@sjcrh/proteinpaint-shared 2.180.0 → 2.180.1

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-shared",
-  "version": "2.180.0",
+  "version": "2.180.1",
   "description": "ProteinPaint code that is shared between server and client-side workspaces",
   "type": "module",
   "main": "src/index.js",
@@ -14,7 +14,7 @@
     "./*": "./src/*"
   },
   "scripts": {
-    "build": "esbuild src/*.ts --platform=node --outdir=src/ --format=esm && prettier --no-semi --use-tabs --write src/urljson.js src/joinUrl.js src/time.js src/doc.js",
+    "build": "esbuild src/*.ts --platform=node --outdir=src/ --format=esm && prettier --no-semi --use-tabs --write src/*.js",
     "prepack": "npm run build",
     "pretest": "mkdir -p test && node emitImports > test/internals-test.ts",
     "spec:coverage": "node test/relevant.js",

package/src/bulk.cnv.js

@@ -4,12 +4,12 @@
 //
 ////////////////////////////////////
 
-import * as common from './common.js'
-import * as bulk from './bulk.js'
+import * as common from "./common.js"
+import * as bulk from "./bulk.js"
 
 export function parseheader(line, flag) {
-	const header = line.toLowerCase().split('\t')
-	if (header.length <= 1) return 'invalid file header for CNV'
+	const header = line.toLowerCase().split("\t")
+	if (header.length <= 1) return "invalid file header for CNV"
 	const htry = (...lst) => {
 		for (const i of lst) {
 			const j = header.indexOf(i)
@@ -17,57 +17,57 @@ export function parseheader(line, flag) {
 		}
 		return -1
 	}
-	let i = htry('gene')
-	if (i == -1) return 'gene missing from header'
-	header[i] = 'gene'
-	i = htry('cnv')
-	if (i == -1) return 'CNV missing from header'
-	header[i] = 'cnv'
-	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('disease')
-	if (i != -1) header[i] = 'disease'
-	i = htry('origin')
-	if (i != -1) header[i] = 'origin'
-	i = htry('sampletype', 'sample type', 'sample_type')
-	if (i != -1) header[i] = 'sampletype'
+	let i = htry("gene")
+	if (i == -1) return "gene missing from header"
+	header[i] = "gene"
+	i = htry("cnv")
+	if (i == -1) return "CNV missing from header"
+	header[i] = "cnv"
+	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("disease")
+	if (i != -1) header[i] = "disease"
+	i = htry("origin")
+	if (i != -1) header[i] = "origin"
+	i = htry("sampletype", "sample type", "sample_type")
+	if (i != -1) header[i] = "sampletype"
 	flag.cnv.header = header
 	flag.cnv.loaded = true
 	return false
 }
 
 export function parseline(i, line, flag) {
-	if (line == '' || line[0] == '#') return
-	const lst = line.split('\t')
+	if (line == "" || line[0] == "#") return
+	const lst = line.split("\t")
 	const m = {}
 	for (let j = 0; j < flag.cnv.header.length; j++) {
 		m[flag.cnv.header[j]] = lst[j]
 	}
 	if (!m.gene) {
-		flag.cnv.badlines.push([i, 'missing gene', lst])
+		flag.cnv.badlines.push([i, "missing gene", lst])
 		return
 	}
 	if (!m.cnv) {
-		flag.cnv.badlines.push([i, 'missing cnv value', lst])
+		flag.cnv.badlines.push([i, "missing cnv value", lst])
 		return
 	}
 	const value = m.cnv.toLowerCase()
 	switch (value) {
-		case 'amplification':
-		case 'gain':
+		case "amplification":
+		case "gain":
 			m.class = common.mclasscnvgain
 			break
-		case 'deletion':
-		case 'loss':
+		case "deletion":
+		case "loss":
 			m.class = common.mclasscnvloss
 			break
-		case 'loh':
+		case "loh":
 			m.class = common.mclasscnvloh
 			break
 		default:
-			flag.cnv.badlines.push([i, 'invalid cnv value: ' + m.cnv, lst])
+			flag.cnv.badlines.push([i, "invalid cnv value: " + m.cnv, lst])
 			m.class = null
 	}
 	if (!m.class) {

package/src/bulk.del.js

@@ -4,12 +4,12 @@
 //
 ////////////////////////////////////
 
-import * as common from './common.js'
-import * as bulk from './bulk.js'
+import * as common from "./common.js"
+import * as bulk from "./bulk.js"
 
 export function parseheader(line, flag) {
-	const header = line.toLowerCase().split('\t')
-	if (header.length <= 1) return 'invalid header line for intragenic deletion'
+	const header = line.toLowerCase().split("\t")
+	if (header.length <= 1) return "invalid header line for intragenic deletion"
 	const htry = (...lst) => {
 		for (const i of lst) {
 			const j = header.indexOf(i)
@@ -17,79 +17,79 @@ export function parseheader(line, flag) {
 		}
 		return -1
 	}
-	let i = htry('gene')
-	if (i == -1) return 'gene missing from header'
-	header[i] = 'gene'
+	let i = htry("gene")
+	if (i == -1) return "gene missing from header"
+	header[i] = "gene"
 	i = htry(
-		'annovar_isoform',
-		'mrna_accession',
-		'mrna accession',
-		'refseq_mrna_id',
-		'annovar_sj_filter_isoform',
-		'refseq',
-		'isoform'
+		"annovar_isoform",
+		"mrna_accession",
+		"mrna accession",
+		"refseq_mrna_id",
+		"annovar_sj_filter_isoform",
+		"refseq",
+		"isoform"
 	)
-	if (i == -1) return 'isoform missing from header'
-	header[i] = 'isoform'
-	i = htry('rnaposition')
+	if (i == -1) return "isoform missing from header"
+	header[i] = "isoform"
+	i = htry("rnaposition")
 	if (i != -1) {
-		header[i] = 'rnaposition'
-		i = htry('rnadellength')
-		if (i == -1) return 'rnadellength is required when rnaPosition is used'
-		header[i] = 'rnadellength'
+		header[i] = "rnaposition"
+		i = htry("rnadellength")
+		if (i == -1) return "rnadellength is required when rnaPosition is used"
+		header[i] = "rnadellength"
 	}
-	i = htry('chromosome', 'chr')
+	i = htry("chromosome", "chr")
 	if (i != -1) {
-		header[i] = 'chr'
-		i = htry('chr_start')
-		if (i == -1) return 'chr_start is required when chr is used'
-		header[i] = 'chrpos1'
-		i = htry('chr_stop')
-		if (i == -1) return 'chr_stop is required when chr is used'
-		header[i] = 'chrpos2'
+		header[i] = "chr"
+		i = htry("chr_start")
+		if (i == -1) return "chr_start is required when chr is used"
+		header[i] = "chrpos1"
+		i = htry("chr_stop")
+		if (i == -1) return "chr_stop is required when chr is used"
+		header[i] = "chrpos2"
 	}
 
-	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('disease')
-	if (i != -1) header[i] = 'disease'
-	i = htry('origin')
-	if (i != -1) header[i] = 'origin'
-	i = htry('sampletype', 'sample type', 'sample_type')
-	if (i != -1) header[i] = 'sampletype'
+	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("disease")
+	if (i != -1) header[i] = "disease"
+	i = htry("origin")
+	if (i != -1) header[i] = "origin"
+	i = htry("sampletype", "sample type", "sample_type")
+	if (i != -1) header[i] = "sampletype"
 	flag.del.header = header
 	flag.del.loaded = true
 	return false
 }
 
 export function parseline(i, line, flag) {
-	if (line == '' || line[0] == '#') return
-	const lst = line.split('\t')
+	if (line == "" || line[0] == "#") return
+	const lst = line.split("\t")
 	const m = {}
 	for (let j = 0; j < flag.del.header.length; j++) {
 		if (lst[j] == undefined) break
 		m[flag.del.header[j]] = lst[j]
 	}
 	if (!m.gene) {
-		flag.del.badlines.push([i, 'missing gene', lst])
+		flag.del.badlines.push([i, "missing gene", lst])
 		return
 	}
 	if (m.rnaposition) {
 		let v = Number.parseInt(m.rnaposition)
 		if (Number.isNaN(v) || v < 0) {
-			flag.del.badlines.push([i, 'invalid rnaPosition value', lst])
+			flag.del.badlines.push([i, "invalid rnaPosition value", lst])
 			return
 		}
 		m.rnaposition = v
 		if (!m.rnadellength) {
-			flag.del.badlines.push([i, 'missing rnaDellength value', lst])
+			flag.del.badlines.push([i, "missing rnaDellength value", lst])
 			return
 		}
 		v = Number.parseInt(m.rnadellength)
 		if (Number.isNaN(v) || v < 0) {
-			flag.del.badlines.push([i, 'invalid rnaDellength value', lst])
+			flag.del.badlines.push([i, "invalid rnaDellength value", lst])
 			return
 		}
 		m.rnadellength = v
@@ -97,13 +97,13 @@ export function parseline(i, line, flag) {
 	if (m.chr) {
 		let v = Number.parseInt(m.chrpos1)
 		if (Number.isNaN(v) || v < 0) {
-			flag.del.badlines.push([i, 'invalid chr_start value', lst])
+			flag.del.badlines.push([i, "invalid chr_start value", lst])
 			return
 		}
 		m.chrpos1 = v
 		v = Number.parseInt(m.chrpos2)
 		if (Number.isNaN(v) || v < 0) {
-			flag.del.badlines.push([i, 'invalid chr_stop value', lst])
+			flag.del.badlines.push([i, "invalid chr_stop value", lst])
 			return
 		}
 		m.chrpos2 = v
@@ -114,7 +114,7 @@ export function parseline(i, line, flag) {
 	}
 	m.dt = common.dtdel
 	m.class = common.mclassdel
-	m.mname = 'DEL'
+	m.mname = "DEL"
 	flag.good++
 	var n = flag.geneToUpper ? m.gene.toUpperCase() : m.gene
 	if (!(n in flag.data)) {

package/src/bulk.itd.js

@@ -4,12 +4,12 @@
 //
 ////////////////////////////////////
 
-import * as common from './common.js'
-import * as bulk from './bulk.js'
+import * as common from "./common.js"
+import * as bulk from "./bulk.js"
 
 export function parseheader(line, flag) {
-	const header = line.toLowerCase().split('\t')
-	if (header.length <= 1) return 'invalid header line for ITD'
+	const header = line.toLowerCase().split("\t")
+	if (header.length <= 1) return "invalid header line for ITD"
 	const htry = (...lst) => {
 		for (const i of lst) {
 			const j = header.indexOf(i)
@@ -17,79 +17,79 @@ export function parseheader(line, flag) {
 		}
 		return -1
 	}
-	let i = htry('gene')
-	if (i == -1) return 'gene missing from header'
-	header[i] = 'gene'
+	let i = htry("gene")
+	if (i == -1) return "gene missing from header"
+	header[i] = "gene"
 	i = htry(
-		'annovar_isoform',
-		'mrna_accession',
-		'mrna accession',
-		'refseq_mrna_id',
-		'annovar_sj_filter_isoform',
-		'refseq',
-		'isoform'
+		"annovar_isoform",
+		"mrna_accession",
+		"mrna accession",
+		"refseq_mrna_id",
+		"annovar_sj_filter_isoform",
+		"refseq",
+		"isoform"
 	)
-	if (i == -1) return 'isoform missing from header'
-	header[i] = 'isoform'
-	i = htry('rnaposition')
+	if (i == -1) return "isoform missing from header"
+	header[i] = "isoform"
+	i = htry("rnaposition")
 	if (i != -1) {
-		header[i] = 'rnaposition'
-		i = htry('rnaduplength')
-		if (i == -1) return 'rnaduplength is required when rnaposition is present'
-		header[i] = 'rnaduplength'
+		header[i] = "rnaposition"
+		i = htry("rnaduplength")
+		if (i == -1) return "rnaduplength is required when rnaposition is present"
+		header[i] = "rnaduplength"
 	}
-	i = htry('chromosome', 'chr')
+	i = htry("chromosome", "chr")
 	if (i != -1) {
-		header[i] = 'chr'
-		i = htry('chr_start')
-		if (i == -1) return 'chr_start is required when chr is present'
-		header[i] = 'chrpos1'
-		i = htry('chr_stop')
-		if (i == -1) return 'chr_stop is required when chr is present'
-		header[i] = 'chrpos2'
+		header[i] = "chr"
+		i = htry("chr_start")
+		if (i == -1) return "chr_start is required when chr is present"
+		header[i] = "chrpos1"
+		i = htry("chr_stop")
+		if (i == -1) return "chr_stop is required when chr is present"
+		header[i] = "chrpos2"
 	}
 
-	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('disease')
-	if (i != -1) header[i] = 'disease'
-	i = htry('origin')
-	if (i != -1) header[i] = 'origin'
-	i = htry('sampletype', 'sample type', 'sample_type')
-	if (i != -1) header[i] = 'sampletype'
+	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("disease")
+	if (i != -1) header[i] = "disease"
+	i = htry("origin")
+	if (i != -1) header[i] = "origin"
+	i = htry("sampletype", "sample type", "sample_type")
+	if (i != -1) header[i] = "sampletype"
 	flag.itd.header = header
 	flag.itd.loaded = true
 	return false
 }
 
 export function parseline(i, line, flag) {
-	if (line == '' || line[0] == '#') return
-	const lst = line.split('\t')
+	if (line == "" || line[0] == "#") return
+	const lst = line.split("\t")
 	const m = {}
 	for (let j = 0; j < flag.itd.header.length; j++) {
 		if (lst[j] == undefined) break
 		m[flag.itd.header[j]] = lst[j]
 	}
 	if (!m.gene) {
-		flag.itd.badlines.push([i, 'missing gene', lst])
+		flag.itd.badlines.push([i, "missing gene", lst])
 		return
 	}
 	if (m.rnaposition) {
 		let v = Number.parseInt(m.rnaposition)
 		if (Number.isNaN(v) || v < 0) {
-			flag.itd.badlines.push([i, 'invalid rnaPosition value', lst])
+			flag.itd.badlines.push([i, "invalid rnaPosition value", lst])
 			return
 		}
 		m.rnaposition = v
 		if (!m.rnaduplength) {
-			flag.itd.badlines.push([i, 'missing rnaDuplength value', lst])
+			flag.itd.badlines.push([i, "missing rnaDuplength value", lst])
 			return
 		}
 		v = Number.parseInt(m.rnaduplength)
 		if (Number.isNaN(v) || v < 0) {
-			flag.itd.badlines.push([i, 'invalid rnaDuplength value', lst])
+			flag.itd.badlines.push([i, "invalid rnaDuplength value", lst])
 			return
 		}
 		m.rnaduplength = v
@@ -97,13 +97,13 @@ export function parseline(i, line, flag) {
 	if (m.chr) {
 		let v = Number.parseInt(m.chrpos1)
 		if (Number.isNaN(v) || v < 0) {
-			flag.itd.badlines.push([i, 'invalid chr_start value', lst])
+			flag.itd.badlines.push([i, "invalid chr_start value", lst])
 			return
 		}
 		m.chrpos1 = v
 		v = Number.parseInt(m.chrpos2)
 		if (Number.isNaN(v) || v < 0) {
-			flag.itd.badlines.push([i, 'invalid chr_stop value', lst])
+			flag.itd.badlines.push([i, "invalid chr_stop value", lst])
 			return
 		}
 		m.chrpos2 = v
@@ -113,7 +113,7 @@ export function parseline(i, line, flag) {
 	}
 	m.dt = common.dtitd
 	m.class = common.mclassitd
-	m.mname = 'ITD'
+	m.mname = "ITD"
 	flag.good++
 	var n = flag.geneToUpper ? m.gene.toUpperCase() : m.gene
 	if (!(n in flag.data)) {

package/src/bulk.js

@@ -4,7 +4,7 @@
 //
 ////////////////////////////////////
 
-import * as common from './common.js'
+import * as common from "./common.js"
 
 export default {}
 
@@ -34,45 +34,45 @@ export function init_bulk_flag(genome) {
 			// jinghui: based on missense/silent ratio of entire dataset to decide whether to include silent when importing...
 			// hard-coded class codes
 			missense: 0,
-			silent: 0
+			silent: 0,
 		},
 		svjson: {
 			loaded: false,
 			header: null,
-			badlines: []
+			badlines: [],
 		},
 		fusion: {
 			loaded: false,
 			header: null,
 			badlines: [],
-			original: []
+			original: [],
 		},
 		sv: {
 			loaded: false,
 			header: null,
 			badlines: [],
-			original: []
+			original: [],
 		},
 		cnv: {
 			loaded: false,
 			header: null,
-			badlines: []
+			badlines: [],
 		},
 		itd: {
 			loaded: false,
 			header: null,
-			badlines: []
+			badlines: [],
 		},
 		del: {
 			loaded: false,
 			header: null,
-			badlines: []
+			badlines: [],
 		},
 		truncation: {
 			loaded: false,
 			header: null,
-			badlines: []
-		}
+			badlines: [],
+		},
 	}
 }
 
@@ -81,25 +81,25 @@ export function parsesample(m, flag, i, lst, badline) {
 	if (m.sampletype) {
 		const s = m.sampletype.toLowerCase()
 		switch (s) {
-			case 'relapse':
+			case "relapse":
 				variantorigin = common.moriginrelapse
 				break
-			case 'germline':
+			case "germline":
 				variantorigin = common.morigingermline
 				break
-			case 'somatic':
-			case 'diagnosis':
+			case "somatic":
+			case "diagnosis":
 				break
 		}
 		if (m.sample) {
 			if (m.patient) {
 				// good
 			} else {
-				m.patient = m.sample + ' ' + m.sampletype
+				m.patient = m.sample + " " + m.sampletype
 			}
 		} else {
 			if (m.patient) {
-				m.sample = m.patient + ' ' + m.sampletype
+				m.sample = m.patient + " " + m.sampletype
 			} else {
 				// neither sample or patient, will quit later
 			}
@@ -123,30 +123,30 @@ export function parsesample(m, flag, i, lst, badline) {
 		// override existing variantorigin
 		const s = m.origin.toLowerCase()
 		switch (s) {
-			case 'r':
-			case 'relapse':
+			case "r":
+			case "relapse":
 				variantorigin = common.moriginrelapse
 				m.isrim2 = true
 				break
-			case 'g':
-			case 'germline':
+			case "g":
+			case "germline":
 				variantorigin = common.morigingermline
 				m.isrim1 = true
 				break
-			case 'gp':
-			case 'germline pathogenic':
+			case "gp":
+			case "germline pathogenic":
 				variantorigin = common.morigingermlinepathogenic
 				m.isrim1 = true
 				break
-			case 'gnp':
-			case 'germline nonpathogenic':
-			case 'germline non-pathogenic':
+			case "gnp":
+			case "germline nonpathogenic":
+			case "germline non-pathogenic":
 				variantorigin = common.morigingermlinenonpathogenic
 				m.isrim1 = true
 				break
-			case 's':
-			case 'somatic':
-			case 'diagnosis':
+			case "s":
+			case "somatic":
+			case "diagnosis":
 				variantorigin = common.moriginsomatic
 				break
 		}
@@ -158,7 +158,7 @@ export function parsesample(m, flag, i, lst, badline) {
 		return
 	}
 
-	const nopatientname = 'no patient/individual name'
+	const nopatientname = "no patient/individual name"
 	let p
 	if (m.patient) {
 		if (!flag.patient2st[m.patient]) {
@@ -182,9 +182,9 @@ export function parsesample(m, flag, i, lst, badline) {
 							m.sample +
 							'": ' +
 							m.disease +
-							', ' +
+							", " +
 							flag.sample2disease[m.sample],
-						lst
+						lst,
 					])
 					return true
 				}