Merge pull request #56 from molgenis/feat/bam

Retrieve embedded bam data
molgenis · May 11, 2021 · e73475c · e73475c
2 parents 8614bd2 + f062aac
commit e73475c
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Showing 7 changed files with 1,746 additions and 1,188 deletions.
diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -1,6 +1,6 @@
 {
   "name": "@molgenis/vip-report-api",
-  "version": "2.2.0",
+  "version": "2.3.0",
   "description": "Report API for Variant Call Format (VCF) Report Templates",
   "main": "dist/index.js",
   "types": "dist/index.d.ts",
@@ -22,21 +22,21 @@
   },
   "homepage": "https://github.com/molgenis/vip-report-api#readme",
   "devDependencies": {
-    "@babel/core": "^7.12.10",
-    "@babel/preset-env": "^7.12.11",
-    "@babel/preset-typescript": "^7.12.7",
-    "@types/jest": "^26.0.20",
-    "@types/node": "^14.14.37",
-    "@typescript-eslint/eslint-plugin": "^4.20.0",
-    "@typescript-eslint/parser": "^4.20.0",
+    "@babel/core": "^7.14.0",
+    "@babel/preset-env": "^7.14.1",
+    "@babel/preset-typescript": "^7.13.0",
+    "@types/jest": "^26.0.23",
+    "@types/node": "^15.0.2",
+    "@typescript-eslint/eslint-plugin": "^4.23.0",
+    "@typescript-eslint/parser": "^4.23.0",
     "babel-jest": "^26.6.3",
-    "eslint": "^7.23.0",
+    "eslint": "^7.26.0",
     "jest": "^26.6.3",
-    "prettier": "2.0.5",
-    "ts-jest": "^26.4.4",
+    "prettier": "2.3.0",
+    "ts-jest": "^26.5.6",
     "tslint": "^6.1.3",
     "tslint-config-prettier": "^1.18.0",
-    "typescript": "^3.9.7"
+    "typescript": "^4.2.4"
   },
   "publishConfig": {
     "access": "public"
@@ -47,6 +47,6 @@
   "dependencies": {
     "ascii85": "^1.0.2",
     "buffer": "^6.0.3",
-    "fflate": "^0.6.9"
+    "fflate": "^0.6.10"
   }
 }
diff --git a/src/ApiClient.ts b/src/ApiClient.ts
@@ -35,6 +35,7 @@ interface BinaryData extends BinaryDataNode {
   vcfGz: Buffer;
   fastaGz: BinaryDataNode;
   genesGz: Buffer;
+  bam: Buffer;
 }
 
 interface BinaryDataNode {
@@ -83,10 +84,14 @@ export class ApiClient implements Api {
     return Promise.resolve(buffer);
   }
 
-  getGenesGz(): Promise<Buffer> {
+  getGenesGz(): Promise<Buffer | null> {
     return Promise.resolve(this.reportData.binary.genesGz);
   }
 
+  getBam(): Promise<Buffer | null> {
+    return Promise.resolve(this.reportData.binary.bam);
+  }
+
   private get<T extends Resource>(resource: string, params: Params = {}): Promise<PagedItems<T>> {
     return new Promise((resolve, reject) => {
       if (!this.reportData.data[resource]) {

diff --git a/src/ApiData.ts b/src/ApiData.ts
@@ -35,6 +35,7 @@ export interface EncodedData extends EncodedDataContainer {
   vcfGz: string;
   fastaGz: EncodedDataContainer;
   genesGz: string;
+  bam: string;
 }
 
 export interface Resource {

diff --git a/src/__tests__/ApiClient.test.ts b/src/__tests__/ApiClient.test.ts
@@ -59,7 +59,8 @@ beforeEach(() => {
           Buffer.from(gzipSync(fs.readFileSync(__dirname + '/interval1.fasta')))
         )
       },
-      genesGz: new Base85().encode(Buffer.from(gzipSync(fs.readFileSync(__dirname + '/example.gff'))))
+      genesGz: new Base85().encode(Buffer.from(gzipSync(fs.readFileSync(__dirname + '/example.gff')))),
+      bam: new Base85().encode(Buffer.from('dummy bam content', 'utf8'))
     }
   };
   api = new ApiClient(reportData);
@@ -668,3 +669,8 @@ test('getGenesGz', async () => {
   // null check, because size check differs between local machine and Travis
   expect(genesGz).not.toBe(null);
 });
+
+test('getBam', async () => {
+  const bam = await api.getBam();
+  expect(bam !== null ? bam.toString('utf-8') : null).toBe('dummy bam content');
+});
diff --git a/src/vcf/MetadataParser.ts b/src/vcf/MetadataParser.ts
@@ -112,7 +112,8 @@ export interface NestedInfoMetadata {
   items: InfoMetadata[];
 }
 
-const REG_EXP_INFO = /##INFO=<ID=(.+?),Number=(.+?),Type=(.+?),Description="(.+?)"(?:,Source="(.+?)")?(?:,Version="(.+?)")?>/;
+const REG_EXP_INFO =
+  /##INFO=<ID=(.+?),Number=(.+?),Type=(.+?),Description="(.+?)"(?:,Source="(.+?)")?(?:,Version="(.+?)")?>/;
 
 export function parseInfoMetadata(token: string): InfoMetadata {
   const result = token.match(REG_EXP_INFO);

diff --git a/src/vcf/__tests__/DataParser.test.ts b/src/vcf/__tests__/DataParser.test.ts
@@ -118,7 +118,7 @@ test('parse value - invalid', () => {
   expect(() =>
     parseValue('', {
       id: 'INT',
-      number: ({ type: 'xx', separator: ',' } as unknown) as NumberMetadata,
+      number: { type: 'xx', separator: ',' } as unknown as NumberMetadata,
       type: 'INTEGER',
       description: 'Integer'
     })