@apollo-annotation/shared 0.3.11 → 0.3.12

package/dist/Checks/TranscriptCheck.js

@@ -1,11 +1,7 @@
-"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");
+import { Check } from '@apollo-annotation/common';
+import { revcom } from '@jbrowse/core/util';
+import ObjectID from 'bson-objectid';
+import { getPrintableId } from './util.js';
 var CAUSES;
 (function (CAUSES) {
     CAUSES[CAUSES["NonCanonicalSpliceSiteAtFivePrime"] = 0] = "NonCanonicalSpliceSiteAtFivePrime";
@@ -41,8 +37,8 @@ async function getSpliceSequences(transcript, getSequence) {
         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);
+            threePrimeSeq = revcom(threePrimeSeq);
+            fivePrimeSeq = revcom(fivePrimeSeq);
         }
         spliceSeq.push({ fivePrimeSeq, fivePrimeMin, threePrimeSeq, threePrimeMin });
     }
@@ -56,26 +52,26 @@ async function checkTranscript(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(),
+                _id: new ObjectID().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: ${spliceSequence.fivePrimeSeq}`,
+                message: `Unexpected 5′ splice site in "${getPrintableId(feature)}". Expected: ${[...VALID_FIVE_PRIME_SEQ].join('|')}, got: ${spliceSequence.fivePrimeSeq}`,
             });
         }
         if (!VALID_THREE_PRIME_SEQ.has(spliceSequence.threePrimeSeq.toUpperCase())) {
             checkResults.push({
-                _id: new bson_objectid_1.default().toHexString(),
+                _id: new ObjectID().toHexString(),
                 name: CHECK_NAME,
                 cause: CAUSES[CAUSES.NonCanonicalSpliceSiteAtThreePrime],
                 ids: [feature._id],
                 refSeq: feature.refSeq.toString(),
                 start: spliceSequence.threePrimeMin,
                 end: spliceSequence.threePrimeMin + 2,
-                message: `Unexpected 3′ splice site in "${(0, util_2.getPrintableId)(feature)}". Expected: ${[...VALID_THREE_PRIME_SEQ].join('|')}, got: ${spliceSequence.threePrimeSeq}`,
+                message: `Unexpected 3′ splice site in "${getPrintableId(feature)}". Expected: ${[...VALID_THREE_PRIME_SEQ].join('|')}, got: ${spliceSequence.threePrimeSeq}`,
             });
         }
     }
@@ -84,7 +80,7 @@ async function checkTranscript(feature, getSequence) {
 function getCauses() {
     return Object.values(CAUSES).filter((x) => Number.isNaN(Number(x)));
 }
-class TranscriptCheck extends common_1.Check {
+export class TranscriptCheck extends Check {
     name = 'TranscriptCheck';
     causes = getCauses();
     version = 1;
@@ -105,5 +101,4 @@ class TranscriptCheck extends common_1.Check {
         return checkResults;
     }
 }
-exports.TranscriptCheck = TranscriptCheck;
 //# sourceMappingURL=TranscriptCheck.js.map

package/dist/Checks/TranscriptCheck.js.map

@@ -1 +1 @@
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+{"version":3,"file":"TranscriptCheck.js","sourceRoot":"","sources":["../../src/Checks/TranscriptCheck.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,2BAA2B,CAAA;AAKjD,OAAO,EAAE,MAAM,EAAE,MAAM,oBAAoB,CAAA;AAC3C,OAAO,QAAQ,MAAM,eAAe,CAAA;AAEpC,OAAO,EAAE,cAAc,EAAE,MAAM,WAAW,CAAA;AAS1C,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,MAAM,CAAC,aAAa,CAAC,CAAA;YACrC,YAAY,GAAG,MAAM,CAAC,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,QAAQ,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,cAAc,CAAC,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,QAAQ,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,cAAc,CAAC,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,MAAM,OAAO,eAAgB,SAAQ,KAAK;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"}

package/dist/Checks/index.d.ts

@@ -1,2 +1,3 @@
-export * from './CDSCheck';
-export * from './TranscriptCheck';
+export * from './CDSCheck.js';
+export * from './TranscriptCheck.js';
+//# sourceMappingURL=index.d.ts.map

package/dist/Checks/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/Checks/index.ts"],"names":[],"mappings":"AAAA,cAAc,eAAe,CAAA;AAC7B,cAAc,sBAAsB,CAAA"}

package/dist/Checks/index.js

@@ -1,6 +1,3 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const tslib_1 = require("tslib");
-tslib_1.__exportStar(require("./CDSCheck"), exports);
-tslib_1.__exportStar(require("./TranscriptCheck"), exports);
+export * from './CDSCheck.js';
+export * from './TranscriptCheck.js';
 //# 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;AAC1B,4DAAiC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/Checks/index.ts"],"names":[],"mappings":"AAAA,cAAc,eAAe,CAAA;AAC7B,cAAc,sBAAsB,CAAA"}

package/dist/Checks/util.d.ts

@@ -1,2 +1,3 @@
-import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
+import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
 export declare function getPrintableId(feature: AnnotationFeatureSnapshot): string;
+//# sourceMappingURL=util.d.ts.map

package/dist/Checks/util.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"util.d.ts","sourceRoot":"","sources":["../../src/Checks/util.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,yBAAyB,EAAE,MAAM,wBAAwB,CAAA;AAEvE,wBAAgB,cAAc,CAAC,OAAO,EAAE,yBAAyB,GAAG,MAAM,CAUzE"}

package/dist/Checks/util.js

@@ -1,7 +1,4 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.getPrintableId = getPrintableId;
-function getPrintableId(feature) {
+export function getPrintableId(feature) {
     const gff_id = feature.attributes?.gff_id?.join(', ');
     if (gff_id) {
         return `${gff_id} (_id: ${feature._id.toString()})`;

package/dist/Checks/util.js.map

@@ -1 +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"}
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../../src/Checks/util.ts"],"names":[],"mappings":"AAEA,MAAM,UAAU,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/Common/index.d.ts

@@ -1 +1,2 @@
-export * from './jwtPayload';
+export * from './jwtPayload.js';
+//# sourceMappingURL=index.d.ts.map

package/dist/Common/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/Common/index.ts"],"names":[],"mappings":"AAAA,cAAc,iBAAiB,CAAA"}

package/dist/Common/index.js

@@ -1,5 +1,2 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const tslib_1 = require("tslib");
-tslib_1.__exportStar(require("./jwtPayload"), exports);
+export * from './jwtPayload.js';
 //# sourceMappingURL=index.js.map

package/dist/Common/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/Common/index.ts"],"names":[],"mappings":";;;AAAA,uDAA4B"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/Common/index.ts"],"names":[],"mappings":"AAAA,cAAc,iBAAiB,CAAA"}

package/dist/Common/jwtPayload.d.ts

@@ -10,3 +10,4 @@ export interface DecodedJWT extends JWTPayload {
 }
 export declare function makeUserSessionId(userOrToken: DecodedJWT | string): string;
 export declare function getDecodedToken(token: string): DecodedJWT;
+//# sourceMappingURL=jwtPayload.d.ts.map

package/dist/Common/jwtPayload.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"jwtPayload.d.ts","sourceRoot":"","sources":["../../src/Common/jwtPayload.ts"],"names":[],"mappings":"AAEA,MAAM,WAAW,UAAU;IACzB,QAAQ,EAAE,MAAM,CAAA;IAChB,KAAK,EAAE,MAAM,CAAA;IACb,IAAI,CAAC,EAAE,OAAO,GAAG,MAAM,GAAG,UAAU,GAAG,MAAM,CAAA;IAC7C,EAAE,EAAE,MAAM,CAAA;CACX;AAED,MAAM,WAAW,UAAW,SAAQ,UAAU;IAC5C,GAAG,EAAE,MAAM,CAAA;IACX,GAAG,EAAE,MAAM,CAAA;CACZ;AAED,wBAAgB,iBAAiB,CAAC,WAAW,EAAE,UAAU,GAAG,MAAM,GAAG,MAAM,CAM1E;AAED,wBAAgB,eAAe,CAAC,KAAK,EAAE,MAAM,GAAG,UAAU,CAEzD"}

package/dist/Common/jwtPayload.js

@@ -1,16 +1,11 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.makeUserSessionId = makeUserSessionId;
-exports.getDecodedToken = getDecodedToken;
-const tslib_1 = require("tslib");
-const jwt_decode_1 = tslib_1.__importDefault(require("jwt-decode"));
-function makeUserSessionId(userOrToken) {
+import jwtDecode from 'jwt-decode';
+export function makeUserSessionId(userOrToken) {
     const user = typeof userOrToken === 'string'
-        ? (0, jwt_decode_1.default)(userOrToken)
+        ? jwtDecode(userOrToken)
         : userOrToken;
     return `${user.id}-${user.iat}`;
 }
-function getDecodedToken(token) {
-    return (0, jwt_decode_1.default)(token);
+export function getDecodedToken(token) {
+    return jwtDecode(token);
 }
 //# sourceMappingURL=jwtPayload.js.map

package/dist/Common/jwtPayload.js.map

@@ -1 +1 @@
-{"version":3,"file":"jwtPayload.js","sourceRoot":"","sources":["../../src/Common/jwtPayload.ts"],"names":[],"mappings":";;AAcA,8CAMC;AAED,0CAEC;;AAxBD,oEAAkC;AAclC,SAAgB,iBAAiB,CAAC,WAAgC;IAChE,MAAM,IAAI,GACR,OAAO,WAAW,KAAK,QAAQ;QAC7B,CAAC,CAAC,IAAA,oBAAS,EAAa,WAAW,CAAC;QACpC,CAAC,CAAC,WAAW,CAAA;IACjB,OAAO,GAAG,IAAI,CAAC,EAAE,IAAI,IAAI,CAAC,GAAG,EAAE,CAAA;AACjC,CAAC;AAED,SAAgB,eAAe,CAAC,KAAa;IAC3C,OAAO,IAAA,oBAAS,EAAa,KAAK,CAAC,CAAA;AACrC,CAAC"}
+{"version":3,"file":"jwtPayload.js","sourceRoot":"","sources":["../../src/Common/jwtPayload.ts"],"names":[],"mappings":"AAAA,OAAO,SAAS,MAAM,YAAY,CAAA;AAclC,MAAM,UAAU,iBAAiB,CAAC,WAAgC;IAChE,MAAM,IAAI,GACR,OAAO,WAAW,KAAK,QAAQ;QAC7B,CAAC,CAAC,SAAS,CAAa,WAAW,CAAC;QACpC,CAAC,CAAC,WAAW,CAAA;IACjB,OAAO,GAAG,IAAI,CAAC,EAAE,IAAI,IAAI,CAAC,GAAG,EAAE,CAAA;AACjC,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,KAAa;IAC3C,OAAO,SAAS,CAAa,KAAK,CAAC,CAAA;AACrC,CAAC"}

package/dist/GFF3/annotationFeatureToGFF3.d.ts

@@ -1,3 +1,4 @@
-import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
-import { type GFF3Feature } from '@gmod/gff';
+import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
+import type { GFF3Feature } from '@gmod/gff';
 export declare function annotationFeatureToGFF3(feature: AnnotationFeatureSnapshot, parentId?: string, refSeqNames?: Record<string, string | undefined>): GFF3Feature;
+//# sourceMappingURL=annotationFeatureToGFF3.d.ts.map

package/dist/GFF3/annotationFeatureToGFF3.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"annotationFeatureToGFF3.d.ts","sourceRoot":"","sources":["../../src/GFF3/annotationFeatureToGFF3.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EACV,yBAAyB,EAG1B,MAAM,wBAAwB,CAAA;AAC/B,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,WAAW,CAAA;AAG5C,wBAAgB,uBAAuB,CACrC,OAAO,EAAE,yBAAyB,EAClC,QAAQ,CAAC,EAAE,MAAM,EACjB,WAAW,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,GAAG,SAAS,CAAC,GAC/C,WAAW,CA0Gb"}

package/dist/GFF3/annotationFeatureToGFF3.js

@@ -1,98 +1,101 @@
-"use strict";
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.annotationFeatureToGFF3 = annotationFeatureToGFF3;
-const util_1 = require("@jbrowse/core/util");
-function annotationFeatureToGFF3(feature, parentId, refSeqNames) {
-    // eslint-disable-next-line unicorn/prefer-structured-clone
-    const attributes = JSON.parse(JSON.stringify(feature.attributes ?? {}));
-    const ontologyTerms = [];
-    const source = feature.attributes?.gff_source?.[0] ?? null;
-    delete attributes.gff_source;
-    if (parentId) {
-        attributes.Parent = [parentId];
-    }
-    if (attributes.gff_id) {
-        attributes.ID = attributes.gff_id;
-        delete attributes.gff_id;
-    }
-    else if (feature.children) {
-        attributes.ID = [feature._id];
-    }
-    if (attributes.gff_name) {
-        attributes.Name = attributes.gff_name;
-        delete attributes.gff_name;
-    }
-    if (attributes.gff_alias) {
-        attributes.Alias = attributes.gff_alias;
-        delete attributes.gff_alias;
-    }
-    if (attributes.gff_target) {
-        attributes.Target = attributes.gff_target;
-        delete attributes.gff_target;
-    }
-    if (attributes.gff_gap) {
-        attributes.Gap = attributes.gff_gap;
-        delete attributes.gff_gap;
-    }
-    if (attributes.gff_derives_from) {
-        attributes.Derives_from = attributes.gff_derives_from;
-        delete attributes.gff_derives_from;
-    }
-    if (attributes.gff_note) {
-        attributes.Note = attributes.gff_note;
-        delete attributes.gff_note;
-    }
-    if (attributes.gff_dbxref) {
-        attributes.Dbxref = attributes.gff_dbxref;
-        delete attributes.gff_dbxref;
-    }
-    if (attributes.gff_is_circular) {
-        attributes.Is_circular = attributes.gff_is_circular;
-        delete attributes.gff_is_circular;
-    }
-    if (attributes.gff_ontology_term) {
-        ontologyTerms.push(...attributes.gff_ontology_term);
-        delete attributes.gff_ontology_term;
-    }
-    if (attributes['Gene Ontology']) {
-        ontologyTerms.push(...attributes['Gene Ontology']);
-        delete attributes['Gene Ontology'];
-    }
-    if (attributes['Sequence Ontology']) {
-        ontologyTerms.push(...attributes['Sequence Ontology']);
-        delete attributes['Sequence Ontology'];
-    }
-    if (ontologyTerms.length > 0) {
-        attributes.Ontology_term = ontologyTerms;
-    }
-    const gff_score = feature.attributes?.gff_score;
-    let score = null;
-    if (gff_score && gff_score.length > 0) {
-        if (gff_score[0]) {
-            score = Number(gff_score[0]);
-            if (Number.isNaN(score)) {
-                score = null;
+import { intersection2 } from '@jbrowse/core/util';
+export function annotationFeatureToGFF3(feature, parentId, refSeqNames) {
+    const locations = feature.type === 'apollo_feature_container'
+        ? Object.values(feature.children ?? {})
+        : [feature];
+    return locations.map((featureLoc) => {
+        // eslint-disable-next-line unicorn/prefer-structured-clone
+        const attributes = JSON.parse(JSON.stringify(featureLoc.attributes ?? {}));
+        const ontologyTerms = [];
+        const source = featureLoc.attributes?.gff_source?.[0] ?? null;
+        delete attributes.gff_source;
+        if (parentId) {
+            attributes.Parent = [parentId];
+        }
+        if (attributes.gff_id) {
+            attributes.ID = attributes.gff_id;
+            delete attributes.gff_id;
+        }
+        else if (featureLoc.children) {
+            attributes.ID = [featureLoc._id];
+        }
+        if (attributes.gff_name) {
+            attributes.Name = attributes.gff_name;
+            delete attributes.gff_name;
+        }
+        if (attributes.gff_alias) {
+            attributes.Alias = attributes.gff_alias;
+            delete attributes.gff_alias;
+        }
+        if (attributes.gff_target) {
+            attributes.Target = attributes.gff_target;
+            delete attributes.gff_target;
+        }
+        if (attributes.gff_gap) {
+            attributes.Gap = attributes.gff_gap;
+            delete attributes.gff_gap;
+        }
+        if (attributes.gff_derives_from) {
+            attributes.Derives_from = attributes.gff_derives_from;
+            delete attributes.gff_derives_from;
+        }
+        if (attributes.gff_note) {
+            attributes.Note = attributes.gff_note;
+            delete attributes.gff_note;
+        }
+        if (attributes.gff_dbxref) {
+            attributes.Dbxref = attributes.gff_dbxref;
+            delete attributes.gff_dbxref;
+        }
+        if (attributes.gff_is_circular) {
+            attributes.Is_circular = attributes.gff_is_circular;
+            delete attributes.gff_is_circular;
+        }
+        if (attributes.gff_ontology_term) {
+            ontologyTerms.push(...attributes.gff_ontology_term);
+            delete attributes.gff_ontology_term;
+        }
+        if (attributes['Gene Ontology']) {
+            ontologyTerms.push(...attributes['Gene Ontology']);
+            delete attributes['Gene Ontology'];
+        }
+        if (attributes['Sequence Ontology']) {
+            ontologyTerms.push(...attributes['Sequence Ontology']);
+            delete attributes['Sequence Ontology'];
+        }
+        if (ontologyTerms.length > 0) {
+            attributes.Ontology_term = ontologyTerms;
+        }
+        const gff_score = featureLoc.attributes?.gff_score;
+        let score = null;
+        if (gff_score && gff_score.length > 0) {
+            if (gff_score[0]) {
+                score = Number(gff_score[0]);
+                if (Number.isNaN(score)) {
+                    score = null;
+                }
             }
+            delete attributes.gff_score;
         }
-        delete attributes.gff_score;
-    }
-    const locations = [{ start: feature.min, end: feature.max }];
-    return locations.map((location) => ({
-        start: Number(location.start) + 1,
-        end: Number(location.end),
-        seq_id: refSeqNames ? refSeqNames[feature.refSeq] ?? null : feature.refSeq,
-        source,
-        type: feature.type,
-        score,
-        strand: feature.strand ? (feature.strand === 1 ? '+' : '-') : null,
-        phase: null,
-        attributes: Object.keys(attributes).length > 0
-            ? attributes
-            : null,
-        derived_features: [],
-        child_features: prepareChildFeatures(feature, attributes.ID?.[0], refSeqNames),
-    }));
+        return {
+            start: Number(featureLoc.min) + 1,
+            end: Number(featureLoc.max),
+            seq_id: refSeqNames
+                ? refSeqNames[featureLoc.refSeq] ?? null
+                : featureLoc.refSeq,
+            source,
+            type: featureLoc.type,
+            score,
+            strand: featureLoc.strand ? (featureLoc.strand === 1 ? '+' : '-') : null,
+            phase: null,
+            attributes: Object.keys(attributes).length > 0
+                ? attributes
+                : null,
+            derived_features: [],
+            child_features: prepareChildFeatures(featureLoc, attributes.ID?.[0], refSeqNames),
+        };
+    });
 }
 function prepareChildFeatures(feature, parentID, refSeqNames) {
     if (!feature.children) {
@@ -158,7 +161,7 @@ function getTranscriptParts(feature) {
             if (lastPart) {
                 parts.push({ min: lastPart.max, max: child.min, type: 'intron' });
             }
-            const [start, end] = (0, util_1.intersection2)(cdsMin, cdsMax, child.min, child.max);
+            const [start, end] = intersection2(cdsMin, cdsMax, child.min, child.max);
             let utrType;
             if (hasIntersected) {
                 utrType = feature.strand === 1 ? 'threePrimeUTR' : 'fivePrimeUTR';

package/dist/GFF3/annotationFeatureToGFF3.js.map

@@ -1 +1 @@
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package/dist/GFF3/annotationFeatureToGFF3.test.d.ts

@@ -1 +1,2 @@
 export {};
+//# sourceMappingURL=annotationFeatureToGFF3.test.d.ts.map

package/dist/GFF3/annotationFeatureToGFF3.test.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"annotationFeatureToGFF3.test.d.ts","sourceRoot":"","sources":["../../src/GFF3/annotationFeatureToGFF3.test.ts"],"names":[],"mappings":""}