@sjcrh/proteinpaint-shared 2.119.0 → 2.121.0

package/README.md

@@ -38,5 +38,9 @@ keep doing this until a dev script or another approach can take care of the `.js
 ## Test
 
 ```sh
+# run all tests
 npm test
+
+# run one script
+node test/mds3tk.unit.spec.js
 ```

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@sjcrh/proteinpaint-shared",
-  "version": "2.119.0",
+  "version": "2.121.0",
   "description": "ProteinPaint code that is shared between server and client-side workspaces",
   "type": "module",
   "main": "src/index.js",

package/src/mds3tk.js

@@ -1,3 +1,5 @@
+import { dtcnv } from './common.js'
+
 // this script should contain mds3 track-related stuff shared between client and backend
 
 /*
@@ -14,3 +16,36 @@ svfusion: dt + chr + pos + strand + pairlstidx + mname
 the separator must avoid conflicting with characters from gene names, and can be changed based on needs
 */
 export const ssmIdFieldsSeparator = '__'
+
+/*
+input: array of mixture of ssm, svfusion and cnv
+
+output: sorted array. each element: [ class/dt, count of m ]
+*/
+export function summarize_mclass(mlst) {
+	const m2c = new Map() // k: mclass, v: {}
+	const cnvs = []
+	for (const m of mlst) {
+		if (m.dt == dtcnv) {
+			cnvs.push(m)
+			continue // process cnv later
+		}
+		// snvindel has m.class=str, svfusion has only dt=int
+		const key = m.class || m.dt
+		m2c.set(key, 1 + (m2c.get(key) || 0))
+	}
+
+	if (cnvs.length) {
+		if (Number.isFinite(cnvs[0].value)) {
+			// first cnv uses numeric value (assumes all the same). record by dt
+			m2c.set(dtcnv, cnvs.length)
+		} else {
+			// cnv not numeric and uses class; record by each class
+			for (const c of cnvs) {
+				if (!c.class) continue // should not happen
+				m2c.set(c.class, 1 + (m2c.get(c.class) || 0))
+			}
+		}
+	}
+	return [...m2c].sort((i, j) => j[1] - i[1])
+}