Update add test

GMOD · Jan 21, 2021 · 2c2fe99 · 2c2fe99
1 parent a0bfd1e
commit 2c2fe99
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Showing 11 changed files with 353 additions and 342 deletions.
diff --git a/plugins/bed/src/BedTabixAdapter/BedTabixAdapter.test.ts b/plugins/bed/src/BedTabixAdapter/BedTabixAdapter.test.ts
@@ -157,3 +157,29 @@ test('adapter can fetch bed with header', async () => {
   const featuresJsonArray = featuresArray.map(f => f.toJSON())
   expect(featuresJsonArray).toMatchSnapshot()
 })
+
+test('adapter can use gwas header', async () => {
+  const adapter = new BedTabixAdapter(
+    MyConfigSchema.create({
+      bedGzLocation: {
+        localPath: require.resolve('./test_data/gwas.bed.gz'),
+      },
+      index: {
+        location: {
+          localPath: require.resolve('./test_data/gwas.bed.gz.tbi'),
+        },
+      },
+    }),
+  )
+
+  const features = adapter.getFeatures({
+    refName: '1',
+    start: 0,
+    end: 100_000,
+    assemblyName: 'hg19',
+  })
+
+  const featuresArray = await features.pipe(toArray()).toPromise()
+  const featuresJsonArray = featuresArray.map(f => f.toJSON())
+  expect(featuresJsonArray).toMatchSnapshot()
+})
diff --git a/plugins/bed/src/BedTabixAdapter/BedTabixAdapter.ts b/plugins/bed/src/BedTabixAdapter/BedTabixAdapter.ts
@@ -46,8 +46,7 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
     })
     this.columnNames = readConfObject(config, 'columnNames')
     this.scoreColumn = readConfObject(config, 'scoreColumn')
-
-    this.parser = autoSql && new BED({ autoSql })
+    this.parser = new BED({ autoSql })
   }
 
   public async getRefNames(opts: BaseOptions = {}) {
@@ -69,11 +68,12 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
     const header = await this.bed.getHeader()
     const defs = header.split('\n').filter(f => !!f)
     const defline = defs[defs.length - 1]
-    const names = defline
-      .slice(1)
-      .split('\t')
-      .map(field => field.trim())
-    return names
+    return defline && defline.includes('\t')
+      ? defline
+          .slice(1)
+          .split('\t')
+          .map(field => field.trim())
+      : null
   }
 
   public getFeatures(query: Region, opts: BaseOptions = {}) {
@@ -85,11 +85,13 @@ export default class BedTabixAdapter extends BaseFeatureDataAdapter {
           const l = line.split('\t')
           const refName = l[meta.columnNumbers.ref - 1]
           const start = +l[meta.columnNumbers.start - 1]
-          const end = +l[meta.columnNumbers.end - 1] + 1
+          const end =
+            +l[meta.columnNumbers.end - 1] +
+            (meta.columnNumbers.end === meta.columnNumbers.start ? 1 : 0)
           const uniqueId = `${this.id}-${fileOffset}`
-          const data = this.parser
-            ? this.parser.parseLine(line, { uniqueId })
-            : this.defaultParser(names, line)
+          const data = names
+            ? this.defaultParser(names, line)
+            : this.parser.parseLine(line, { uniqueId })
 
           const { blockCount, blockSizes, blockStarts, chromStarts } = data