@apollo-annotation/shared 0.3.7 → 0.3.8

package/dist/util.d.ts

@@ -1,3 +1,6 @@
 import { type Feature } from '@apollo-annotation/schemas';
+import { type IKeyValueMap } from 'mobx';
 export declare function splitStringIntoChunks(input: string, chunkSize: number): string[];
 export declare function getPrintableId(feature: Feature): string;
+export declare function attributesToRecords(attributes: IKeyValueMap<readonly string[] | undefined> | undefined): Record<string, string[] | undefined>;
+export declare function stringifyAttributes(attributes: Record<string, string[] | undefined> | undefined): string;

package/dist/util.js

@@ -2,6 +2,8 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.splitStringIntoChunks = splitStringIntoChunks;
 exports.getPrintableId = getPrintableId;
+exports.attributesToRecords = attributesToRecords;
+exports.stringifyAttributes = stringifyAttributes;
 function splitStringIntoChunks(input, chunkSize) {
     const chunks = [];
     for (let i = 0; i < input.length; i += chunkSize) {
@@ -22,4 +24,35 @@ function getPrintableId(feature) {
     }
     return `_id: ${feature._id.toString()}`;
 }
+function attributesToRecords(attributes) {
+    const records = {};
+    if (!attributes) {
+        return records;
+    }
+    for (const [key, value] of Object.entries(attributes)) {
+        records[key] = value?.slice();
+    }
+    return records;
+}
+function stringifyAttributes(attributes) {
+    if (!attributes) {
+        return '';
+    }
+    const str = [];
+    for (const [key, value] of Object.entries(attributes)) {
+        let attributeName = key;
+        if (attributeName.startsWith('gff_')) {
+            attributeName = attributeName.slice(4);
+            attributeName =
+                attributeName.charAt(0).toUpperCase() + attributeName.slice(1);
+        }
+        if (value) {
+            str.push(`${attributeName}=${value.join(',')}`);
+        }
+        else {
+            str.push(attributeName);
+        }
+    }
+    return encodeURIComponent(str.join(';'));
+}
 //# sourceMappingURL=util.js.map

package/dist/util.js.map

@@ -1 +1 @@
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+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;AAIA,sDAUC;AAED,wCAWC;AAED,kDAWC;AAED,kDAqBC;AA3DD,SAAgB,qBAAqB,CACnC,KAAa,EACb,SAAiB;IAEjB,MAAM,MAAM,GAAa,EAAE,CAAA;IAC3B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,IAAI,SAAS,EAAE,CAAC;QACjD,MAAM,KAAK,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,SAAS,CAAC,CAAA;QAC3C,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;IACpB,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAED,SAAgB,cAAc,CAAC,OAAgB;IAC7C,MAAM,EAAE,GAAG,OAAuC,CAAA;IAClD,MAAM,MAAM,GAAG,EAAE,CAAC,UAAU,CAAC,GAAG,CAAC,QAAQ,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAA;IACrD,IAAI,MAAM,EAAE,CAAC;QACX,OAAO,MAAM,MAAM,UAAU,OAAO,CAAC,GAAG,CAAC,QAAQ,EAAE,GAAG,CAAA;IACxD,CAAC;IACD,MAAM,QAAQ,GAAG,EAAE,CAAC,UAAU,CAAC,GAAG,CAAC,UAAU,CAAC,EAAE,IAAI,CAAC,GAAG,CAAC,CAAA;IACzD,IAAI,QAAQ,EAAE,CAAC;QACb,OAAO,QAAQ,QAAQ,UAAU,OAAO,CAAC,GAAG,CAAC,QAAQ,EAAE,GAAG,CAAA;IAC5D,CAAC;IACD,OAAO,QAAQ,OAAO,CAAC,GAAG,CAAC,QAAQ,EAAE,EAAE,CAAA;AACzC,CAAC;AAED,SAAgB,mBAAmB,CACjC,UAAmE;IAEnE,MAAM,OAAO,GAAyC,EAAE,CAAA;IACxD,IAAI,CAAC,UAAU,EAAE,CAAC;QAChB,OAAO,OAAO,CAAA;IAChB,CAAC;IACD,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,UAAU,CAAC,EAAE,CAAC;QACtD,OAAO,CAAC,GAAG,CAAC,GAAG,KAAK,EAAE,KAAK,EAAE,CAAA;IAC/B,CAAC;IACD,OAAO,OAAO,CAAA;AAChB,CAAC;AAED,SAAgB,mBAAmB,CACjC,UAA4D;IAE5D,IAAI,CAAC,UAAU,EAAE,CAAC;QAChB,OAAO,EAAE,CAAA;IACX,CAAC;IACD,MAAM,GAAG,GAAG,EAAE,CAAA;IACd,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,UAAU,CAAC,EAAE,CAAC;QACtD,IAAI,aAAa,GAAG,GAAG,CAAA;QACvB,IAAI,aAAa,CAAC,UAAU,CAAC,MAAM,CAAC,EAAE,CAAC;YACrC,aAAa,GAAG,aAAa,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YACtC,aAAa;gBACX,aAAa,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,WAAW,EAAE,GAAG,aAAa,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;QAClE,CAAC;QACD,IAAI,KAAK,EAAE,CAAC;YACV,GAAG,CAAC,IAAI,CAAC,GAAG,aAAa,IAAI,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAA;QACjD,CAAC;aAAM,CAAC;YACN,GAAG,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;QACzB,CAAC;IACH,CAAC;IACD,OAAO,kBAAkB,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAA;AAC1C,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/shared",
-  "version": "0.3.7",
+  "version": "0.3.8",
   "main": "./dist/index.js",
   "scripts": {
     "build": "yarn clean && tsc --build",
@@ -10,12 +10,12 @@
     "test:ci": "NODE_V8_COVERAGE=./coverage glob -c \"tsx --test --test-reporter spec --experimental-test-coverage \" \"**/*.test.ts\""
   },
   "dependencies": {
-    "@apollo-annotation/common": "^0.3.7",
-    "@apollo-annotation/mst": "^0.3.7",
-    "@apollo-annotation/schemas": "^0.3.7",
+    "@apollo-annotation/common": "^0.3.8",
+    "@apollo-annotation/mst": "^0.3.8",
+    "@apollo-annotation/schemas": "^0.3.8",
     "@gmod/gff": "1.2.0",
     "@gmod/indexedfasta": "^2.0.4",
-    "@jbrowse/core": "^3.0.1",
+    "@jbrowse/core": "^3.6.5",
     "bson-objectid": "^2.0.4",
     "generic-filehandle": "^3.0.0",
     "jwt-decode": "^3.1.2",
@@ -39,8 +39,8 @@
     "typescript": "^5.5.3"
   },
   "peerDependencies": {
-    "@mui/material": "^6.0.0",
-    "@mui/x-data-grid": "^7.0.0",
+    "@mui/material": "^7.0.0",
+    "@mui/x-data-grid": "^8.0.0",
     "mobx": "^6.6.1",
     "mobx-react": "^7.2.1",
     "mobx-state-tree": "^5.4.0",

package/src/Changes/AddAssemblyAndFeaturesFromFileChange.ts

@@ -90,7 +90,8 @@ export class AddAssemblyAndFeaturesFromFileChange extends FromFileBaseChange {
         throw new Error(`Assembly "${assemblyName}" already exists`)
       }
       // get checks
-      const checkDocs = await checkModel.find({ default: true }).exec()
+      const checkDocs = await checkModel.find({ isDefault: true }).exec()
+
       const checks = checkDocs.map((checkDoc) => checkDoc._id.toHexString())
       // Add assembly
       const [newAssemblyDoc] = await assemblyModel.create([

package/src/Changes/AddAssemblyFromFileChange.ts

@@ -128,7 +128,7 @@ export class AddAssemblyFromFileChange extends FromFileBaseChange {
     if (assemblyDoc) {
       throw new Error(`Assembly "${assemblyName}" already exists`)
     }
-    const checkDocs = await checkModel.find({ default: true }).exec()
+    const checkDocs = await checkModel.find({ isDefault: true }).exec()
     const checks = checkDocs.map((checkDoc) => checkDoc._id.toHexString())
     const [newAssemblyDoc] = await assemblyModel.create([
       {

package/src/Changes/AddRefSeqAliasesChange.ts

@@ -36,9 +36,8 @@ export class AddRefSeqAliasesChange extends AssemblySpecificChange {
       throw new Error(`assembly ${this.assembly} not found`)
     }
     const sessionAliases = assembly.refNameAliases
-    const sessionLCAliases = assembly.lowerCaseRefNameAliases
 
-    if (!sessionAliases || !sessionLCAliases) {
+    if (!sessionAliases) {
       throw new Error('Session refNameAliases not found in assembly')
     }
 
@@ -46,10 +45,9 @@ export class AddRefSeqAliasesChange extends AssemblySpecificChange {
       const { aliases, refName } = refSeqAlias
       for (const alias of aliases) {
         sessionAliases[alias] = refName
-        sessionLCAliases[alias.toLowerCase()] = refName
       }
     }
-    assembly.setRefNameAliases(sessionAliases, sessionLCAliases)
+    assembly.setRefNameAliases(sessionAliases)
     return Promise.resolve()
   }
 

package/src/Changes/ImportJBrowseConfigChange.ts

@@ -75,7 +75,7 @@ export function filterJBrowseConfig(config: JBrowseConfig): JBrowseConfig {
     filteredConfig.plugins = plugins.filter((p) => p.name !== 'Apollo')
   }
   if (tracks) {
-    filteredConfig.trackss = tracks.filter((t) => t.type !== 'ApolloTrack')
+    filteredConfig.tracks = tracks.filter((t) => t.type !== 'ApolloTrack')
   }
   return filteredConfig
 }

package/src/Changes/MergeExonsChange.ts

@@ -1,3 +1,4 @@
+/* eslint-disable unicorn/prefer-structured-clone */
 /* eslint-disable @typescript-eslint/require-await */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 
@@ -11,6 +12,8 @@ import {
 } from '@apollo-annotation/common'
 import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 
+import { attributesToRecords, stringifyAttributes } from '../util'
+
 import { findAndDeleteChildFeature } from './DeleteFeatureChange'
 import { UndoMergeExonsChange } from './UndoMergeExonsChange'
 
@@ -89,7 +92,15 @@ export class MergeExonsChange extends FeatureChange {
       }
       mergedExon.min = Math.min(firstExon.min, secondExon.min)
       mergedExon.max = Math.max(firstExon.max, secondExon.max)
-      mergedExon.attributes = this.mergeAttributes(firstExon, secondExon)
+
+      const mergedAttributes: Record<string, string[]> = mergedExon.attributes
+        ? JSON.parse(JSON.stringify(mergedExon.attributes))
+        : {}
+      mergedAttributes.merged_with = [
+        stringifyAttributes(attributesToRecords(secondExon.attributes)),
+      ]
+      mergedExon.attributes = mergedAttributes
+
       const deletedIds = findAndDeleteChildFeature(
         topLevelFeature,
         secondExon._id,
@@ -123,11 +134,16 @@ export class MergeExonsChange extends FeatureChange {
       }
       mergedExon.setMin(Math.min(firstExon.min, secondExon.min))
       mergedExon.setMax(Math.max(firstExon.max, secondExon.max))
-      const mergedAttrs = this.mergeAttributes(firstExon, secondExon)
-      mergedExon.setAttributes(new Map())
-      for (const key of Object.keys(mergedAttrs)) {
-        mergedExon.setAttribute(key, mergedAttrs[key])
+
+      const mrg = mergedExon.attributes.get('merged_with')?.slice() ?? []
+      const mergedWith = stringifyAttributes(
+        attributesToRecords(secondExon.attributes),
+      )
+      if (!mrg.includes(mergedWith)) {
+        mrg.push(mergedWith)
       }
+      mergedExon.setAttribute('merged_with', mrg)
+
       mergedExon.parent?.deleteChild(secondExon._id)
     }
   }
@@ -151,35 +167,35 @@ export class MergeExonsChange extends FeatureChange {
     )
   }
 
-  mergeAttributes(
-    firstExon: AnnotationFeatureSnapshot,
-    secondExon: AnnotationFeatureSnapshot,
-  ): Record<string, string[]> {
-    let mergedAttrs: Record<string, string[]> = {}
-    if (firstExon.attributes) {
-      // eslint-disable-next-line unicorn/prefer-structured-clone
-      mergedAttrs = JSON.parse(JSON.stringify(firstExon.attributes))
-    }
-
-    if (secondExon.attributes) {
-      // eslint-disable-next-line unicorn/prefer-structured-clone
-      const attrs: Record<string, string[]> = JSON.parse(
-        JSON.stringify(secondExon.attributes),
-      )
-      for (const key of Object.keys(attrs)) {
-        if (key === '_id' || key === 'gff_id') {
-          continue
-        }
-        if (!Object.keys(mergedAttrs).includes(key)) {
-          mergedAttrs[key] = []
-        }
-        attrs[key].map((x) => {
-          if (!mergedAttrs[key].includes(x)) {
-            mergedAttrs[key].push(x)
-          }
-        })
-      }
-    }
-    return mergedAttrs
-  }
+  // mergeAttributes(
+  //   firstExon: AnnotationFeatureSnapshot,
+  //   secondExon: AnnotationFeatureSnapshot,
+  // ): Record<string, string[]> {
+  //   let mergedAttrs: Record<string, string[]> = {}
+  //   if (firstExon.attributes) {
+  //     // eslint-disable-next-line unicorn/prefer-structured-clone
+  //     mergedAttrs = JSON.parse(JSON.stringify(firstExon.attributes))
+  //   }
+
+  //   if (secondExon.attributes) {
+  //     // eslint-disable-next-line unicorn/prefer-structured-clone
+  //     const attrs: Record<string, string[]> = JSON.parse(
+  //       JSON.stringify(secondExon.attributes),
+  //     )
+  //     for (const key of Object.keys(attrs)) {
+  //       if (key === '_id' || key === 'gff_id') {
+  //         continue
+  //       }
+  //       if (!Object.keys(mergedAttrs).includes(key)) {
+  //         mergedAttrs[key] = []
+  //       }
+  //       attrs[key].map((x) => {
+  //         if (!mergedAttrs[key].includes(x)) {
+  //           mergedAttrs[key].push(x)
+  //         }
+  //       })
+  //     }
+  //   }
+  //   return mergedAttrs
+  // }
 }

package/src/Changes/MergeTranscriptsChange.ts

@@ -16,6 +16,9 @@ import {
 } from '@apollo-annotation/mst'
 import { type Feature } from '@apollo-annotation/schemas'
 import { doesIntersect2 } from '@jbrowse/core/util'
+import { getSnapshot } from 'mobx-state-tree'
+
+import { attributesToRecords, stringifyAttributes } from '../util'
 
 import { findAndDeleteChildFeature } from './DeleteFeatureChange'
 import { UndoMergeTranscriptsChange } from './UndoMergeTranscriptsChange'
@@ -42,6 +45,7 @@ interface SerializedMergeTranscriptsChangeMultiple
 export type SerializedMergeTranscriptsChange =
   | SerializedMergeTranscriptsChangeSingle
   | SerializedMergeTranscriptsChangeMultiple
+
 export class MergeTranscriptsChange extends FeatureChange {
   typeName = 'MergeTranscriptsChange' as const
   changes: MergeTranscriptsChangeDetails[]
@@ -50,6 +54,10 @@ export class MergeTranscriptsChange extends FeatureChange {
     super(json, options)
     this.changes = 'changes' in json ? json.changes : [json]
   }
+  // eslint-disable-next-line @typescript-eslint/class-literal-property-style
+  get notification() {
+    return 'Transcripts successfully merged'
+  }
 
   toJSON(): SerializedMergeTranscriptsChange {
     const { assembly, changedIds, changes, typeName } = this
@@ -111,7 +119,21 @@ export class MergeTranscriptsChange extends FeatureChange {
   ) {
     firstTranscript.min = Math.min(firstTranscript.min, secondTranscript.min)
     firstTranscript.max = Math.max(firstTranscript.max, secondTranscript.max)
-    this.mergeTranscriptAttributes(firstTranscript, secondTranscript)
+
+    const mergedAttributes: Record<string, string[]> =
+      firstTranscript.attributes
+        ? JSON.parse(JSON.stringify(firstTranscript.attributes))
+        : {}
+    if (secondTranscript.attributes) {
+      if (!Object.keys(mergedAttributes).includes('merged_with')) {
+        mergedAttributes.merged_with = []
+      }
+      mergedAttributes.merged_with.push(
+        stringifyAttributes(attributesToRecords(secondTranscript.attributes)),
+      )
+    }
+    firstTranscript.attributes = mergedAttributes
+
     if (secondTranscript.children) {
       for (const [, secondFeatureChild] of Object.entries(
         secondTranscript.children,
@@ -133,9 +155,13 @@ export class MergeTranscriptsChange extends FeatureChange {
     }
     let merged = false
     let mrgChild: Feature | undefined
-    for (const [fKey, firstFeatureChild] of firstTranscript.children) {
+    let toDelete
+    for (const [, firstFeatureChild] of firstTranscript.children) {
       if (!merged || !mrgChild) {
+        toDelete = false
         mrgChild = firstFeatureChild
+      } else {
+        toDelete = true
       }
       if (
         mrgChild.type === secondFeatureChild.type &&
@@ -163,9 +189,36 @@ export class MergeTranscriptsChange extends FeatureChange {
           mrgChild.max,
           firstFeatureChild.max,
         )
-        const mergedAttrs = this.mergeAttributes(mrgChild, secondFeatureChild)
-        mrgChild.attributes = mergedAttrs
-        firstTranscript.children.delete(fKey)
+
+        if (!mrgChild.attributes) {
+          mrgChild.attributes = {}
+        }
+
+        const mrgChildAttr: Record<string, string[]> = JSON.parse(
+          JSON.stringify(mrgChild.attributes),
+        )
+
+        if (!Object.keys(mrgChildAttr).includes('merged_with')) {
+          mrgChildAttr.merged_with = []
+        }
+        const mergedWithAttributes = mrgChildAttr.merged_with
+        mergedWithAttributes.push(
+          stringifyAttributes(
+            attributesToRecords(secondFeatureChild.attributes),
+          ),
+        )
+
+        if (toDelete) {
+          const recs: Record<string, string[] | undefined> =
+            firstFeatureChild.attributes
+              ? JSON.parse(JSON.stringify(firstFeatureChild.attributes))
+              : undefined
+          mergedWithAttributes.push(stringifyAttributes(recs))
+          firstTranscript.children.delete(firstFeatureChild._id.toString())
+        }
+
+        mrgChildAttr.merged_with = [...new Set(mergedWithAttributes)]
+        mrgChild.attributes = mrgChildAttr
         merged = true
       }
     }
@@ -215,7 +268,16 @@ export class MergeTranscriptsChange extends FeatureChange {
     firstTranscript.setMin(Math.min(firstTranscript.min, secondTranscript.min))
     firstTranscript.setMax(Math.max(firstTranscript.max, secondTranscript.max))
 
-    this.mergeTranscriptAttributes(firstTranscript, secondTranscript)
+    const mrg = firstTranscript.attributes.get('merged_with')?.slice() ?? []
+    const mergedWith = stringifyAttributes(
+      attributesToRecords(secondTranscript.attributes),
+    )
+
+    if (!mrg.includes(mergedWith)) {
+      // executeOnClient runs twice (?!) so avoid adding this key again
+      mrg.push(mergedWith)
+    }
+    firstTranscript.setAttribute('merged_with', mrg)
 
     if (secondTranscript.children) {
       for (const [, secondFeatureChild] of Object.entries(
@@ -269,15 +331,20 @@ export class MergeTranscriptsChange extends FeatureChange {
           Math.max(secondFeatureChild.max, mrgChild.max, firstFeatureChild.max),
         )
 
-        const mergedAttrs = this.mergeAttributes(mrgChild, secondFeatureChild)
-        Object.entries(mergedAttrs).map(([key, value]) => {
-          if (mrgChild) {
-            mrgChild.setAttribute(key, value)
-          }
-        })
+        const mergedWithAttributes =
+          mrgChild.attributes.get('merged_with')?.slice() ?? []
+        mergedWithAttributes.push(
+          stringifyAttributes(
+            attributesToRecords(secondFeatureChild.attributes),
+          ),
+        )
         if (toDelete) {
+          mergedWithAttributes.push(
+            stringifyAttributes(getSnapshot(firstFeatureChild).attributes),
+          )
           firstTranscript.deleteChild(firstFeatureChild._id)
         }
+        mrgChild.setAttribute('merged_with', [...new Set(mergedWithAttributes)])
         merged = true
       }
     }
@@ -288,71 +355,19 @@ export class MergeTranscriptsChange extends FeatureChange {
       })
     }
 
-    if (!(merged && mrgChild)) {
+    if (merged && mrgChild) {
+      firstTranscript.addChild(getSnapshot(mrgChild))
+    } else {
       // This secondFeatureChild has no overlap with any feature in the
       // receiving transcript so we add it as it is to the receiving transcript
       firstTranscript.addChild(secondFeatureChild)
     }
   }
 
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  isAnnotationFeature(obj: any): obj is AnnotationFeature {
-    return (
-      // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
-      typeof obj.setMin === 'function' &&
-      // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
-      typeof obj.setMax === 'function' &&
-      // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
-      typeof obj.addChild === 'function' &&
-      // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
-      typeof obj.deleteChild === 'function'
-    )
-  }
-
   async executeOnLocalGFF3(_backend: LocalGFF3DataStore) {
     throw new Error('executeOnLocalGFF3 not implemented')
   }
 
-  /* Merge attributes from source into destination */
-  mergeAttributes(
-    destination: Feature | AnnotationFeature,
-    source: AnnotationFeatureSnapshot,
-  ): Record<string, string[]> {
-    const destAttrs: Record<string, string[]> = destination.attributes
-      ? JSON.parse(JSON.stringify(destination.attributes))
-      : {}
-    if (source.attributes) {
-      const sourceAttrs: Record<string, string[]> = JSON.parse(
-        JSON.stringify(source.attributes),
-      )
-      Object.entries(sourceAttrs).map(([key, value]) => {
-        if (!(key in destAttrs)) {
-          destAttrs[key] = []
-        }
-        value.map((x) => {
-          if (!destAttrs[key].includes(x)) {
-            destAttrs[key].push(x)
-          }
-        })
-      })
-    }
-    return destAttrs
-  }
-
-  mergeTranscriptAttributes(
-    firstTranscript: Feature | AnnotationFeature,
-    secondTranscript: AnnotationFeatureSnapshot,
-  ) {
-    const txAttrs = this.mergeAttributes(firstTranscript, secondTranscript)
-    if (this.isAnnotationFeature(firstTranscript)) {
-      Object.entries(txAttrs).map(([key, value]) => {
-        firstTranscript.setAttribute(key, value)
-      })
-    } else {
-      firstTranscript.attributes = txAttrs
-    }
-  }
-
   getInverse() {
     const { assembly, changedIds, changes, logger } = this
     const inverseChangedIds = [...changedIds].reverse()

package/src/Checks/CDSCheck.ts

@@ -22,7 +22,6 @@ enum CAUSES {
   'InternalStopCodon',
   'MissingStartCodon',
   'MissingStopCodon',
-  'MultipleOfThree',
 }
 
 const iupacComplements: Record<string, string | undefined> = {
@@ -156,6 +155,10 @@ async function checkMRNA(
   for (const cdsLocation of cdsLocations) {
     const sequence = await getCDSSequence(cdsLocation, strand, getSequence)
     const codons = splitSequenceInCodons(sequence)
+    const cdsEnd =
+      strand === -1
+        ? cdsLocation.at(0)?.min ?? min
+        : cdsLocation.at(-1)?.max ?? max
     if (sequence.length % 3 === 0) {
       const start_codon = codons.at(0)
       if (start_codon && !(start_codon.toUpperCase() in START_CODONS)) {
@@ -175,12 +178,9 @@ async function checkMRNA(
           message: `Unexpected start codon in feature "${_id}": ${start_codon}`,
         })
       }
+
       const lastCodon = codons.at(-1) // Last codon is supposed to be a stop
       if (lastCodon && !(lastCodon.toUpperCase() in STOP_CODONS)) {
-        const cdsEnd =
-          strand === -1
-            ? cdsLocation.at(0)?.min ?? min
-            : cdsLocation.at(-1)?.max ?? max
         checkResults.push({
           _id: new ObjectID().toHexString(),
           name: CHECK_NAME,
@@ -196,12 +196,12 @@ async function checkMRNA(
       checkResults.push({
         _id: new ObjectID().toHexString(),
         name: CHECK_NAME,
-        cause: CAUSES[CAUSES.MultipleOfThree],
+        cause: CAUSES[CAUSES.MissingStopCodon],
         ids,
         refSeq: refSeq.toString(),
-        start: min,
-        end: max,
-        message: `The coding sequence for feature "${_id}" is not a multiple of three`,
+        start: cdsEnd,
+        end: cdsEnd,
+        message: `Missing stop codon: The coding sequence for feature "${_id}" is not a multiple of three`,
       })
     }
     for (const [idx, codon] of codons.entries()) {
@@ -285,7 +285,7 @@ export class CDSCheck extends Check {
   name = CHECK_NAME
   causes = getCauses()
   version = 1
-  default = true
+  isDefault = true
 
   async checkFeature(
     feature: AnnotationFeatureSnapshot,