@sjcrh/proteinpaint-shared 2.129.1 → 2.129.5

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-shared",
-  "version": "2.129.1",
+  "version": "2.129.5",
   "description": "ProteinPaint code that is shared between server and client-side workspaces",
   "type": "module",
   "main": "src/index.js",

package/src/common.js

@@ -530,8 +530,7 @@ export const tkt = {
 	bigwigstranded: 'bigwigstranded',
 	junction: 'junction',
 	mdsjunction: 'mdsjunction',
-	mdscnv: 'mdscnv',
-	mdssvcnv: 'mdssvcnv', // no longer use as driver
+	mdssvcnv: 'mdssvcnv', // replaced by mds3
 	mdsexpressionrank: 'mdsexpressionrank',
 	mdsvcf: 'mdsvcf', // for snv/indels, currently vcf, may include MAF
 	//mdsgeneral:'mdsgeneral', // replaces mdssvcnv   ****** not ready yet
@@ -542,8 +541,7 @@ export const tkt = {
 	expressionrank: 'expressionrank',
 	aicheck: 'aicheck',
 	ase: 'ase',
-	mds2: 'mds2', // mds 2nd gen
-	mds3: 'mds3', // 3rd gen
+	mds3: 'mds3', //
 	bedgraphdot: 'bedgraphdot',
 	bam: 'bam',
 	ld: 'ld'
@@ -1234,3 +1232,100 @@ export const colorScaleMap = {
 	// when hierCluster z-score transformation is not performed, should use two-color scale
 	whiteRed: { domain: [0, 1], range: ['white', 'red'] }
 }
+
+export function invalidcoord(thisgenome, chrom, start, stop) {
+	if (!thisgenome) return 'no genome'
+	if (!chrom) return 'no chr name'
+	const chr = thisgenome.chrlookup[chrom.toUpperCase()]
+	if (!chr) return 'Invalid chromosome name: ' + chr
+	if (!Number.isInteger(start)) return 'Non-numerical position: ' + start
+	if (start < 0 || start >= chr.len) return 'Position out of range: ' + start
+	if (!Number.isInteger(stop)) return 'Non-numerical position: ' + stop
+	if (stop < 0 || stop > chr.len) return 'Position out of range: ' + stop
+	if (start > stop) return 'Start position is greater than stop'
+	return false
+}
+
+export function string2pos(s, genome, donotextend) {
+	s = s.replace(/,/g, '')
+	const chr = genome.chrlookup[s.toUpperCase()]
+	if (chr) {
+		// chr name only, to middle
+		return {
+			chr: chr.name,
+			chrlen: chr.len,
+			start: Math.max(0, Math.ceil(chr.len / 2) - 10000),
+			stop: Math.min(chr.len, Math.ceil(chr.len / 2) + 10000)
+		}
+	}
+	{
+		// special handling for snv4
+		const tmp = s.split('.')
+		if (tmp.length >= 2) {
+			const chr = genome.chrlookup[tmp[0].toUpperCase()]
+			const pos = Number.parseInt(tmp[1])
+			const e = invalidcoord(genome, tmp[0], pos, pos + 1)
+			if (!e) {
+				// valid snv4
+				const bpspan = 400
+				return {
+					chr: chr.name,
+					chrlen: chr.len,
+					start: Math.max(0, pos - Math.ceil(bpspan / 2)),
+					stop: Math.min(chr.len, pos + Math.ceil(bpspan / 2)),
+					actualposition: { position: pos, len: 1 }
+				}
+			}
+		}
+	}
+	const tmp = s.split(/[-:\s]+/)
+	if (tmp.length == 2) {
+		// must be chr - pos
+		const pos = Number.parseInt(tmp[1])
+		const e = invalidcoord(genome, tmp[0], pos, pos + 1)
+		if (e) {
+			return null
+		}
+		const chr = genome.chrlookup[tmp[0].toUpperCase()]
+		const bpspan = 400
+		return {
+			chr: chr.name,
+			chrlen: chr.len,
+			start: Math.max(0, pos - Math.ceil(bpspan / 2)),
+			stop: Math.min(chr.len, pos + Math.ceil(bpspan / 2)),
+			actualposition: { position: pos, len: 1 }
+		}
+	}
+	if (tmp.length == 3) {
+		// must be chr - start - stop
+		let start = Number.parseInt(tmp[1]),
+			stop = Number.parseInt(tmp[2])
+		const e = invalidcoord(genome, tmp[0], start, stop)
+		if (e) {
+			return null
+		}
+		const actualposition = { position: start, len: stop - start }
+		const chr = genome.chrlookup[tmp[0].toUpperCase()]
+
+		if (!donotextend) {
+			const minspan = 400
+			if (stop - start < minspan) {
+				let center = Math.ceil((start + stop) / 2)
+				if (center + minspan / 2 >= chr.len) {
+					center = chr.len - Math.ceil(minspan / 2)
+				}
+				start = Math.max(0, center - Math.ceil(minspan / 2))
+				stop = start + minspan
+			}
+		}
+
+		return {
+			chr: chr.name,
+			chrlen: chr.len,
+			start,
+			stop,
+			actualposition
+		}
+	}
+	return null
+}