@sjcrh/proteinpaint-client 2.182.0 → 2.182.1

package/dist/chunk-IGEQI6MR.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../shared/utils/src/filter.js", "../../shared/utils/src/common.js"],
-  "sourcesContent": ["function getFilteredSamples(sampleAnno, filter) {\n\tsetDatasetAnnotations(filter)\n\tconst samples = /* @__PURE__ */ new Set()\n\tfor (const anno of sampleAnno) {\n\t\tif (samples.has(anno.sample)) continue\n\t\tconst data = anno.s || anno.data\n\t\tif (data && sample_match_termvaluesetting(data, filter)) {\n\t\t\tsamples.add(anno.sample)\n\t\t}\n\t}\n\treturn samples\n}\nfunction sample_match_termvaluesetting(row, filter, _term = null, sample = null) {\n\tconst lst = filter.type == 'tvslst' ? filter.lst : [filter]\n\tlet numberofmatchedterms = 0\n\tfor (const item of lst) {\n\t\tif ('type' in item && item.type == 'tvslst') {\n\t\t\tif (sample_match_termvaluesetting(row, item, _term, sample)) {\n\t\t\t\tnumberofmatchedterms++\n\t\t\t}\n\t\t} else {\n\t\t\tconst itemCopy = JSON.parse(JSON.stringify(item))\n\t\t\tconst t = itemCopy.tvs\n\t\t\tif (_term && t.term) {\n\t\t\t\tif (!(_term.name == t.term.name && _term.type == t.term.type)) {\n\t\t\t\t\tnumberofmatchedterms++\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t}\n\t\t\tlet samplevalue\n\t\t\tif (_term && !t.term) {\n\t\t\t\tif (t.term$type && t.term$type !== _term.type) {\n\t\t\t\t\tnumberofmatchedterms++\n\t\t\t\t\tcontinue\n\t\t\t\t}\n\t\t\t\tt.term = _term\n\t\t\t\tsamplevalue = typeof row === 'object' && t.term.id in row ? row[t.term.id] : row\n\t\t\t} else if (sample && t.term.$id) {\n\t\t\t\tsamplevalue = sample[t.term.$id].value\n\t\t\t} else {\n\t\t\t\tsamplevalue = t.term.id in row ? row[t.term.id] : row\n\t\t\t}\n\t\t\tsetDatasetAnnotations(itemCopy)\n\t\t\tlet thistermmatch\n\t\t\tif (t.term.type == 'categorical') {\n\t\t\t\tif (samplevalue === void 0) continue\n\t\t\t\tthistermmatch = t.valueset.has(samplevalue)\n\t\t\t} else if (t.term.type == 'integer' || t.term.type == 'float') {\n\t\t\t\tif (samplevalue === void 0) continue\n\t\t\t\tfor (const range of t.ranges) {\n\t\t\t\t\tif ('value' in range) {\n\t\t\t\t\t\tthistermmatch = samplevalue === range.value\n\t\t\t\t\t\tif (thistermmatch) break\n\t\t\t\t\t} else if (samplevalue == range.name) {\n\t\t\t\t\t\tthistermmatch = true\n\t\t\t\t\t\tbreak\n\t\t\t\t\t} else {\n\t\t\t\t\t\tif (t.term.values) {\n\t\t\t\t\t\t\tconst v = t.term.values[samplevalue.toString()]\n\t\t\t\t\t\t\tif (v && v.uncomputable) {\n\t\t\t\t\t\t\t\tcontinue\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tlet left, right\n\t\t\t\t\t\tif (range.startunbounded) {\n\t\t\t\t\t\t\tleft = true\n\t\t\t\t\t\t} else if ('start' in range) {\n\t\t\t\t\t\t\tif (range.startinclusive) {\n\t\t\t\t\t\t\t\tleft = samplevalue >= range.start\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tleft = samplevalue > range.start\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tif (range.stopunbounded) {\n\t\t\t\t\t\t\tright = true\n\t\t\t\t\t\t} else if ('stop' in range) {\n\t\t\t\t\t\t\tif (range.stopinclusive) {\n\t\t\t\t\t\t\t\tright = samplevalue <= range.stop\n\t\t\t\t\t\t\t} else {\n\t\t\t\t\t\t\t\tright = samplevalue < range.stop\n\t\t\t\t\t\t\t}\n\t\t\t\t\t\t}\n\t\t\t\t\t\tthistermmatch = left && right\n\t\t\t\t\t}\n\t\t\t\t\tif (thistermmatch) break\n\t\t\t\t}\n\t\t\t} else if (t.term.type == 'condition') {\n\t\t\t\tconst key = getPrecomputedKey(t)\n\t\t\t\tconst anno = samplevalue && samplevalue[key]\n\t\t\t\tif (anno) {\n\t\t\t\t\tthistermmatch = Array.isArray(anno)\n\t\t\t\t\t\t? t.values.find(d => anno.includes(d.key))\n\t\t\t\t\t\t: t.values.find(d => d.key == anno)\n\t\t\t\t}\n\t\t\t} else if (t.term.type == 'geneVariant') {\n\t\t\t\tconst svalues = samplevalue.values || [samplevalue]\n\t\t\t\tfor (const sv of svalues) {\n\t\t\t\t\tthistermmatch =\n\t\t\t\t\t\tt.values.find(\n\t\t\t\t\t\t\tv =>\n\t\t\t\t\t\t\t\tv.dt == sv.dt &&\n\t\t\t\t\t\t\t\t(!v.origin || sv.origin == v.origin) &&\n\t\t\t\t\t\t\t\t(!v.mclasslst || v.mclasslst.includes(sv.class))\n\t\t\t\t\t\t) && true\n\t\t\t\t\tif (thistermmatch) break\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tthrow 'unknown term type [sample_match_termvaluesetting() shared/utils/src/filter.ts]'\n\t\t\t}\n\t\t\tif (t.isnot) {\n\t\t\t\tthistermmatch = !thistermmatch\n\t\t\t}\n\t\t\tif (thistermmatch) numberofmatchedterms++\n\t\t}\n\t\tif (filter.join == 'or') {\n\t\t\tif (numberofmatchedterms && filter.in) return true\n\t\t\tif (!numberofmatchedterms && !filter.in) return true\n\t\t}\n\t}\n\tif (!('in' in filter)) filter.in = true\n\treturn filter.in == (numberofmatchedterms == lst.length)\n}\nfunction setDatasetAnnotations(item, ds = null) {\n\tif (item.type == 'tvslst') {\n\t\tfor (const subitem of item.lst) {\n\t\t\tsetDatasetAnnotations(subitem, ds)\n\t\t}\n\t} else {\n\t\tif (ds && typeof ds.setAnnoByTermId == 'function') {\n\t\t\tds.setAnnoByTermId(item.tvs.term.id)\n\t\t}\n\t\tif (item.tvs.term.type == 'categorical') {\n\t\t\tconst tvsAny = item.tvs\n\t\t\ttvsAny.valueset = new Set(tvsAny.values.map(i => i.key))\n\t\t}\n\t}\n}\nfunction getPrecomputedKey(q) {\n\tconst precomputedKey =\n\t\tq.bar_by_children && q.value_by_max_grade\n\t\t\t? 'childrenAtMaxGrade'\n\t\t\t: q.bar_by_children && q.value_by_most_recent\n\t\t\t? 'childrenAtMostRecent'\n\t\t\t: q.bar_by_children && q.value_by_computable_grade\n\t\t\t? 'children'\n\t\t\t: q.bar_by_grade && q.value_by_max_grade\n\t\t\t? 'maxGrade'\n\t\t\t: q.bar_by_grade && q.value_by_most_recent\n\t\t\t? 'mostRecentGrades'\n\t\t\t: q.bar_by_grade && q.value_by_computable_grade\n\t\t\t? 'computableGrades'\n\t\t\t: ''\n\tif (!precomputedKey) throw `unknown condition term bar_by_* and/or value_by_*`\n\treturn precomputedKey\n}\nfunction filterJoin(lst) {\n\tif (!lst || lst.length == 0) return\n\tlet f = JSON.parse(JSON.stringify(lst[0]))\n\tif (lst.length == 1) return f\n\tif (f.lst.length < 2) {\n\t\tif (f.join !== '') throw 'filter.join must be an empty string \"\" when filter.lst.length < 2'\n\t\tf.join = 'and'\n\t} else if (f.join == 'or') {\n\t\tf = {\n\t\t\ttype: 'tvslst',\n\t\t\tjoin: 'and',\n\t\t\tin: true,\n\t\t\tlst: [f]\n\t\t}\n\t} else if (f.join != 'and') {\n\t\tthrow 'filter.join must be either \"and\" or \"or\" when .lst length > 1'\n\t}\n\tfor (let i = 1; i < lst.length; i++) {\n\t\tconst f2 = JSON.parse(JSON.stringify(lst[i]))\n\t\tif (f2.join == 'or') f.lst.push(f2)\n\t\telse f.lst.push(...f2.lst)\n\t}\n\tif (f.lst.length == 1 && f.lst[0].type == 'tvs') {\n\t\tf.join = ''\n\t}\n\treturn f\n}\nfunction getWrappedTvslst(lst = [], join = '', $id = null) {\n\tconst filter = {\n\t\ttype: 'tvslst',\n\t\tin: true,\n\t\tjoin,\n\t\tlst\n\t}\n\tif ($id !== null) filter.$id = $id\n\treturn filter\n}\nfunction validateTermCollectionTvs(lst1, lst2) {\n\tif (!Array.isArray(lst1)) throw new Error('numerator not array')\n\tif (!Array.isArray(lst2)) throw new Error('denominator not array')\n\tif (lst1.length == 0) throw new Error('numerator empty')\n\tif (lst2.length == 0) throw new Error('denominator empty')\n\tif (lst1.length > lst2.length) throw new Error('numerator longer than denominator')\n\tfor (const s of lst1) {\n\t\tif (typeof s != 'string') throw new Error('one of numerator not string')\n\t\tif (!s) throw new Error('empty string in numerator')\n\t\tif (!lst2.includes(s)) throw new Error('one of numerator not in denominator')\n\t}\n}\nexport {\n\tfilterJoin,\n\tgetFilteredSamples,\n\tgetWrappedTvslst,\n\tsample_match_termvaluesetting,\n\tsetDatasetAnnotations,\n\tvalidateTermCollectionTvs\n}\n", "/*\nshared between client and server\n\nexported functions\n- bplen()\n- mclasstester()\n- basecompliment()\n\n\n*/\nimport { rgb } from 'd3-color'\nimport * as d3scale from 'd3-scale'\nimport * as d3 from 'd3'\nimport { getWrappedTvslst } from './filter.js'\n\n// moved from `#shared/terms` to here, so that this can be passed as\n// part of 'common' argument to exported dataset js function, at server runtime\n// 3/30/2026 - changed from literal object to a class with static properties\n// to make it easier for IDEs and tsc compiler to catch typos in consumer code\nexport class TermTypeGroups {\n\tstatic DICTIONARY_VARIABLES = 'Dictionary Variables'\n\tstatic DNA_METHYLATION = 'DNA Methylation'\n\tstatic GENE_DEPENDENCY = 'Gene Dependency'\n\tstatic GENE_EXPRESSION = 'Gene Expression'\n\tstatic ISOFORM_EXPRESSION = 'Isoform Expression'\n\tstatic GSEA = 'GSEA'\n\tstatic METABOLITE_INTENSITY = 'Metabolite Intensity'\n\tstatic PROTEOME_ABUNDANCE = 'Whole Proteome Abundance'\n\tstatic MUTATION_CNV_FUSION = 'Mutation/CNV/Fusion'\n\tstatic MUTATION_SIGNATURE = 'Mutation Signature'\n\tstatic PROTEIN_EXPRESSION = 'Protein Expression'\n\tstatic SINGLECELL_CELLTYPE = 'Single-cell Cell Type'\n\tstatic SINGLECELL_GENE_EXPRESSION = 'Single-cell Gene Expression'\n\tstatic SNP = 'SNP Genotype'\n\tstatic SNP_LIST = 'SNP List'\n\tstatic SNP_LOCUS = 'SNP Locus'\n\tstatic SPLICE_JUNCTION = 'Splice Junction'\n\tstatic SSGSEA = 'Geneset Expression'\n\tstatic TERM_COLLECTION = 'Term Collection'\n\tstatic VARIANT_GENOTYPE = 'Variant Genotype'\n}\n// freeze so that mutating any of the static properties above will throw at runtime\nObject.freeze(TermTypeGroups)\n\nexport const defaultcolor = rgb('#8AB1D4').darker()\nexport const default_text_color = rgb('#aaa').darker().darker()\n\nexport const exoncolor = '#4F8053'\nexport const plotColor = '#ce768e'\n\n// something that has something to do with coding gene reading frame\nexport const IN_frame = true\nexport const OUT_frame = false\n\n/********************************\n*        on dt usage            *\n*********************************\n- once a dt value is decided and used with actual dataset,\n  the value must not be altered, since dataset file may hardcode such value and reassigning to a new integer will break!\n- never test dt value by range e.g. if(dt>10), it breaks! only test equality!\n- in code import variable from here and DO NOT use literal values, to make code tractable\n*/\nexport const dtsnvindel = 1\nexport const dtfusionrna = 2\nexport const dtgeneexpression = 3\nexport const dtcnv = 4\nexport const dtsv = 5\nexport const dtitd = 6\nexport const dtdel = 7\nexport const dtnloss = 8\nexport const dtcloss = 9\nexport const dtloh = 10\nexport const dtmetaboliteintensity = 11\nexport const dtssgsea = 12\nexport const dtdnamethylation = 13\nexport const dtproteomeabundance = 14\n// add new dt value here. !!!DO NOT change value of existing dt!!!\n\nexport const dt2label = {\n\t[dtsnvindel]: 'SNV/indel',\n\t[dtfusionrna]: 'Fusion RNA',\n\t[dtcnv]: 'CNV',\n\t[dtsv]: 'SV',\n\t[dtitd]: 'ITD',\n\t[dtdel]: 'Deletion',\n\t[dtnloss]: 'N-loss',\n\t[dtcloss]: 'C-loss',\n\t[dtloh]: 'LOH',\n\t[dtgeneexpression]: 'Gene Expression',\n\t[dtmetaboliteintensity]: 'Metabolite Intensity',\n\t[dtproteomeabundance]: 'Whole Proteome Abundance'\n}\n\n// Maps dt types to UI labels and lesion types for GRIN2\n// All dt types use lesionTypes array for consistency\nexport const dt2lesion = {\n\t[dtsnvindel]: {\n\t\tuilabel: 'SNV/INDEL (Mutation)',\n\t\tlesionTypes: [{ name: 'Mutation', lesionType: 'mutation', color: '#44AA44' }]\n\t},\n\t[dtcnv]: {\n\t\tuilabel: 'CNV (Copy Number Variation)',\n\t\tlesionTypes: [\n\t\t\t{ name: 'Loss', lesionType: 'loss', color: '#4444FF' },\n\t\t\t{ name: 'Gain', lesionType: 'gain', color: '#FF4444' }\n\t\t]\n\t},\n\t[dtsv]: {\n\t\tuilabel: 'SV (Structural Variation)',\n\t\tlesionTypes: [{ name: 'SV', lesionType: 'sv', color: '#9932CC' }]\n\t},\n\t[dtfusionrna]: {\n\t\tuilabel: 'Fusion (RNA Fusion)',\n\t\tlesionTypes: [{ name: 'Fusion', lesionType: 'fusion', color: '#FFA500' }]\n\t}\n}\n\n// Maps GRIN2 option types to their corresponding dt values\nexport const optionToDt = {\n\tsnvindelOptions: dtsnvindel,\n\tcnvOptions: dtcnv,\n\tfusionOptions: dtfusionrna,\n\tsvOptions: dtsv\n}\n\nexport const mclass = {\n\tM: {\n\t\tlabel: 'MISSENSE',\n\t\tcolor: '#3987CC',\n\t\tdt: dtsnvindel,\n\t\tdesc: 'A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved',\n\t\tkey: 'M'\n\t},\n\tE: { label: 'EXON', color: '#bcbd22', dt: dtsnvindel, desc: 'A variant in the exon of a non-coding RNA.', key: 'E' },\n\tF: {\n\t\tlabel: 'FRAMESHIFT',\n\t\tcolor: 'rgb(200, 61, 61)',\n\t\tdt: dtsnvindel,\n\t\tdesc: 'A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three',\n\t\tkey: 'F'\n\t},\n\tN: {\n\t\tlabel: 'NONSENSE',\n\t\tcolor: '#ff7f0e',\n\t\tdt: dtsnvindel,\n\t\tdesc: 'A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript',\n\t\tkey: 'N'\n\t},\n\tS: {\n\t\tlabel: 'SILENT',\n\t\tcolor: '#2ca02c',\n\t\tdt: dtsnvindel,\n\t\tdesc: 'A sequence variant where there is no resulting change to the encoded amino acid',\n\t\tkey: 'S'\n\t},\n\tD: {\n\t\tlabel: 'PROTEINDEL',\n\t\tcolor: 'rgb(100, 100, 100)',\n\t\tdt: dtsnvindel,\n\t\tdesc: 'An inframe non synonymous variant that deletes bases from the coding sequence',\n\t\tkey: 'D'\n\t},\n\tI: {\n\t\tlabel: 'PROTEININS',\n\t\tcolor: '#8c564b',\n\t\tdt: dtsnvindel,\n\t\tdesc: 'An inframe non synonymous variant that inserts bases into in the coding sequence',\n\t\tkey: 'I'\n\t},\n\tProteinAltering: {\n\t\tlabel: 'PROTEINALTERING',\n\t\tcolor: '#5a0034',\n\t\tdt: dtsnvindel,\n\t\tdesc: 'An inframe complex change to the coding sequence',\n\t\tkey: 'ProteinAltering'\n\t},\n\tP: {\n\t\tlabel: 'SPLICE_REGION',\n\t\tcolor: '#9467bd',\n\t\tdt: dtsnvindel,\n\t\tdesc: 'A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron',\n\t\tkey: 'P'\n\t},\n\tL: {\n\t\tlabel: 'SPLICE',\n\t\tcolor: '#6633FF',\n\t\tdt: dtsnvindel,\n\t\tdesc: 'A variant near an exon edge that may affect splicing functionality',\n\t\tkey: 'L'\n\t},\n\tIntron: { label: 'INTRON', color: '#656565', dt: dtsnvindel, desc: 'An intronic variant.', key: 'Intron' },\n\n\tStopLost: {\n\t\tlabel: 'Stop lost',\n\t\tcolor: '#ff7f0e',\n\t\tdt: dtsnvindel,\n\t\tdesc: 'A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript',\n\t\tkey: 'StopLost'\n\t},\n\tStartLost: {\n\t\tlabel: 'Start lost',\n\t\tcolor: '#ff7f0e',\n\t\tdt: dtsnvindel,\n\t\tdesc: 'A codon variant that changes at least one base of the canonical start codon',\n\t\tkey: 'StartLost'\n\t},\n\n\t// quick fix!! for showing genes that are not tested in samples (e.g. gene panels) in the heatmap\n\tBlank: { label: 'Not tested', color: '#fff', dt: dtsnvindel, desc: 'This gene is not tested.', key: 'Blank' },\n\n\tWT: { label: 'Wildtype', color: '#D3D3D3', dt: dtsnvindel, desc: 'Wildtype', key: 'WT' }\n}\nexport const mclassitd = 'ITD'\nmclass[mclassitd] = {\n\tlabel: 'ITD',\n\tcolor: '#ff70ff',\n\tdt: dtitd,\n\tdesc: 'In-frame internal tandem duplication.',\n\tkey: mclassitd\n}\n\nexport const mclassdel = 'DEL'\nmclass[mclassdel] = {\n\tlabel: 'DELETION, intragenic',\n\tcolor: '#858585',\n\tdt: dtdel,\n\tdesc: 'Intragenic deletion.',\n\tkey: mclassdel\n}\n\nexport const mclassnloss = 'NLOSS'\nmclass[mclassnloss] = {\n\tlabel: 'N-terminus loss',\n\tcolor: '#545454',\n\tdt: dtnloss,\n\tdesc: 'N-terminus loss due to translocation',\n\tkey: mclassnloss\n}\n\nexport const mclasscloss = 'CLOSS'\nmclass[mclasscloss] = {\n\tlabel: 'C-terminus loss',\n\tcolor: '#545454',\n\tdt: dtcloss,\n\tdesc: 'C-terminus loss due to translocation',\n\tkey: mclasscloss\n}\n\nexport const mclassutr3 = 'Utr3'\nmclass[mclassutr3] = {\n\tlabel: 'UTR_3',\n\tcolor: '#998199',\n\tdt: dtsnvindel,\n\tdesc: \"A variant in the 3' untranslated region.\",\n\tkey: mclassutr3\n}\n\nexport const mclassutr5 = 'Utr5'\nmclass[mclassutr5] = {\n\tlabel: 'UTR_5',\n\tcolor: '#819981',\n\tdt: dtsnvindel,\n\tdesc: \"A variant in the 5' untranslated region.\",\n\tkey: mclassutr5\n}\n\nexport const mclassnonstandard = 'X'\nmclass[mclassnonstandard] = {\n\tlabel: 'NONSTANDARD',\n\tcolor: 'black',\n\tdt: dtsnvindel,\n\tdesc: 'A mutation class that either does not match our notation, or is unspecified.',\n\tkey: mclassnonstandard\n}\n\nexport const mclassnoncoding = 'noncoding'\nmclass[mclassnoncoding] = {\n\tlabel: 'NONCODING',\n\tcolor: 'black',\n\tdt: dtsnvindel,\n\tdesc: 'Noncoding mutation.',\n\tkey: mclassnoncoding\n}\n\n/*\nincludes full list of consequences from\nhttps://www.ensembl.org/info/genome/variation/prediction/predicted_data.html\neach entry is SO term with matching pp class\nentries that cannot be mapped to dtsnvindel classes are commented off\norder of entries is severity\n\n* since source of data! *\nfrom this array derives multiple types of lookup tables to perform mapping on both ways\n*/\nconst SOterms = [\n\t//transcript_ablation // not supported: 1) do not expect this in maf/vcf 2) should be represented as cnv deletion but not the legacy unused value \"dtdel\"; if needed can reenable\n\t['splice_acceptor_variant', 'L'],\n\t['splice_donor_variant', 'L'],\n\t['stop_gained', 'N'],\n\t['frameshift_variant', 'F'],\n\t['stop_lost', 'StopLost'],\n\t['start_lost', 'StartLost'],\n\t//transcript_amplification // not supported, should be represented by cnv instead\n\t['feature_elongation', mclassnoncoding],\n\t['feature_truncation', mclassnoncoding],\n\t['inframe_insertion', 'I'],\n\t['inframe_deletion', 'D'],\n\t['missense_variant', 'M'],\n\t['protein_altering_variant', 'ProteinAltering'],\n\t['splice_donor_5th_base_variant', 'P'],\n\t['splice_region_variant', 'P'],\n\t['splice_donor_region_variant', 'P'],\n\t['splice_polypyrimidine_tract_variant', 'P'],\n\t['incomplete_terminal_codon_variant', 'N'],\n\t['start_retained_variant', 'S'],\n\t['stop_retained_variant', 'S'],\n\t['synonymous_variant', 'S'],\n\t['coding_sequence_variant', 'E'],\n\t['mature_miRNA_variant', 'E'],\n\t['5_prime_UTR_variant', mclassutr5],\n\t['3_prime_UTR_variant', mclassutr3],\n\t['non_coding_transcript_exon_variant', 'E'],\n\t['intron_variant', 'Intron'],\n\t['NMD_transcript_variant', 'F'],\n\t['non_coding_transcript_variant', 'E'],\n\t['coding_transcript_variant', 'E'],\n\t['upstream_gene_variant', mclassnoncoding],\n\t['downstream_gene_variant', mclassnoncoding],\n\t['TFBS_ablation', mclassnoncoding],\n\t['TFBS_amplification', mclassnoncoding],\n\t['TF_binding_site_variant', mclassnoncoding],\n\t['regulatory_region_ablation', mclassnoncoding],\n\t['regulatory_region_amplification', mclassnoncoding],\n\t['regulatory_region_variant', mclassnoncoding],\n\t['intergenic_variant', mclassnoncoding],\n\t['sequence_variant', mclassnonstandard]\n]\n\n// maps a pp class to an array of consequences\n// k: pp class, v: array of consequences. case sensitive\nexport const class2SOterm = new Map()\nfor (const [csq, cls] of SOterms) {\n\tif (!class2SOterm.has(cls)) class2SOterm.set(cls, [])\n\tclass2SOterm.get(cls).push(csq)\n}\n\n// maps a consequence to a pp class. no severity info. use vepinfo() if needs severity\n// k: consequence, v: pp class. case sensitive.\nexport const SOterm2class = new Map()\nfor (const [csq, cls] of SOterms) {\n\tSOterm2class.set(csq, cls)\n}\n\n// outdated function to match with adhoc nonstandard notations, only used in legacy code utils/src/bulk.snv.js\n// DO NOT USE to map vep consequences\nexport function mclasstester(s) {\n\tswitch (s.toLowerCase()) {\n\t\tcase 'missense_mutation':\n\t\t\treturn 'M'\n\t\tcase 'nonsense_mutation':\n\t\t\treturn 'N'\n\t\tcase 'splice_site':\n\t\t\treturn 'L'\n\t\tcase 'splice_region':\n\t\t\treturn 'P'\n\t\tcase 'rna':\n\t\t\treturn mclassnoncoding\n\t\tcase 'frame_shift_del':\n\t\t\treturn 'F'\n\t\tcase 'frame_shift_ins':\n\t\t\treturn 'F'\n\t\tcase 'in_frame_del':\n\t\t\treturn 'D'\n\t\tcase 'in_frame_ins':\n\t\t\treturn 'I'\n\t\tcase 'protein_altering_variant':\n\t\t\treturn 'ProteinAltering'\n\t\tcase 'translation_start_site':\n\t\t\treturn mclassnonstandard\n\t\tcase 'nonstop_mutation':\n\t\t\treturn 'N'\n\t\tcase \"3'utr\":\n\t\t\treturn mclassutr3\n\t\tcase \"3'flank\":\n\t\t\treturn mclassnoncoding\n\t\tcase \"5'utr\":\n\t\t\treturn mclassutr5\n\t\tcase \"5'flank\":\n\t\t\treturn mclassnoncoding\n\t\tcase 'silent':\n\t\t\treturn 'S'\n\t\tcase 'blank':\n\t\t\treturn 'Blank'\n\t\tdefault:\n\t\t\treturn null\n\t}\n}\n\nexport const mclassfusionrna = 'Fuserna'\nmclass[mclassfusionrna] = {\n\tlabel: 'Fusion transcript',\n\tcolor: '#545454',\n\tdt: dtfusionrna,\n\tdesc:\n\t\t'Marks the break points leading to fusion transcripts.<br>' +\n\t\t'<span style=\"font-size:150%\">&#9680;</span> - 3\\' end of the break point is fused to the 5\\' end of another break point in a different gene.<br>' +\n\t\t'<span style=\"font-size:150%\">&#9681;</span> - 5\\' end of the break point is fused to the 3\\' end of another break point in a different gene.',\n\tkey: mclassfusionrna\n}\nexport const mclasssv = 'SV'\nmclass[mclasssv] = {\n\tlabel: 'Structural variation',\n\tcolor: '#858585',\n\tdt: dtsv,\n\tdesc:\n\t\t'<span style=\"font-size:150%\">&#9680;</span> - 3\\' end of the break point is fused to the 5\\' end of another break point in a different gene.<br>' +\n\t\t'<span style=\"font-size:150%\">&#9681;</span> - 5\\' end of the break point is fused to the 3\\' end of another break point in a different gene.',\n\tkey: mclasssv\n}\n\n// \"CNV_amp\" represents \"CNV Gain\" and is used in both 2-category and 5-category CNV data representation\n// \"CNV_amplification\" represents CNV amplification and is used in 5-category CNV\n// \"CNV_amp\" have to stay as-is since it may be hardcoded in lots of data beyond portal code.\nexport const mclasscnvgain = 'CNV_amp'\nmclass[mclasscnvgain] = {\n\tlabel: 'Copy number gain', // TODO change to 'Gain'\n\tcolor: '#e9a3c9',\n\tdt: dtcnv,\n\tdesc: 'Copy number gain',\n\tkey: mclasscnvgain\n}\n\nexport const mclasscnvloss = 'CNV_loss'\nmclass[mclasscnvloss] = {\n\tlabel: 'Copy number loss',\n\tcolor: '#a1d76a',\n\tdt: dtcnv,\n\tdesc: 'Copy number loss',\n\tkey: mclasscnvloss\n}\n\n// mclasscnvAmp is next level above mclasscnvgain and is used in 5-category CNV data\nexport const mclasscnvAmp = 'CNV_amplification'\nmclass[mclasscnvAmp] = {\n\tlabel: 'Copy number amplification',\n\tcolor: '#ff0000',\n\tdt: dtcnv,\n\tdesc: 'Copy number amplification',\n\tkey: mclasscnvAmp\n}\n\nexport const mclasscnvHomozygousDel = 'CNV_homozygous_deletion'\nmclass[mclasscnvHomozygousDel] = {\n\tlabel: 'Copy number homozygous deletion',\n\tcolor: '#0000ff',\n\tdt: dtcnv,\n\tdesc: 'Copy number homozygous deletion',\n\tkey: mclasscnvHomozygousDel\n}\n\nexport const mclasscnvloh = 'CNV_loh'\nmclass[mclasscnvloh] = { label: 'LOH', color: '#12EDFC', dt: dtcnv, desc: 'Loss of heterozygosity', key: mclasscnvloh }\n\n// for VCF\nexport const mclasssnv = 'snv'\nmclass[mclasssnv] = {\n\tlabel: 'SNV',\n\tcolor: '#92a2d4',\n\tdt: dtsnvindel,\n\tdesc: 'Single nucleotide variation',\n\tkey: mclasssnv\n}\n\nexport const mclassmnv = 'mnv'\nmclass[mclassmnv] = {\n\tlabel: 'MNV',\n\tcolor: '#92a2d4',\n\tdt: dtsnvindel,\n\tdesc: 'Multiple nucleotide variation',\n\tkey: mclassmnv\n}\n\nexport const mclassinsertion = 'insertion'\nmclass[mclassinsertion] = {\n\tlabel: 'Sequence insertion',\n\tcolor: '#bd8e91',\n\tdt: dtsnvindel,\n\tdesc: 'Sequence insertion',\n\tkey: mclassinsertion\n}\n\nexport const mclassdeletion = 'deletion'\nmclass[mclassdeletion] = {\n\tlabel: 'Sequence deletion',\n\tcolor: '#b5a174',\n\tdt: dtsnvindel,\n\tdesc: 'Sequence deletion',\n\tkey: mclassdeletion\n}\n// TODO complex indel\n\n/* tricky\nwhen a mds3 tk uses numeric cnv, data points from tk.cnv.cnvLst[] has .class=dtcnv but no class!\na \"cnv\" entry needs to be present in mclass legend, and thus this wrapper function over mclass{} to allow dtcnv as key\nthe tricky case doesn't apply to other plots\n*/\nexport function mds3tkMclass(k) {\n\tif (k == dtcnv) {\n\t\treturn {\n\t\t\tcolor: '#858585',\n\t\t\tlabel: 'CNV',\n\t\t\tdesc: 'Copy number variation'\n\t\t}\n\t}\n\treturn mclass[k]\n}\n\nexport const dt2color = {\n\t[dtsnvindel]: mclass.M.color // general color for snvindel irrespective of class (when class is not available)\n\t// add new dt as needed\n}\n\n// option to override mutation class attribute values\nexport function applyOverrides(overrides = {}) {\n\tif (overrides.mclass) {\n\t\tfor (const key in overrides.mclass) {\n\t\t\t// allow to fill-in mutation class that are missing from mclass;\n\t\t\t// may be useful for things like 'Not tested', etc, that may not be in mclass by default\n\t\t\t// but are used by a customer with its own PP server instance\n\t\t\tif (!mclass[key]) mclass[key] = {}\n\t\t\tfor (const subkey in overrides.mclass[key]) {\n\t\t\t\tmclass[key][subkey] = overrides.mclass[key][subkey]\n\t\t\t}\n\t\t}\n\t}\n}\n\n/* legacy function. input is comma-joined multiple consequences\nperforms case insensitive match and returns severity rank\nTODO share data with SOterms\n*/\nexport const vepinfo = function (s) {\n\tconst l = s.toLowerCase().split(',')\n\tlet rank = 1\n\tif (l.indexOf('transcript_ablation') != -1) {\n\t\t// FIXME no class for whole gene deletion\n\t\treturn [dtdel, mclassdel, rank]\n\t}\n\trank++\n\tif (l.indexOf('splice_acceptor_variant') != -1) return [dtsnvindel, 'L', rank]\n\trank++\n\tif (l.indexOf('splice_donor_variant') != -1) return [dtsnvindel, 'L', rank]\n\trank++\n\tif (l.indexOf('stop_gained') != -1) return [dtsnvindel, 'N', rank]\n\trank++\n\tif (l.indexOf('frameshift_variant') != -1) return [dtsnvindel, 'F', rank]\n\trank++\n\tif (l.indexOf('stop_lost') != -1) return [dtsnvindel, 'N', rank]\n\trank++\n\tif (l.indexOf('start_lost') != -1) return [dtsnvindel, 'N', rank]\n\trank++\n\tif (l.indexOf('transcript_amplification') != -1) {\n\t\t// FIXME no class for whole gene amp\n\t\treturn [dtsnvindel, mclassnonstandard, rank]\n\t}\n\trank++\n\tif (\n\t\tl.indexOf('inframe_insertion') != -1 ||\n\t\tl.indexOf('conservative_inframe_insertion') != -1 ||\n\t\tl.indexOf('disruptive_inframe_insertion') != -1\n\t)\n\t\treturn [dtsnvindel, 'I', rank]\n\trank++\n\tif (\n\t\tl.indexOf('inframe_deletion') != -1 ||\n\t\tl.indexOf('conservative_inframe_deletion') != -1 ||\n\t\tl.indexOf('disruptive_inframe_deletion') != -1\n\t)\n\t\treturn [dtsnvindel, 'D', rank]\n\trank++\n\tif (l.indexOf('missense_variant') != -1) return [dtsnvindel, 'M', rank]\n\trank++\n\tif (l.indexOf('protein_altering_variant') != -1) return [dtsnvindel, 'ProteinAltering', rank]\n\trank++\n\tif (l.indexOf('splice_region_variant') != -1) return [dtsnvindel, 'P', rank]\n\trank++\n\tif (l.indexOf('incomplete_terminal_codon_variant') != -1) return [dtsnvindel, 'N', rank]\n\trank++\n\tif (l.indexOf('stop_retained_variant') != -1) return [dtsnvindel, 'S', rank]\n\trank++\n\tif (l.indexOf('synonymous_variant') != -1) return [dtsnvindel, 'S', rank]\n\trank++\n\tif (l.indexOf('coding_sequence_variant') != -1) return [dtsnvindel, mclassnonstandard, rank]\n\trank++\n\tif (l.indexOf('mature_mirna_variant') != -1) return [dtsnvindel, 'E', rank]\n\trank++\n\tif (l.indexOf('5_prime_utr_variant') != -1) return [dtsnvindel, mclassutr5, rank]\n\trank++\n\tif (l.indexOf('3_prime_utr_variant') != -1) return [dtsnvindel, mclassutr3, rank]\n\trank++\n\tif (l.indexOf('non_coding_transcript_exon_variant') != -1) return [dtsnvindel, 'E', rank]\n\trank++\n\tif (l.indexOf('intron_variant') != -1) return [dtsnvindel, 'Intron', rank]\n\trank++\n\tif (l.indexOf('nmd_transcript_variant') != -1) return [dtsnvindel, 'S', rank]\n\trank++\n\tif (l.indexOf('non_coding_transcript_variant') != -1) return [dtsnvindel, 'E', rank]\n\trank++\n\tif (l.indexOf('upstream_gene_variant') != -1) return [dtsnvindel, mclassnoncoding, rank]\n\trank++\n\tif (l.indexOf('downstream_gene_variant') != -1) return [dtsnvindel, mclassnoncoding, rank]\n\trank++\n\tif (l.indexOf('tfbs_ablation') != -1) return [dtsnvindel, mclassnoncoding, rank]\n\trank++\n\tif (l.indexOf('tfbs_amplification') != -1) return [dtsnvindel, mclassnoncoding, rank]\n\trank++\n\tif (l.indexOf('tf_binding_site_variant') != -1) return [dtsnvindel, mclassnoncoding, rank]\n\trank++\n\tif (l.indexOf('regulatory_region_ablation') != -1) return [dtsnvindel, mclassnoncoding, rank]\n\trank++\n\tif (l.indexOf('regulatory_region_amplification') != -1) return [dtsnvindel, mclassnoncoding, rank]\n\trank++\n\tif (l.indexOf('feature_elongation') != -1) return [dtsnvindel, mclassnoncoding, rank]\n\trank++\n\tif (l.indexOf('regulatory_region_variant') != -1) return [dtsnvindel, mclassnoncoding, rank]\n\trank++\n\tif (l.indexOf('feature_truncation') != -1) return [dtsnvindel, mclassnoncoding, rank]\n\trank++\n\tif (l.indexOf('intergenic_variant') != -1) return [dtsnvindel, mclassnoncoding, rank]\n\trank++\n\treturn [dtsnvindel, mclassnonstandard, rank]\n}\n\n// m orgin\nexport const germlinelegend =\n\t'<circle cx=\"7\" cy=\"12\" r=\"7\" fill=\"#b1b1b1\"></circle><path d=\"M6.735557395310443e-16,-11A11,11 0 0,1 11,0L9,0A9,9 0 0,0 5.51091059616309e-16,-9Z\" transform=\"translate(7,12)\" fill=\"#858585\" stroke=\"none\"></path>'\n\nexport const morigin = {}\n\nexport const moriginsomatic = 'S'\nmorigin[moriginsomatic] = {\n\tlabel: 'Somatic',\n\tdesc: 'A variant found only in a tumor sample. The proportion is indicated by lack of any arc.',\n\tlegend: '<circle cx=\"7\" cy=\"12\" r=\"7\" fill=\"#b1b1b1\"></circle>'\n}\nexport const morigingermline = 'G'\nmorigin[morigingermline] = {\n\tlabel: 'Germline',\n\tdesc: 'A constitutional variant found in a normal sample. The proportion is indicated by the span of the solid arc within the whole circle.',\n\tlegend: germlinelegend\n}\n\nmorigin.germline = morigin[morigingermline]\nmorigin.somatic = morigin[moriginsomatic]\n\nexport const moriginrelapse = 'R'\nmorigin[moriginrelapse] = {\n\tlabel: 'Relapse',\n\tdesc: 'A somatic variant found only in a relapse sample. The proportion is indicated by the span of the hollow arc within the whole circle.',\n\tlegend:\n\t\t'<circle cx=\"7\" cy=\"12\" r=\"7\" fill=\"#b1b1b1\"></circle><path d=\"M6.735557395310443e-16,-11A11,11 0 0,1 11,0L9,0A9,9 0 0,0 5.51091059616309e-16,-9Z\" transform=\"translate(7,12)\" fill=\"none\" stroke=\"#858585\"></path>'\n}\nexport const morigingermlinepathogenic = 'GP'\nmorigin[morigingermlinepathogenic] = {\n\tlabel: 'Germline pathogenic',\n\tdesc: 'A constitutional variant with pathogenic allele.',\n\tlegend: germlinelegend\n}\nexport const morigingermlinenonpathogenic = 'GNP'\nmorigin[morigingermlinenonpathogenic] = {\n\tlabel: 'Germline non-pathogenic',\n\tdesc: 'A constitutional variant with non-pathogenic allele.',\n\tlegend: germlinelegend,\n\thidden: true\n}\n\nexport const tkt = {\n\tusegm: 'usegm',\n\tds: 'dataset',\n\tbigwig: 'bigwig',\n\tbigwigstranded: 'bigwigstranded',\n\tjunction: 'junction',\n\tmdsjunction: 'mdsjunction',\n\tmdssvcnv: 'mdssvcnv', // replaced by mds3\n\tmdsexpressionrank: 'mdsexpressionrank',\n\tmdsvcf: 'mdsvcf', // for snv/indels, currently vcf, may include MAF\n\t//mdsgeneral:'mdsgeneral', // replaces mdssvcnv   ****** not ready yet\n\tbedj: 'bedj',\n\tpgv: 'profilegenevalue',\n\tbampile: 'bampile',\n\thicstraw: 'hicstraw',\n\texpressionrank: 'expressionrank',\n\taicheck: 'aicheck',\n\tase: 'ase',\n\tmds3: 'mds3', //\n\tbedgraphdot: 'bedgraphdot',\n\tbam: 'bam',\n\tld: 'ld'\n}\n\nexport function validtkt(what) {\n\tfor (const k in tkt) {\n\t\tif (what == tkt[k]) {\n\t\t\treturn true\n\t\t}\n\t}\n\treturn false\n}\n\n/*\nmember track types from mdsvcf\nto get rid of hardcoded strings\nin future may include MAF format files\n*/\nexport const mdsvcftype = {\n\tvcf: 'vcf'\n}\n\n/*\nfor custom mdssvcnv track\nor general track\nto avoid using hard-coded string\n*/\nexport const custommdstktype = {\n\tvcf: 'vcf',\n\tsvcnvitd: 'svcnvitd',\n\tgeneexpression: 'geneexpression'\n}\n\n// codons that are not here are stop codon!!\nexport const codon = {\n\tGCT: 'A',\n\tGCC: 'A',\n\tGCA: 'A',\n\tGCG: 'A',\n\tCGT: 'R',\n\tCGC: 'R',\n\tCGA: 'R',\n\tCGG: 'R',\n\tAGA: 'R',\n\tAGG: 'R',\n\tAAT: 'N',\n\tAAC: 'N',\n\tGAT: 'D',\n\tGAC: 'D',\n\tTGT: 'C',\n\tTGC: 'C',\n\tCAA: 'Q',\n\tCAG: 'Q',\n\tGAA: 'E',\n\tGAG: 'E',\n\tGGT: 'G',\n\tGGC: 'G',\n\tGGA: 'G',\n\tGGG: 'G',\n\tCAT: 'H',\n\tCAC: 'H',\n\tATT: 'I',\n\tATC: 'I',\n\tATA: 'I',\n\tTTA: 'L',\n\tTTG: 'L',\n\tCTT: 'L',\n\tCTC: 'L',\n\tCTA: 'L',\n\tCTG: 'L',\n\tAAA: 'K',\n\tAAG: 'K',\n\tATG: 'M',\n\tTTT: 'F',\n\tTTC: 'F',\n\tCCT: 'P',\n\tCCC: 'P',\n\tCCA: 'P',\n\tCCG: 'P',\n\tTCT: 'S',\n\tTCC: 'S',\n\tTCA: 'S',\n\tTCG: 'S',\n\tAGT: 'S',\n\tAGC: 'S',\n\tACT: 'T',\n\tACC: 'T',\n\tACA: 'T',\n\tACG: 'T',\n\tTGG: 'W',\n\tTAT: 'Y',\n\tTAC: 'Y',\n\tGTT: 'V',\n\tGTC: 'V',\n\tGTA: 'V',\n\tGTG: 'V'\n}\n\nexport const codon_stop = '*'\n\nexport function nt2aa(gm) {\n\t// must convert genome seq to upper case!!!\n\tif (!gm.genomicseq) return undefined\n\tconst enlst = []\n\tif (gm.coding) {\n\t\tfor (const [i, e] of gm.coding.entries()) {\n\t\t\tconst s = gm.genomicseq.substr(e[0] - gm.start, e[1] - e[0])\n\t\t\tif (gm.strand == '-') {\n\t\t\t\tenlst.push(reversecompliment(s))\n\t\t\t} else {\n\t\t\t\tenlst.push(s)\n\t\t\t}\n\t\t}\n\t}\n\tconst nt = enlst.join('')\n\tconst pep = []\n\n\t/*\n\tif startCodonFrame is set, will not begin translation from first nt, but will skip 1 or 2 nt at the beginning\n\tin case of IGKC, frame=1 means it will borrow 1 nt from the previous IGKJ exons\n\tso the first two nucleotides from the current exon will have to be skipped when translating IGKC alone\n\t*/\n\tconst startntidx = gm.startCodonFrame ? 3 - gm.startCodonFrame : 0\n\tfor (let i = startntidx; i < nt.length; i += 3) {\n\t\tconst a = codon[nt.substr(i, 3)]\n\t\tpep.push(a || codon_stop)\n\t}\n\tgm.cdseq = nt\n\treturn pep.join('')\n}\n\nexport function bplen(len, isfile) {\n\t// if \"isfile\" is true, to measure file size instead of basepair len\n\tif (len >= 1000000000) return (len / 1000000000).toFixed(1) + ' Gb'\n\tif (len >= 10000000) return Math.ceil(len / 1000000) + ' Mb'\n\tif (len >= 1000000) return (len / 1000000).toFixed(1) + ' Mb'\n\tif (len >= 10000) return Math.ceil(len / 1000) + ' Kb'\n\tif (len >= 1000) return (len / 1000).toFixed(1) + ' Kb'\n\treturn len + (isfile ? 'bytes' : ' bp')\n}\n\nexport const basecolor = {\n\tA: '#ca0020',\n\tT: '#f4a582',\n\tC: '#92c5de',\n\tG: '#0571b0'\n}\n\nexport function basecompliment(nt) {\n\tswitch (nt) {\n\t\tcase 'A':\n\t\t\treturn 'T'\n\t\tcase 'T':\n\t\t\treturn 'A'\n\t\tcase 'C':\n\t\t\treturn 'G'\n\t\tcase 'G':\n\t\t\treturn 'C'\n\t\tcase 'a':\n\t\t\treturn 't'\n\t\tcase 't':\n\t\t\treturn 'a'\n\t\tcase 'c':\n\t\t\treturn 'g'\n\t\tcase 'g':\n\t\t\treturn 'c'\n\t\tdefault:\n\t\t\treturn nt\n\t}\n}\n\nexport function reversecompliment(s) {\n\tconst tmp = []\n\tfor (let i = s.length - 1; i >= 0; i--) {\n\t\ttmp.push(basecompliment(s[i]))\n\t}\n\treturn tmp.join('')\n}\n\nexport function spliceeventchangegmexon(gm, evt) {\n\t/*\n\talter gm.coding[], by exon-skip/alt events\n\tfor frame checking\n\tgm must have coding\n\t*/\n\tconst gm2 = {\n\t\tchr: gm.chr,\n\t\tstart: gm.start,\n\t\tstop: gm.stop,\n\t\tstrand: gm.strand,\n\t\tcoding: []\n\t}\n\tif (evt.isskipexon || evt.isaltexon) {\n\t\tfor (let i = 0; i < gm.exon.length; i++) {\n\t\t\tconst codingstart = Math.max(gm.codingstart, gm.exon[i][0])\n\t\t\tconst codingstop = Math.min(gm.codingstop, gm.exon[i][1])\n\t\t\tif (codingstart > codingstop) {\n\t\t\t\t// not coding exon\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tif (evt.skippedexon.indexOf(i) == -1) {\n\t\t\t\t// not skipped\n\t\t\t\tgm2.coding.push([codingstart, codingstop])\n\t\t\t} else {\n\t\t\t\t// skipped\n\t\t\t}\n\t\t}\n\t} else if (evt.a5ss || evt.a3ss) {\n\t\t// still equal number of exons\n\t\t// adjust the affected exon first, then figure out coding[]\n\t\tconst exons = gm.exon.map(e => [e[0], e[1]])\n\t\tconst forward = gm.strand == '+'\n\t\tif (evt.a5ss) {\n\t\t\tif (forward) {\n\t\t\t\texons[evt.exon5idx][1] = evt.junctionB.start\n\t\t\t} else {\n\t\t\t\texons[evt.exon5idx + 1][0] = evt.junctionB.stop\n\t\t\t}\n\t\t} else {\n\t\t\tif (forward) {\n\t\t\t\texons[evt.exon5idx + 1][0] = evt.junctionB.stop\n\t\t\t} else {\n\t\t\t\texons[evt.exon5idx][1] = evt.junctionB.start\n\t\t\t}\n\t\t}\n\t\t// from new exons, figure out coding exons\n\t\tfor (const e of exons) {\n\t\t\tconst codingstart = Math.max(gm.codingstart, e[0])\n\t\t\tconst codingstop = Math.min(gm.codingstop, e[1])\n\t\t\tif (codingstart > codingstop) {\n\t\t\t\t// not coding exon\n\t\t\t\tcontinue\n\t\t\t}\n\t\t\tgm2.coding.push([codingstart, codingstop])\n\t\t}\n\t}\n\treturn gm2\n}\n\nexport function fasta2gmframecheck(gm, str) {\n\t/*\n\tgm{}\n\t\t.chr\n\t\t.start\n\t\t.stop\n\t\t\tstart/stop is transcript position\n\t\t.strand\n\t\t.coding[]\n\tstr\n\t\tsamtools faidx output\n\t*/\n\tconst lines = str.split('\\n')\n\t// remove fasta header\n\tlines.shift()\n\tgm.genomicseq = lines.join('').toUpperCase()\n\n\tconst aaseq = nt2aa(gm)\n\n\tlet thisframe = OUT_frame\n\tconst stopcodonidx = aaseq.indexOf(codon_stop)\n\tif (stopcodonidx == aaseq.length - 1) {\n\t\t// the first appearance of stop codon is at the last of translation\n\t\tthisframe = IN_frame\n\t}\n\treturn thisframe\n}\n\nexport function validate_vcfinfofilter(obj) {\n\t/*\n\tvalidate vcfinfofilter as from embedding api or dataset\n\t*/\n\n\tif (!obj.lst) return '.lst missing'\n\n\tif (!Array.isArray(obj.lst)) return 'input is not an array'\n\n\tfor (const set of obj.lst) {\n\t\tif (!set.name) return 'name missing from a set of .vcfinfofilter.lst'\n\n\t\tif (set.autocategory || set.categories) {\n\t\t\t// categorical info, auto or defined\n\n\t\t\tif (!set.autocategory) {\n\t\t\t\tfor (const k in set.categories) {\n\t\t\t\t\tconst v = set.categories[k]\n\t\t\t\t\tif (!set.autocolor && !v.color)\n\t\t\t\t\t\treturn '.color missing for class ' + k + ' from .categories of set ' + set.name\n\t\t\t\t\tif (!v.label) {\n\t\t\t\t\t\tv.label = k\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\n\t\t\tif (set.categoryhidden) {\n\t\t\t\tfor (const k in set.categoryhidden) {\n\t\t\t\t\tif (!set.categories[k]) return 'unknown hidden-by-default category ' + k + ' from set ' + set.name\n\t\t\t\t}\n\t\t\t} else {\n\t\t\t\tset.categoryhidden = {}\n\t\t\t}\n\t\t} else if (set.numericfilter) {\n\t\t\t// otherwise, numerical value, the style of population frequency filter\n\t\t\tconst lst = []\n\t\t\tfor (const v of set.numericfilter) {\n\t\t\t\tif (typeof v == 'number') {\n\t\t\t\t\t/*\n\t\t\t\t\tjust a number, defaults to 'lower-than'\n\t\t\t\t\t*/\n\t\t\t\t\tlst.push({ side: '<', value: v })\n\t\t\t\t} else {\n\t\t\t\t\tlst.push({\n\t\t\t\t\t\tside: v.side || '<',\n\t\t\t\t\t\tvalue: v.value\n\t\t\t\t\t})\n\t\t\t\t}\n\t\t\t}\n\t\t\tset.numericfilter = lst\n\n\t\t\t//return 'no .categories or .numericfilter from set '+set.name\n\t\t}\n\n\t\tif (set.altalleleinfo) {\n\t\t\tif (!set.altalleleinfo.key) {\n\t\t\t\treturn '.key missing from .altalleleinfo from set ' + set.name\n\t\t\t}\n\t\t} else if (set.locusinfo) {\n\t\t\tif (!set.locusinfo.key) {\n\t\t\t\treturn '.key missing from .locusinfo from set ' + set.name\n\t\t\t}\n\t\t} else {\n\t\t\treturn 'neither .altalleleinfo or .locusinfo is available from set ' + set.name\n\t\t}\n\t}\n}\n\nexport function contigNameNoChr(genome, chrlst) {\n\t/*\n\tFIXME hard-coded for human genome styled chromosome names\n\t*/\n\tfor (const n in genome.majorchr) {\n\t\tif (chrlst.indexOf(n.replace('chr', '')) != -1) {\n\t\t\treturn true\n\t\t}\n\t}\n\tif (genome.minorchr) {\n\t\tfor (const n in genome.minorchr) {\n\t\t\tif (chrlst.indexOf(n.replace('chr', '')) != -1) {\n\t\t\t\treturn true\n\t\t\t}\n\t\t}\n\t}\n\treturn false\n}\nexport function contigNameNoChr2(genome, chrlst) {\n\t// returns number of matching chr names that either includes \"chr\" or not\n\t// for detecting if chrlst entirely mismatch with what's in the genome build\n\t// TODO replace contigNameNoChr\n\tlet nochrcount = 0,\n\t\thaschrcount = 0\n\tfor (const n in genome.majorchr) {\n\t\tif (chrlst.includes(n)) {\n\t\t\thaschrcount++\n\t\t} else if (chrlst.includes(n.replace('chr', ''))) {\n\t\t\tnochrcount++\n\t\t}\n\t}\n\tif (genome.minorchr) {\n\t\tfor (const n in genome.minorchr) {\n\t\t\tif (chrlst.includes(n)) {\n\t\t\t\thaschrcount++\n\t\t\t} else if (chrlst.includes(n.replace('chr', ''))) {\n\t\t\t\tnochrcount++\n\t\t\t}\n\t\t}\n\t}\n\treturn [nochrcount, haschrcount]\n}\n\nexport function getMax_byiqr(lst, novaluemax) {\n\t/*\n\tlst: array of numbers\n\tnovaluemax: when lst is empty, return this value\n\tcutoff value based on IQR to exclude outlier values\n\t*/\n\tif (lst.length == 0) return novaluemax\n\tlst.sort((i, j) => i - j)\n\tconst max = lst[lst.length - 1]\n\tif (lst.length <= 5) return max\n\tconst q1 = lst[Math.floor(lst.length / 4)]\n\tconst q2 = lst[Math.floor((lst.length * 3) / 4)]\n\treturn Math.min(q2 + (q2 - q1) * 1.5, max)\n}\n\nexport function alleleInGenotypeStr(genotype, allele) {\n\tif (!genotype) return false\n\tif (genotype.indexOf('/') != -1) {\n\t\treturn genotype.split('/').indexOf(allele) != -1\n\t}\n\treturn genotype.split('|').indexOf(allele) != -1\n}\n\nexport const gmmode = {\n\tgenomic: 'genomic',\n\tsplicingrna: 'splicing RNA', // if just 1 exon, use \"RNA\" as label\n\texononly: 'exon only',\n\tprotein: 'protein',\n\tgmsum: 'aggregated exons'\n}\n\n/*\ninput:\n\nm={}\n\tm.csq=[]\n\t\telement: {\n\t\t\tAllele: str,\n\t\t\tConsequence: str,\n\t\t\tCANONICAL: str, // true if _isoform is canonical\n\t\t\t...\n\t\t\t_isoform: str,\n\t\t\t_class: str,\n\t\t\t_csqrank: int\n\t\t}\n\tm.ann=[]\n\t\tannovar output. may be derelict\nblock={}\n\tblock.usegm={ isoform }\n\tcan be a mock object when running this function in node!\n\ndoes:\n\tfind an annotation from m.csq[] that's fitting the circumstance\n\t- current gm isoform displayed in block gene mode\n\t- any canonical isoform from m.csq[] (can be missing if vep is not instructed to do it)\n\t- one with highest _csqrank\n\tthen, copy its class/mname to m{}\n\thas many fall-back and always try to assign class/mname\n\nno return\n*/\nexport function vcfcopymclass(m, block) {\n\tif (m.csq) {\n\t\tlet useone // point to the element of m.csq[], from this class/mname is copied to m{}\n\n\t\tif (block.usegm) {\n\t\t\t// block is in gm mode, find a csq matching with the genemodel isoform\n\t\t\tuseone = m.csq.find(i => i._isoform == block.usegm.isoform)\n\t\t}\n\n\t\tif (!useone) {\n\t\t\t// no match to usegm isoform; can be due to in genomic mode and zoomed out, where this variant is from a neighboring gene near block.usegm\n\t\t\t// find one using canonical isoform\n\t\t\tuseone = m.csq.find(i => i.CANONICAL)\n\n\t\t\tif (!useone) {\n\t\t\t\t// none of the elements in m.csq[] is using a canonical isoform, as that's a vep optional output\n\t\t\t\t// last method: choose *colorful* annotation based on if is canonical, _csqrank\n\t\t\t\tuseone = m.csq[0]\n\t\t\t\tfor (const q of m.csq) {\n\t\t\t\t\tif (q._csqrank < useone._csqrank) {\n\t\t\t\t\t\tuseone = q\n\t\t\t\t\t}\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\n\t\tif (useone) {\n\t\t\tm.gene = useone._gene\n\t\t\tm.isoform = useone._isoform\n\t\t\tm.class = useone._class\n\t\t\tm.dt = useone._dt\n\t\t\tm.mname = useone._mname\n\n\t\t\tif (m.class == mclassnoncoding) {\n\t\t\t\t// noncoding converted from csq is not a meaningful, drab color, has no mname label, delete so later will be converted to non-protein class\n\t\t\t\tdelete m.class\n\t\t\t}\n\t\t}\n\t} else if (m.ann) {\n\t\t// there could be many applicable annotations, the first one not always desirable\n\t\t// choose *colorful* annotation based on _csqrank\n\t\tlet useone = null\n\t\tif (block.usegm) {\n\t\t\tfor (const q of m.ann) {\n\t\t\t\tif (q._isoform != block.usegm.isoform) continue\n\t\t\t\tif (useone) {\n\t\t\t\t\tif (q._csqrank < useone._csqrank) {\n\t\t\t\t\t\tuseone = q\n\t\t\t\t\t}\n\t\t\t\t} else {\n\t\t\t\t\tuseone = q\n\t\t\t\t}\n\t\t\t}\n\t\t\tif (!useone && block.gmmode == gmmode.genomic) {\n\t\t\t\t// no match to this gene, but in genomic mode, maybe from other genes?\n\t\t\t\tuseone = m.ann[0]\n\t\t\t}\n\t\t} else {\n\t\t\tuseone = m.ann[0]\n\t\t\tfor (const q of m.ann) {\n\t\t\t\tif (q._csqrank < useone._csqrank) {\n\t\t\t\t\tuseone = q\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t\tif (useone) {\n\t\t\tm.gene = useone._gene\n\t\t\tm.isoform = useone._isoform\n\t\t\tm.class = useone._class\n\t\t\tm.dt = useone._dt\n\t\t\tm.mname = useone._mname\n\n\t\t\tif (m.class == mclassnoncoding) {\n\t\t\t\tdelete m.class\n\t\t\t}\n\t\t}\n\t}\n\n\tif (m.class == undefined) {\n\t\t// infer class from m.type, which was assigned by vcf.js\n\t\tif (mclass[m.type]) {\n\t\t\tm.class = m.type\n\t\t\tm.dt = mclass[m.type].dt\n\t\t\tm.mname = m.id && m.id != '.' ? m.id : m.ref + '>' + m.alt\n\t\t\tif (m.mname.length > 15) {\n\t\t\t\t// avoid long indel\n\t\t\t\tm.mname = m.type\n\t\t\t}\n\t\t} else {\n\t\t\tm.class = mclassnonstandard\n\t\t\tm.dt = dtsnvindel\n\t\t\tm.mname = m.type\n\t\t}\n\t}\n\n\tdelete m.type\n}\n\n/*\nused in:\n\tmdssvcnv track, mutation attributes, items that are not annotated by an attribute for showing in legend, and server-side filtering\n*/\nexport const not_annotated = 'Unannotated'\n\n// kernal density estimator as from https://www.d3-graph-gallery.com/graph/density_basic.html\n\nexport function kernelDensityEstimator(kernel, X) {\n\treturn function (V) {\n\t\treturn X.map(x => {\n\t\t\treturn [x, V.map(v => kernel(x - v)).reduce((i, j) => i + j, 0) / V.length]\n\t\t})\n\t}\n}\n\nexport function kernelEpanechnikov(k) {\n\treturn function (v) {\n\t\treturn Math.abs((v /= k)) <= 1 ? (0.75 * (1 - v * v)) / k : 0\n\t}\n}\n\n/////////////////////// color sets /////////////////////////\n\nexport const schemeCategory20 = [\n\t'#1f77b4',\n\t'#aec7e8',\n\t'#ff7f0e',\n\t'#ffbb78',\n\t'#2ca02c',\n\t'#98df8a',\n\t'#d62728',\n\t'#ff9896',\n\t'#9467bd',\n\t'#c5b0d5',\n\t'#8c564b',\n\t'#c49c94',\n\t'#e377c2',\n\t'#f7b6d2',\n\t'#7f7f7f',\n\t'#c7c7c7',\n\t'#bcbd22',\n\t'#dbdb8d',\n\t'#17becf',\n\t'#9edae5'\n]\nexport const schemeCategory2 = ['#e75480', 'blue']\n\nexport function getColorScheme(number) {\n\tif (number > 20) {\n\t\tconst scheme = []\n\t\tfor (let i = 0; i < number; i++) scheme.push(d3.interpolateRainbow(i / number))\n\t\treturn scheme\n\t}\n\tif (number > 12) return schemeCategory20\n\telse if (number > 8) return d3.schemePaired\n\telse if (number > 2) return d3.schemeDark2\n\telse return schemeCategory2\n}\nexport function getColors(number) {\n\tconst scheme = getColorScheme(number)\n\treturn d3scale.scaleOrdinal(scheme)\n}\n\n// for now not using getColorScheme() for protein domains, because this color list have been in use since 2015...\nconst proteinDomainColors = [\n\t'#8dd3c7',\n\t'#bebada',\n\t'#fb8072',\n\t'#80b1d3',\n\t'#E8E89E',\n\t'#a6d854',\n\t'#fdb462',\n\t'#ffd92f',\n\t'#e5c494',\n\t'#b3b3b3'\n]\nexport function proteinDomainColorScale() {\n\treturn d3scale.scaleOrdinal().range(proteinDomainColors)\n}\n\n/////////////////////// end of color sets /////////////////////////\n\nexport const truncatingMutations = ['F', 'N', 'L', 'P']\nexport const proteinChangingMutations = ['F', 'N', 'L', 'P', 'D', 'I', 'ProteinAltering', 'M']\nexport const synonymousMutations = ['S', 'Intron', 'Utr3', 'Utr5', 'noncoding', 'E']\nexport const mutationClasses = Object.values(mclass)\n\t.filter(m => m.dt == dtsnvindel)\n\t.map(m => m.key)\nexport const CNVClasses = Object.values(mclass)\n\t.filter(m => m.dt == dtcnv)\n\t.map(m => m.key)\n\n// dt terms used for filtering variants for geneVariant term\nconst dtTerms_temp = [\n\t{\n\t\tid: 'snvindel',\n\t\tquery: 'snvindel',\n\t\tname: dt2label[dtsnvindel],\n\t\tparent_id: null,\n\t\tisleaf: true,\n\t\ttype: 'dtsnvindel',\n\t\tdt: dtsnvindel,\n\t\tvalues: {}\n\t},\n\t{\n\t\tid: 'cnv',\n\t\tquery: 'cnv',\n\t\tname: dt2label[dtcnv],\n\t\tparent_id: null,\n\t\tisleaf: true,\n\t\ttype: 'dtcnv',\n\t\tdt: dtcnv,\n\t\tvalues: {}\n\t},\n\t{\n\t\tid: 'fusion',\n\t\tquery: 'svfusion',\n\t\tname: dt2label[dtfusionrna],\n\t\tparent_id: null,\n\t\tisleaf: true,\n\t\ttype: 'dtfusion',\n\t\tdt: dtfusionrna,\n\t\tvalues: {}\n\t},\n\t{\n\t\tid: 'sv',\n\t\tquery: 'svfusion',\n\t\tname: dt2label[dtsv],\n\t\tparent_id: null,\n\t\tisleaf: true,\n\t\ttype: 'dtsv',\n\t\tdt: dtsv,\n\t\tvalues: {}\n\t}\n]\n// add origin annotations to dt terms\nconst dtTerms_temp2 = []\nfor (const dtTerm of dtTerms_temp) {\n\tdtTerm.name_noOrigin = dtTerm.name // for labeling groups in groupsetting\n\tdtTerms_temp2.push(dtTerm) // no origin\n\tfor (const origin of ['somatic', 'germline']) {\n\t\t// add origins\n\t\tconst addOrigin = {\n\t\t\tid: `${dtTerm.id}_${origin}`,\n\t\t\tname: `${dtTerm.name} (${origin})`,\n\t\t\torigin\n\t\t}\n\t\tdtTerms_temp2.push(Object.assign({}, dtTerm, addOrigin))\n\t}\n}\nexport const dtTerms = dtTerms_temp2\n\nexport const colorScaleMap = {\n\tblueWhiteRed: { domain: [0, 0.5, 1], range: ['blue', 'white', 'red'] },\n\tgreenWhiteRed: { domain: [0, 0.5, 1], range: ['green', 'white', 'red'] },\n\tblueYellowRed: {\n\t\tdomain: [0, 0.17, 0.33, 0.5, 0.67, 0.83, 1],\n\t\trange: ['#313695', '#649AC7', '#BCE1ED', '#FFFFBF', '#FDBE70', '#EA5839', '#A50026']\n\t},\n\tgreenBlackRed: {\n\t\tdomain: [0, 0.17, 0.33, 0.5, 0.67, 0.83, 1],\n\t\trange: ['#00FF00', '#14E10C', '#1AAF10', '#000000', '#B01205', '#E20E03', '#FF0000']\n\t},\n\tblueBlackYellow: {\n\t\tdomain: [0, 0.17, 0.33, 0.5, 0.67, 0.83, 1],\n\t\trange: ['#0000FF', '#0000CC', '#000099', '#202020', '#999900', '#CCCC00', '#FFFF00']\n\t},\n\t// when hierCluster z-score transformation is not performed, should use two-color scale\n\twhiteRed: { domain: [0, 1], range: ['white', 'red'] }\n}\n\nexport function invalidcoord(thisgenome, chrom, start, stop) {\n\tif (!thisgenome) return 'no genome'\n\tif (!chrom) return 'no chr name'\n\tconst chr = thisgenome.chrlookup[chrom.toUpperCase()]\n\tif (!chr) return 'Invalid chromosome name: ' + chr\n\tif (!Number.isInteger(start)) return 'Non-numerical position: ' + start\n\tif (start < 0 || start >= chr.len) return 'Position out of range: ' + start\n\tif (!Number.isInteger(stop)) return 'Non-numerical position: ' + stop\n\tif (stop < 0 || stop > chr.len) return 'Position out of range: ' + stop\n\tif (start > stop) return 'Start position is greater than stop'\n\treturn false\n}\n\nexport function string2pos(s, genome, donotextend) {\n\ts = s.replace(/,/g, '')\n\tconst chr = genome.chrlookup[s.toUpperCase()]\n\tif (chr) {\n\t\t// chr name only, to middle\n\t\treturn {\n\t\t\tchr: chr.name,\n\t\t\tchrlen: chr.len,\n\t\t\tstart: Math.max(0, Math.ceil(chr.len / 2) - 10000),\n\t\t\tstop: Math.min(chr.len, Math.ceil(chr.len / 2) + 10000)\n\t\t}\n\t}\n\t{\n\t\t// special handling for snv4\n\t\tconst tmp = s.split('.')\n\t\tif (tmp.length >= 2) {\n\t\t\tconst chr = genome.chrlookup[tmp[0].toUpperCase()]\n\t\t\tconst pos = Number.parseInt(tmp[1])\n\t\t\tconst e = invalidcoord(genome, tmp[0], pos, pos + 1)\n\t\t\tif (!e) {\n\t\t\t\t// valid snv4\n\t\t\t\tconst bpspan = 400\n\t\t\t\treturn {\n\t\t\t\t\tchr: chr.name,\n\t\t\t\t\tchrlen: chr.len,\n\t\t\t\t\tstart: Math.max(0, pos - Math.ceil(bpspan / 2)),\n\t\t\t\t\tstop: Math.min(chr.len, pos + Math.ceil(bpspan / 2)),\n\t\t\t\t\tactualposition: { position: pos, len: 1 }\n\t\t\t\t}\n\t\t\t}\n\t\t}\n\t}\n\tconst tmp = s.split(/[-:\\s]+/)\n\tif (tmp.length == 2) {\n\t\t// must be chr - pos\n\t\tconst pos = Number.parseInt(tmp[1])\n\t\tconst e = invalidcoord(genome, tmp[0], pos, pos + 1)\n\t\tif (e) {\n\t\t\treturn null\n\t\t}\n\t\tconst chr = genome.chrlookup[tmp[0].toUpperCase()]\n\t\tconst bpspan = 400\n\t\treturn {\n\t\t\tchr: chr.name,\n\t\t\tchrlen: chr.len,\n\t\t\tstart: Math.max(0, pos - Math.ceil(bpspan / 2)),\n\t\t\tstop: Math.min(chr.len, pos + Math.ceil(bpspan / 2)),\n\t\t\tactualposition: { position: pos, len: 1 }\n\t\t}\n\t}\n\tif (tmp.length == 3) {\n\t\t// must be chr - start - stop\n\t\tlet start = Number.parseInt(tmp[1]),\n\t\t\tstop = Number.parseInt(tmp[2])\n\t\tconst e = invalidcoord(genome, tmp[0], start, stop)\n\t\tif (e) {\n\t\t\treturn null\n\t\t}\n\t\tconst actualposition = { position: start, len: stop - start }\n\t\tconst chr = genome.chrlookup[tmp[0].toUpperCase()]\n\n\t\tif (!donotextend) {\n\t\t\tconst minspan = 400\n\t\t\tif (stop - start < minspan) {\n\t\t\t\tlet center = Math.ceil((start + stop) / 2)\n\t\t\t\tif (center + minspan / 2 >= chr.len) {\n\t\t\t\t\tcenter = chr.len - Math.ceil(minspan / 2)\n\t\t\t\t}\n\t\t\t\tstart = Math.max(0, center - Math.ceil(minspan / 2))\n\t\t\t\tstop = start + minspan\n\t\t\t}\n\t\t}\n\n\t\treturn {\n\t\t\tchr: chr.name,\n\t\t\tchrlen: chr.len,\n\t\t\tstart,\n\t\t\tstop,\n\t\t\tactualposition\n\t\t}\n\t}\n\treturn null\n}\n"],
-  "mappings": 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-}