@sjcrh/proteinpaint-shared 2.187.0 → 2.188.0

package/src/vcf.js

@@ -1,654 +0,0 @@
-import { mclass } from "./common.js"
-import { dissect_INFO } from "./vcf.info.js"
-import { parse_CSQ } from "./vcf.csq.js"
-import { parse_ANN } from "./vcf.ann.js"
-import { getVariantType } from "./vcf.type.js"
-
-/*
-Only for parsing vcf files
-is not involved in creating vcf tracks
-
-shared between client-server
-*/
-
-// for telling symbolic alleles e.g. <*:DEL>
-const getallelename = new RegExp(/<(.+)>/)
-
-const mclasslabel2key = {}
-for (const k in mclass) {
-	mclasslabel2key[mclass[k].label.toUpperCase()] = k
-}
-
-export function vcfparsemeta(lines) {
-	/*
-	input: array of string, as lines separated by linebreak
-
-	##INFO for meta lines
-	#CHROM for header, to get samples
-
-	*/
-
-	let sample = [],
-		errlst = [],
-		info = {},
-		hasinfo = false,
-		format = {},
-		hasformat = false
-
-	for (const line of lines) {
-		if (!line.startsWith("#")) {
-			continue
-		}
-
-		if (line.startsWith("#C")) {
-			// header, get samples
-			sample = line.split("\t").slice(9)
-			continue
-		}
-
-		if (line.startsWith("##INFO")) {
-			const e = tohash(line.substring(8, line.length - 1), info)
-			if (e) {
-				errlst.push("INFO error: " + e)
-			} else {
-				hasinfo = true
-			}
-			continue
-		}
-
-		if (line.startsWith("##FORMAT")) {
-			const e = tohash(line.substring(10, line.length - 1), format)
-			if (e) {
-				errlst.push("FORMAT error: " + e)
-			} else {
-				hasformat = true
-			}
-		}
-	}
-
-	const sampleobjlst = []
-	for (const samplename of sample) {
-		const a = { name: samplename }
-
-		// this enables adding key4annotation to match with .ds.cohort.annotation
-
-		sampleobjlst.push(a)
-	}
-
-	// reserved INFO fields
-	if (info.CSQ) {
-		const lst = info.CSQ.Description.split(" Format: ")
-		if (lst[1]) {
-			const lst2 = lst[1].split("|")
-			if (lst2.length > 1) {
-				// fix csq headers so to allow configuring show/hide of csq fields
-				info.CSQ.csqheader = []
-				for (const str of lst2) {
-					const attr = { name: str }
-					info.CSQ.csqheader.push(attr)
-				}
-			} else {
-				errlst.push("unknown format for CSQ header: " + info.CSQ.Description)
-			}
-		} else {
-			errlst.push("unknown format for CSQ header: " + info.CSQ.Description)
-		}
-	}
-
-	if (info.ANN) {
-		const lst = info.ANN.Description.split("'")
-		if (lst[1]) {
-			const lst2 = lst[1].split(" | ")
-			if (lst2.length) {
-				info.ANN.annheader = []
-				for (const s of lst2) {
-					const attr = { name: s }
-					info.ANN.annheader.push(attr)
-				}
-			} else {
-				errlst.push(
-					'no " | " joined annotation fields for ANN (snpEff annotation): ' +
-						info.ANN.Description
-				)
-			}
-		} else {
-			errlst.push(
-				"no single-quote enclosed annotation fields for ANN (snpEff annotation): " +
-					info.ANN.Description
-			)
-		}
-	}
-
-	return [
-		hasinfo ? info : null,
-		hasformat ? format : null,
-		sampleobjlst,
-		errlst.length ? errlst : null,
-	]
-}
-
-export function vcfparseline(line, vcf) {
-	/*
-	vcf, samples/info is generated by vcfparsemeta()
-		.nochr BOOL
-		.samples [ {} ]
-			.name
-		.info {}
-		.format {}
-
-	return:
-		error message STR
-		altinvalid []
-		mlst [ m ]   one m per alt allele
-			chr
-			pos
-			name
-			type
-			ref
-			alt
-			altstr
-			sampledata []
-			altinfo
-	*/
-
-	const lst = line.split("\t")
-	if (lst.length < 8) {
-		// no good
-		return ["line has less than 8 fields", null, null]
-	}
-
-	const rawpos = Number.parseInt(lst[2 - 1])
-	if (!Number.isInteger(rawpos)) {
-		return ["invalid value for genomic position", null, null]
-	}
-
-	const refallele = lst[4 - 1]
-
-	const m = {
-		vcf_ID: lst[3 - 1],
-		chr: (vcf.nochr ? "chr" : "") + lst[1 - 1],
-		pos: rawpos - 1,
-		ref: refallele,
-		//refstr:refallele, // e.g. GA>GCC, ref:A, refstr:GA, "refstr" is required for matching in FORMAT
-		altstr: lst[5 - 1],
-		alleles: [
-			{
-				/*
-				ref allele only a placeholder, to be removed, this array only contains alt alleles
-				this is a must
-				also allows GT allele index to work
-				*/
-				allele: refallele,
-				sampledata: [],
-			},
-		],
-
-		info: {}, // locus info, do not contain allele info
-
-		name: lst[3 - 1] == "." ? null : lst[3 - 1],
-	}
-
-	// parse alt
-	const altinvalid = []
-	for (const alt of lst[5 - 1].split(",")) {
-		const a = {
-			ref: m.ref, // may be corrected just below!
-			allele: alt,
-			// 5078356.TATCAGAGAA.GGGAGGA keep original allele for matching with csq which hardcodes original allele
-			allele_original: alt,
-			sampledata: [],
-			_m: m,
-			info: {}, // allele info, do not contain locus info
-		}
-		m.alleles.push(a)
-		if (alt[0] == "<") {
-			/*
-			symbolic allele, show text within <> as name
-			FIXME match INFO
-			*/
-			const tmp = alt.match(getallelename)
-			if (!tmp) {
-				altinvalid.push(alt)
-				continue
-			}
-			a.type = tmp[1]
-
-			a.allele = tmp[1]
-			a.issymbolicallele = true
-		} else {
-			// normal nucleotide
-
-			const [p, ref, alt] = correctRefAlt(m.pos, m.ref, a.allele)
-			a.pos = p
-			a.ref = ref
-			a.allele = alt
-		}
-	}
-
-	if (lst[9 - 1] && lst[10 - 1]) {
-		parse_FORMAT2(lst, m, vcf)
-	}
-
-	/*
-	remove ref allele so it only contain alternative alleles
-	so that parse_INFO can safely apply Number=A fields to m.alleles
-	*/
-	m.alleles.shift()
-
-	// info
-	const tmp = lst[8 - 1] == "." ? [] : dissect_INFO(lst[8 - 1])
-	let badinfokeys = []
-
-	if (vcf.info) {
-		badinfokeys = parse_INFO(tmp, m, vcf)
-	} else {
-		// vcf meta lines told nothing about INFO, do not parse
-		m.info = tmp
-	}
-
-	const mlst = []
-	for (const a of m.alleles) {
-		const m2 = {}
-		for (const k in m) {
-			if (k != "alleles") {
-				m2[k] = m[k]
-			}
-		}
-		for (const k in a) {
-			if (k == "allele") {
-				m2.alt = a[k]
-			} else if (k == "info") {
-				m2.altinfo = a[k]
-			} else {
-				m2[k] = a[k]
-			}
-		}
-		if (!m2.issymbolicallele && m2.alt != "NON_REF") {
-			m2.type = getVariantType(m2.ref, m2.alt)
-			/*
-			// valid alt allele, apply Dr. J's cool method
-			const [p,ref,alt]=correctRefAlt(m2.pos, m2.ref, m2.alt)
-			m2.pos=p
-			m2.ref=ref
-			m2.alt=alt
-			*/
-		}
-		mlst.push(m2)
-	}
-	return [
-		badinfokeys.length ? "unknown info keys: " + badinfokeys.join(",") : null,
-		mlst,
-		altinvalid.length > 0 ? altinvalid : null,
-	]
-}
-
-function correctRefAlt(p, ref, alt) {
-	// for oligos, always trim the last identical base
-	while (
-		ref.length > 1 &&
-		alt.length > 1 &&
-		ref[ref.length - 1] == alt[alt.length - 1]
-	) {
-		ref = ref.substr(0, ref.length - 1)
-		alt = alt.substr(0, alt.length - 1)
-	}
-	// move position up as long as first positions are equal
-	while (ref.length > 1 && alt.length > 1 && ref[0] == alt[0]) {
-		ref = ref.substr(1)
-		alt = alt.substr(1)
-		p++
-	}
-	return [p, ref, alt]
-}
-
-function parse_FORMAT2(lst, m, vcf) {
-	/*
-	m.alleles[0] is ref allele
-
-	each allele:
-		.ref
-		.allele
-		.allele_original
-		.sampledata[]     blank array
-	*/
-	const formatfields = lst[9 - 1].split(":")
-
-	for (let _sampleidx = 9; _sampleidx < lst.length; _sampleidx++) {
-		// for each sample
-
-		const valuelst = lst[_sampleidx].split(":")
-		{
-			// tell if this sample have any data in this line (variant), if .:., then skip
-			let none = true
-			for (const v of valuelst) {
-				if (v != ".") {
-					none = false
-					break
-				}
-			}
-			if (none) {
-				// this sample has no format value
-				continue
-			}
-		}
-
-		/* should create an object of {format:value} of this sample
-		with this object, for each alt allele this sample has,
-		put a copy in m.allele[x].sampledata[]
-		*/
-
-		const sampleidx = _sampleidx - 9
-
-		/*
-		for each alt allele, initialize obj of this sample and store in this allele
-		later, to iterate over format fields and put in appropriate values
-		note that this sample may not actually have this allele
-		*/
-		for (let i = 1; i < m.alleles.length; i++) {
-			const sobj = {}
-			if (vcf.samples && vcf.samples[sampleidx]) {
-				for (const k in vcf.samples[sampleidx]) {
-					sobj[k] = vcf.samples[sampleidx][k]
-				}
-			} else {
-				sobj.name = "missing_samplename_from_vcf_header"
-			}
-			m.alleles[i].sampledata.push({
-				sampleobj: sobj,
-			})
-		}
-
-		for (let fi = 0; fi < formatfields.length; fi++) {
-			// for each field of this sample
-
-			const field = formatfields[fi]
-			const value = valuelst[fi]
-			if (value == ".") {
-				// no value for this field
-				continue
-			}
-
-			if (field == "GT") {
-				const splitter = value.indexOf("/") != -1 ? "/" : "|"
-				let gtsum = 0 // for calculating gtallref=true, old
-				let unknowngt = false // if any is '.', then won't calculate gtallref
-				const gtalleles = []
-				for (const i of value.split(splitter)) {
-					if (i == ".") {
-						unknowngt = true
-						continue
-					}
-					const j = Number.parseInt(i)
-					if (Number.isNaN(j)) {
-						unknowngt = true
-						continue
-					}
-					gtsum += j
-					const ale = m.alleles[j]
-					if (ale) {
-						gtalleles.push(ale.allele)
-					}
-				}
-				let gtallref = false
-				if (!unknowngt) {
-					gtallref = gtsum == 0
-				}
-
-				const genotype = gtalleles.join(splitter)
-				for (let i = 1; i < m.alleles.length; i++) {
-					const ms = m.alleles[i].sampledata[m.alleles[i].sampledata.length - 1]
-					ms.GT = value
-					ms.genotype = genotype
-					if (gtallref) {
-						ms.gtallref = true
-					}
-
-					// for mds vcf to drop out samples that do not have this alt allele
-					ms.__gtalleles = gtalleles
-				}
-				continue
-			}
-
-			// other data fields
-			const formatdesc = vcf.format ? vcf.format[field] : null
-			if (!formatdesc) {
-				// unspecified field, put to all alt alleles
-				for (let i = 1; i < m.alleles.length; i++) {
-					m.alleles[i].sampledata[m.alleles[i].sampledata.length - 1][field] =
-						value
-				}
-				continue
-			}
-
-			const isinteger = formatdesc.Type == "Integer"
-			const isfloat = formatdesc.Type == "Float"
-
-			if ((formatdesc.Number && formatdesc.Number == "R") || field == "AD") {
-				/*
-				per-allele value, including ref
-				v4.1 has AD not with "R", must process as R
-				*/
-				const fvlst = value.split(",").map((i) => {
-					if (isinteger) return Number.parseInt(i)
-					if (isfloat) return Number.parseFloat(i)
-					return i
-				})
-				for (let i = 1; i < m.alleles.length; i++) {
-					if (fvlst[i] != undefined) {
-						// this allele has value
-						const m2 = m.alleles[i]
-						const m2s = m2.sampledata[m2.sampledata.length - 1]
-						// use this allele's ref/alt (after nt trimming)
-						m2s[field] = {}
-						m2s[field][m2.ref] = fvlst[0]
-						m2s[field][m2.allele] = fvlst[i]
-					}
-				}
-				continue
-			}
-			if (formatdesc.Number && formatdesc.Number == "A") {
-				// per alt-allele value
-				const fvlst = value.split(",").map((i) => {
-					if (isinteger) return Number.parseInt(i)
-					if (isfloat) return Number.parseFloat(i)
-					return i
-				})
-				for (let i = 1; i < m.alleles.length; i++) {
-					if (fvlst[i - 1] != undefined) {
-						// this allele has value
-						const m2 = m.alleles[i]
-						const m2s = m2.sampledata[m2.sampledata.length - 1]
-						// use this allele's ref/alt (after nt trimming)
-						m2s[field] = {}
-						m2s[field][m2.allele] = fvlst[i - 1]
-					}
-				}
-				continue
-			}
-			// otherwise, append this field to all alt
-			for (let i = 1; i < m.alleles.length; i++) {
-				m.alleles[i].sampledata[m.alleles[i].sampledata.length - 1][field] =
-					value
-			}
-		}
-	}
-
-	// compatible with old ds: make allele2readcount from AD
-	for (const a of m.alleles) {
-		for (const s of a.sampledata) {
-			if (s.AD) {
-				s.allele2readcount = {}
-				for (const k in s.AD) {
-					s.allele2readcount[k] = s.AD[k]
-				}
-			}
-		}
-	}
-}
-
-function tohash(s, hash) {
-	/*
-	parse INFO
-	*/
-	const h = {},
-		err = []
-	let prev = 0,
-		prevdoublequote = false,
-		k = null
-	for (let i = 0; i < s.length; i++) {
-		if (s[i] == '"') {
-			i++
-			const thisstart = i
-			while (s[i] != '"') {
-				i++
-			}
-			if (k) {
-				h[k] = s.substring(thisstart, i)
-				k = null
-			} else {
-				err.push("k undefined before double quotes")
-			}
-			prevdoublequote = true
-			continue
-		}
-		if (s[i] == "=") {
-			k = s.substring(prev, i)
-			prev = i + 1
-			continue
-		}
-		if (s[i] == ",") {
-			if (prevdoublequote) {
-				prevdoublequote = false
-			} else {
-				if (k) {
-					h[k] = s.substring(prev, i)
-					k = null
-				} else {
-					err.push("k undefined")
-				}
-			}
-			prev = i + 1
-			continue
-		}
-	}
-	if (k) {
-		h[k] = s.substring(prev, i)
-	}
-	if (h.ID) {
-		hash[h.ID] = h
-	} else {
-		return "no ID"
-	}
-	if (err.length) return err.join("\n")
-}
-
-function parse_INFO(tmp, m, vcf) {
-	/*
-	this function fills in both m.info{} and m.alleles[].info{}
-
-	the m.alleles[] will later be converted to [m], each carrying one alt allele
-	each m will have .info{} for locus info, and .altinfo{} for alt allele info
-
-	*/
-
-	const badinfokeys = []
-
-	for (const key in tmp) {
-		if (vcf.info[key] == undefined) {
-			badinfokeys.push(key)
-			continue
-		}
-
-		const value = tmp[key]
-
-		////////////////// hard-coded fields
-
-		if (key == "CSQ") {
-			const okay = parse_CSQ(value, vcf.info.CSQ.csqheader, m)
-			if (!okay) {
-				m.info[key] = value
-			}
-			continue
-		}
-		if (key == "ANN") {
-			const okay = parse_ANN(value, vcf.info.ANN.annheader, m)
-			if (!okay) {
-				m.info[key] = value
-			}
-			continue
-		}
-
-		////////////////// end of hardcoded fields
-
-		if (vcf.info[key].Type == "Flag") {
-			// flag has no value
-			m.info[key] = key
-			continue
-		}
-
-		const __number = vcf.info[key].Number
-		const isinteger = vcf.info[key].Type == "Integer"
-		const isfloat = vcf.info[key].Type == "Float"
-
-		if (__number == "0") {
-			/*
-			no value, should be a Flag
-			*/
-			m.info[key] = key
-			continue
-		}
-
-		if (__number == "A") {
-			/*
-			per alt allele
-			*/
-			const tt = value.split(",")
-			for (let j = 0; j < tt.length; j++) {
-				if (m.alleles[j]) {
-					m.alleles[j].info[key] = isinteger
-						? Number.parseInt(tt[j])
-						: isfloat
-						? Number.parseFloat(tt[j])
-						: tt[j]
-				}
-			}
-			continue
-		}
-
-		if (__number == "R") {
-			/*
-			FIXME "R" is not considered, m.alleles only contain alt, which .info{} for each
-			the current datastructure does not support info for ref allele!
-			*/
-		}
-
-		if (__number == "1") {
-			/*
-			single value
-			*/
-			m.info[key] = isinteger
-				? Number.parseInt(value)
-				: isfloat
-				? Number.parseFloat(value)
-				: value
-			continue
-		}
-
-		if (!value.split) {
-			// unknown error
-			continue
-		}
-
-		// number of values unknown, "commas are permitted only as delimiters for lists of values"
-
-		const lst = value.split(",") // value is always array!!
-		if (isinteger) {
-			m.info[key] = lst.map(Number.parseInt)
-		} else if (isfloat) {
-			m.info[key] = lst.map(Number.parseFloat)
-		} else {
-			m.info[key] = lst
-		}
-	}
-	return badinfokeys
-}

package/src/vcf.type.js

@@ -1,24 +0,0 @@
-import {
-	mclassdeletion,
-	mclasssnv,
-	mclassmnv,
-	mclassinsertion,
-	mclassnonstandard,
-} from "./common.js"
-
-export function getVariantType(ref, alt) {
-	if (ref.length == 1 && alt.length == 1) {
-		// both alleles length of 1
-		if (alt == ".") {
-			// alt is missing
-			return mclassdeletion
-		}
-		// snv
-		return mclasssnv
-	}
-	if (ref.length == alt.length) return mclassmnv
-	// FIXME only when empty length of one allele
-	if (ref.length < alt.length) return mclassinsertion
-	if (ref.length > alt.length) return mclassdeletion
-	return mclassnonstandard
-}