@apollo-annotation/shared 0.3.4 → 0.3.6

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/shared",
-  "version": "0.3.4",
+  "version": "0.3.6",
   "main": "./dist/index.js",
   "scripts": {
     "build": "yarn clean && tsc --build",
@@ -10,9 +10,9 @@
     "test:ci": "NODE_V8_COVERAGE=./coverage glob -c \"tsx --test --test-reporter spec --experimental-test-coverage \" \"**/*.test.ts\""
   },
   "dependencies": {
-    "@apollo-annotation/common": "^0.3.4",
-    "@apollo-annotation/mst": "^0.3.4",
-    "@apollo-annotation/schemas": "^0.3.4",
+    "@apollo-annotation/common": "^0.3.6",
+    "@apollo-annotation/mst": "^0.3.6",
+    "@apollo-annotation/schemas": "^0.3.6",
     "@gmod/gff": "1.2.0",
     "@gmod/indexedfasta": "^2.0.4",
     "@jbrowse/core": "^3.0.1",

package/src/Changes/AddAssemblyAndFeaturesFromFileChange.ts

@@ -1,13 +1,13 @@
 /* eslint-disable @typescript-eslint/require-await */
 
 import {
-  ChangeOptions,
-  ClientDataStore,
-  LocalGFF3DataStore,
-  SerializedAssemblySpecificChange,
-  ServerDataStore,
+  type ChangeOptions,
+  type ClientDataStore,
+  type LocalGFF3DataStore,
+  type SerializedAssemblySpecificChange,
+  type ServerDataStore,
 } from '@apollo-annotation/common'
-import { GFF3Feature } from '@gmod/gff'
+import { type GFF3Feature } from '@gmod/gff'
 
 import { FromFileBaseChange } from './FromFileBaseChange'
 

package/src/Changes/AddAssemblyFromExternalChange.ts

@@ -4,11 +4,11 @@
 /* eslint-disable @typescript-eslint/require-await */
 import {
   AssemblySpecificChange,
-  ChangeOptions,
-  ClientDataStore,
-  LocalGFF3DataStore,
-  SerializedAssemblySpecificChange,
-  ServerDataStore,
+  type ChangeOptions,
+  type ClientDataStore,
+  type LocalGFF3DataStore,
+  type SerializedAssemblySpecificChange,
+  type ServerDataStore,
 } from '@apollo-annotation/common'
 import { BgzipIndexedFasta, IndexedFasta } from '@gmod/indexedfasta'
 import { RemoteFile } from 'generic-filehandle'

package/src/Changes/AddAssemblyFromFileChange.ts

@@ -1,11 +1,11 @@
 /* eslint-disable @typescript-eslint/restrict-template-expressions */
 /* eslint-disable @typescript-eslint/require-await */
 import {
-  ChangeOptions,
-  ClientDataStore,
-  LocalGFF3DataStore,
-  SerializedAssemblySpecificChange,
-  ServerDataStore,
+  type ChangeOptions,
+  type ClientDataStore,
+  type LocalGFF3DataStore,
+  type SerializedAssemblySpecificChange,
+  type ServerDataStore,
 } from '@apollo-annotation/common'
 import { BgzipIndexedFasta } from '@gmod/indexedfasta'
 
@@ -100,19 +100,19 @@ export class AddAssemblyFromFileChange extends FromFileBaseChange {
     const faDoc = await fileModel.findById(faId)
     const faChecksum = faDoc?.checksum
     if (!faChecksum) {
-      throw new Error(`No checksum for file document ${faDoc}`)
+      throw new Error(`No checksum for file document ${faDoc?.id}`)
     }
 
     const faiDoc = await fileModel.findById(faiId)
     const faiChecksum = faiDoc?.checksum
     if (!faiChecksum) {
-      throw new Error(`No checksum for file document ${faiDoc}`)
+      throw new Error(`No checksum for file document ${faiDoc?.id}`)
     }
 
     const gziDoc = await fileModel.findById(gziId)
     const gziChecksum = gziDoc?.checksum
     if (!gziChecksum) {
-      throw new Error(`No checksum for file document ${gziDoc}`)
+      throw new Error(`No checksum for file document ${gziDoc?.id}`)
     }
 
     const fasta = filesService.getFileHandle(faDoc)

package/src/Changes/AddFeatureChange.ts

@@ -3,14 +3,14 @@
 /* eslint-disable @typescript-eslint/require-await */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import {
-  ChangeOptions,
-  ClientDataStore,
+  type ChangeOptions,
+  type ClientDataStore,
   FeatureChange,
-  LocalGFF3DataStore,
-  SerializedFeatureChange,
-  ServerDataStore,
+  type LocalGFF3DataStore,
+  type SerializedFeatureChange,
+  type ServerDataStore,
 } from '@apollo-annotation/common'
-import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 
 import { DeleteFeatureChange } from './DeleteFeatureChange'
 
@@ -143,6 +143,7 @@ export class AddFeatureChange extends FeatureChange {
             }
             attributes = {
               _id: [parentFeature._id.toString()],
+              // eslint-disable-next-line unicorn/prefer-structured-clone
               ...JSON.parse(JSON.stringify(attributes)),
             }
             parentFeature.attributes = attributes

package/src/Changes/AddFeaturesFromFileChange.ts

@@ -1,12 +1,12 @@
 /* eslint-disable @typescript-eslint/require-await */
 import {
-  ChangeOptions,
-  ClientDataStore,
-  LocalGFF3DataStore,
-  SerializedAssemblySpecificChange,
-  ServerDataStore,
+  type ChangeOptions,
+  type ClientDataStore,
+  type LocalGFF3DataStore,
+  type SerializedAssemblySpecificChange,
+  type ServerDataStore,
 } from '@apollo-annotation/common'
-import { GFF3Feature } from '@gmod/gff'
+import { type GFF3Feature } from '@gmod/gff'
 
 import { FromFileBaseChange } from './FromFileBaseChange'
 

package/src/Changes/AddRefSeqAliasesChange.ts

@@ -1,11 +1,11 @@
 import {
   AssemblySpecificChange,
-  Change,
-  ChangeOptions,
-  ClientDataStore,
-  LocalGFF3DataStore,
-  SerializedAssemblySpecificChange,
-  ServerDataStore,
+  type Change,
+  type ChangeOptions,
+  type ClientDataStore,
+  type LocalGFF3DataStore,
+  type SerializedAssemblySpecificChange,
+  type ServerDataStore,
 } from '@apollo-annotation/common'
 import { getSession } from '@jbrowse/core/util'
 

package/src/Changes/DeleteAssemblyChange.ts

@@ -4,10 +4,10 @@
 /* eslint-disable @typescript-eslint/no-unsafe-call */
 import {
   AssemblySpecificChange,
-  ClientDataStore,
-  LocalGFF3DataStore,
-  SerializedAssemblySpecificChange,
-  ServerDataStore,
+  type ClientDataStore,
+  type LocalGFF3DataStore,
+  type SerializedAssemblySpecificChange,
+  type ServerDataStore,
 } from '@apollo-annotation/common'
 import { getSession } from '@jbrowse/core/util'
 

package/src/Changes/DeleteFeatureChange.ts

@@ -2,15 +2,15 @@
 /* eslint-disable @typescript-eslint/require-await */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import {
-  ChangeOptions,
-  ClientDataStore,
+  type ChangeOptions,
+  type ClientDataStore,
   FeatureChange,
-  LocalGFF3DataStore,
-  SerializedFeatureChange,
-  ServerDataStore,
+  type LocalGFF3DataStore,
+  type SerializedFeatureChange,
+  type ServerDataStore,
 } from '@apollo-annotation/common'
-import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
-import { Feature } from '@apollo-annotation/schemas'
+import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import { type Feature } from '@apollo-annotation/schemas'
 
 import { AddFeatureChange } from './AddFeatureChange'
 

package/src/Changes/DeleteUserChange.ts

@@ -1,11 +1,11 @@
 /* eslint-disable @typescript-eslint/require-await */
 import {
   Change,
-  ChangeOptions,
-  ClientDataStore,
-  LocalGFF3DataStore,
-  SerializedChange,
-  ServerDataStore,
+  type ChangeOptions,
+  type ClientDataStore,
+  type LocalGFF3DataStore,
+  type SerializedChange,
+  type ServerDataStore,
 } from '@apollo-annotation/common'
 
 export interface SerializedDeleteUserChangeBase extends SerializedChange {

package/src/Changes/FeatureAttributeChange.ts

@@ -2,14 +2,14 @@
 /* eslint-disable @typescript-eslint/require-await */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import {
-  ChangeOptions,
-  ClientDataStore,
+  type ChangeOptions,
+  type ClientDataStore,
   FeatureChange,
-  LocalGFF3DataStore,
-  SerializedFeatureChange,
-  ServerDataStore,
+  type LocalGFF3DataStore,
+  type SerializedFeatureChange,
+  type ServerDataStore,
 } from '@apollo-annotation/common'
-import { Feature, FeatureDocument } from '@apollo-annotation/schemas'
+import { type Feature, type FeatureDocument } from '@apollo-annotation/schemas'
 
 interface SerializedFeatureAttributeChangeBase extends SerializedFeatureChange {
   typeName: 'FeatureAttributeChange'

package/src/Changes/FromFileBaseChange.ts

@@ -5,10 +5,13 @@
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
 import {
   AssemblySpecificChange,
-  ServerDataStore,
+  type ServerDataStore,
 } from '@apollo-annotation/common'
-import { FileDocument, RefSeqDocument } from '@apollo-annotation/schemas'
-import { GFF3Feature } from '@gmod/gff'
+import {
+  type FileDocument,
+  type RefSeqDocument,
+} from '@apollo-annotation/schemas'
+import { type GFF3Feature } from '@gmod/gff'
 
 import { gff3ToAnnotationFeature } from '../GFF3'
 

package/src/Changes/ImportJBrowseConfigChange.ts

@@ -1,10 +1,10 @@
 /* eslint-disable @typescript-eslint/require-await */
 import {
   Change,
-  ChangeOptions,
-  ClientDataStore,
-  LocalGFF3DataStore,
-  ServerDataStore,
+  type ChangeOptions,
+  type ClientDataStore,
+  type LocalGFF3DataStore,
+  type ServerDataStore,
 } from '@apollo-annotation/common'
 
 interface JBrowseAssembly {

package/src/Changes/LocationEndChange.ts

@@ -2,14 +2,14 @@
 /* eslint-disable @typescript-eslint/require-await */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import {
-  ChangeOptions,
-  ClientDataStore,
+  type ChangeOptions,
+  type ClientDataStore,
   FeatureChange,
-  LocalGFF3DataStore,
-  SerializedFeatureChange,
-  ServerDataStore,
+  type LocalGFF3DataStore,
+  type SerializedFeatureChange,
+  type ServerDataStore,
 } from '@apollo-annotation/common'
-import { Feature, FeatureDocument } from '@apollo-annotation/schemas'
+import { type Feature, type FeatureDocument } from '@apollo-annotation/schemas'
 
 interface SerializedLocationEndChangeBase extends SerializedFeatureChange {
   typeName: 'LocationEndChange'

package/src/Changes/LocationStartChange.ts

@@ -2,14 +2,14 @@
 /* eslint-disable @typescript-eslint/require-await */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import {
-  ChangeOptions,
-  ClientDataStore,
+  type ChangeOptions,
+  type ClientDataStore,
   FeatureChange,
-  LocalGFF3DataStore,
-  SerializedFeatureChange,
-  ServerDataStore,
+  type LocalGFF3DataStore,
+  type SerializedFeatureChange,
+  type ServerDataStore,
 } from '@apollo-annotation/common'
-import { Feature, FeatureDocument } from '@apollo-annotation/schemas'
+import { type Feature, type FeatureDocument } from '@apollo-annotation/schemas'
 
 interface SerializedLocationStartChangeBase extends SerializedFeatureChange {
   typeName: 'LocationStartChange'

package/src/Changes/StrandChange.ts

@@ -2,14 +2,14 @@
 /* eslint-disable @typescript-eslint/require-await */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import {
-  ChangeOptions,
-  ClientDataStore,
+  type ChangeOptions,
+  type ClientDataStore,
   FeatureChange,
-  LocalGFF3DataStore,
-  SerializedFeatureChange,
-  ServerDataStore,
+  type LocalGFF3DataStore,
+  type SerializedFeatureChange,
+  type ServerDataStore,
 } from '@apollo-annotation/common'
-import { Feature, FeatureDocument } from '@apollo-annotation/schemas'
+import { type Feature, type FeatureDocument } from '@apollo-annotation/schemas'
 
 interface SerializedStrandChangeBase extends SerializedFeatureChange {
   typeName: 'StrandChange'

package/src/Changes/TypeChange.ts

@@ -2,14 +2,14 @@
 /* eslint-disable @typescript-eslint/require-await */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import {
-  ChangeOptions,
-  ClientDataStore,
+  type ChangeOptions,
+  type ClientDataStore,
   FeatureChange,
-  LocalGFF3DataStore,
-  SerializedFeatureChange,
-  ServerDataStore,
+  type LocalGFF3DataStore,
+  type SerializedFeatureChange,
+  type ServerDataStore,
 } from '@apollo-annotation/common'
-import { Feature, FeatureDocument } from '@apollo-annotation/schemas'
+import { type Feature, type FeatureDocument } from '@apollo-annotation/schemas'
 
 interface SerializedTypeChangeBase extends SerializedFeatureChange {
   typeName: 'TypeChange'

package/src/Changes/UserChange.ts

@@ -1,11 +1,11 @@
 /* eslint-disable @typescript-eslint/require-await */
 import {
   Change,
-  ChangeOptions,
-  ClientDataStore,
-  LocalGFF3DataStore,
-  SerializedChange,
-  ServerDataStore,
+  type ChangeOptions,
+  type ClientDataStore,
+  type LocalGFF3DataStore,
+  type SerializedChange,
+  type ServerDataStore,
 } from '@apollo-annotation/common'
 
 export interface SerializedUserChangeBase extends SerializedChange {

package/src/Checks/CDSCheck.ts

@@ -1,7 +1,7 @@
 import { Check } from '@apollo-annotation/common'
 import {
-  AnnotationFeatureSnapshot,
-  CheckResultSnapshot,
+  type AnnotationFeatureSnapshot,
+  type CheckResultSnapshot,
 } from '@apollo-annotation/mst'
 import { intersection2 } from '@jbrowse/core/util'
 import ObjectID from 'bson-objectid'
@@ -12,6 +12,19 @@ enum STOP_CODONS {
   'TGA',
 }
 
+enum START_CODONS {
+  'ATG',
+}
+
+const CHECK_NAME = 'CDSCheck'
+
+enum CAUSES {
+  'InternalStopCodon',
+  'MissingStartCodon',
+  'MissingStopCodon',
+  'MultipleOfThree',
+}
+
 const iupacComplements: Record<string, string | undefined> = {
   G: 'C',
   A: 'T',
@@ -57,10 +70,11 @@ async function getCDSSequence(
   const sequences = await Promise.all(
     cdsLocation.map(({ max, min }) => getSequence(min, max)),
   )
+  let seq = sequences.join('')
   if (strand === -1) {
-    return sequences.map((seq) => reverseComplement(seq)).join('')
+    seq = reverseComplement(seq)
   }
-  return sequences.join('')
+  return seq
 }
 
 function splitSequenceInCodons(cds: string): string[] {
@@ -71,33 +85,59 @@ function splitSequenceInCodons(cds: string): string[] {
   return codons
 }
 
+function cmp(pos: number, max: number, strand: -1 | 1 | undefined): boolean {
+  if (strand === -1) {
+    return pos > max
+  }
+  return pos < max
+}
+
 function getOriginalCodonLocation(
   cdsLocation: CDSLocation,
   strand: 1 | -1 | undefined,
   index: number,
 ): [number, number] | undefined {
-  let lengthToStart = index * 3
-  let lengthToEnd = lengthToStart + 3
-
-  let startLocation: number | undefined = undefined,
-    endLocation: number | undefined = undefined
-  for (const loc of cdsLocation) {
-    const locLength = loc.max - loc.min
-    if (startLocation === undefined && locLength > lengthToStart) {
-      startLocation = loc.min + lengthToStart
-    } else {
-      lengthToStart -= locLength
-    }
-    if (endLocation === undefined && locLength > lengthToEnd) {
-      endLocation = loc.min + lengthToEnd
-    } else {
-      lengthToEnd -= locLength
-    }
-    if (startLocation !== undefined && endLocation !== undefined) {
-      return [startLocation, endLocation]
+  // Index 0 is the start codon, so reverse the CDS locations if strand is -1
+  const sortedLocation: CDSLocation = structuredClone(cdsLocation)
+  if (strand === -1) {
+    sortedLocation.sort((a, b) => (a.min < b.min ? 1 : -1))
+  } else {
+    sortedLocation.sort((a, b) => (a.min < b.min ? -1 : 1))
+  }
+  let i = 0
+  let currentStart: number | undefined = undefined
+  let currentEnd: number | undefined = undefined
+  for (let iloc = 0; iloc < sortedLocation.length; iloc++) {
+    const loc = sortedLocation[iloc]
+    const { phase } = loc
+    // On the reverse strand start iterating from the right and end on the left
+    const startAt = strand === -1 ? loc.max - phase : loc.min + phase
+    const endAt = strand === -1 ? loc.min : loc.max
+    for (
+      let pos = startAt;
+      cmp(pos, endAt, strand);
+      pos = strand === -1 ? pos - 3 : pos + 3
+    ) {
+      currentStart = pos
+      currentEnd = strand === -1 ? currentStart - 3 : currentStart + 3
+      // These if conditions occur if a codon is split between two exons
+      if (strand === -1 && currentEnd < loc.min) {
+        currentEnd =
+          sortedLocation[iloc + 1].max - sortedLocation[iloc + 1].phase
+      } else if (currentEnd > loc.max) {
+        currentEnd =
+          sortedLocation[iloc + 1].min + sortedLocation[iloc + 1].phase
+      }
+      if (i === index) {
+        return [currentStart, currentEnd].sort((a, b) => a - b) as [
+          number,
+          number,
+        ]
+      }
+      i++
     }
   }
-  return
+  return undefined
 }
 
 async function checkMRNA(
@@ -106,7 +146,9 @@ async function checkMRNA(
 ): Promise<CheckResultSnapshot[]> {
   const checkResults: CheckResultSnapshot[] = []
   const { _id, max, min, refSeq, strand } = feature
+
   const cdsLocations = getCDSLocations(feature)
+
   if (!cdsLocations) {
     return checkResults
   }
@@ -115,22 +157,46 @@ async function checkMRNA(
     const sequence = await getCDSSequence(cdsLocation, strand, getSequence)
     const codons = splitSequenceInCodons(sequence)
     if (sequence.length % 3 === 0) {
-      const lastCodon = codons.pop() // Last codon is supposed to be a stop
+      const start_codon = codons.at(0)
+      if (start_codon && !(start_codon.toUpperCase() in START_CODONS)) {
+        let cdsStart =
+          strand === -1
+            ? cdsLocation.at(-1)?.max ?? max
+            : cdsLocation.at(0)?.min ?? min
+        cdsStart = strand === -1 ? cdsStart - 3 : cdsStart
+        checkResults.push({
+          _id: new ObjectID().toHexString(),
+          name: CHECK_NAME,
+          cause: CAUSES[CAUSES.MissingStartCodon],
+          ids,
+          refSeq: refSeq.toString(),
+          start: cdsStart,
+          end: cdsStart,
+          message: `Unexpected start codon in feature "${_id}": ${start_codon}`,
+        })
+      }
+      const lastCodon = codons.at(-1) // Last codon is supposed to be a stop
       if (lastCodon && !(lastCodon.toUpperCase() in STOP_CODONS)) {
+        const cdsEnd =
+          strand === -1
+            ? cdsLocation.at(0)?.min ?? min
+            : cdsLocation.at(-1)?.max ?? max
         checkResults.push({
           _id: new ObjectID().toHexString(),
-          name: 'MissingStopCodonCheck',
+          name: CHECK_NAME,
+          cause: CAUSES[CAUSES.MissingStopCodon],
           ids,
           refSeq: refSeq.toString(),
-          start: max,
-          end: max,
-          message: `Missing stop codon`,
+          start: cdsEnd,
+          end: cdsEnd,
+          message: `Missing stop codon for feature "${_id}"`,
         })
       }
     } else {
       checkResults.push({
         _id: new ObjectID().toHexString(),
-        name: 'MultipleOfThreeCheck',
+        name: CHECK_NAME,
+        cause: CAUSES[CAUSES.MultipleOfThree],
         ids,
         refSeq: refSeq.toString(),
         start: min,
@@ -139,12 +205,17 @@ async function checkMRNA(
       })
     }
     for (const [idx, codon] of codons.entries()) {
+      if (idx === codons.length - 1) {
+        // Don't test last codon as it is supposed to be a stop
+        break
+      }
       const location = getOriginalCodonLocation(cdsLocation, strand, idx)
       if (location && codon.toUpperCase() in STOP_CODONS) {
         const [codonStart, codonEnd] = location
         checkResults.push({
           _id: new ObjectID().toHexString(),
-          name: 'InternalStopCodonCheck',
+          name: CHECK_NAME,
+          cause: CAUSES[CAUSES.InternalStopCodon],
           ids,
           refSeq: refSeq.toString(),
           start: codonStart,
@@ -196,13 +267,23 @@ function getCDSLocations(
       nextPhase = ((3 - ((loc.max - loc.min - phase + 3) % 3)) % 3) as 0 | 1 | 2
       return { ...loc, phase }
     })
+    phasedLocs.sort((a, b) => (a.min < b.min ? -1 : 1))
     cdsLocations.push(phasedLocs)
   }
+  if (cdsLocations.length > 1) {
+    cdsLocations.sort((a, b) => (a[0].min < b[0].min ? -1 : 1))
+  }
   return cdsLocations
 }
 
+function getCauses(): string[] {
+  return Object.values(CAUSES).filter((x) =>
+    Number.isNaN(Number(x)),
+  ) as string[]
+}
 export class CDSCheck extends Check {
-  name = 'CDSCheck'
+  name = CHECK_NAME
+  causes = getCauses()
   version = 1
   default = true
 

package/src/GFF3/annotationFeatureToGFF3.test.ts

@@ -1,10 +1,12 @@
 /* eslint-disable prefer-destructuring */
 /* eslint-disable @typescript-eslint/no-floating-promises */
 import { describe, it } from 'node:test'
+
+import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 import { assert } from 'chai'
-import { readAnnotationFeatureSnapshot } from './gff3ToAnnotationFeature.test'
+
 import { annotationFeatureToGFF3 } from './annotationFeatureToGFF3'
-import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import { readAnnotationFeatureSnapshot } from './gff3ToAnnotationFeature.test'
 
 describe('annotationFeatureToGFF3', () => {
   it('Test mandatory columns', () => {

package/src/GFF3/annotationFeatureToGFF3.ts

@@ -1,11 +1,11 @@
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 
 import {
-  AnnotationFeatureSnapshot,
-  TranscriptPartLocation,
-  TranscriptPartNonCoding,
+  type AnnotationFeatureSnapshot,
+  type TranscriptPartLocation,
+  type TranscriptPartNonCoding,
 } from '@apollo-annotation/mst'
-import { GFF3Feature } from '@gmod/gff'
+import { type GFF3Feature } from '@gmod/gff'
 import { intersection2 } from '@jbrowse/core/util'
 
 export function annotationFeatureToGFF3(
@@ -13,6 +13,7 @@ export function annotationFeatureToGFF3(
   parentId?: string,
   refSeqNames?: Record<string, string | undefined>,
 ): GFF3Feature {
+  // eslint-disable-next-line unicorn/prefer-structured-clone
   const attributes: Record<string, string[] | undefined> = JSON.parse(
     JSON.stringify(feature.attributes ?? {}),
   )
@@ -126,6 +127,7 @@ function prepareChildFeatures(
       const gffChild = annotationFeatureToGFF3(child, parentID, refSeqNames)
       if (child.type === 'CDS') {
         for (const loc of cdsLocations[cds_idx]) {
+          // eslint-disable-next-line unicorn/prefer-structured-clone
           const gffCds = JSON.parse(JSON.stringify(gffChild)) as GFF3Feature
           if (gffCds.length != 1) {
             // Do we need this check?