Add test for null ALT

GMOD · Sep 13, 2024 · 041be88 · 041be88
1 parent 8b8fdb3
commit 041be88
Show file tree

Hide file tree

Showing 5 changed files with 181 additions and 122 deletions.
diff --git a/plugins/variants/src/VcfFeature/__snapshots__/index.test.ts.snap b/plugins/variants/src/VcfFeature/__snapshots__/index.test.ts.snap
@@ -0,0 +1,29 @@
+// Jest Snapshot v1, https://goo.gl/fbAQLP
+
+exports[`null ALT 1`] = `
+{
+  "ALT": null,
+  "CHROM": "chr1",
+  "FILTER": "PASS",
+  "ID": [
+    "rs123",
+  ],
+  "INFO": {
+    "HELLO": [
+      "world",
+    ],
+  },
+  "POS": 100,
+  "QUAL": 29,
+  "REF": "G",
+  "aliases": undefined,
+  "description": "no alternative alleles",
+  "end": 100,
+  "name": "rs123",
+  "refName": "chr1",
+  "samples": {},
+  "start": 99,
+  "type": "remark",
+  "uniqueId": "myuniqueid",
+}
+`;
diff --git a/plugins/variants/src/VcfFeature/index.test.ts b/plugins/variants/src/VcfFeature/index.test.ts
@@ -142,3 +142,22 @@ test('multiple SNV2', () => {
   })
   expect(f.get('description')).toEqual('insertion G -> AT,<*>')
 })
+
+// see example 1.1 in VCF 4.3 spec, indicates the . in ALT field indicates
+// "a site that is called monomorphic reference (i.e. with no alternate alleles"
+test('null ALT', () => {
+  const parser = new VcfParser({
+    header:
+      '#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tBAMs/caudaus.sorted.sam',
+  })
+  const line = 'chr1\t100\trs123\tG\t.\t29\tPASS\tHELLO=world'
+
+  const variant = parser.parseLine(line)
+
+  const f = new VcfFeature({
+    parser,
+    variant,
+    id: 'myuniqueid',
+  })
+  expect(f.toJSON()).toMatchSnapshot()
+})
diff --git a/plugins/variants/src/VcfFeature/index.ts b/plugins/variants/src/VcfFeature/index.ts
@@ -64,16 +64,16 @@ export default class VCFFeature implements Feature {
   dataFromVariant(variant: {
     REF: string
     POS: number
-    ALT: string[]
+    ALT?: string[]
     CHROM: string
     INFO: any
     ID?: string[]
   }): FeatureData {
     const { REF, ALT, POS, CHROM, INFO, ID } = variant
     const start = POS - 1
     const [type, description] = getSOTermAndDescription(REF, ALT, this.parser)
-    const isTRA = ALT.includes('<TRA>')
-    const isSymbolic = ALT.some(f => f.includes('<'))
+    const isTRA = ALT?.includes('<TRA>')
+    const isSymbolic = ALT?.some(f => f.includes('<'))
 
     return {
       refName: CHROM,

diff --git a/products/jbrowse-cli/src/commands/text-index.ts b/products/jbrowse-cli/src/commands/text-index.ts
@@ -361,7 +361,7 @@ export default class TextIndex extends JBrowseCommand {
     await this.indexDriver({
       trackConfigs,
       outLocation: outFlag,
-      name: trackConfigs.length > 1 ? 'aggregate' : path.basename(file[0]!),
+      name: trackConfigs.length > 1 ? 'aggregate' : path.basename(file[0]),
       quiet,
       attributes: attributes.split(','),
       typesToExclude: exclude.split(','),