@apollo-annotation/shared 0.3.8 → 0.3.10

package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.d.ts

@@ -8,6 +8,9 @@ export interface AddAssemblyAndFeaturesFromFileChangeDetails {
     fileIds: {
         fa: string;
     };
+    parseOptions?: {
+        bufferSize: number;
+    };
 }
 export interface SerializedAddAssemblyAndFeaturesFromFileChangeSingle extends SerializedAddAssemblyAndFeaturesFromFileChangeBase, AddAssemblyAndFeaturesFromFileChangeDetails {
 }

package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.js

@@ -30,7 +30,7 @@ class AddAssemblyAndFeaturesFromFileChange extends FromFileBaseChange_1.FromFile
         const { assemblyModel, checkModel, fileModel, filesService, user } = backend;
         const { assembly, changes, logger } = this;
         for (const change of changes) {
-            const { assemblyName, fileIds } = change;
+            const { assemblyName, fileIds, parseOptions } = change;
             const fileId = fileIds.fa;
             const { FILE_UPLOAD_FOLDER } = process.env;
             if (!FILE_UPLOAD_FOLDER) {
@@ -61,9 +61,10 @@ class AddAssemblyAndFeaturesFromFileChange extends FromFileBaseChange_1.FromFile
             // Add refSeqs
             // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
             await this.addRefSeqIntoDb(fileDoc, newAssemblyDoc._id.toString(), backend);
-            // Loop all features
-            logger.debug?.(`**************** LOOPATAAN KAIKKI FEATURET SEURAAVAKSI File type: "${fileDoc.type}"`);
-            const featureStream = filesService.parseGFF3(filesService.getFileStream(fileDoc));
+            const { bufferSize = 10_000 } = parseOptions ?? {};
+            const featureStream = filesService.parseGFF3(filesService.getFileStream(fileDoc), { bufferSize });
+            // @ts-expect-error type is wrong here
+            // eslint-disable-next-line @typescript-eslint/await-thenable
             for await (const f of featureStream) {
                 const gff3Feature = f;
                 logger.verbose?.(`ENTRY=${JSON.stringify(gff3Feature)}`);

package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.js.map

@@ -1 +1 @@
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package/dist/Changes/AddFeatureChange.js

@@ -53,6 +53,11 @@ class AddFeatureChange extends common_1.FeatureChange {
         }
         let featureCnt = 0;
         logger.debug?.(`changes: ${JSON.stringify(changes)}`);
+        const { INDEXED_IDS } = process.env;
+        let idsToIndex;
+        if (INDEXED_IDS) {
+            idsToIndex = INDEXED_IDS.split(',');
+        }
         // Loop the changes
         for (const change of changes) {
             logger.debug?.(`change: ${JSON.stringify(change)}`);
@@ -67,8 +72,9 @@ class AddFeatureChange extends common_1.FeatureChange {
             }
             // CopyFeature is called from CopyFeature.tsx
             if (copyFeature) {
+                const indexedIds = this.getIndexedIds(addedFeature, idsToIndex);
                 // Add into Mongo
-                const [newFeatureDoc] = await featureModel.create([{ ...addedFeature, allIds, status: -1, user }], { session });
+                const [newFeatureDoc] = await featureModel.create([{ ...addedFeature, allIds, indexedIds, status: -1, user }], { session });
                 logger.debug?.(`Copied feature, docId "${newFeatureDoc._id}" to assembly "${assembly}"`);
                 featureCnt++;
             }
@@ -94,7 +100,8 @@ class AddFeatureChange extends common_1.FeatureChange {
                 else {
                     const childIds = this.getChildFeatureIds(addedFeature);
                     const allIdsV2 = [_id, ...childIds];
-                    const [newFeatureDoc] = await featureModel.create([{ allIds: allIdsV2, status: 0, ...addedFeature }], { session });
+                    const indexedIds = this.getIndexedIds(addedFeature, idsToIndex);
+                    const [newFeatureDoc] = await featureModel.create([{ allIds: allIdsV2, indexedIds, status: 0, ...addedFeature }], { session });
                     logger.verbose?.(`Added docId "${newFeatureDoc._id}"`);
                 }
             }
@@ -113,9 +120,21 @@ class AddFeatureChange extends common_1.FeatureChange {
         for (const change of changes) {
             const { addedFeature, parentFeatureId } = change;
             if (parentFeatureId) {
-                const parentFeature = dataStore.getFeature(parentFeatureId);
+                let parentFeature = dataStore.getFeature(parentFeatureId);
+                // maybe the parent feature hasn't been loaded yet
                 if (!parentFeature) {
-                    throw new Error(`Could not find parent feature "${parentFeatureId}"`);
+                    await dataStore.loadFeatures([
+                        {
+                            assemblyName: assembly,
+                            refName: addedFeature.refSeq,
+                            start: addedFeature.min,
+                            end: addedFeature.max,
+                        },
+                    ]);
+                    parentFeature = dataStore.getFeature(parentFeatureId);
+                    if (!parentFeature) {
+                        throw new Error(`Could not find parent feature "${parentFeatureId}"`);
+                    }
                 }
                 // create an ID for the parent feature if it does not have one
                 if (!parentFeature.attributes.get('_id')) {

package/dist/Changes/AddFeatureChange.js.map

@@ -1 +1 @@
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package/dist/Changes/AddFeaturesFromFileChange.d.ts

@@ -6,6 +6,9 @@ export interface SerializedAddFeaturesFromFileChangeBase extends SerializedAssem
 }
 export interface AddFeaturesFromFileChangeDetails {
     fileId: string;
+    parseOptions?: {
+        bufferSize: number;
+    };
 }
 export interface SerializedAddFeaturesFromFileChangeSingle extends SerializedAddFeaturesFromFileChangeBase, AddFeaturesFromFileChangeDetails {
 }

package/dist/Changes/AddFeaturesFromFileChange.js

@@ -35,7 +35,7 @@ class AddFeaturesFromFileChange extends FromFileBaseChange_1.FromFileBaseChange
             await this.removeExistingFeatures(backend);
         }
         for (const change of changes) {
-            const { fileId } = change;
+            const { fileId, parseOptions } = change;
             const { FILE_UPLOAD_FOLDER } = process.env;
             if (!FILE_UPLOAD_FOLDER) {
                 throw new Error('No FILE_UPLOAD_FOLDER found in .env file');
@@ -47,8 +47,11 @@ class AddFeaturesFromFileChange extends FromFileBaseChange_1.FromFileBaseChange
             }
             logger.debug?.(`FileId "${fileId}", checksum "${fileDoc.checksum}"`);
             // Read data from compressed file and parse the content
-            const featureStream = filesService.parseGFF3(filesService.getFileStream(fileDoc));
+            const { bufferSize = 10_000 } = parseOptions ?? {};
+            const featureStream = filesService.parseGFF3(filesService.getFileStream(fileDoc), { bufferSize });
             let featureCount = 0;
+            // @ts-expect-error type is wrong here
+            // eslint-disable-next-line @typescript-eslint/await-thenable
             for await (const f of featureStream) {
                 const gff3Feature = f;
                 // Add new feature into database

package/dist/Changes/AddFeaturesFromFileChange.js.map

@@ -1 +1 @@
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+{"version":3,"file":"AddFeaturesFromFileChange.js","sourceRoot":"","sources":["../../src/Changes/AddFeaturesFromFileChange.ts"],"names":[],"mappings":";;;AAUA,6DAAyD;AA0BzD,MAAa,yBAA0B,SAAQ,uCAAkB;IAC/D,QAAQ,GAAG,2BAAoC,CAAA;IAC/C,OAAO,CAAoC;IAC3C,sBAAsB,GAAG,KAAK,CAAA;IAE9B,YACE,IAAyC,EACzC,OAAuB;QAEvB,KAAK,CAAC,IAAI,EAAE,OAAO,CAAC,CAAA;QACpB,IAAI,CAAC,sBAAsB,GAAG,IAAI,CAAC,sBAAsB,IAAI,KAAK,CAAA;QAClE,IAAI,CAAC,OAAO,GAAG,SAAS,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;IAC1D,CAAC;IAED,2EAA2E;IAC3E,IAAI,YAAY;QACd,OAAO,iEAAiE,CAAA;IAC1E,CAAC;IAED,MAAM;QACJ,MAAM,EAAE,QAAQ,EAAE,OAAO,EAAE,sBAAsB,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAA;QACpE,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACzB,MAAM,CAAC,EAAE,MAAM,EAAE,CAAC,GAAG,OAAO,CAAA;YAC5B,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,MAAM,EAAE,sBAAsB,EAAE,CAAA;QAC/D,CAAC;QACD,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,OAAO,EAAE,sBAAsB,EAAE,CAAA;IAChE,CAAC;IAED;;;;OAIG;IACH,KAAK,CAAC,eAAe,CAAC,OAAwB;QAC5C,MAAM,EAAE,SAAS,EAAE,YAAY,EAAE,GAAG,OAAO,CAAA;QAC3C,MAAM,EAAE,OAAO,EAAE,sBAAsB,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;QAExD,IAAI,sBAAsB,EAAE,CAAC;YAC3B,MAAM,IAAI,CAAC,sBAAsB,CAAC,OAAO,CAAC,CAAA;QAC5C,CAAC;QAED,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;YAC7B,MAAM,EAAE,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,CAAA;YAEvC,MAAM,EAAE,kBAAkB,EAAE,GAAG,OAAO,CAAC,GAAG,CAAA;YAC1C,IAAI,CAAC,kBAAkB,EAAE,CAAC;gBACxB,MAAM,IAAI,KAAK,CAAC,0CAA0C,CAAC,CAAA;YAC7D,CAAC;YACD,oBAAoB;YACpB,MAAM,OAAO,GAAG,MAAM,SAAS,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,CAAA;YACvD,IAAI,CAAC,OAAO,EAAE,CAAC;gBACb,MAAM,IAAI,KAAK,CAAC,SAAS,MAAM,sBAAsB,CAAC,CAAA;YACxD,CAAC;YACD,MAAM,CAAC,KAAK,EAAE,CAAC,WAAW,MAAM,gBAAgB,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAA;YAEpE,uDAAuD;YACvD,MAAM,EAAE,UAAU,GAAG,MAAM,EAAE,GAAG,YAAY,IAAI,EAAE,CAAA;YAClD,MAAM,aAAa,GAAG,YAAY,CAAC,SAAS,CAC1C,YAAY,CAAC,aAAa,CAAC,OAAO,CAAC,EACnC,EAAE,UAAU,EAAE,CACf,CAAA;YACD,IAAI,YAAY,GAAG,CAAC,CAAA;YACpB,sCAAsC;YACtC,6DAA6D;YAC7D,IAAI,KAAK,EAAE,MAAM,CAAC,IAAI,aAAa,EAAE,CAAC;gBACpC,MAAM,WAAW,GAAG,CAAgB,CAAA;gBAEpC,gCAAgC;gBAChC,iGAAiG;gBACjG,MAAM,IAAI,CAAC,gBAAgB,CAAC,WAAW,EAAE,OAAO,CAAC,CAAA;gBACjD,YAAY,EAAE,CAAA;gBACd,IAAI,YAAY,GAAG,IAAI,KAAK,CAAC,EAAE,CAAC;oBAC9B,MAAM,CAAC,KAAK,EAAE,CAAC,aAAa,YAAY,WAAW,CAAC,CAAA;gBACtD,CAAC;YACH,CAAC;QACH,CAAC;QACD,MAAM,CAAC,KAAK,EAAE,CAAC,mCAAmC,CAAC,CAAA;IACrD,CAAC;IAED,KAAK,CAAC,kBAAkB,CAAC,QAA4B;QACnD,MAAM,IAAI,KAAK,CAAC,oCAAoC,CAAC,CAAA;IACvD,CAAC;IAED,gEAAgE;IAChE,KAAK,CAAC,eAAe,CAAC,UAA2B,IAAG,CAAC;IAErD,UAAU;QACR,MAAM,EAAE,QAAQ,EAAE,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAA;QACpD,OAAO,IAAI,yBAAyB,CAClC,EAAE,QAAQ,EAAE,OAAO,EAAE,QAAQ,EAAE,EAC/B,EAAE,MAAM,EAAE,CACX,CAAA;IACH,CAAC;CACF;AA7FD,8DA6FC"}

package/dist/Changes/AddRefSeqAliasesChange.js

@@ -16,10 +16,7 @@ class AddRefSeqAliasesChange extends common_1.AssemblySpecificChange {
         if (!assembly) {
             throw new Error(`assembly ${this.assembly} not found`);
         }
-        const sessionAliases = assembly.refNameAliases;
-        if (!sessionAliases) {
-            throw new Error('Session refNameAliases not found in assembly');
-        }
+        const sessionAliases = assembly.refNameAliases ?? {};
         for (const refSeqAlias of this.refSeqAliases) {
             const { aliases, refName } = refSeqAlias;
             for (const alias of aliases) {

package/dist/Changes/AddRefSeqAliasesChange.js.map

@@ -1 +1 @@
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+{"version":3,"file":"AddRefSeqAliasesChange.js","sourceRoot":"","sources":["../../src/Changes/AddRefSeqAliasesChange.ts"],"names":[],"mappings":";;;AAAA,sDAQkC;AAClC,6CAA+C;AAa/C,MAAa,sBAAuB,SAAQ,+BAAsB;IAChE,QAAQ,GAAG,wBAAiC,CAAA;IAC5C,aAAa,CAA2B;IAExC,YAAY,IAAmC,EAAE,OAAuB;QACtE,KAAK,CAAC,IAAI,EAAE,OAAO,CAAC,CAAA;QACpB,IAAI,CAAC,aAAa,GAAG,IAAI,CAAC,aAAa,CAAA;IACzC,CAAC;IAED,eAAe,CAAC,eAAgC;QAC9C,MAAM,EAAE,eAAe,EAAE,GAAG,IAAA,iBAAU,EAAC,eAAe,CAAC,CAAA;QACvD,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;QACnD,IAAI,CAAC,QAAQ,EAAE,CAAC;YACd,MAAM,IAAI,KAAK,CAAC,YAAY,IAAI,CAAC,QAAQ,YAAY,CAAC,CAAA;QACxD,CAAC;QACD,MAAM,cAAc,GAAG,QAAQ,CAAC,cAAc,IAAI,EAAE,CAAA;QAEpD,KAAK,MAAM,WAAW,IAAI,IAAI,CAAC,aAAa,EAAE,CAAC;YAC7C,MAAM,EAAE,OAAO,EAAE,OAAO,EAAE,GAAG,WAAW,CAAA;YACxC,KAAK,MAAM,KAAK,IAAI,OAAO,EAAE,CAAC;gBAC5B,cAAc,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;YACjC,CAAC;QACH,CAAC;QACD,QAAQ,CAAC,iBAAiB,CAAC,cAAc,CAAC,CAAA;QAC1C,OAAO,OAAO,CAAC,OAAO,EAAE,CAAA;IAC1B,CAAC;IAED,UAAU;QACR,MAAM,IAAI,KAAK,CAAC,yBAAyB,CAAC,CAAA;IAC5C,CAAC;IAED,MAAM;QACJ,MAAM,EAAE,QAAQ,EAAE,aAAa,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAA;QAClD,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,aAAa,EAAE,CAAA;IAC9C,CAAC;IAED,KAAK,CAAC,eAAe,CAAC,OAAwB;QAC5C,MAAM,EAAE,WAAW,EAAE,OAAO,EAAE,GAAG,OAAO,CAAA;QACxC,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,aAAa,EAAE,GAAG,IAAI,CAAA;QAEhD,KAAK,MAAM,WAAW,IAAI,aAAa,EAAE,CAAC;YACxC,MAAM,CAAC,KAAK,EAAE,CACZ,wCAAwC,QAAQ,kBAAkB,IAAI,CAAC,SAAS,CAAC,WAAW,CAAC,EAAE,CAChG,CAAA;YACD,MAAM,EAAE,OAAO,EAAE,OAAO,EAAE,GAAG,WAAW,CAAA;YACxC,MAAM,WAAW;iBACd,SAAS,CAAC,EAAE,QAAQ,EAAE,IAAI,EAAE,OAAO,EAAE,EAAE,EAAE,IAAI,EAAE,EAAE,OAAO,EAAE,EAAE,CAAC;iBAC7D,OAAO,CAAC,OAAO,CAAC,CAAA;QACrB,CAAC;IACH,CAAC;IAED,kBAAkB,CAAC,QAA4B;QAC7C,MAAM,IAAI,KAAK,CAAC,yBAAyB,CAAC,CAAA;IAC5C,CAAC;IAED,2EAA2E;IAC3E,IAAI,YAAY;QACd,OAAO,iCAAiC,CAAA;IAC1C,CAAC;CACF;AA3DD,wDA2DC"}

package/dist/Changes/FromFileBaseChange.d.ts

@@ -1,4 +1,5 @@
 import { AssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
+import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
 import { type FileDocument } from '@apollo-annotation/schemas';
 import { type GFF3Feature } from '@gmod/gff';
 export declare abstract class FromFileBaseChange extends AssemblySpecificChange {
@@ -6,4 +7,5 @@ export declare abstract class FromFileBaseChange extends AssemblySpecificChange
     private refSeqCache;
     removeExistingFeatures(backend: ServerDataStore): Promise<void>;
     addFeatureIntoDb(gff3Feature: GFF3Feature, backend: ServerDataStore): Promise<void>;
+    getAllIds(feature: AnnotationFeatureSnapshot): string[];
 }

package/dist/Changes/FromFileBaseChange.js

@@ -1,10 +1,7 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.FromFileBaseChange = void 0;
-/* eslint-disable @typescript-eslint/restrict-plus-operands */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
-/* eslint-disable @typescript-eslint/no-unsafe-member-access */
-/* eslint-disable @typescript-eslint/no-unsafe-call */
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
 const common_1 = require("@apollo-annotation/common");
 const GFF3_1 = require("../GFF3");
@@ -26,8 +23,11 @@ class FromFileBaseChange extends common_1.AssemblySpecificChange {
         let parsingStarted = false;
         logger.debug?.('starting sequence stream');
         let lineCount = 0;
+        const decoder = new TextDecoder();
+        // @ts-expect-error type is wrong here
+        // eslint-disable-next-line @typescript-eslint/await-thenable
         for await (const data of sequenceStream) {
-            const chunk = data.toString();
+            const chunk = decoder.decode(data);
             lastLineIsIncomplete = !chunk.endsWith('\n');
             // chunk is small enough that you can split the whole thing into lines without having to make it into smaller chunks first.
             const lines = chunk.split(/\r?\n/);
@@ -36,9 +36,9 @@ class FromFileBaseChange extends common_1.AssemblySpecificChange {
                 incompleteLine = '';
             }
             if (lastLineIsIncomplete) {
-                incompleteLine = lines.pop() || '';
+                incompleteLine = lines.pop() ?? '';
             }
-            for await (const line of lines) {
+            for (const line of lines) {
                 lineCount++;
                 if (lineCount % 1_000_000 === 0) {
                     logger.debug?.(`Processed ${lineCount} lines`);
@@ -155,8 +155,13 @@ class FromFileBaseChange extends common_1.AssemblySpecificChange {
         }
     }
     async addFeatureIntoDb(gff3Feature, backend) {
-        const { featureModel, refSeqModel, user } = backend;
+        const { INDEXED_IDS } = process.env;
+        let idsToIndex;
+        if (INDEXED_IDS) {
+            idsToIndex = INDEXED_IDS.split(',');
+        }
         const { assembly, refSeqCache } = this;
+        const { featureModel, refSeqModel, user } = backend;
         const [{ seq_id: refName }] = gff3Feature;
         if (!refName) {
             throw new Error(`Valid seq_id not found in feature ${JSON.stringify(gff3Feature)}`);
@@ -173,15 +178,25 @@ class FromFileBaseChange extends common_1.AssemblySpecificChange {
         if (!refSeqDoc) {
             throw new Error(`RefSeq was not found by assembly "${assembly}" and seq_id "${refName}" not found`);
         }
-        // Let's add featureId to parent feature
-        const featureIds = [];
-        const newFeature = (0, GFF3_1.gff3ToAnnotationFeature)(gff3Feature, refSeqDoc._id, featureIds);
+        const newFeature = (0, GFF3_1.gff3ToAnnotationFeature)(gff3Feature, refSeqDoc._id);
+        const allIds = this.getAllIds(newFeature);
+        const indexedIds = this.getIndexedIds(newFeature, idsToIndex);
         // Add into Mongo
         // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
         await featureModel.create([
-            { allIds: featureIds, ...newFeature, user, status: -1 },
+            { allIds, indexedIds, ...newFeature, user, status: -1 },
         ]);
     }
+    getAllIds(feature) {
+        const allIds = [feature._id];
+        if (feature.children) {
+            for (const child of Object.values(feature.children)) {
+                const childIds = this.getAllIds(child);
+                allIds.push(...childIds);
+            }
+        }
+        return allIds;
+    }
 }
 exports.FromFileBaseChange = FromFileBaseChange;
 //# sourceMappingURL=FromFileBaseChange.js.map

package/dist/Changes/FromFileBaseChange.js.map

@@ -1 +1 @@
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package/dist/Checks/CDSCheck.js

@@ -5,6 +5,7 @@ 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"));
+const util_2 = require("./util");
 var STOP_CODONS;
 (function (STOP_CODONS) {
     STOP_CODONS[STOP_CODONS["TAG"] = 0] = "TAG";
@@ -143,7 +144,7 @@ async function checkMRNA(feature, getSequence) {
                     refSeq: refSeq.toString(),
                     start: cdsStart,
                     end: cdsStart,
-                    message: `Unexpected start codon in feature "${_id}": ${start_codon}`,
+                    message: `Unexpected start codon "${start_codon}" in feature "${(0, util_2.getPrintableId)(feature)}": `,
                 });
             }
             const lastCodon = codons.at(-1); // Last codon is supposed to be a stop
@@ -156,7 +157,7 @@ async function checkMRNA(feature, getSequence) {
                     refSeq: refSeq.toString(),
                     start: cdsEnd,
                     end: cdsEnd,
-                    message: `Missing stop codon for feature "${_id}"`,
+                    message: `Missing stop codon in feature "${(0, util_2.getPrintableId)(feature)}"`,
                 });
             }
         }
@@ -169,7 +170,7 @@ async function checkMRNA(feature, getSequence) {
                 refSeq: refSeq.toString(),
                 start: cdsEnd,
                 end: cdsEnd,
-                message: `Missing stop codon: The coding sequence for feature "${_id}" is not a multiple of three`,
+                message: `Missing stop codon in feature "${(0, util_2.getPrintableId)(feature)}"`,
             });
         }
         for (const [idx, codon] of codons.entries()) {
@@ -188,7 +189,7 @@ async function checkMRNA(feature, getSequence) {
                     refSeq: refSeq.toString(),
                     start: codonStart,
                     end: codonEnd,
-                    message: `The coding sequence for feature "${_id}" has an internal stop codon`,
+                    message: `Internal stop codon in feature "${(0, util_2.getPrintableId)(feature)}"`,
                 });
             }
         }

package/dist/Checks/CDSCheck.js.map

@@ -1 +1 @@
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package/dist/Checks/TranscriptCheck.js

@@ -5,6 +5,7 @@ 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"));
+const util_2 = require("./util");
 var CAUSES;
 (function (CAUSES) {
     CAUSES[CAUSES["NonCanonicalSpliceSiteAtFivePrime"] = 0] = "NonCanonicalSpliceSiteAtFivePrime";
@@ -24,14 +25,18 @@ async function getSpliceSequences(transcript, getSequence) {
     if (exons.length < 2) {
         return [];
     }
+    exons.sort((a, b) => (a.min < b.min ? -1 : 1));
     const spliceSeq = [];
     for (let i = 0; i < exons.length - 1; i++) {
         let fivePrimeMin = exons[i].max;
-        let threePrimeMin = exons[i + 1].min - 2;
+        let threePrimeMin = exons[i + 1].min;
         if (transcript.strand === -1) {
-            const _fivePrimeMin = fivePrimeMin;
-            fivePrimeMin = threePrimeMin;
-            threePrimeMin = _fivePrimeMin;
+            ;
+            [threePrimeMin, fivePrimeMin] = [fivePrimeMin, threePrimeMin];
+            fivePrimeMin -= 2;
+        }
+        else {
+            threePrimeMin -= 2;
         }
         let fivePrimeSeq = await getSequence(fivePrimeMin, fivePrimeMin + 2);
         let threePrimeSeq = await getSequence(threePrimeMin, threePrimeMin + 2);
@@ -39,12 +44,7 @@ async function getSpliceSequences(transcript, getSequence) {
             threePrimeSeq = (0, util_1.revcom)(threePrimeSeq);
             fivePrimeSeq = (0, util_1.revcom)(fivePrimeSeq);
         }
-        spliceSeq.push({
-            fivePrimeSeq,
-            fivePrimeMin,
-            threePrimeSeq,
-            threePrimeMin,
-        });
+        spliceSeq.push({ fivePrimeSeq, fivePrimeMin, threePrimeSeq, threePrimeMin });
     }
     return spliceSeq;
 }
@@ -63,7 +63,7 @@ async function checkTranscript(feature, getSequence) {
                 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: ${spliceSequence.fivePrimeSeq}`,
+                message: `Unexpected 5′ splice site in "${(0, util_2.getPrintableId)(feature)}". Expected: ${[...VALID_FIVE_PRIME_SEQ].join('|')}, got: ${spliceSequence.fivePrimeSeq}`,
             });
         }
         if (!VALID_THREE_PRIME_SEQ.has(spliceSequence.threePrimeSeq.toUpperCase())) {
@@ -75,7 +75,7 @@ async function checkTranscript(feature, getSequence) {
                 refSeq: feature.refSeq.toString(),
                 start: spliceSequence.threePrimeMin,
                 end: spliceSequence.threePrimeMin + 2,
-                message: `Unexpected 3' splice site in "${feature._id}". Expected: ${[...VALID_THREE_PRIME_SEQ].join('|')}, got: ${spliceSequence.threePrimeSeq}`,
+                message: `Unexpected 3′ splice site in "${(0, util_2.getPrintableId)(feature)}". Expected: ${[...VALID_THREE_PRIME_SEQ].join('|')}, got: ${spliceSequence.threePrimeSeq}`,
             });
         }
     }

package/dist/Checks/TranscriptCheck.js.map

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

@@ -0,0 +1,2 @@
+import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
+export declare function getPrintableId(feature: AnnotationFeatureSnapshot): string;

package/dist/Checks/util.js

@@ -0,0 +1,15 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getPrintableId = getPrintableId;
+function getPrintableId(feature) {
+    const gff_id = feature.attributes?.gff_id?.join(', ');
+    if (gff_id) {
+        return `${gff_id} (_id: ${feature._id.toString()})`;
+    }
+    const gff_name = feature.attributes?.gff_name?.join(', ');
+    if (gff_name) {
+        return `${gff_name} (_id: ${feature._id.toString()})`;
+    }
+    return `_id: ${feature._id.toString()}`;
+}
+//# sourceMappingURL=util.js.map

package/dist/Checks/util.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/Checks/util.ts"],"names":[],"mappings":";;AAEA,wCAUC;AAVD,SAAgB,cAAc,CAAC,OAAkC;IAC/D,MAAM,MAAM,GAAG,OAAO,CAAC,UAAU,EAAE,MAAM,EAAE,IAAI,CAAC,IAAI,CAAC,CAAA;IACrD,IAAI,MAAM,EAAE,CAAC;QACX,OAAO,GAAG,MAAM,UAAU,OAAO,CAAC,GAAG,CAAC,QAAQ,EAAE,GAAG,CAAA;IACrD,CAAC;IACD,MAAM,QAAQ,GAAG,OAAO,CAAC,UAAU,EAAE,QAAQ,EAAE,IAAI,CAAC,IAAI,CAAC,CAAA;IACzD,IAAI,QAAQ,EAAE,CAAC;QACb,OAAO,GAAG,QAAQ,UAAU,OAAO,CAAC,GAAG,CAAC,QAAQ,EAAE,GAAG,CAAA;IACvD,CAAC;IACD,OAAO,QAAQ,OAAO,CAAC,GAAG,CAAC,QAAQ,EAAE,EAAE,CAAA;AACzC,CAAC"}

package/dist/GFF3/annotationFeatureToGFF3.js

@@ -87,7 +87,9 @@ function annotationFeatureToGFF3(feature, parentId, refSeqNames) {
         score,
         strand: feature.strand ? (feature.strand === 1 ? '+' : '-') : null,
         phase: null,
-        attributes: Object.keys(attributes).length > 0 ? attributes : null,
+        attributes: Object.keys(attributes).length > 0
+            ? attributes
+            : null,
         derived_features: [],
         child_features: prepareChildFeatures(feature, attributes.ID?.[0], refSeqNames),
     }));

package/dist/GFF3/annotationFeatureToGFF3.js.map

@@ -1 +1 @@
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