@apollo-annotation/shared 0.3.7 → 0.3.9

package/dist/Changes/MergeTranscriptsChange.js

@@ -6,6 +6,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.MergeTranscriptsChange = void 0;
 const common_1 = require("@apollo-annotation/common");
 const util_1 = require("@jbrowse/core/util");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const util_2 = require("../util");
 const DeleteFeatureChange_1 = require("./DeleteFeatureChange");
 const UndoMergeTranscriptsChange_1 = require("./UndoMergeTranscriptsChange");
 class MergeTranscriptsChange extends common_1.FeatureChange {
@@ -15,6 +17,10 @@ class MergeTranscriptsChange extends common_1.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() {
         const { assembly, changedIds, changes, typeName } = this;
         if (changes.length === 1) {
@@ -60,7 +66,16 @@ class MergeTranscriptsChange extends common_1.FeatureChange {
     mergeTranscriptsOnServer(firstTranscript, secondTranscript) {
         firstTranscript.min = Math.min(firstTranscript.min, secondTranscript.min);
         firstTranscript.max = Math.max(firstTranscript.max, secondTranscript.max);
-        this.mergeTranscriptAttributes(firstTranscript, secondTranscript);
+        const mergedAttributes = 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((0, util_2.stringifyAttributes)((0, util_2.attributesToRecords)(secondTranscript.attributes)));
+        }
+        firstTranscript.attributes = mergedAttributes;
         if (secondTranscript.children) {
             for (const [, secondFeatureChild] of Object.entries(secondTranscript.children)) {
                 this.mergeFeatureIntoTranscriptOnServer(secondFeatureChild, firstTranscript);
@@ -73,19 +88,39 @@ class MergeTranscriptsChange extends common_1.FeatureChange {
         }
         let merged = false;
         let mrgChild;
-        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 &&
                 mrgChild.type === firstFeatureChild.type &&
                 (0, util_1.doesIntersect2)(secondFeatureChild.min, secondFeatureChild.max, mrgChild.min, mrgChild.max) &&
                 (0, util_1.doesIntersect2)(firstFeatureChild.min, firstFeatureChild.max, mrgChild.min, mrgChild.max)) {
                 mrgChild.min = Math.min(secondFeatureChild.min, mrgChild.min, firstFeatureChild.min);
                 mrgChild.max = Math.max(secondFeatureChild.max, mrgChild.max, firstFeatureChild.max);
-                const mergedAttrs = this.mergeAttributes(mrgChild, secondFeatureChild);
-                mrgChild.attributes = mergedAttrs;
-                firstTranscript.children.delete(fKey);
+                if (!mrgChild.attributes) {
+                    mrgChild.attributes = {};
+                }
+                const mrgChildAttr = JSON.parse(JSON.stringify(mrgChild.attributes));
+                if (!Object.keys(mrgChildAttr).includes('merged_with')) {
+                    mrgChildAttr.merged_with = [];
+                }
+                const mergedWithAttributes = mrgChildAttr.merged_with;
+                mergedWithAttributes.push((0, util_2.stringifyAttributes)((0, util_2.attributesToRecords)(secondFeatureChild.attributes)));
+                if (toDelete) {
+                    const recs = firstFeatureChild.attributes
+                        ? JSON.parse(JSON.stringify(firstFeatureChild.attributes))
+                        : undefined;
+                    mergedWithAttributes.push((0, util_2.stringifyAttributes)(recs));
+                    firstTranscript.children.delete(firstFeatureChild._id.toString());
+                }
+                mrgChildAttr.merged_with = [...new Set(mergedWithAttributes)];
+                mrgChild.attributes = mrgChildAttr;
                 merged = true;
             }
         }
@@ -124,7 +159,13 @@ class MergeTranscriptsChange extends common_1.FeatureChange {
     mergeTranscriptsOnClient(firstTranscript, secondTranscript) {
         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 = (0, util_2.stringifyAttributes)((0, util_2.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(secondTranscript.children)) {
                 this.mergeFeatureIntoTranscriptOnClient(secondFeatureChild, firstTranscript);
@@ -152,15 +193,13 @@ class MergeTranscriptsChange extends common_1.FeatureChange {
                 (0, util_1.doesIntersect2)(firstFeatureChild.min, firstFeatureChild.max, mrgChild.min, mrgChild.max)) {
                 mrgChild.setMin(Math.min(secondFeatureChild.min, mrgChild.min, firstFeatureChild.min));
                 mrgChild.setMax(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((0, util_2.stringifyAttributes)((0, util_2.attributesToRecords)(secondFeatureChild.attributes)));
                 if (toDelete) {
+                    mergedWithAttributes.push((0, util_2.stringifyAttributes)((0, mobx_state_tree_1.getSnapshot)(firstFeatureChild).attributes));
                     firstTranscript.deleteChild(firstFeatureChild._id);
                 }
+                mrgChild.setAttribute('merged_with', [...new Set(mergedWithAttributes)]);
                 merged = true;
             }
         }
@@ -169,58 +208,18 @@ class MergeTranscriptsChange extends common_1.FeatureChange {
                 mrgChild.addChild(child);
             });
         }
-        if (!(merged && mrgChild)) {
+        if (merged && mrgChild) {
+            firstTranscript.addChild((0, mobx_state_tree_1.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) {
-        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) {
         throw new Error('executeOnLocalGFF3 not implemented');
     }
-    /* Merge attributes from source into destination */
-    mergeAttributes(destination, source) {
-        const destAttrs = destination.attributes
-            ? JSON.parse(JSON.stringify(destination.attributes))
-            : {};
-        if (source.attributes) {
-            const sourceAttrs = 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, secondTranscript) {
-        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/dist/Changes/MergeTranscriptsChange.js.map

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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

@@ -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";
@@ -21,7 +22,6 @@ 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 +126,9 @@ 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)) {
@@ -141,14 +144,11 @@ 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 "${(0, util_2.getPrintableId)(feature)}": `,
                 });
             }
             const lastCodon = codons.at(-1); // Last codon is supposed to be a stop
             if (lastCodon && !(lastCodon.toUpperCase() in STOP_CODONS)) {
-                const cdsEnd = strand === -1
-                    ? cdsLocation.at(0)?.min ?? min
-                    : cdsLocation.at(-1)?.max ?? max;
                 checkResults.push({
                     _id: new bson_objectid_1.default().toHexString(),
                     name: CHECK_NAME,
@@ -157,7 +157,7 @@ async function checkMRNA(feature, getSequence) {
                     refSeq: refSeq.toString(),
                     start: cdsEnd,
                     end: cdsEnd,
-                    message: `Missing stop codon for feature "${_id}"`,
+                    message: `Missing stop codon in feature "${(0, util_2.getPrintableId)(feature)}"`,
                 });
             }
         }
@@ -165,12 +165,12 @@ async function checkMRNA(feature, getSequence) {
             checkResults.push({
                 _id: new bson_objectid_1.default().toHexString(),
                 name: CHECK_NAME,
-                cause: CAUSES[CAUSES.MultipleOfThree],
+                cause: CAUSES[CAUSES.MissingStopCodon],
                 ids,
                 refSeq: refSeq.toString(),
-                start: min,
-                end: max,
-                message: `The coding sequence for feature "${_id}" is not a multiple of three`,
+                start: cdsEnd,
+                end: cdsEnd,
+                message: `Missing stop codon in feature "${(0, util_2.getPrintableId)(feature)}"`,
             });
         }
         for (const [idx, codon] of codons.entries()) {
@@ -189,7 +189,7 @@ async function checkMRNA(feature, getSequence) {
                     refSeq: refSeq.toString(),
                     start: codonStart,
                     end: codonEnd,
-                    message: `The coding sequence for feature "${_id}" has an internal stop codon`,
+                    message: `Internal stop codon in feature "${(0, util_2.getPrintableId)(feature)}"`,
                 });
             }
         }
@@ -246,7 +246,7 @@ 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"));
+const util_2 = require("./util");
+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 [];
+    }
+    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;
+        if (transcript.strand === -1) {
+            ;
+            [threePrimeMin, fivePrimeMin] = [fivePrimeMin, threePrimeMin];
+            fivePrimeMin -= 2;
+        }
+        else {
+            threePrimeMin -= 2;
+        }
+        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 "${(0, util_2.getPrintableId)(feature)}". Expected: ${[...VALID_FIVE_PRIME_SEQ].join('|')}, got: ${spliceSequence.fivePrimeSeq}`,
+            });
+        }
+        if (!VALID_THREE_PRIME_SEQ.has(spliceSequence.threePrimeSeq.toUpperCase())) {
+            checkResults.push({
+                _id: new bson_objectid_1.default().toHexString(),
+                name: CHECK_NAME,
+                cause: CAUSES[CAUSES.NonCanonicalSpliceSiteAtThreePrime],
+                ids: [feature._id],
+                refSeq: feature.refSeq.toString(),
+                start: spliceSequence.threePrimeMin,
+                end: spliceSequence.threePrimeMin + 2,
+                message: `Unexpected 3′ splice site in "${(0, util_2.getPrintableId)(feature)}". 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 @@
+{"version":3,"file":"TranscriptCheck.js","sourceRoot":"","sources":["../../src/Checks/TranscriptCheck.ts"],"names":[],"mappings":";;;;AAAA,sDAAiD;AAKjD,6CAA2C;AAC3C,0EAAoC;AAEpC,iCAAuC;AASvC,IAAK,MAGJ;AAHD,WAAK,MAAM;IACT,6FAAmC,CAAA;IACnC,+FAAoC,CAAA;AACtC,CAAC,EAHI,MAAM,KAAN,MAAM,QAGV;AACD,MAAM,UAAU,GAAG,iBAAiB,CAAA;AAEpC,KAAK,UAAU,kBAAkB,CAC/B,UAAqC,EACrC,WAA4D;IAE5D,IAAI,CAAC,UAAU,CAAC,QAAQ,EAAE,CAAC;QACzB,OAAO,EAAE,CAAA;IACX,CAAC;IACD,MAAM,KAAK,GAAgC,EAAE,CAAA;IAC7C,KAAK,MAAM,CAAC,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,UAAU,CAAC,QAAQ,CAAC,EAAE,CAAC;QAC5D,IAAI,KAAK,CAAC,IAAI,KAAK,MAAM,EAAE,CAAC;YAC1B,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;QACnB,CAAC;IACH,CAAC;IACD,IAAI,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACrB,OAAO,EAAE,CAAA;IACX,CAAC;IACD,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;IAE9C,MAAM,SAAS,GAAqB,EAAE,CAAA;IACtC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;QAC1C,IAAI,YAAY,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAA;QAC/B,IAAI,aAAa,GAAG,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAA;QACpC,IAAI,UAAU,CAAC,MAAM,KAAK,CAAC,CAAC,EAAE,CAAC;YAC7B,CAAC;YAAA,CAAC,aAAa,EAAE,YAAY,CAAC,GAAG,CAAC,YAAY,EAAE,aAAa,CAAC,CAAA;YAC9D,YAAY,IAAI,CAAC,CAAA;QACnB,CAAC;aAAM,CAAC;YACN,aAAa,IAAI,CAAC,CAAA;QACpB,CAAC;QAED,IAAI,YAAY,GAAG,MAAM,WAAW,CAAC,YAAY,EAAE,YAAY,GAAG,CAAC,CAAC,CAAA;QACpE,IAAI,aAAa,GAAG,MAAM,WAAW,CAAC,aAAa,EAAE,aAAa,GAAG,CAAC,CAAC,CAAA;QACvE,IAAI,UAAU,CAAC,MAAM,KAAK,CAAC,CAAC,EAAE,CAAC;YAC7B,aAAa,GAAG,IAAA,aAAM,EAAC,aAAa,CAAC,CAAA;YACrC,YAAY,GAAG,IAAA,aAAM,EAAC,YAAY,CAAC,CAAA;QACrC,CAAC;QAED,SAAS,CAAC,IAAI,CAAC,EAAE,YAAY,EAAE,YAAY,EAAE,aAAa,EAAE,aAAa,EAAE,CAAC,CAAA;IAC9E,CAAC;IACD,OAAO,SAAS,CAAA;AAClB,CAAC;AAED,KAAK,UAAU,eAAe,CAC5B,OAAkC,EAClC,WAA4D;IAE5D,MAAM,YAAY,GAA0B,EAAE,CAAA;IAE9C,MAAM,oBAAoB,GAAG,IAAI,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,CAAA;IAC5C,MAAM,qBAAqB,GAAG,IAAI,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,CAAA;IAC7C,MAAM,eAAe,GAAG,MAAM,kBAAkB,CAAC,OAAO,EAAE,WAAW,CAAC,CAAA;IACtE,KAAK,MAAM,cAAc,IAAI,eAAe,EAAE,CAAC;QAC7C,IAAI,CAAC,oBAAoB,CAAC,GAAG,CAAC,cAAc,CAAC,YAAY,CAAC,WAAW,EAAE,CAAC,EAAE,CAAC;YACzE,YAAY,CAAC,IAAI,CAAC;gBAChB,GAAG,EAAE,IAAI,uBAAQ,EAAE,CAAC,WAAW,EAAE;gBACjC,IAAI,EAAE,UAAU;gBAChB,KAAK,EAAE,MAAM,CAAC,MAAM,CAAC,iCAAiC,CAAC;gBACvD,GAAG,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC;gBAClB,MAAM,EAAE,OAAO,CAAC,MAAM,CAAC,QAAQ,EAAE;gBACjC,KAAK,EAAE,cAAc,CAAC,YAAY;gBAClC,GAAG,EAAE,cAAc,CAAC,YAAY,GAAG,CAAC;gBACpC,OAAO,EAAE,iCAAiC,IAAA,qBAAc,EAAC,OAAO,CAAC,gBAAgB,CAAC,GAAG,oBAAoB,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,UAAU,cAAc,CAAC,YAAY,EAAE;aAC5J,CAAC,CAAA;QACJ,CAAC;QACD,IACE,CAAC,qBAAqB,CAAC,GAAG,CAAC,cAAc,CAAC,aAAa,CAAC,WAAW,EAAE,CAAC,EACtE,CAAC;YACD,YAAY,CAAC,IAAI,CAAC;gBAChB,GAAG,EAAE,IAAI,uBAAQ,EAAE,CAAC,WAAW,EAAE;gBACjC,IAAI,EAAE,UAAU;gBAChB,KAAK,EAAE,MAAM,CAAC,MAAM,CAAC,kCAAkC,CAAC;gBACxD,GAAG,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC;gBAClB,MAAM,EAAE,OAAO,CAAC,MAAM,CAAC,QAAQ,EAAE;gBACjC,KAAK,EAAE,cAAc,CAAC,aAAa;gBACnC,GAAG,EAAE,cAAc,CAAC,aAAa,GAAG,CAAC;gBACrC,OAAO,EAAE,iCAAiC,IAAA,qBAAc,EAAC,OAAO,CAAC,gBAAgB,CAAC,GAAG,qBAAqB,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,UAAU,cAAc,CAAC,aAAa,EAAE;aAC9J,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;IACD,OAAO,YAAY,CAAA;AACrB,CAAC;AAED,SAAS,SAAS;IAChB,OAAO,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CACxC,MAAM,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CACZ,CAAA;AACf,CAAC;AACD,MAAa,eAAgB,SAAQ,cAAK;IACxC,IAAI,GAAG,iBAAiB,CAAA;IACxB,MAAM,GAAG,SAAS,EAAE,CAAA;IACpB,OAAO,GAAG,CAAC,CAAA;IACX,SAAS,GAAG,IAAI,CAAA;IAEhB,KAAK,CAAC,YAAY,CAChB,OAAkC,EAClC,WAA4D;QAE5D,IACE,OAAO,CAAC,IAAI,KAAK,MAAM;YACvB,OAAO,CAAC,IAAI,KAAK,YAAY;YAC7B,OAAO,CAAC,IAAI,KAAK,wBAAwB,EACzC,CAAC;YACD,OAAO,eAAe,CAAC,OAAO,EAAE,WAAW,CAAC,CAAA;QAC9C,CAAC;QAED,IAAI,CAAC,OAAO,CAAC,QAAQ,EAAE,CAAC;YACtB,OAAO,EAAE,CAAA;QACX,CAAC;QAED,MAAM,YAAY,GAA0B,EAAE,CAAA;QAC9C,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,QAAQ,CAAC,EAAE,CAAC;YACpD,YAAY,CAAC,IAAI,CAAC,GAAG,CAAC,MAAM,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,WAAW,CAAC,CAAC,CAAC,CAAA;QACrE,CAAC;QACD,OAAO,YAAY,CAAA;IACrB,CAAC;CACF;AA5BD,0CA4BC"}

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"}

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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package/dist/GFF3/gff3ToAnnotationFeature.js

@@ -93,7 +93,7 @@ function convertFeatureAttributes(gff3Feature) {
     if (attributesCollections.length > 0) {
         for (const attributesCollection of attributesCollections) {
             for (const [key, val] of Object.entries(attributesCollection)) {
-                if (!val || key === 'Parent') {
+                if (key === 'Parent') {
                     continue;
                 }
                 const newKey = (0, gffReservedKeys_1.isGFFReservedAttribute)(key) ? gffReservedKeys_1.gffToInternal[key] : key;