i = lineidx + 1; i < lines.length; i++) {\n\t\tif (lines[i] == '') continue\n\t\tif (lines[i][0] == '#') continue\n\t\tbulksv.parseline(i, lines[i], flag, isSv)\n\t}\n}\n", "import * as client from './client'\nimport vcf2dstk from './vcf.tkconvert'\nimport { bulkin } from './bulk.ui'\nimport { string2pos, invalidcoord } from './coord'\nimport { scaleOrdinal } from 'd3-scale'\nimport { schemeCategory10 } from 'd3-scale-chromatic'\nimport * as common from '#shared/common.js'\nimport { getsjcharts } from './getsjcharts'\n\n/*\nparse and validate study configuration, including assays\n\n********************** EXPORTED\n\ntpinit()\n\nloadstudycohort()\n\n\n\n********************** INTERNAL\n\ncohort2genometkset()\ntidy_qtk()\n\n*/\n\nexport function tpinit(cohort) {\n\tif (!cohort.p2st) {\n\t\tcohort.p2st = {}\n\t}\n\tif (!cohort.assays) {\n\t\tcohort.assays = []\n\t}\n\tif (!Array.isArray(cohort.assays)) {\n\t\treturn '.assays should be an array'\n\t}\n\n\t/**********************\n\t\t qc check assays\n\t\t replace .assays with .assaylst\n\t**********************/\n\n\tcohort.assaylst = []\n\tlet assaynum = 0\n\tfor (const assayname of cohort.assays) {\n\t\tconst rawassay = cohort[assayname]\n\t\tif (!rawassay) {\n\t\t\treturn 'Assay \"' + assayname + '\" not found in cohort'\n\t\t}\n\t\tconst config = rawassay.config\n\t\tif (!config) {\n\t\t\treturn '.config object missing for assay \"' + assayname + '\"'\n\t\t}\n\t\tdelete rawassay.config\n\t\tif (!config.type) {\n\t\t\treturn '.config.type missing for assay \"' + assayname + '\"'\n\t\t}\n\t\tif (config.type.toLowerCase() == 'vcf') {\n\t\t\tconfig.type = client.tkt.ds\n\t\t\tconfig.isvcf = true\n\t\t} else {\n\t\t\tif (!common.validtkt(config.type)) {\n\t\t\t\treturn 'unknown .config.type \"' + config.type + '\" for assay \"' + assayname + '\"'\n\t\t\t}\n\t\t}\n\t\tconfig.id = (++assaynum).toString()\n\t\tif (!config.name) {\n\t\t\tconfig.name = assayname\n\t\t}\n\t\tif (config.type == client.tkt.junction) {\n\t\t\tif (config.readcountcutoff) {\n\t\t\t\tif (!Number.isInteger(config.readcountcutoff) || config.readcountcutoff < 0) {\n\t\t\t\t\treturn 'invalid .config.readcountcutoff for assay \"' + assayname + '\"'\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tcohort.assaylst.push(config)\n\n\t\tfor (const pn in rawassay) {\n\t\t\tif (!cohort.p2st[pn]) {\n\t\t\t\tcohort.p2st[pn] = {}\n\t\t\t}\n\t\t\tfor (const st in rawassay[pn]) {\n\t\t\t\tif (!cohort.p2st[pn][st]) {\n\t\t\t\t\tcohort.p2st[pn][st] = {\n\t\t\t\t\t\ttktemplate: []\n\t\t\t\t\t}\n\t\t\t\t}\n\n\t\t\t\t/*\n\t\t\t\tspecial cases, not singlar tk per sample\n\t\t\t\tnot in use\n\t\t\t\t*/\n\t\t\t\tif (config.type == client.tkt.vafs1) {\n\t\t\t\t\tfor (const name in rawassay[pn][st]) {\n\t\t\t\t\t\tconst tk = rawassay[pn][st][name]\n\t\t\t\t\t\tif (!tk.file && !tk.url) {\n\t\t\t\t\t\t\treturn 'no file or URL for ' + name + ' vafs1 of ' + pn + ', ' + st\n\t\t\t\t\t\t}\n\t\t\t\t\t\ttk.type = client.tkt.vafs1\n\t\t\t\t\t\ttk.patient = pn\n\t\t\t\t\t\ttk.sampletype = st\n\t\t\t\t\t\ttk.assayname = assayname\n\t\t\t\t\t\ttk.id = config.id\n\t\t\t\t\t\ttk.tkid = Math.random().toString()\n\t\t\t\t\t\tif (!tk.name) {\n\t\t\t\t\t\t\ttk.name = name + ' vaf'\n\t\t\t\t\t\t}\n\t\t\t\t\t\tcohort.p2st[pn][st].tktemplate.push(tk)\n\t\t\t\t\t}\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\n\t\t\t\t/*\n\t\t\t\tcommon steps applied to common tk types\n\t\t\t\tallow to be array of multiple tracks, or a single track {}\n\t\t\t\t*/\n\t\t\t\tlet rawtklst = []\n\t\t\t\tif (Array.isArray(rawassay[pn][st])) {\n\t\t\t\t\t// multiple tracks\n\t\t\t\t\trawtklst = rawassay[pn][st]\n\t\t\t\t} else {\n\t\t\t\t\t// single\n\t\t\t\t\trawtklst.push(rawassay[pn][st])\n\t\t\t\t}\n\t\t\t\tfor (const _tk of rawtklst) {\n\t\t\t\t\t/*\n\t\t\t\t\ttk will be overwritten in case of vcf track\n\t\t\t\t\t*/\n\t\t\t\t\tlet tk = _tk\n\t\t\t\t\tif (!tk.file && !tk.url) {\n\t\t\t\t\t\treturn 'track has no file or url (sample: ' + pn + ', assay: ' + assayname + ')'\n\t\t\t\t\t}\n\t\t\t\t\tif (tk.name) {\n\t\t\t\t\t\t// keep name\n\t\t\t\t\t} else if (tk.partname) {\n\t\t\t\t\t\t// partname is provided as a short way to distinguish multiple tracks of same sample-assay\n\t\t\t\t\t\ttk.name = pn + (st == pn ? '' : ' ' + st) + ' ' + assayname + ' ' + tk.partname\n\t\t\t\t\t} else {\n\t\t\t\t\t\t// no name\n\t\t\t\t\t\ttk.name = pn + (st == pn ? '' : ' ' + st) + ' ' + assayname\n\t\t\t\t\t}\n\t\t\t\t\tif (config.isvcf) {\n\t\t\t\t\t\tconst [err, tk2] = vcf2dstk({\n\t\t\t\t\t\t\tname: tk.name,\n\t\t\t\t\t\t\tfile: tk.file,\n\t\t\t\t\t\t\turl: tk.url\n\t\t\t\t\t\t})\n\t\t\t\t\t\tif (err) {\n\t\t\t\t\t\t\treturn 'VCF track error: ' + err\n\t\t\t\t\t\t}\n\t\t\t\t\t\ttk = tk2\n\t\t\t\t\t} else {\n\t\t\t\t\t\t/*\n\t\t\t\t\t\tby default, each tk will *inherit* config.type\n\t\t\t\t\t\tbut allow the track to have its own type \n\t\t\t\t\t\t*/\n\t\t\t\t\t\tif (tk.type) {\n\t\t\t\t\t\t\tif (!common.validtkt(tk.type)) {\n\t\t\t\t\t\t\t\treturn 'invalid track type \"' + tk.type + '\" (sample: ' + pn + ', assay: ' + assayname + ')'\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\ttk.type = config.type\n\t\t\t\t\t\t}\n\t\t\t\t\t}\n\t\t\t\t\ttk.patient = pn\n\t\t\t\t\ttk.sampletype = st\n\t\t\t\t\ttk.assayname = assayname\n\t\t\t\t\ttk.id = config.id\n\t\t\t\t\ttk.tkid = Math.random().toString()\n\t\t\t\t\tcohort.p2st[pn][st].tktemplate.push(tk)\n\n\t\t\t\t\t// type-specific procedures\n\t\t\t\t\tswitch (config.type) {\n\t\t\t\t\t\tcase client.tkt.bigwig:\n\t\t\t\t\t\t\tconst e = tidy_qtk(tk, config)\n\t\t\t\t\t\t\tif (e) {\n\t\t\t\t\t\t\t\treturn 'Assay ' + assayname + ': ' + config.type + ' track error: ' + e\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t\tcase client.tkt.junction:\n\t\t\t\t\t\t\ttk.categories = config.categories\n\t\t\t\t\t\t\ttk.readcountcutoff = config.readcountcutoff\n\t\t\t\t\t\t\tbreak\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\tdelete cohort.assays\n\n\t{\n\t\tconst err = cohort2genometkset(cohort)\n\t\tif (err) {\n\t\t\treturn 'Error: ' + err\n\t\t}\n\t}\n\n\t/*******************\n\t   metadata, not in use\n\t********************/\n\n\tif (cohort.patientannotation) {\n\t\tconst err = parse_patientannotation(cohort)\n\t\tif (err) return err\n\t}\n\n\tif (cohort.browserview) {\n\t\tconst err = parse_browserview(cohort)\n\t\tif (err) return err\n\t}\n\n\tif (cohort.e2pca) {\n\t\tif (!cohort.e2pca.list) return '.list missing from e2pca'\n\t\tif (!Array.isArray(cohort.e2pca.list)) return 'e2pca.list should be an array'\n\t\tif (cohort.e2pca.list.length == 0) return 'e2pca.list[] length 0'\n\t\tif (!cohort.e2pca.label) {\n\t\t\tcohort.e2pca.label = 'Expression - PCA'\n\t\t}\n\t\tfor (const obj of cohort.e2pca.list) {\n\t\t\tif (!obj.vectorfile) return 'vectorfile missing from e2pca'\n\t\t\tif (!obj.dbfile) return 'dbfile missing from e2pca'\n\t\t}\n\t}\n\treturn\n}\n\nexport function loadstudycohort(genomes, file, holder, hostURL, jwt, noshow, app) {\n\t/*\n\ttp entry point\n\tapp.js calls this to load a study json file from server\n\n\tnoshow will not call tpui, to load assay tracks only, to work with block view and make the tracks searchable there\n\t*/\n\n\tconst wait = holder.append('div').style('color', '#858585')\n\twait.text('Loading ' + file + ' ...')\n\treturn fetch(hostURL + '/study', {\n\t\tmethod: 'POST',\n\t\tbody: JSON.stringify({ file: file, jwt: jwt })\n\t})\n\t\t.then(res => res.json())\n\t\t.then(data => {\n\t\t\tif (!data) {\n\t\t\t\twait.text('Server error!')\n\t\t\t\treturn\n\t\t\t}\n\t\t\tif (data.error) {\n\t\t\t\twait.text('Error loading study: ' + data.error)\n\t\t\t\treturn\n\t\t\t}\n\t\t\tconst cohort = data.cohort\n\t\t\tif (!cohort) {\n\t\t\t\twait.text('.cohort missing')\n\t\t\t\treturn\n\t\t\t}\n\t\t\tif (!cohort.genome) {\n\t\t\t\twait.text('No genome specified in the cohort JSON content')\n\t\t\t\treturn\n\t\t\t}\n\t\t\tconst g = genomes[cohort.genome]\n\t\t\tif (!g) {\n\t\t\t\twait.text('Invalid genome from cohort: ' + cohort.genome)\n\t\t\t\treturn\n\t\t\t}\n\n\t\t\tcohort.genome = g\n\t\t\tcohort.jwt = jwt\n\n\t\t\tif (!data.flagset) {\n\t\t\t\twait.text('.flagset missing')\n\t\t\t\treturn\n\t\t\t}\n\t\t\twait.text('')\n\t\t\tcohort.dsset = {}\n\t\t\tfor (const k in data.flagset) {\n\t\t\t\tconst flag = data.flagset[k]\n\t\t\t\tflag.genome = g\n\t\t\t\tbulkin({\n\t\t\t\t\tflag: flag,\n\t\t\t\t\tfilename: file,\n\t\t\t\t\tcohort: cohort,\n\t\t\t\t\terr: m => client.sayerror(wait, m)\n\t\t\t\t})\n\t\t\t}\n\t\t\tconst err = tpinit(cohort)\n\t\t\tif (err) {\n\t\t\t\tclient.sayerror(wait, err)\n\t\t\t}\n\n\t\t\tif (!noshow) {\n\t\t\t\treturn import('./tp.ui').then(async p => {\n\t\t\t\t\tgetsjcharts().catch(console.error)\n\t\t\t\t\tp.default(cohort, holder, hostURL, app)\n\t\t\t\t\treturn app\n\t\t\t\t})\n\t\t\t}\n\t\t})\n}\n\nfunction tidy_qtk(tk, config) {\n\t// bedgraph or bigwig\n\tif (!config) {\n\t\tconfig = {}\n\t}\n\tif (!tk.file && !tk.url) {\n\t\treturn 'no file or url'\n\t}\n\tif (!tk.pcolor) {\n\t\ttk.pcolor = config.pcolor || '#0066CC'\n\t}\n\tif (!tk.pcolor2) {\n\t\ttk.pcolor2 = config.pcolor2 || '#CC0000'\n\t}\n\tif (!tk.ncolor) {\n\t\ttk.ncolor = config.ncolor || '#FF850A'\n\t}\n\tif (!tk.ncolor2) {\n\t\ttk.ncolor2 = config.ncolor2 || '#0A85FF'\n\t}\n\tif (!tk.height) 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assayname in cohort.browserview.assays) {\n\t\t\tconst assayview = cohort.browserview.assays[assayname]\n\t\t\tif (assayview.combined && assayview.combinetk) {\n\t\t\t\tlst.push(assayview.combinetk)\n\t\t\t}\n\t\t}\n\t}\n\tif (!cohort.genome.tkset) {\n\t\tcohort.genome.tkset = []\n\t}\n\tconst thisset = {\n\t\tname: cohort.name,\n\t\ttklst: lst\n\t}\n\n\tif (cohort.trackfacets) {\n\t\t/*\n\t\tlight validation\n\t\t*/\n\t\tif (!Array.isArray(cohort.trackfacets)) {\n\t\t\treturn '.trackfacets is not an array'\n\t\t}\n\t\tconst lst = []\n\t\tfor (const fc of cohort.trackfacets) {\n\t\t\tif (!fc.samples) {\n\t\t\t\treturn 'trackfacets: .samples missing from facet ' + fc.name\n\t\t\t}\n\t\t\tif (!Array.isArray(fc.samples)) {\n\t\t\t\treturn 'trackfacets: .samples is not array from facet ' + fc.name\n\t\t\t}\n\t\t\tif (!fc.assays) {\n\t\t\t\treturn 'trackfacets: .assays missing from a facet ' + fc.name\n\t\t\t}\n\t\t\tif (!Array.isArray(fc.assays)) {\n\t\t\t\treturn 'trackfacets: .assays is not array from a facet ' + fc.name\n\t\t\t}\n\t\t\tlst.push(fc)\n\t\t}\n\t\tif (lst.length) {\n\t\t\tthisset.facetlst = lst\n\t\t}\n\t}\n\n\tcohort.genome.tkset.push(thisset)\n\n\treturn null\n}\n\nfunction parse_browserview(cohort) {\n\tif (cohort.browserview.position) {\n\t\tlet pos\n\t\tif (typeof cohort.browserview.position == 'string') {\n\t\t\tpos = string2pos(cohort.browserview.position, cohort.genome)\n\t\t\tif (!pos) {\n\t\t\t\treturn '.browserview.position invalid value'\n\t\t\t}\n\t\t} else {\n\t\t\tpos = cohort.browserview.position\n\t\t}\n\t\tconst e = invalidcoord(cohort.genome, pos.chr, pos.start, pos.stop)\n\t\tif (e) {\n\t\t\treturn '.browserview.position error: ' + e\n\t\t}\n\t\tcohort.browserview.position = pos\n\t} else {\n\t\tcohort.browserview.position = {\n\t\t\tchr: cohort.genome.defaultcoord.chr,\n\t\t\tstart: cohort.genome.defaultcoord.start,\n\t\t\tstop: cohort.genome.defaultcoord.stop\n\t\t}\n\t}\n\tif (cohort.browserview.assays) {\n\t\tfor (const assayname in cohort.browserview.assays) {\n\t\t\tif (typeof cohort.browserview.assays[assayname] != 'object') {\n\t\t\t\tcohort.browserview.assays[assayname] = {}\n\t\t\t}\n\t\t\tconst assayview = cohort.browserview.assays[assayname]\n\t\t\tfor (const a of cohort.assaylst) {\n\t\t\t\tif (a.name == assayname) {\n\t\t\t\t\tassayview.assayobj = a\n\t\t\t\t\tbreak\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (!assayview.assayobj) {\n\t\t\t\t// abandon\n\t\t\t\tconsole.log('missing assayobj for assayview of ' + assayname)\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tif (assayview.sum_view) {\n\t\t\t\t// obsolete trigger name\n\t\t\t\tdelete assayview.sum_view\n\t\t\t\tassayview.combined = true\n\t\t\t}\n\t\t\tif (assayview.combined) {\n\t\t\t\t// this assay has a combined view\n\t\t\t\t// sum into one big tk\n\t\t\t\t// TODO do not support associated assay, e.g. bigwig for junction\n\t\t\t\tconst combinetk = {}\n\t\t\t\t// copy attr from assayobj\n\t\t\t\tfor (const k in assayview.assayobj) {\n\t\t\t\t\tcombinetk[k] = assayview.assayobj[k]\n\t\t\t\t}\n\t\t\t\t// for attr in assayview, override\n\t\t\t\tfor (const k in assayview) {\n\t\t\t\t\tif (k == 'assayobj') continue\n\t\t\t\t\tcombinetk[k] = assayview[k]\n\t\t\t\t}\n\t\t\t\tif (!combinetk.name) {\n\t\t\t\t\tcombinetk.name = assayname\n\t\t\t\t}\n\t\t\t\tcombinetk.tracks = []\n\t\t\t\tfor (const pn in cohort.p2st) {\n\t\t\t\t\tfor (const st in cohort.p2st[pn]) {\n\t\t\t\t\t\tfor (const t of cohort.p2st[pn][st].tktemplate) {\n\t\t\t\t\t\t\tif (t.id == assayview.assayobj.id) {\n\t\t\t\t\t\t\t\tt.patient = pn\n\t\t\t\t\t\t\t\tt.sampletype = st\n\t\t\t\t\t\t\t\tcombinetk.tracks.push(t)\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}\n\t\t\t\tif (combinetk.isvcf) {\n\t\t\t\t\t// gather vcf tracks into ds\n\t\t\t\t\tcombinetk.ds = {\n\t\t\t\t\t\tid2vcf: {},\n\t\t\t\t\t\tlabel: combinetk.name\n\t\t\t\t\t}\n\t\t\t\t\tfor (const t of combinetk.tracks) {\n\t\t\t\t\t\tfor (const i in t.ds.id2vcf) {\n\t\t\t\t\t\t\tt.__vcfobj = 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+  "names": ["parseheader", "flag", "i", "parseline", "parseheader", "flag", "parseline", "parseheader", "flag", "i", "parseline", "parseheader", "flag", "i", "parseline", "parseheader", "flag", "i", "parseline", "parseheader", "flag", "parseline", "text", "event", "reader", "flag", "event", "err", "parseheader", "parseline", "err", "flag", "lst"]
+}

package/dist/chunk-RZ5JP44H.js

@@ -0,0 +1,276 @@
+import {
+  parsesample
+} from "./chunk-TCPU43TU.js";
+import {
+  dtfusionrna,
+  dtsv,
+  mclassfusionrna,
+  mclasssv
+} from "./chunk-IGEQI6MR.js";
+
+// ../shared/utils/src/bulk.sv.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 (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 ? dtsv : dtfusionrna,
+      class: issv ? mclasssv : 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 ? dtsv : dtfusionrna,
+      class: issv ? mclasssv : 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 {
+  parseheader,
+  parseline,
+  duplicate
+};
+//# sourceMappingURL=chunk-RZ5JP44H.js.map