@apollo-annotation/shared 0.3.6 → 0.3.8

package/dist/Changes/UndoMergeTranscriptsChange.js

@@ -0,0 +1,104 @@
+"use strict";
+/* eslint-disable @typescript-eslint/require-await */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.UndoMergeTranscriptsChange = void 0;
+const common_1 = require("@apollo-annotation/common");
+const MergeTranscriptsChange_1 = require("./MergeTranscriptsChange");
+class UndoMergeTranscriptsChange extends common_1.FeatureChange {
+    typeName = 'UndoMergeTranscriptsChange';
+    changes;
+    constructor(json, options) {
+        super(json, options);
+        this.changes = 'changes' in json ? json.changes : [json];
+    }
+    toJSON() {
+        const { assembly, changedIds, changes, typeName } = this;
+        if (changes.length === 1) {
+            const [{ transcriptsToRestore, parentFeatureId }] = changes;
+            return {
+                typeName,
+                changedIds,
+                assembly,
+                transcriptsToRestore,
+                parentFeatureId,
+            };
+        }
+        return { typeName, changedIds, assembly, changes };
+    }
+    async executeOnServer(backend) {
+        const { featureModel, session } = backend;
+        const { changes } = this;
+        for (const change of changes) {
+            const { transcriptsToRestore, parentFeatureId } = change;
+            if (transcriptsToRestore.length !== 2) {
+                throw new Error(`Expected exactly two transcripts to restore. Got :${transcriptsToRestore.length}`);
+            }
+            const topLevelFeature = await featureModel
+                .findOne({ allIds: parentFeatureId })
+                .session(session)
+                .exec();
+            if (!topLevelFeature) {
+                throw new Error(`Could not find feature with ID "${parentFeatureId}"`);
+            }
+            const parentFeature = this.getFeatureFromId(topLevelFeature, parentFeatureId);
+            if (!parentFeature) {
+                throw new Error(`Could not find feature with ID "${parentFeatureId}" in feature "${topLevelFeature._id.toString()}"`);
+            }
+            if (!parentFeature.children) {
+                parentFeature.children = new Map();
+            }
+            for (const transcript of transcriptsToRestore) {
+                this.addChild(parentFeature, transcript);
+                const childIds = this.getChildFeatureIds(transcript);
+                topLevelFeature.allIds.push(transcript._id, ...childIds);
+            }
+            await topLevelFeature.save();
+        }
+    }
+    async executeOnLocalGFF3(_backend) {
+        throw new Error('executeOnLocalGFF3 not implemented');
+    }
+    async executeOnClient(dataStore) {
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+        if (!dataStore) {
+            throw new Error('No data store');
+        }
+        const { changes } = this;
+        for (const change of changes) {
+            const { transcriptsToRestore, parentFeatureId } = change;
+            if (!parentFeatureId) {
+                throw new Error('Parent ID is missing');
+            }
+            const parentFeature = dataStore.getFeature(parentFeatureId);
+            if (!parentFeature) {
+                throw new Error(`Could not find parent feature "${parentFeatureId}"`);
+            }
+            // create an ID for the parent feature if it does not have one
+            if (!parentFeature.attributes.get('_id')) {
+                parentFeature.setAttribute('_id', [parentFeature._id]);
+            }
+            for (const transcript of transcriptsToRestore) {
+                parentFeature.addChild(transcript);
+            }
+        }
+    }
+    getInverse() {
+        const { assembly, changedIds, changes, logger } = this;
+        const inverseChangedIds = [...changedIds].reverse();
+        const inverseChanges = [...changes]
+            .reverse()
+            .map((undoMergeTranscriptsChange) => ({
+            firstTranscript: undoMergeTranscriptsChange.transcriptsToRestore[0],
+            secondTranscript: undoMergeTranscriptsChange.transcriptsToRestore[1],
+            parentFeatureId: undoMergeTranscriptsChange.parentFeatureId,
+        }));
+        return new MergeTranscriptsChange_1.MergeTranscriptsChange({
+            changedIds: inverseChangedIds,
+            typeName: 'MergeTranscriptsChange',
+            changes: inverseChanges,
+            assembly,
+        }, { logger });
+    }
+}
+exports.UndoMergeTranscriptsChange = UndoMergeTranscriptsChange;
+//# sourceMappingURL=UndoMergeTranscriptsChange.js.map

package/dist/Changes/UndoMergeTranscriptsChange.js.map

@@ -0,0 +1 @@
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package/dist/Changes/UndoSplitExonChange.d.ts

@@ -0,0 +1,32 @@
+import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
+import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
+import { SplitExonChange } from './SplitExonChange';
+interface SerializedUndoSplitExonChangeBase extends SerializedFeatureChange {
+    typeName: 'UndoSplitExonChange';
+}
+export interface UndoSplitExonChangeDetails {
+    exonToRestore: AnnotationFeatureSnapshot;
+    parentFeatureId: string;
+    idsToDelete: string[];
+    upstreamCut: number;
+    downstreamCut: number;
+    leftExonId: string;
+    rightExonId: string;
+}
+interface SerializedUndoSplitExonChangeSingle extends SerializedUndoSplitExonChangeBase, UndoSplitExonChangeDetails {
+}
+interface SerializedUndoSplitExonChangeMultiple extends SerializedUndoSplitExonChangeBase {
+    changes: UndoSplitExonChangeDetails[];
+}
+export type SerializedUndoSplitExonChange = SerializedUndoSplitExonChangeSingle | SerializedUndoSplitExonChangeMultiple;
+export declare class UndoSplitExonChange extends FeatureChange {
+    typeName: "UndoSplitExonChange";
+    changes: UndoSplitExonChangeDetails[];
+    constructor(json: SerializedUndoSplitExonChange, options?: ChangeOptions);
+    toJSON(): SerializedUndoSplitExonChange;
+    executeOnServer(backend: ServerDataStore): Promise<void>;
+    executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<void>;
+    executeOnClient(dataStore: ClientDataStore): Promise<void>;
+    getInverse(): SplitExonChange;
+}
+export {};

package/dist/Changes/UndoSplitExonChange.js

@@ -0,0 +1,111 @@
+"use strict";
+/* eslint-disable @typescript-eslint/require-await */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.UndoSplitExonChange = void 0;
+const common_1 = require("@apollo-annotation/common");
+const DeleteFeatureChange_1 = require("./DeleteFeatureChange");
+const SplitExonChange_1 = require("./SplitExonChange");
+class UndoSplitExonChange extends common_1.FeatureChange {
+    typeName = 'UndoSplitExonChange';
+    changes;
+    constructor(json, options) {
+        super(json, options);
+        this.changes = 'changes' in json ? json.changes : [json];
+    }
+    toJSON() {
+        const { assembly, changedIds, changes, typeName } = this;
+        if (changes.length === 1) {
+            const [{ exonToRestore, parentFeatureId, idsToDelete, upstreamCut, downstreamCut, leftExonId, rightExonId, },] = changes;
+            return {
+                typeName,
+                changedIds,
+                assembly,
+                exonToRestore,
+                parentFeatureId,
+                idsToDelete,
+                upstreamCut,
+                downstreamCut,
+                leftExonId,
+                rightExonId,
+            };
+        }
+        return { typeName, changedIds, assembly, changes };
+    }
+    async executeOnServer(backend) {
+        const { featureModel, session } = backend;
+        const { changes } = this;
+        for (const change of changes) {
+            const { exonToRestore, parentFeatureId, idsToDelete } = change;
+            const topLevelFeature = await featureModel
+                .findOne({ allIds: parentFeatureId })
+                .session(session)
+                .exec();
+            if (!topLevelFeature) {
+                throw new Error(`Could not find feature with ID "${parentFeatureId}"`);
+            }
+            const parentFeature = this.getFeatureFromId(topLevelFeature, parentFeatureId);
+            if (!parentFeature) {
+                throw new Error(`Could not find feature with ID "${parentFeatureId}" in feature "${topLevelFeature._id.toString()}"`);
+            }
+            if (!parentFeature.children) {
+                parentFeature.children = new Map();
+            }
+            this.addChild(parentFeature, exonToRestore);
+            const childIds = this.getChildFeatureIds(exonToRestore);
+            topLevelFeature.allIds.push(exonToRestore._id, ...childIds);
+            topLevelFeature.allIds = topLevelFeature.allIds.filter((id) => !idsToDelete.includes(id));
+            idsToDelete.map((id) => (0, DeleteFeatureChange_1.findAndDeleteChildFeature)(topLevelFeature, id, this));
+            await topLevelFeature.save();
+        }
+    }
+    async executeOnLocalGFF3(_backend) {
+        throw new Error('executeOnLocalGFF3 not implemented');
+    }
+    async executeOnClient(dataStore) {
+        // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+        if (!dataStore) {
+            throw new Error('No data store');
+        }
+        const { changes } = this;
+        for (const change of changes) {
+            const { exonToRestore, parentFeatureId, idsToDelete } = change;
+            if (!parentFeatureId) {
+                throw new Error('Parent ID is missing');
+            }
+            const parentFeature = dataStore.getFeature(parentFeatureId);
+            if (!parentFeature) {
+                throw new Error(`Could not find parent feature "${parentFeatureId}"`);
+            }
+            // create an ID for the parent feature if it does not have one
+            if (!parentFeature.attributes.get('_id')) {
+                parentFeature.setAttribute('_id', [parentFeature._id]);
+            }
+            parentFeature.addChild(exonToRestore);
+            idsToDelete.map((id) => {
+                parentFeature.deleteChild(id);
+            });
+        }
+    }
+    getInverse() {
+        const { assembly, changedIds, changes, logger } = this;
+        const inverseChangedIds = [...changedIds].reverse();
+        const inverseChanges = [...changes]
+            .reverse()
+            .map((undoSplitExonChange) => ({
+            parentFeatureId: undoSplitExonChange.parentFeatureId,
+            exonToBeSplit: undoSplitExonChange.exonToRestore,
+            upstreamCut: undoSplitExonChange.upstreamCut,
+            downstreamCut: undoSplitExonChange.downstreamCut,
+            leftExonId: undoSplitExonChange.leftExonId,
+            rightExonId: undoSplitExonChange.rightExonId,
+        }));
+        return new SplitExonChange_1.SplitExonChange({
+            changedIds: inverseChangedIds,
+            typeName: 'SplitExonChange',
+            changes: inverseChanges,
+            assembly,
+        }, { logger });
+    }
+}
+exports.UndoSplitExonChange = UndoSplitExonChange;
+//# sourceMappingURL=UndoSplitExonChange.js.map

package/dist/Changes/UndoSplitExonChange.js.map

@@ -0,0 +1 @@
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package/dist/Changes/index.d.ts

@@ -1,3 +1,4 @@
+import { AddAssemblyAliasesChange } from './AddAssemblyAliasesChange';
 import { AddAssemblyAndFeaturesFromFileChange } from './AddAssemblyAndFeaturesFromFileChange';
 import { AddAssemblyFromExternalChange } from './AddAssemblyFromExternalChange';
 import { AddAssemblyFromFileChange } from './AddAssemblyFromFileChange';
@@ -11,8 +12,14 @@ import { FeatureAttributeChange } from './FeatureAttributeChange';
 import { ImportJBrowseConfigChange } from './ImportJBrowseConfigChange';
 import { LocationEndChange } from './LocationEndChange';
 import { LocationStartChange } from './LocationStartChange';
+import { MergeExonsChange } from './MergeExonsChange';
+import { MergeTranscriptsChange } from './MergeTranscriptsChange';
+import { SplitExonChange } from './SplitExonChange';
 import { StrandChange } from './StrandChange';
 import { TypeChange } from './TypeChange';
+import { UndoMergeExonsChange } from './UndoMergeExonsChange';
+import { UndoMergeTranscriptsChange } from './UndoMergeTranscriptsChange';
+import { UndoSplitExonChange } from './UndoSplitExonChange';
 import { UserChange } from './UserChange';
 export declare const changes: {
     AddAssemblyAndFeaturesFromFileChange: typeof AddAssemblyAndFeaturesFromFileChange;
@@ -27,10 +34,17 @@ export declare const changes: {
     ImportJBrowseConfigChange: typeof ImportJBrowseConfigChange;
     LocationEndChange: typeof LocationEndChange;
     LocationStartChange: typeof LocationStartChange;
+    MergeExonsChange: typeof MergeExonsChange;
+    SplitExonChange: typeof SplitExonChange;
+    MergeTranscriptsChange: typeof MergeTranscriptsChange;
+    UndoMergeExonsChange: typeof UndoMergeExonsChange;
+    UndoSplitExonChange: typeof UndoSplitExonChange;
+    UndoMergeTranscriptsChange: typeof UndoMergeTranscriptsChange;
     StrandChange: typeof StrandChange;
     TypeChange: typeof TypeChange;
     UserChange: typeof UserChange;
     AddRefSeqAliasesChange: typeof AddRefSeqAliasesChange;
+    AddAssemblyAliasesChange: typeof AddAssemblyAliasesChange;
 };
 export * from './AddAssemblyAndFeaturesFromFileChange';
 export * from './AddAssemblyFromFileChange';
@@ -44,7 +58,14 @@ export * from './FeatureAttributeChange';
 export * from './ImportJBrowseConfigChange';
 export * from './LocationEndChange';
 export * from './LocationStartChange';
+export * from './MergeExonsChange';
+export * from './SplitExonChange';
+export * from './MergeTranscriptsChange';
+export * from './UndoMergeExonsChange';
+export * from './UndoSplitExonChange';
+export * from './UndoMergeTranscriptsChange';
 export * from './StrandChange';
 export * from './TypeChange';
 export * from './UserChange';
 export * from './AddRefSeqAliasesChange';
+export * from './AddAssemblyAliasesChange';

package/dist/Changes/index.js

@@ -2,6 +2,7 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.changes = void 0;
 const tslib_1 = require("tslib");
+const AddAssemblyAliasesChange_1 = require("./AddAssemblyAliasesChange");
 const AddAssemblyAndFeaturesFromFileChange_1 = require("./AddAssemblyAndFeaturesFromFileChange");
 const AddAssemblyFromExternalChange_1 = require("./AddAssemblyFromExternalChange");
 const AddAssemblyFromFileChange_1 = require("./AddAssemblyFromFileChange");
@@ -15,8 +16,14 @@ const FeatureAttributeChange_1 = require("./FeatureAttributeChange");
 const ImportJBrowseConfigChange_1 = require("./ImportJBrowseConfigChange");
 const LocationEndChange_1 = require("./LocationEndChange");
 const LocationStartChange_1 = require("./LocationStartChange");
+const MergeExonsChange_1 = require("./MergeExonsChange");
+const MergeTranscriptsChange_1 = require("./MergeTranscriptsChange");
+const SplitExonChange_1 = require("./SplitExonChange");
 const StrandChange_1 = require("./StrandChange");
 const TypeChange_1 = require("./TypeChange");
+const UndoMergeExonsChange_1 = require("./UndoMergeExonsChange");
+const UndoMergeTranscriptsChange_1 = require("./UndoMergeTranscriptsChange");
+const UndoSplitExonChange_1 = require("./UndoSplitExonChange");
 const UserChange_1 = require("./UserChange");
 exports.changes = {
     AddAssemblyAndFeaturesFromFileChange: AddAssemblyAndFeaturesFromFileChange_1.AddAssemblyAndFeaturesFromFileChange,
@@ -31,10 +38,17 @@ exports.changes = {
     ImportJBrowseConfigChange: ImportJBrowseConfigChange_1.ImportJBrowseConfigChange,
     LocationEndChange: LocationEndChange_1.LocationEndChange,
     LocationStartChange: LocationStartChange_1.LocationStartChange,
+    MergeExonsChange: MergeExonsChange_1.MergeExonsChange,
+    SplitExonChange: SplitExonChange_1.SplitExonChange,
+    MergeTranscriptsChange: MergeTranscriptsChange_1.MergeTranscriptsChange,
+    UndoMergeExonsChange: UndoMergeExonsChange_1.UndoMergeExonsChange,
+    UndoSplitExonChange: UndoSplitExonChange_1.UndoSplitExonChange,
+    UndoMergeTranscriptsChange: UndoMergeTranscriptsChange_1.UndoMergeTranscriptsChange,
     StrandChange: StrandChange_1.StrandChange,
     TypeChange: TypeChange_1.TypeChange,
     UserChange: UserChange_1.UserChange,
     AddRefSeqAliasesChange: AddRefSeqAliasesChange_1.AddRefSeqAliasesChange,
+    AddAssemblyAliasesChange: AddAssemblyAliasesChange_1.AddAssemblyAliasesChange,
 };
 tslib_1.__exportStar(require("./AddAssemblyAndFeaturesFromFileChange"), exports);
 tslib_1.__exportStar(require("./AddAssemblyFromFileChange"), exports);
@@ -48,8 +62,15 @@ tslib_1.__exportStar(require("./FeatureAttributeChange"), exports);
 tslib_1.__exportStar(require("./ImportJBrowseConfigChange"), exports);
 tslib_1.__exportStar(require("./LocationEndChange"), exports);
 tslib_1.__exportStar(require("./LocationStartChange"), exports);
+tslib_1.__exportStar(require("./MergeExonsChange"), exports);
+tslib_1.__exportStar(require("./SplitExonChange"), exports);
+tslib_1.__exportStar(require("./MergeTranscriptsChange"), exports);
+tslib_1.__exportStar(require("./UndoMergeExonsChange"), exports);
+tslib_1.__exportStar(require("./UndoSplitExonChange"), exports);
+tslib_1.__exportStar(require("./UndoMergeTranscriptsChange"), exports);
 tslib_1.__exportStar(require("./StrandChange"), exports);
 tslib_1.__exportStar(require("./TypeChange"), exports);
 tslib_1.__exportStar(require("./UserChange"), exports);
 tslib_1.__exportStar(require("./AddRefSeqAliasesChange"), exports);
+tslib_1.__exportStar(require("./AddAssemblyAliasesChange"), exports);
 //# sourceMappingURL=index.js.map

package/dist/Changes/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/Changes/index.ts"],"names":[],"mappings":";;;;AAAA,yEAAqE;AACrE,iGAA6F;AAC7F,mFAA+E;AAC/E,2EAAuE;AACvE,yDAAqD;AACrD,2EAAuE;AACvE,qEAAiE;AACjE,iEAA6D;AAC7D,+DAA2D;AAC3D,yDAAqD;AACrD,qEAAiE;AACjE,2EAAuE;AACvE,2DAAuD;AACvD,+DAA2D;AAC3D,yDAAqD;AACrD,qEAAiE;AACjE,uDAAmD;AACnD,iDAA6C;AAC7C,6CAAyC;AACzC,iEAA6D;AAC7D,6EAAyE;AACzE,+DAA2D;AAC3D,6CAAyC;AAE5B,QAAA,OAAO,GAAG;IACrB,oCAAoC,EAApC,2EAAoC;IACpC,yBAAyB,EAAzB,qDAAyB;IACzB,6BAA6B,EAA7B,6DAA6B;IAC7B,gBAAgB,EAAhB,mCAAgB;IAChB,yBAAyB,EAAzB,qDAAyB;IACzB,oBAAoB,EAApB,2CAAoB;IACpB,mBAAmB,EAAnB,yCAAmB;IACnB,gBAAgB,EAAhB,mCAAgB;IAChB,sBAAsB,EAAtB,+CAAsB;IACtB,yBAAyB,EAAzB,qDAAyB;IACzB,iBAAiB,EAAjB,qCAAiB;IACjB,mBAAmB,EAAnB,yCAAmB;IACnB,gBAAgB,EAAhB,mCAAgB;IAChB,eAAe,EAAf,iCAAe;IACf,sBAAsB,EAAtB,+CAAsB;IACtB,oBAAoB,EAApB,2CAAoB;IACpB,mBAAmB,EAAnB,yCAAmB;IACnB,0BAA0B,EAA1B,uDAA0B;IAC1B,YAAY,EAAZ,2BAAY;IACZ,UAAU,EAAV,uBAAU;IACV,UAAU,EAAV,uBAAU;IACV,sBAAsB,EAAtB,+CAAsB;IACtB,wBAAwB,EAAxB,mDAAwB;CACzB,CAAA;AAED,iFAAsD;AACtD,sEAA2C;AAC3C,0EAA+C;AAC/C,6DAAkC;AAClC,sEAA2C;AAC3C,iEAAsC;AACtC,gEAAqC;AACrC,6DAAkC;AAClC,mEAAwC;AACxC,sEAA2C;AAC3C,8DAAmC;AACnC,gEAAqC;AACrC,6DAAkC;AAClC,4DAAiC;AACjC,mEAAwC;AACxC,iEAAsC;AACtC,gEAAqC;AACrC,uEAA4C;AAC5C,yDAA8B;AAC9B,uDAA4B;AAC5B,uDAA4B;AAC5B,mEAAwC;AACxC,qEAA0C"}

package/dist/Checks/CDSCheck.d.ts

@@ -4,6 +4,6 @@ export declare class CDSCheck extends Check {
     name: string;
     causes: string[];
     version: number;
-    default: boolean;
+    isDefault: boolean;
     checkFeature(feature: AnnotationFeatureSnapshot, getSequence: (start: number, end: number) => Promise<string>): Promise<CheckResultSnapshot[]>;
 }

package/dist/Checks/CDSCheck.js

@@ -21,7 +21,6 @@ var CAUSES;
     CAUSES[CAUSES["InternalStopCodon"] = 0] = "InternalStopCodon";
     CAUSES[CAUSES["MissingStartCodon"] = 1] = "MissingStartCodon";
     CAUSES[CAUSES["MissingStopCodon"] = 2] = "MissingStopCodon";
-    CAUSES[CAUSES["MultipleOfThree"] = 3] = "MultipleOfThree";
 })(CAUSES || (CAUSES = {}));
 const iupacComplements = {
     G: 'C',
@@ -126,6 +125,9 @@ async function checkMRNA(feature, getSequence) {
     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)) {
@@ -146,9 +148,6 @@ async function checkMRNA(feature, getSequence) {
             }
             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 bson_objectid_1.default().toHexString(),
                     name: CHECK_NAME,
@@ -165,12 +164,12 @@ async function checkMRNA(feature, getSequence) {
             checkResults.push({
                 _id: new bson_objectid_1.default().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()) {
@@ -246,7 +245,7 @@ class CDSCheck extends common_1.Check {
     name = CHECK_NAME;
     causes = getCauses();
     version = 1;
-    default = true;
+    isDefault = true;
     async checkFeature(feature, getSequence) {
         if (feature.type === 'mRNA') {
             return checkMRNA(feature, getSequence);

package/dist/Checks/CDSCheck.js.map

@@ -1 +1 @@
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package/dist/Checks/TranscriptCheck.d.ts

@@ -0,0 +1,9 @@
+import { Check } from '@apollo-annotation/common';
+import { type AnnotationFeatureSnapshot, type CheckResultSnapshot } from '@apollo-annotation/mst';
+export declare class TranscriptCheck extends Check {
+    name: string;
+    causes: string[];
+    version: number;
+    isDefault: boolean;
+    checkFeature(feature: AnnotationFeatureSnapshot, getSequence: (start: number, end: number) => Promise<string>): Promise<CheckResultSnapshot[]>;
+}

package/dist/Checks/TranscriptCheck.js

@@ -0,0 +1,109 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.TranscriptCheck = void 0;
+const tslib_1 = require("tslib");
+const common_1 = require("@apollo-annotation/common");
+const util_1 = require("@jbrowse/core/util");
+const bson_objectid_1 = tslib_1.__importDefault(require("bson-objectid"));
+var CAUSES;
+(function (CAUSES) {
+    CAUSES[CAUSES["NonCanonicalSpliceSiteAtFivePrime"] = 0] = "NonCanonicalSpliceSiteAtFivePrime";
+    CAUSES[CAUSES["NonCanonicalSpliceSiteAtThreePrime"] = 1] = "NonCanonicalSpliceSiteAtThreePrime";
+})(CAUSES || (CAUSES = {}));
+const CHECK_NAME = 'TranscriptCheck';
+async function getSpliceSequences(transcript, getSequence) {
+    if (!transcript.children) {
+        return [];
+    }
+    const exons = [];
+    for (const [, child] of Object.entries(transcript.children)) {
+        if (child.type === 'exon') {
+            exons.push(child);
+        }
+    }
+    if (exons.length < 2) {
+        return [];
+    }
+    const spliceSeq = [];
+    for (let i = 0; i < exons.length - 1; i++) {
+        let fivePrimeMin = exons[i].max;
+        let threePrimeMin = exons[i + 1].min - 2;
+        if (transcript.strand === -1) {
+            const _fivePrimeMin = fivePrimeMin;
+            fivePrimeMin = threePrimeMin;
+            threePrimeMin = _fivePrimeMin;
+        }
+        let fivePrimeSeq = await getSequence(fivePrimeMin, fivePrimeMin + 2);
+        let threePrimeSeq = await getSequence(threePrimeMin, threePrimeMin + 2);
+        if (transcript.strand === -1) {
+            threePrimeSeq = (0, util_1.revcom)(threePrimeSeq);
+            fivePrimeSeq = (0, util_1.revcom)(fivePrimeSeq);
+        }
+        spliceSeq.push({
+            fivePrimeSeq,
+            fivePrimeMin,
+            threePrimeSeq,
+            threePrimeMin,
+        });
+    }
+    return spliceSeq;
+}
+async function checkTranscript(feature, getSequence) {
+    const checkResults = [];
+    const VALID_FIVE_PRIME_SEQ = new Set(['GT']);
+    const VALID_THREE_PRIME_SEQ = new Set(['AG']);
+    const spliceSequences = await getSpliceSequences(feature, getSequence);
+    for (const spliceSequence of spliceSequences) {
+        if (!VALID_FIVE_PRIME_SEQ.has(spliceSequence.fivePrimeSeq.toUpperCase())) {
+            checkResults.push({
+                _id: new bson_objectid_1.default().toHexString(),
+                name: CHECK_NAME,
+                cause: CAUSES[CAUSES.NonCanonicalSpliceSiteAtFivePrime],
+                ids: [feature._id],
+                refSeq: feature.refSeq.toString(),
+                start: spliceSequence.fivePrimeMin,
+                end: spliceSequence.fivePrimeMin + 2,
+                message: `Unexpected 5' splice site in "${feature._id}". Expected: ${[...VALID_FIVE_PRIME_SEQ].join('|')}, got: ${spliceSequence.fivePrimeSeq}`,
+            });
+        }
+        if (!VALID_THREE_PRIME_SEQ.has(spliceSequence.threePrimeSeq.toUpperCase())) {
+            checkResults.push({
+                _id: new bson_objectid_1.default().toHexString(),
+                name: CHECK_NAME,
+                cause: CAUSES[CAUSES.NonCanonicalSpliceSiteAtThreePrime],
+                ids: [feature._id],
+                refSeq: feature.refSeq.toString(),
+                start: spliceSequence.threePrimeMin,
+                end: spliceSequence.threePrimeMin + 2,
+                message: `Unexpected 3' splice site in "${feature._id}". Expected: ${[...VALID_THREE_PRIME_SEQ].join('|')}, got: ${spliceSequence.threePrimeSeq}`,
+            });
+        }
+    }
+    return checkResults;
+}
+function getCauses() {
+    return Object.values(CAUSES).filter((x) => Number.isNaN(Number(x)));
+}
+class TranscriptCheck extends common_1.Check {
+    name = 'TranscriptCheck';
+    causes = getCauses();
+    version = 1;
+    isDefault = true;
+    async checkFeature(feature, getSequence) {
+        if (feature.type === 'mRNA' ||
+            feature.type === 'transcript' ||
+            feature.type === 'pseudogenic_transcript') {
+            return checkTranscript(feature, getSequence);
+        }
+        if (!feature.children) {
+            return [];
+        }
+        const checkResults = [];
+        for (const child of Object.values(feature.children)) {
+            checkResults.push(...(await this.checkFeature(child, getSequence)));
+        }
+        return checkResults;
+    }
+}
+exports.TranscriptCheck = TranscriptCheck;
+//# sourceMappingURL=TranscriptCheck.js.map

package/dist/Checks/TranscriptCheck.js.map

@@ -0,0 +1 @@
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package/dist/Checks/index.d.ts

@@ -1 +1,2 @@
 export * from './CDSCheck';
+export * from './TranscriptCheck';

package/dist/Checks/index.js

@@ -2,4 +2,5 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 const tslib_1 = require("tslib");
 tslib_1.__exportStar(require("./CDSCheck"), exports);
+tslib_1.__exportStar(require("./TranscriptCheck"), exports);
 //# sourceMappingURL=index.js.map

package/dist/Checks/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/Checks/index.ts"],"names":[],"mappings":";;;AAAA,qDAA0B"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/Checks/index.ts"],"names":[],"mappings":";;;AAAA,qDAA0B;AAC1B,4DAAiC"}