@sjcrh/proteinpaint-shared 2.187.0 → 2.188.1

package/src/vcf.csq.js

@@ -1,153 +0,0 @@
-import { vepinfo } from "./common.js"
-/*
-parse csq field from a variant line, not header
-CSQ header must have already been parsed
-
-str: the csq value for a vcf line
-header: [ // something like this
-  { name: 'Allele' },
-  { name: 'Consequence' },
-  { name: 'IMPACT' },
-  { name: 'SYMBOL' },
-  { name: 'Gene' },
-  { name: 'Feature_type' },
-  { name: 'Feature' },
-  { name: 'BIOTYPE' },
-  { name: 'EXON' },
-  { name: 'INTRON' },
-  { name: 'HGVSc' },
-  { name: 'HGVSp' },
-  { name: 'cDNA_position' },
-  { name: 'CDS_position' },
-  { name: 'Protein_position' },
-  { name: 'Amino_acids' },
-  { name: 'Codons' },
-  { name: 'Existing_variation' },
-  { name: 'DISTANCE' },
-  { name: 'STRAND' },
-  { name: 'FLAGS' },
-  { name: 'SYMBOL_SOURCE' },
-  { name: 'HGNC_ID' },
-  { name: 'CANONICAL' },
-  { name: 'REFSEQ_MATCH' },
-  { name: 'GIVEN_REF' },
-  { name: 'USED_REF' },
-  { name: 'BAM_EDIT' },
-  { name: 'HGVS_OFFSET' },
-  { name: 'CLIN_SIG' },
-  { name: 'SOMATIC' },
-  { name: 'PHENO' }
-]
-
-m: {
-	mlst[ {} ]
-		.allele_original
-		.csq[ {} ] // parse_CSQ will add this array to this allele
-			._class
-			._csqrank
-			._dt
-			._gene
-			._isoform
-			._mname
-}
-
-*/
-
-export function parse_CSQ(str, header, m) {
-	if (!header) {
-		return null
-	}
-	for (const thisannotation of str.split(",")) {
-		const lst = thisannotation.replace(/&/g, ",").split("|")
-
-		const o = {}
-
-		for (let i = 0; i < header.length; i++) {
-			if (lst[i]) {
-				o[header[i].name] = lst[i]
-			}
-		}
-		if (!o.Allele) {
-			continue
-		}
-		let allele = null
-
-		//////////////////////////////////////
-		// NOTE
-		// mds2delete
-		// m.alleles[] is based on old vcf parsing and may delete?
-		// latest spec is m.mlst[]
-		//////////////////////////////////////
-
-		for (const a of m.mlst || m.alleles) {
-			if (a.allele_original == o.Allele) {
-				allele = a
-				break
-			}
-		}
-		if (!allele) {
-			if (o.Allele == "-") {
-				// deletion
-				if (m.mlst) {
-					if (m.mlst.length == 1) {
-						allele = m.mlst[0]
-					}
-				} else if (m.alleles) {
-					if (m.alleles.length == 1) {
-						allele = m.alleles[0]
-					}
-				}
-			} else {
-				for (const a of m.mlst || m.alleles) {
-					if (a.allele_original.substr(1) == o.Allele) {
-						// insertion, without first padding base
-						allele = a
-						break
-					}
-				}
-			}
-			if (!allele) {
-				// cannot match to allele!!!
-				continue
-			}
-		}
-		if (!allele.csq) {
-			allele.csq = []
-		}
-		allele.csq.push(o)
-
-		// gene
-		o._gene = o.SYMBOL || o.Gene
-
-		// isoform
-		if (o.Feature_type && o.Feature_type == "Transcript") {
-			o._isoform = o.Feature.split(".")[0] // remove version
-		} else {
-			o._isoform = o._gene
-		}
-
-		// class
-		if (o.Consequence) {
-			const [dt, cls, rank] = vepinfo(o.Consequence)
-			o._dt = dt
-			o._class = cls
-			o._csqrank = rank
-		} else {
-			// FIXME
-			o._dt = dtsnvindel
-			o._class = mclassnonstandard
-		}
-		// mname
-		if (o.HGVSp) {
-			o._mname = decodeURIComponent(o.HGVSp.substr(o.HGVSp.indexOf(":") + 1))
-		} else if (o.Protein_position && o.Amino_acids) {
-			o._mname = decodeURIComponent(o.Protein_position + o.Amino_acids)
-		} else if (o.HGVSc) {
-			o._mname = o.HGVSc.substr(o.HGVSc.indexOf(":") + 1)
-		} else if (o.Existing_variation) {
-			o._name = o.Existing_variation
-		} else {
-		}
-	}
-	return true
-}

package/src/vcf.info.js

@@ -1,50 +0,0 @@
-/*
-to parse a variant line, not header
-
-cannot simply slice by /[;=]/, but read char by char
-case  CLNVI=Breast_Cancer_Information_Core__(BRCA2):745-4&base_change=C_to_G;
-case  k1=v1;DB;k2=v2;
-*/
-export function dissect_INFO(str) {
-	//let findequal=true
-	let findsemicolon = false
-	let findequalorsemicolon = true
-
-	let i = 0
-	let idx = 0
-
-	const k2v = {}
-	let lastkey
-
-	while (i < str.length) {
-		const c = str[i]
-		if (findequalorsemicolon) {
-			if (c == "=") {
-				findsemicolon = true
-				findequalorsemicolon = false
-				lastkey = str.substring(idx, i)
-				idx = i + 1
-			} else if (c == ";") {
-				// should be a flag
-				k2v[str.substring(idx, i)] = 1
-				idx = i + 1
-			}
-		} else if (findsemicolon && c == ";") {
-			findequalorsemicolon = true
-			findsemicolon = false
-			k2v[lastkey] = str.substring(idx, i)
-			lastkey = null
-			idx = i + 1
-		}
-		i++
-	}
-
-	const remainstr = str.substr(idx, i)
-	if (lastkey) {
-		k2v[lastkey] = remainstr
-	} else {
-		k2v[remainstr] = 1
-	}
-
-	return k2v
-}