@jbrowse/plugin-variants 2.3.4 → 2.4.1

package/src/VcfFeature/util.ts

@@ -92,7 +92,7 @@ export function getSOAndDescFromAltDefs(
   if (modAlt.length > 1) {
     return getSOAndDescFromAltDefs(
       ref,
-      `<${modAlt.slice(0, modAlt.length - 1).join(':')}>`,
+      `<${modAlt.slice(0, -1).join(':')}>`,
       parser,
     )
   }
@@ -121,11 +121,9 @@ export function getSOAndDescByExamination(ref: string, alt: string) {
   } else if (alt.includes('<')) {
     return ['sv', alt]
   } else if (ref.length === alt.length) {
-    if (ref.split('').reverse().join('') === alt) {
-      return ['inversion', makeDescriptionString('inversion', ref, alt)]
-    } else {
-      return ['substitution', makeDescriptionString('substitution', ref, alt)]
-    }
+    return ref.split('').reverse().join('') === alt
+      ? ['inversion', makeDescriptionString('inversion', ref, alt)]
+      : ['substitution', makeDescriptionString('substitution', ref, alt)]
   } else if (ref.length <= alt.length) {
     return ['insertion', makeDescriptionString('insertion', ref, alt)]
   } else if (ref.length > alt.length) {

package/src/VcfTabixAdapter/VcfTabixAdapter.ts

@@ -2,7 +2,7 @@ import {
   BaseFeatureDataAdapter,
   BaseOptions,
 } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { FileLocation, NoAssemblyRegion } from '@jbrowse/core/util/types'
+import { NoAssemblyRegion } from '@jbrowse/core/util/types'
 import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 import { Feature } from '@jbrowse/core/util'
@@ -24,7 +24,7 @@ export default class extends BaseFeatureDataAdapter {
     const location = this.getConf(['index', 'location'])
     const indexType = this.getConf(['index', 'indexType'])
 
-    const filehandle = openLocation(vcfGzLocation as FileLocation, pm)
+    const filehandle = openLocation(vcfGzLocation, pm)
     const isCSI = indexType === 'CSI'
     const vcf = new TabixIndexedFile({
       filehandle,

package/src/VcfTabixAdapter/__snapshots__/VcfTabixAdapter.test.ts.snap

@@ -66,7 +66,7 @@ exports[`adapter can fetch variants from volvox.vcf.gz 2`] = `
     },
     "start": 276,
     "type": "SNV",
-    "uniqueId": "test-vcf-604452",
+    "uniqueId": "test-vcf-604453",
   },
   {
     "ALT": [
@@ -132,7 +132,7 @@ exports[`adapter can fetch variants from volvox.vcf.gz 2`] = `
     },
     "start": 1693,
     "type": "SNV",
-    "uniqueId": "test-vcf-604550",
+    "uniqueId": "test-vcf-604551",
   },
   {
     "ALT": [
@@ -198,7 +198,7 @@ exports[`adapter can fetch variants from volvox.vcf.gz 2`] = `
     },
     "start": 2643,
     "type": "SNV",
-    "uniqueId": "test-vcf-604667",
+    "uniqueId": "test-vcf-604668",
   },
   {
     "ALT": [
@@ -258,7 +258,7 @@ exports[`adapter can fetch variants from volvox.vcf.gz 2`] = `
     },
     "start": 3212,
     "type": "SNV",
-    "uniqueId": "test-vcf-604784",
+    "uniqueId": "test-vcf-604785",
   },
   {
     "ALT": [
@@ -319,7 +319,7 @@ exports[`adapter can fetch variants from volvox.vcf.gz 2`] = `
     },
     "start": 3857,
     "type": "deletion",
-    "uniqueId": "test-vcf-604886",
+    "uniqueId": "test-vcf-604887",
   },
 ]
 `;