@apollo-annotation/shared 1.0.1 → 1.1.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/Changes/MergeAndUndoMergeTranscriptsChanges.d.ts.map +1 -1
- package/dist/Changes/MergeAndUndoMergeTranscriptsChanges.js +3 -9
- package/dist/Changes/MergeAndUndoMergeTranscriptsChanges.js.map +1 -1
- package/dist/Checks/CDSCheck.js +6 -6
- package/dist/Checks/CDSCheck.js.map +1 -1
- package/dist/Checks/TranscriptCheck.js +2 -2
- package/dist/Checks/TranscriptCheck.js.map +1 -1
- package/dist/Checks/util.js +3 -3
- package/dist/Checks/util.js.map +1 -1
- package/dist/GFF3/annotationFeatureToGFF3.js +3 -3
- package/dist/GFF3/annotationFeatureToGFF3.js.map +1 -1
- package/dist/GFF3/annotationFeatureToGFF3.test.js +2 -2
- package/dist/GFF3/annotationFeatureToGFF3.test.js.map +1 -1
- package/dist/tsconfig.tsbuildinfo +1 -1
- package/package.json +8 -8
- package/src/Changes/MergeAndUndoMergeTranscriptsChanges.ts +3 -9
- package/src/Checks/CDSCheck.ts +6 -6
- package/src/Checks/TranscriptCheck.ts +2 -2
- package/src/Checks/util.ts +3 -3
- package/src/GFF3/annotationFeatureToGFF3.test.ts +2 -2
- package/src/GFF3/annotationFeatureToGFF3.ts +3 -3
- package/test_data/gene.json +2 -2
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{"version":3,"file":"MergeAndUndoMergeTranscriptsChanges.d.ts","sourceRoot":"","sources":["../../src/Changes/MergeAndUndoMergeTranscriptsChanges.ts"],"names":[],"mappings":"AAGA,OAAO,EACL,KAAK,aAAa,EAClB,aAAa,EACb,KAAK,uBAAuB,EAC7B,MAAM,2BAA2B,CAAA;AAClC,OAAO,KAAK,EACV,iBAAiB,EACjB,yBAAyB,EAC1B,MAAM,wBAAwB,CAAA;AAC/B,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,4BAA4B,CAAA;AAMzD,UAAU,oCAAqC,SAAQ,uBAAuB;IAC5E,QAAQ,EAAE,wBAAwB,CAAA;CACnC;AAED,MAAM,WAAW,6BAA6B;IAC5C,eAAe,EAAE,yBAAyB,CAAA;IAC1C,gBAAgB,EAAE,yBAAyB,CAAA;IAC3C,eAAe,EAAE,MAAM,CAAA;CACxB;AAED,UAAU,sCACR,SAAQ,oCAAoC,EAC1C,6BAA6B;CAAG;AAEpC,UAAU,wCACR,SAAQ,oCAAoC;IAC5C,OAAO,EAAE,6BAA6B,EAAE,CAAA;CACzC;AAED,MAAM,MAAM,gCAAgC,GACxC,sCAAsC,GACtC,wCAAwC,CAAA;AAE5C,UAAU,wCACR,SAAQ,uBAAuB;IAC/B,QAAQ,EAAE,4BAA4B,CAAA;CACvC;AAED,MAAM,WAAW,iCAAiC;IAChD,oBAAoB,EAAE,yBAAyB,EAAE,CAAA;IACjD,eAAe,EAAE,MAAM,CAAA;CACxB;AAED,UAAU,0CACR,SAAQ,wCAAwC,EAC9C,iCAAiC;CAAG;AAExC,UAAU,4CACR,SAAQ,wCAAwC;IAChD,OAAO,EAAE,iCAAiC,EAAE,CAAA;CAC7C;AAED,MAAM,MAAM,oCAAoC,GAC5C,0CAA0C,GAC1C,4CAA4C,CAAA;AAEhD,qBAAa,sBAAuB,SAAQ,aAAa;IACvD,QAAQ,2BAAoC;IAC5C,OAAO,EAAE,6BAA6B,EAAE,CAAA;gBAE5B,IAAI,EAAE,gCAAgC,EAAE,OAAO,CAAC,EAAE,aAAa;IAK3E,IAAI,YAAY,WAEf;IAED,MAAM,IAAI,gCAAgC;IAiB1C,wBAAwB,CACtB,eAAe,EAAE,OAAO,EACxB,gBAAgB,EAAE,yBAAyB;IA+B7C,kCAAkC,CAChC,kBAAkB,EAAE,yBAAyB,EAC7C,eAAe,EAAE,OAAO;
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{"version":3,"file":"MergeAndUndoMergeTranscriptsChanges.d.ts","sourceRoot":"","sources":["../../src/Changes/MergeAndUndoMergeTranscriptsChanges.ts"],"names":[],"mappings":"AAGA,OAAO,EACL,KAAK,aAAa,EAClB,aAAa,EACb,KAAK,uBAAuB,EAC7B,MAAM,2BAA2B,CAAA;AAClC,OAAO,KAAK,EACV,iBAAiB,EACjB,yBAAyB,EAC1B,MAAM,wBAAwB,CAAA;AAC/B,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,4BAA4B,CAAA;AAMzD,UAAU,oCAAqC,SAAQ,uBAAuB;IAC5E,QAAQ,EAAE,wBAAwB,CAAA;CACnC;AAED,MAAM,WAAW,6BAA6B;IAC5C,eAAe,EAAE,yBAAyB,CAAA;IAC1C,gBAAgB,EAAE,yBAAyB,CAAA;IAC3C,eAAe,EAAE,MAAM,CAAA;CACxB;AAED,UAAU,sCACR,SAAQ,oCAAoC,EAC1C,6BAA6B;CAAG;AAEpC,UAAU,wCACR,SAAQ,oCAAoC;IAC5C,OAAO,EAAE,6BAA6B,EAAE,CAAA;CACzC;AAED,MAAM,MAAM,gCAAgC,GACxC,sCAAsC,GACtC,wCAAwC,CAAA;AAE5C,UAAU,wCACR,SAAQ,uBAAuB;IAC/B,QAAQ,EAAE,4BAA4B,CAAA;CACvC;AAED,MAAM,WAAW,iCAAiC;IAChD,oBAAoB,EAAE,yBAAyB,EAAE,CAAA;IACjD,eAAe,EAAE,MAAM,CAAA;CACxB;AAED,UAAU,0CACR,SAAQ,wCAAwC,EAC9C,iCAAiC;CAAG;AAExC,UAAU,4CACR,SAAQ,wCAAwC;IAChD,OAAO,EAAE,iCAAiC,EAAE,CAAA;CAC7C;AAED,MAAM,MAAM,oCAAoC,GAC5C,0CAA0C,GAC1C,4CAA4C,CAAA;AAEhD,qBAAa,sBAAuB,SAAQ,aAAa;IACvD,QAAQ,2BAAoC;IAC5C,OAAO,EAAE,6BAA6B,EAAE,CAAA;gBAE5B,IAAI,EAAE,gCAAgC,EAAE,OAAO,CAAC,EAAE,aAAa;IAK3E,IAAI,YAAY,WAEf;IAED,MAAM,IAAI,gCAAgC;IAiB1C,wBAAwB,CACtB,eAAe,EAAE,OAAO,EACxB,gBAAgB,EAAE,yBAAyB;IA+B7C,kCAAkC,CAChC,kBAAkB,EAAE,yBAAyB,EAC7C,eAAe,EAAE,OAAO;IA2F1B,wBAAwB,CACtB,eAAe,EAAE,iBAAiB,EAClC,gBAAgB,EAAE,yBAAyB;IA4B7C,kCAAkC,CAChC,kBAAkB,EAAE,yBAAyB,EAC7C,eAAe,EAAE,iBAAiB;IAqEpC,UAAU;CAuBX;AAED,qBAAa,0BAA2B,SAAQ,aAAa;IAC3D,QAAQ,+BAAwC;IAChD,OAAO,EAAE,iCAAiC,EAAE,CAAA;gBAG1C,IAAI,EAAE,oCAAoC,EAC1C,OAAO,CAAC,EAAE,aAAa;IAMzB,MAAM,IAAI,oCAAoC;IAgB9C,UAAU;CAqBX"}
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@@ -50,9 +50,7 @@ export class MergeTranscriptsChange extends FeatureChange {
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}
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}
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mergeFeatureIntoTranscriptOnServer(secondFeatureChild, firstTranscript) {
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firstTranscript.children = new Map();
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}
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firstTranscript.children ??= new Map();
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let merged = false;
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let mrgChild;
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let toDelete;
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@@ -70,9 +68,7 @@ export class MergeTranscriptsChange extends FeatureChange {
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doesIntersect2(firstFeatureChild.min, firstFeatureChild.max, mrgChild.min, mrgChild.max)) {
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mrgChild.min = Math.min(secondFeatureChild.min, mrgChild.min, firstFeatureChild.min);
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mrgChild.max = Math.max(secondFeatureChild.max, mrgChild.max, firstFeatureChild.max);
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mrgChild.attributes = {};
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}
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mrgChild.attributes ??= {};
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const mrgChildAttr = JSON.parse(JSON.stringify(mrgChild.attributes));
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if (!Object.keys(mrgChildAttr).includes('merged_with')) {
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mrgChildAttr.merged_with = [];
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@@ -124,9 +120,7 @@ export class MergeTranscriptsChange extends FeatureChange {
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}
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}
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mergeFeatureIntoTranscriptOnClient(secondFeatureChild, firstTranscript) {
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firstTranscript.children = new Map();
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}
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firstTranscript.children ??= new Map();
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let merged = false;
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let mrgChild;
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let toDelete;
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+
{"version":3,"file":"MergeAndUndoMergeTranscriptsChanges.js","sourceRoot":"","sources":["../../src/Changes/MergeAndUndoMergeTranscriptsChanges.ts"],"names":[],"mappings":"AAAA,oDAAoD;AACpD,4DAA4D;AAE5D,OAAO,EAEL,aAAa,GAEd,MAAM,2BAA2B,CAAA;AAMlC,OAAO,EAAE,cAAc,EAAE,MAAM,oBAAoB,CAAA;AACnD,OAAO,EAAE,WAAW,EAAE,MAAM,0BAA0B,CAAA;AAEtD,OAAO,EAAE,mBAAmB,EAAE,mBAAmB,EAAE,MAAM,YAAY,CAAA;AAgDrE,MAAM,OAAO,sBAAuB,SAAQ,aAAa;IACvD,QAAQ,GAAG,wBAAiC,CAAA;IAC5C,OAAO,CAAiC;IAExC,YAAY,IAAsC,EAAE,OAAuB;QACzE,KAAK,CAAC,IAAI,EAAE,OAAO,CAAC,CAAA;QACpB,IAAI,CAAC,OAAO,GAAG,SAAS,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;IAC1D,CAAC;IACD,2EAA2E;IAC3E,IAAI,YAAY;QACd,OAAO,iCAAiC,CAAA;IAC1C,CAAC;IAED,MAAM;QACJ,MAAM,EAAE,QAAQ,EAAE,UAAU,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAA;QACxD,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACzB,MAAM,CAAC,EAAE,eAAe,EAAE,gBAAgB,EAAE,eAAe,EAAE,CAAC,GAAG,OAAO,CAAA;YAExE,OAAO;gBACL,QAAQ;gBACR,UAAU;gBACV,QAAQ;gBACR,eAAe;gBACf,gBAAgB;gBAChB,eAAe;aAChB,CAAA;QACH,CAAC;QACD,OAAO,EAAE,QAAQ,EAAE,UAAU,EAAE,QAAQ,EAAE,OAAO,EAAE,CAAA;IACpD,CAAC;IAED,wBAAwB,CACtB,eAAwB,EACxB,gBAA2C;QAE3C,eAAe,CAAC,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,eAAe,CAAC,GAAG,EAAE,gBAAgB,CAAC,GAAG,CAAC,CAAA;QACzE,eAAe,CAAC,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,eAAe,CAAC,GAAG,EAAE,gBAAgB,CAAC,GAAG,CAAC,CAAA;QAEzE,MAAM,gBAAgB,GACpB,eAAe,CAAC,UAAU;YACxB,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,eAAe,CAAC,UAAU,CAAC,CAAC;YACxD,CAAC,CAAC,EAAE,CAAA;QACR,IAAI,gBAAgB,CAAC,UAAU,EAAE,CAAC;YAChC,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC,QAAQ,CAAC,aAAa,CAAC,EAAE,CAAC;gBAC3D,gBAAgB,CAAC,WAAW,GAAG,EAAE,CAAA;YACnC,CAAC;YACD,gBAAgB,CAAC,WAAW,CAAC,IAAI,CAC/B,mBAAmB,CAAC,mBAAmB,CAAC,gBAAgB,CAAC,UAAU,CAAC,CAAC,CACtE,CAAA;QACH,CAAC;QACD,eAAe,CAAC,UAAU,GAAG,gBAAgB,CAAA;QAE7C,IAAI,gBAAgB,CAAC,QAAQ,EAAE,CAAC;YAC9B,KAAK,MAAM,CAAC,EAAE,kBAAkB,CAAC,IAAI,MAAM,CAAC,OAAO,CACjD,gBAAgB,CAAC,QAAQ,CAC1B,EAAE,CAAC;gBACF,IAAI,CAAC,kCAAkC,CACrC,kBAAkB,EAClB,eAAe,CAChB,CAAA;YACH,CAAC;QACH,CAAC;IACH,CAAC;IAED,kCAAkC,CAChC,kBAA6C,EAC7C,eAAwB;QAExB,eAAe,CAAC,QAAQ,KAAK,IAAI,GAAG,EAAmB,CAAA;QACvD,IAAI,MAAM,GAAG,KAAK,CAAA;QAClB,IAAI,QAA6B,CAAA;QACjC,IAAI,QAAQ,CAAA;QACZ,KAAK,MAAM,CAAC,EAAE,iBAAiB,CAAC,IAAI,eAAe,CAAC,QAAQ,EAAE,CAAC;YAC7D,IAAI,CAAC,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAC;gBACzB,QAAQ,GAAG,KAAK,CAAA;gBAChB,QAAQ,GAAG,iBAAiB,CAAA;YAC9B,CAAC;iBAAM,CAAC;gBACN,QAAQ,GAAG,IAAI,CAAA;YACjB,CAAC;YACD,IACE,QAAQ,CAAC,IAAI,KAAK,kBAAkB,CAAC,IAAI;gBACzC,QAAQ,CAAC,IAAI,KAAK,iBAAiB,CAAC,IAAI;gBACxC,cAAc,CACZ,kBAAkB,CAAC,GAAG,EACtB,kBAAkB,CAAC,GAAG,EACtB,QAAQ,CAAC,GAAG,EACZ,QAAQ,CAAC,GAAG,CACb;gBACD,cAAc,CACZ,iBAAiB,CAAC,GAAG,EACrB,iBAAiB,CAAC,GAAG,EACrB,QAAQ,CAAC,GAAG,EACZ,QAAQ,CAAC,GAAG,CACb,EACD,CAAC;gBACD,QAAQ,CAAC,GAAG,GAAG,IAAI,CAAC,GAAG,CACrB,kBAAkB,CAAC,GAAG,EACtB,QAAQ,CAAC,GAAG,EACZ,iBAAiB,CAAC,GAAG,CACtB,CAAA;gBACD,QAAQ,CAAC,GAAG,GAAG,IAAI,CAAC,GAAG,CACrB,kBAAkB,CAAC,GAAG,EACtB,QAAQ,CAAC,GAAG,EACZ,iBAAiB,CAAC,GAAG,CACtB,CAAA;gBAED,QAAQ,CAAC,UAAU,KAAK,EAAE,CAAA;gBAE1B,MAAM,YAAY,GAA6B,IAAI,CAAC,KAAK,CACvD,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,UAAU,CAAC,CACpC,CAAA;gBAED,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,QAAQ,CAAC,aAAa,CAAC,EAAE,CAAC;oBACvD,YAAY,CAAC,WAAW,GAAG,EAAE,CAAA;gBAC/B,CAAC;gBACD,MAAM,oBAAoB,GAAG,YAAY,CAAC,WAAW,CAAA;gBACrD,oBAAoB,CAAC,IAAI,CACvB,mBAAmB,CACjB,mBAAmB,CAAC,kBAAkB,CAAC,UAAU,CAAC,CACnD,CACF,CAAA;gBAED,IAAI,QAAQ,EAAE,CAAC;oBACb,MAAM,IAAI,GACR,iBAAiB,CAAC,UAAU;wBAC1B,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,iBAAiB,CAAC,UAAU,CAAC,CAAC;wBAC1D,CAAC,CAAC,SAAS,CAAA;oBACf,oBAAoB,CAAC,IAAI,CAAC,mBAAmB,CAAC,IAAI,CAAC,CAAC,CAAA;oBACpD,eAAe,CAAC,QAAQ,CAAC,MAAM,CAAC,iBAAiB,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAA;gBACnE,CAAC;gBAED,YAAY,CAAC,WAAW,GAAG,CAAC,GAAG,IAAI,GAAG,CAAC,oBAAoB,CAAC,CAAC,CAAA;gBAC7D,QAAQ,CAAC,UAAU,GAAG,YAAY,CAAA;gBAClC,MAAM,GAAG,IAAI,CAAA;YACf,CAAC;QACH,CAAC;QAED,IAAI,MAAM,IAAI,QAAQ,IAAI,kBAAkB,CAAC,QAAQ,EAAE,CAAC;YACtD,yCAAyC;YACzC,iEAAiE;YACjE,MAAM,CAAC,OAAO,CAAC,kBAAkB,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,KAAK,CAAC,EAAE,EAAE;gBAC5D,IAAI,CAAC,QAAQ,CAAC,QAAQ,EAAE,KAAK,CAAC,CAAA;YAChC,CAAC,CAAC,CAAA;QACJ,CAAC;QAED,IAAI,MAAM,IAAI,QAAQ,EAAE,CAAC;YACvB,IAAI,CAAC,QAAQ,CACX,eAAe,EACf,QAAgD,CACjD,CAAA;QACH,CAAC;aAAM,CAAC;YACN,iEAAiE;YACjE,yEAAyE;YACzE,IAAI,CAAC,QAAQ,CAAC,eAAe,EAAE,kBAAkB,CAAC,CAAA;QACpD,CAAC;IACH,CAAC;IAED,wBAAwB,CACtB,eAAkC,EAClC,gBAA2C;QAE3C,eAAe,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,eAAe,CAAC,GAAG,EAAE,gBAAgB,CAAC,GAAG,CAAC,CAAC,CAAA;QAC3E,eAAe,CAAC,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,eAAe,CAAC,GAAG,EAAE,gBAAgB,CAAC,GAAG,CAAC,CAAC,CAAA;QAE3E,MAAM,GAAG,GAAG,eAAe,CAAC,UAAU,CAAC,GAAG,CAAC,aAAa,CAAC,EAAE,KAAK,EAAE,IAAI,EAAE,CAAA;QACxE,MAAM,UAAU,GAAG,mBAAmB,CACpC,mBAAmB,CAAC,gBAAgB,CAAC,UAAU,CAAC,CACjD,CAAA;QAED,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,UAAU,CAAC,EAAE,CAAC;YAC9B,iEAAiE;YACjE,GAAG,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;QACtB,CAAC;QACD,eAAe,CAAC,YAAY,CAAC,aAAa,EAAE,GAAG,CAAC,CAAA;QAEhD,IAAI,gBAAgB,CAAC,QAAQ,EAAE,CAAC;YAC9B,KAAK,MAAM,CAAC,EAAE,kBAAkB,CAAC,IAAI,MAAM,CAAC,OAAO,CACjD,gBAAgB,CAAC,QAAQ,CAC1B,EAAE,CAAC;gBACF,IAAI,CAAC,kCAAkC,CACr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|
package/dist/Checks/CDSCheck.js
CHANGED
|
@@ -79,8 +79,8 @@ function getOriginalCodonLocation(cdsLocation, strand, index) {
|
|
|
79
79
|
? cdsLocation.toSorted((a, b) => (a.min < b.min ? 1 : -1))
|
|
80
80
|
: cdsLocation.toSorted((a, b) => (a.min < b.min ? -1 : 1));
|
|
81
81
|
let i = 0;
|
|
82
|
-
let currentStart
|
|
83
|
-
let currentEnd
|
|
82
|
+
let currentStart;
|
|
83
|
+
let currentEnd;
|
|
84
84
|
for (let iloc = 0; iloc < sortedLocation.length; iloc++) {
|
|
85
85
|
const loc = sortedLocation[iloc];
|
|
86
86
|
const { phase } = loc;
|
|
@@ -133,7 +133,7 @@ async function checkMRNA(feature, getSequence) {
|
|
|
133
133
|
name: CHECK_NAME,
|
|
134
134
|
cause: CAUSES[CAUSES.MissingStartCodon],
|
|
135
135
|
ids,
|
|
136
|
-
refSeq
|
|
136
|
+
refSeq,
|
|
137
137
|
start: cdsStart,
|
|
138
138
|
end: cdsStart,
|
|
139
139
|
message: `Unexpected start codon "${start_codon}" in feature "${getPrintableId(feature)}": `,
|
|
@@ -146,7 +146,7 @@ async function checkMRNA(feature, getSequence) {
|
|
|
146
146
|
name: CHECK_NAME,
|
|
147
147
|
cause: CAUSES[CAUSES.MissingStopCodon],
|
|
148
148
|
ids,
|
|
149
|
-
refSeq
|
|
149
|
+
refSeq,
|
|
150
150
|
start: cdsEnd,
|
|
151
151
|
end: cdsEnd,
|
|
152
152
|
message: `Missing stop codon in feature "${getPrintableId(feature)}"`,
|
|
@@ -159,7 +159,7 @@ async function checkMRNA(feature, getSequence) {
|
|
|
159
159
|
name: CHECK_NAME,
|
|
160
160
|
cause: CAUSES[CAUSES.MissingStopCodon],
|
|
161
161
|
ids,
|
|
162
|
-
refSeq
|
|
162
|
+
refSeq,
|
|
163
163
|
start: cdsEnd,
|
|
164
164
|
end: cdsEnd,
|
|
165
165
|
message: `Missing stop codon in feature "${getPrintableId(feature)}"`,
|
|
@@ -178,7 +178,7 @@ async function checkMRNA(feature, getSequence) {
|
|
|
178
178
|
name: CHECK_NAME,
|
|
179
179
|
cause: CAUSES[CAUSES.InternalStopCodon],
|
|
180
180
|
ids,
|
|
181
|
-
refSeq
|
|
181
|
+
refSeq,
|
|
182
182
|
start: codonStart,
|
|
183
183
|
end: codonEnd,
|
|
184
184
|
message: `Internal stop codon in feature "${getPrintableId(feature)}"`,
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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+
{"version":3,"file":"CDSCheck.js","sourceRoot":"","sources":["../../src/Checks/CDSCheck.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,2BAA2B,CAAA;AAKjD,OAAO,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAA;AAClD,OAAO,QAAQ,MAAM,eAAe,CAAA;AAEpC,OAAO,EAAE,cAAc,EAAE,MAAM,WAAW,CAAA;AAE1C,IAAK,WAIJ;AAJD,WAAK,WAAW;IACd,2CAAK,CAAA;IACL,2CAAK,CAAA;IACL,2CAAK,CAAA;AACP,CAAC,EAJI,WAAW,KAAX,WAAW,QAIf;AAED,IAAK,YAEJ;AAFD,WAAK,YAAY;IACf,6CAAK,CAAA;AACP,CAAC,EAFI,YAAY,KAAZ,YAAY,QAEhB;AAED,MAAM,UAAU,GAAG,UAAU,CAAA;AAE7B,IAAK,MAIJ;AAJD,WAAK,MAAM;IACT,6DAAmB,CAAA;IACnB,6DAAmB,CAAA;IACnB,2DAAkB,CAAA;AACpB,CAAC,EAJI,MAAM,KAAN,MAAM,QAIV;AAED,MAAM,gBAAgB,GAAuC;IAC3D,CAAC,EAAE,GAAG;IACN,CAAC,EAAE,GAAG;IACN,CAAC,EAAE,GAAG;IACN,CAAC,EAAE,GAAG;IACN,CAAC,CAAC,YAAY,EAAE,GAAG;IACnB,CAAC,CAAC,YAAY,EAAE,GAAG;IACnB,CAAC,CAAC,YAAY,EAAE,GAAG;IACnB,CAAC,CAAC,YAAY,EAAE,GAAG;IACnB,CAAC,CAAC,YAAY,EAAE,GAAG;IACnB,CAAC,CAAC,YAAY,EAAE,GAAG;IACnB,CAAC,CAAC,iBAAiB,EAAE,GAAG;IACxB,CAAC,CAAC,iBAAiB,EAAE,GAAG;IACxB,CAAC,CAAC,iBAAiB,EAAE,GAAG;IACxB,CAAC,CAAC,iBAAiB,EAAE,GAAG;IACxB,CAAC,CAAC,sBAAsB,EAAE,GAAG;CAC9B,CAAA;AAKD,SAAS,iBAAiB,CAAC,GAAW;IACpC,MAAM,UAAU,GAAa,EAAE,CAAA;IAC/B,KAAK,MAAM,EAAE,IAAI,GAAG,EAAE,CAAC;QACrB,MAAM,EAAE,GAAG,gBAAgB,CAAC,EAAE,CAAC,WAAW,EAAE,CAAC,CAAA;QAC7C,IAAI,EAAE,KAAK,SAAS,EAAE,CAAC;YACrB,MAAM,IAAI,SAAS,CAAC,kCAAkC,EAAE,GAAG,CAAC,CAAA;QAC9D,CAAC;QACD,IAAI,EAAE,KAAK,EAAE,CAAC,WAAW,EAAE,EAAE,CAAC;YAC5B,UAAU,CAAC,IAAI,CAAC,EAAE,CAAC,WAAW,EAAE,CAAC,CAAA;QACnC,CAAC;aAAM,CAAC;YACN,UAAU,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;QACrB,CAAC;IACH,CAAC;IACD,OAAO,UAAU,CAAC,OAAO,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;AACtC,CAAC;AAED,KAAK,UAAU,cAAc,CAC3B,WAAwB,EACxB,MAA0B,EAC1B,WAA4D;IAE5D,MAAM,SAAS,GAAG,MAAM,OAAO,CAAC,GAAG,CACjC,WAAW,CAAC,GAAG,CAAC,CAAC,EAAE,GAAG,EAAE,GAAG,EAAE,EAAE,EAAE,CAAC,WAAW,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,CACzD,CAAA;IACD,IAAI,GAAG,GAAG,SAAS,CAAC,IAAI,CAAC,EAAE,CAAC,CAAA;IAC5B,IAAI,MAAM,KAAK,CAAC,CAAC,EAAE,CAAC;QAClB,GAAG,GAAG,iBAAiB,CAAC,GAAG,CAAC,CAAA;IAC9B,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AAED,SAAS,qBAAqB,CAAC,GAAW;IACxC,MAAM,MAAM,GAAa,EAAE,CAAA;IAC3B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,GAAG,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;QAC5C,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;IAClC,CAAC;IACD,OAAO,MAAM,CAAA;AACf,CAAC;AAED,SAAS,GAAG,CAAC,GAAW,EAAE,GAAW,EAAE,MAA0B;IAC/D,IAAI,MAAM,KAAK,CAAC,CAAC,EAAE,CAAC;QAClB,OAAO,GAAG,GAAG,GAAG,CAAA;IAClB,CAAC;IACD,OAAO,GAAG,GAAG,GAAG,CAAA;AAClB,CAAC;AAED,SAAS,wBAAwB,CAC/B,WAAwB,EACxB,MAA0B,EAC1B,KAAa;IAEb,2EAA2E;IAC3E,MAAM,cAAc,GAClB,MAAM,KAAK,CAAC,CAAC;QACX,CAAC,CAAC,WAAW,CAAC,QAAQ,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;QAC1D,CAAC,CAAC,WAAW,CAAC,QAAQ,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;IAC9D,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,IAAI,YAAgC,CAAA;IACpC,IAAI,UAA8B,CAAA;IAClC,KAAK,IAAI,IAAI,GAAG,CAAC,EAAE,IAAI,GAAG,cAAc,CAAC,MAAM,EAAE,IAAI,EAAE,EAAE,CAAC;QACxD,MAAM,GAAG,GAAG,cAAc,CAAC,IAAI,CAAC,CAAA;QAChC,MAAM,EAAE,KAAK,EAAE,GAAG,GAAG,CAAA;QACrB,2EAA2E;QAC3E,MAAM,OAAO,GAAG,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,GAAG,KAAK,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,GAAG,KAAK,CAAA;QACjE,MAAM,KAAK,GAAG,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAA;QAC/C,KACE,IAAI,GAAG,GAAG,OAAO,EACjB,GAAG,CAAC,GAAG,EAAE,KAAK,EAAE,MAAM,CAAC,EACvB,GAAG,GAAG,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,EACvC,CAAC;YACD,YAAY,GAAG,GAAG,CAAA;YAClB,UAAU,GAAG,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,CAAC,YAAY,GAAG,CAAC,CAAA;YAChE,kEAAkE;YAClE,IAAI,MAAM,KAAK,CAAC,CAAC,IAAI,UAAU,GAAG,GAAG,CAAC,GAAG,EAAE,CAAC;gBAC1C,UAAU;oBACR,cAAc,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,GAAG,GAAG,cAAc,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAA;YACjE,CAAC;iBAAM,IAAI,UAAU,GAAG,GAAG,CAAC,GAAG,EAAE,CAAC;gBAChC,UAAU;oBACR,cAAc,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,GAAG,GAAG,cAAc,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,KAAK,CAAA;YACjE,CAAC;YACD,IAAI,CAAC,KAAK,KAAK,EAAE,CAAC;gBAChB,OAAO,CAAC,YAAY,EAAE,UAAU,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAGrD,CAAA;YACH,CAAC;YACD,CAAC,EAAE,CAAA;QACL,CAAC;IACH,CAAC;IACD,OAAO,SAAS,CAAA;AAClB,CAAC;AAED,KAAK,UAAU,SAAS,CACtB,OAAkC,EAClC,WAA4D;IAE5D,MAAM,YAAY,GAA0B,EAAE,CAAA;IAC9C,MAAM,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,MAAM,EAAE,MAAM,EAAE,GAAG,OAAO,CAAA;IAEjD,MAAM,YAAY,GAAG,eAAe,CAAC,OAAO,CAAC,CAAA;IAE7C,IAAI,CAAC,YAAY,EAAE,CAAC;QAClB,OAAO,YAAY,CAAA;IACrB,CAAC;IACD,MAAM,GAAG,GAAG,CAAC,GAAG,CAAC,CAAA;IACjB,KAAK,MAAM,WAAW,IAAI,YAAY,EAAE,CAAC;QACvC,MAAM,QAAQ,GAAG,MAAM,cAAc,CAAC,WAAW,EAAE,MAAM,EAAE,WAAW,CAAC,CAAA;QACvE,MAAM,MAAM,GAAG,qBAAqB,CAAC,QAAQ,CAAC,CAAA;QAC9C,MAAM,MAAM,GACV,MAAM,KAAK,CAAC,CAAC;YACX,CAAC,CAAC,WAAW,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,GAAG,IAAI,GAAG;YAC/B,CAAC,CAAC,WAAW,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,EAAE,GAAG,IAAI,GAAG,CAAA;QACpC,IAAI,QAAQ,CAAC,MAAM,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC;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|
|
@@ -56,7 +56,7 @@ async function checkTranscript(feature, getSequence) {
|
|
|
56
56
|
name: CHECK_NAME,
|
|
57
57
|
cause: CAUSES[CAUSES.NonCanonicalSpliceSiteAtFivePrime],
|
|
58
58
|
ids: [feature._id],
|
|
59
|
-
refSeq: feature.refSeq
|
|
59
|
+
refSeq: feature.refSeq,
|
|
60
60
|
start: spliceSequence.fivePrimeMin,
|
|
61
61
|
end: spliceSequence.fivePrimeMin + 2,
|
|
62
62
|
message: `Unexpected 5′ splice site in "${getPrintableId(feature)}". Expected: ${[...VALID_FIVE_PRIME_SEQ].join('|')}, got: ${spliceSequence.fivePrimeSeq}`,
|
|
@@ -68,7 +68,7 @@ async function checkTranscript(feature, getSequence) {
|
|
|
68
68
|
name: CHECK_NAME,
|
|
69
69
|
cause: CAUSES[CAUSES.NonCanonicalSpliceSiteAtThreePrime],
|
|
70
70
|
ids: [feature._id],
|
|
71
|
-
refSeq: feature.refSeq
|
|
71
|
+
refSeq: feature.refSeq,
|
|
72
72
|
start: spliceSequence.threePrimeMin,
|
|
73
73
|
end: spliceSequence.threePrimeMin + 2,
|
|
74
74
|
message: `Unexpected 3′ splice site in "${getPrintableId(feature)}". Expected: ${[...VALID_THREE_PRIME_SEQ].join('|')}, got: ${spliceSequence.threePrimeSeq}`,
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"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
|
|
1
|
+
{"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;gBACtB,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;gBACtB,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/util.js
CHANGED
|
@@ -1,12 +1,12 @@
|
|
|
1
1
|
export function getPrintableId(feature) {
|
|
2
2
|
const gff_id = feature.attributes?.gff_id?.join(', ');
|
|
3
3
|
if (gff_id) {
|
|
4
|
-
return `${gff_id} (_id: ${feature._id
|
|
4
|
+
return `${gff_id} (_id: ${feature._id})`;
|
|
5
5
|
}
|
|
6
6
|
const gff_name = feature.attributes?.gff_name?.join(', ');
|
|
7
7
|
if (gff_name) {
|
|
8
|
-
return `${gff_name} (_id: ${feature._id
|
|
8
|
+
return `${gff_name} (_id: ${feature._id})`;
|
|
9
9
|
}
|
|
10
|
-
return `_id: ${feature._id
|
|
10
|
+
return `_id: ${feature._id}`;
|
|
11
11
|
}
|
|
12
12
|
//# sourceMappingURL=util.js.map
|
package/dist/Checks/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"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,
|
|
1
|
+
{"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,GAAG,CAAA;IAC1C,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,GAAG,CAAA;IAC5C,CAAC;IACD,OAAO,QAAQ,OAAO,CAAC,GAAG,EAAE,CAAA;AAC9B,CAAC"}
|
|
@@ -79,8 +79,8 @@ export function annotationFeatureToGFF3(feature, parentId, refSeqNames) {
|
|
|
79
79
|
delete attributes.gff_score;
|
|
80
80
|
}
|
|
81
81
|
return {
|
|
82
|
-
start:
|
|
83
|
-
end:
|
|
82
|
+
start: featureLoc.min + 1,
|
|
83
|
+
end: featureLoc.max,
|
|
84
84
|
seq_id: refSeqNames
|
|
85
85
|
? refSeqNames[featureLoc.refSeq] ?? null
|
|
86
86
|
: featureLoc.refSeq,
|
|
@@ -210,7 +210,7 @@ function getTranscriptParts(feature) {
|
|
|
210
210
|
return transcriptParts;
|
|
211
211
|
}
|
|
212
212
|
function getCdsLocations(feature) {
|
|
213
|
-
let transcriptParts
|
|
213
|
+
let transcriptParts;
|
|
214
214
|
try {
|
|
215
215
|
transcriptParts = getTranscriptParts(feature);
|
|
216
216
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"annotationFeatureToGFF3.js","sourceRoot":"","sources":["../../src/GFF3/annotationFeatureToGFF3.ts"],"names":[],"mappings":"AAAA,4DAA4D;AAQ5D,OAAO,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAA;AAElD,MAAM,UAAU,uBAAuB,CACrC,OAAkC,EAClC,QAAiB,EACjB,WAAgD;IAEhD,MAAM,SAAS,GACb,OAAO,CAAC,IAAI,KAAK,0BAA0B;QACzC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,QAAQ,IAAI,EAAE,CAAC;QACvC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAA;IACf,OAAO,SAAS,CAAC,GAAG,CAAC,CAAC,UAAU,EAAE,EAAE;QAClC,2DAA2D;QAC3D,MAAM,UAAU,GAAyC,IAAI,CAAC,KAAK,CACjE,IAAI,CAAC,SAAS,CAAC,UAAU,CAAC,UAAU,IAAI,EAAE,CAAC,CAC5C,CAAA;QACD,MAAM,aAAa,GAAa,EAAE,CAAA;QAClC,MAAM,MAAM,GAAG,UAAU,CAAC,UAAU,EAAE,UAAU,EAAE,CAAC,CAAC,CAAC,IAAI,IAAI,CAAA;QAE7D,OAAO,UAAU,CAAC,UAAU,CAAA;QAC5B,IAAI,QAAQ,EAAE,CAAC;YACb,UAAU,CAAC,MAAM,GAAG,CAAC,QAAQ,CAAC,CAAA;QAChC,CAAC;QACD,IAAI,UAAU,CAAC,MAAM,EAAE,CAAC;YACtB,UAAU,CAAC,EAAE,GAAG,UAAU,CAAC,MAAM,CAAA;YACjC,OAAO,UAAU,CAAC,MAAM,CAAA;QAC1B,CAAC;aAAM,IAAI,UAAU,CAAC,QAAQ,EAAE,CAAC;YAC/B,UAAU,CAAC,EAAE,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,CAAA;QAClC,CAAC;QACD,IAAI,UAAU,CAAC,QAAQ,EAAE,CAAC;YACxB,UAAU,CAAC,IAAI,GAAG,UAAU,CAAC,QAAQ,CAAA;YACrC,OAAO,UAAU,CAAC,QAAQ,CAAA;QAC5B,CAAC;QACD,IAAI,UAAU,CAAC,SAAS,EAAE,CAAC;YACzB,UAAU,CAAC,KAAK,GAAG,UAAU,CAAC,SAAS,CAAA;YACvC,OAAO,UAAU,CAAC,SAAS,CAAA;QAC7B,CAAC;QACD,IAAI,UAAU,CAAC,UAAU,EAAE,CAAC;YAC1B,UAAU,CAAC,MAAM,GAAG,UAAU,CAAC,UAAU,CAAA;YACzC,OAAO,UAAU,CAAC,UAAU,CAAA;QAC9B,CAAC;QACD,IAAI,UAAU,CAAC,OAAO,EAAE,CAAC;YACvB,UAAU,CAAC,GAAG,GAAG,UAAU,CAAC,OAAO,CAAA;YACnC,OAAO,UAAU,CAAC,OAAO,CAAA;QAC3B,CAAC;QACD,IAAI,UAAU,CAAC,gBAAgB,EAAE,CAAC;YAChC,UAAU,CAAC,YAAY,GAAG,UAAU,CAAC,gBAAgB,CAAA;YACrD,OAAO,UAAU,CAAC,gBAAgB,CAAA;QACpC,CAAC;QACD,IAAI,UAAU,CAAC,QAAQ,EAAE,CAAC;YACxB,UAAU,CAAC,IAAI,GAAG,UAAU,CAAC,QAAQ,CAAA;YACrC,OAAO,UAAU,CAAC,QAAQ,CAAA;QAC5B,CAAC;QACD,IAAI,UAAU,CAAC,UAAU,EAAE,CAAC;YAC1B,UAAU,CAAC,MAAM,GAAG,UAAU,CAAC,UAAU,CAAA;YACzC,OAAO,UAAU,CAAC,UAAU,CAAA;QAC9B,CAAC;QACD,IAAI,UAAU,CAAC,eAAe,EAAE,CAAC;YAC/B,UAAU,CAAC,WAAW,GAAG,UAAU,CAAC,eAAe,CAAA;YACnD,OAAO,UAAU,CAAC,eAAe,CAAA;QACnC,CAAC;QACD,IAAI,UAAU,CAAC,iBAAiB,EAAE,CAAC;YACjC,aAAa,CAAC,IAAI,CAAC,GAAG,UAAU,CAAC,iBAAiB,CAAC,CAAA;YACnD,OAAO,UAAU,CAAC,iBAAiB,CAAA;QACrC,CAAC;QACD,IAAI,UAAU,CAAC,eAAe,CAAC,EAAE,CAAC;YAChC,aAAa,CAAC,IAAI,CAAC,GAAG,UAAU,CAAC,eAAe,CAAC,CAAC,CAAA;YAClD,OAAO,UAAU,CAAC,eAAe,CAAC,CAAA;QACpC,CAAC;QACD,IAAI,UAAU,CAAC,mBAAmB,CAAC,EAAE,CAAC;YACpC,aAAa,CAAC,IAAI,CAAC,GAAG,UAAU,CAAC,mBAAmB,CAAC,CAAC,CAAA;YACtD,OAAO,UAAU,CAAC,mBAAmB,CAAC,CAAA;QACxC,CAAC;QACD,IAAI,aAAa,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC7B,UAAU,CAAC,aAAa,GAAG,aAAa,CAAA;QAC1C,CAAC;QAED,MAAM,SAAS,GAAG,UAAU,CAAC,UAAU,EAAE,SAAS,CAAA;QAClD,IAAI,KAAK,GAAkB,IAAI,CAAA;QAC/B,IAAI,SAAS,IAAI,SAAS,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACtC,IAAI,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC;gBACjB,KAAK,GAAG,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAA;gBAC5B,IAAI,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC;oBACxB,KAAK,GAAG,IAAI,CAAA;gBACd,CAAC;YACH,CAAC;YACD,OAAO,UAAU,CAAC,SAAS,CAAA;QAC7B,CAAC;QAED,OAAO;YACL,KAAK,EAAE,
|
|
1
|
+
{"version":3,"file":"annotationFeatureToGFF3.js","sourceRoot":"","sources":["../../src/GFF3/annotationFeatureToGFF3.ts"],"names":[],"mappings":"AAAA,4DAA4D;AAQ5D,OAAO,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAA;AAElD,MAAM,UAAU,uBAAuB,CACrC,OAAkC,EAClC,QAAiB,EACjB,WAAgD;IAEhD,MAAM,SAAS,GACb,OAAO,CAAC,IAAI,KAAK,0BAA0B;QACzC,CAAC,CAAC,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,QAAQ,IAAI,EAAE,CAAC;QACvC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAA;IACf,OAAO,SAAS,CAAC,GAAG,CAAC,CAAC,UAAU,EAAE,EAAE;QAClC,2DAA2D;QAC3D,MAAM,UAAU,GAAyC,IAAI,CAAC,KAAK,CACjE,IAAI,CAAC,SAAS,CAAC,UAAU,CAAC,UAAU,IAAI,EAAE,CAAC,CAC5C,CAAA;QACD,MAAM,aAAa,GAAa,EAAE,CAAA;QAClC,MAAM,MAAM,GAAG,UAAU,CAAC,UAAU,EAAE,UAAU,EAAE,CAAC,CAAC,CAAC,IAAI,IAAI,CAAA;QAE7D,OAAO,UAAU,CAAC,UAAU,CAAA;QAC5B,IAAI,QAAQ,EAAE,CAAC;YACb,UAAU,CAAC,MAAM,GAAG,CAAC,QAAQ,CAAC,CAAA;QAChC,CAAC;QACD,IAAI,UAAU,CAAC,MAAM,EAAE,CAAC;YACtB,UAAU,CAAC,EAAE,GAAG,UAAU,CAAC,MAAM,CAAA;YACjC,OAAO,UAAU,CAAC,MAAM,CAAA;QAC1B,CAAC;aAAM,IAAI,UAAU,CAAC,QAAQ,EAAE,CAAC;YAC/B,UAAU,CAAC,EAAE,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC,CAAA;QAClC,CAAC;QACD,IAAI,UAAU,CAAC,QAAQ,EAAE,CAAC;YACxB,UAAU,CAAC,IAAI,GAAG,UAAU,CAAC,QAAQ,CAAA;YACrC,OAAO,UAAU,CAAC,QAAQ,CAAA;QAC5B,CAAC;QACD,IAAI,UAAU,CAAC,SAAS,EAAE,CAAC;YACzB,UAAU,CAAC,KAAK,GAAG,UAAU,CAAC,SAAS,CAAA;YACvC,OAAO,UAAU,CAAC,SAAS,CAAA;QAC7B,CAAC;QACD,IAAI,UAAU,CAAC,UAAU,EAAE,CAAC;YAC1B,UAAU,CAAC,MAAM,GAAG,UAAU,CAAC,UAAU,CAAA;YACzC,OAAO,UAAU,CAAC,UAAU,CAAA;QAC9B,CAAC;QACD,IAAI,UAAU,CAAC,OAAO,EAAE,CAAC;YACvB,UAAU,CAAC,GAAG,GAAG,UAAU,CAAC,OAAO,CAAA;YACnC,OAAO,UAAU,CAAC,OAAO,CAAA;QAC3B,CAAC;QACD,IAAI,UAAU,CAAC,gBAAgB,EAAE,CAAC;YAChC,UAAU,CAAC,YAAY,GAAG,UAAU,CAAC,gBAAgB,CAAA;YACrD,OAAO,UAAU,CAAC,gBAAgB,CAAA;QACpC,CAAC;QACD,IAAI,UAAU,CAAC,QAAQ,EAAE,CAAC;YACxB,UAAU,CAAC,IAAI,GAAG,UAAU,CAAC,QAAQ,CAAA;YACrC,OAAO,UAAU,CAAC,QAAQ,CAAA;QAC5B,CAAC;QACD,IAAI,UAAU,CAAC,UAAU,EAAE,CAAC;YAC1B,UAAU,CAAC,MAAM,GAAG,UAAU,CAAC,UAAU,CAAA;YACzC,OAAO,UAAU,CAAC,UAAU,CAAA;QAC9B,CAAC;QACD,IAAI,UAAU,CAAC,eAAe,EAAE,CAAC;YAC/B,UAAU,CAAC,WAAW,GAAG,UAAU,CAAC,eAAe,CAAA;YACnD,OAAO,UAAU,CAAC,eAAe,CAAA;QACnC,CAAC;QACD,IAAI,UAAU,CAAC,iBAAiB,EAAE,CAAC;YACjC,aAAa,CAAC,IAAI,CAAC,GAAG,UAAU,CAAC,iBAAiB,CAAC,CAAA;YACnD,OAAO,UAAU,CAAC,iBAAiB,CAAA;QACrC,CAAC;QACD,IAAI,UAAU,CAAC,eAAe,CAAC,EAAE,CAAC;YAChC,aAAa,CAAC,IAAI,CAAC,GAAG,UAAU,CAAC,eAAe,CAAC,CAAC,CAAA;YAClD,OAAO,UAAU,CAAC,eAAe,CAAC,CAAA;QACpC,CAAC;QACD,IAAI,UAAU,CAAC,mBAAmB,CAAC,EAAE,CAAC;YACpC,aAAa,CAAC,IAAI,CAAC,GAAG,UAAU,CAAC,mBAAmB,CAAC,CAAC,CAAA;YACtD,OAAO,UAAU,CAAC,mBAAmB,CAAC,CAAA;QACxC,CAAC;QACD,IAAI,aAAa,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC7B,UAAU,CAAC,aAAa,GAAG,aAAa,CAAA;QAC1C,CAAC;QAED,MAAM,SAAS,GAAG,UAAU,CAAC,UAAU,EAAE,SAAS,CAAA;QAClD,IAAI,KAAK,GAAkB,IAAI,CAAA;QAC/B,IAAI,SAAS,IAAI,SAAS,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YACtC,IAAI,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC;gBACjB,KAAK,GAAG,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAA;gBAC5B,IAAI,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC;oBACxB,KAAK,GAAG,IAAI,CAAA;gBACd,CAAC;YACH,CAAC;YACD,OAAO,UAAU,CAAC,SAAS,CAAA;QAC7B,CAAC;QAED,OAAO;YACL,KAAK,EAAE,UAAU,CAAC,GAAG,GAAG,CAAC;YACzB,GAAG,EAAE,UAAU,CAAC,GAAG;YACnB,MAAM,EAAE,WAAW;gBACjB,CAAC,CAAC,WAAW,CAAC,UAAU,CAAC,MAAM,CAAC,IAAI,IAAI;gBACxC,CAAC,CAAC,UAAU,CAAC,MAAM;YACrB,MAAM;YACN,IAAI,EAAE,UAAU,CAAC,IAAI;YACrB,KAAK;YACL,MAAM,EAAE,UAAU,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI;YACxE,KAAK,EAAE,IAAI;YACX,UAAU,EACR,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC,MAAM,GAAG,CAAC;gBAChC,CAAC,CAAE,UAAuC;gBAC1C,CAAC,CAAC,IAAI;YACV,gBAAgB,EAAE,EAAE;YACpB,cAAc,EAAE,oBAAoB,CAClC,UAAU,EACV,UAAU,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,EAClB,WAAW,CACZ;SACF,CAAA;IACH,CAAC,CAAC,CAAA;AACJ,CAAC;AAED,SAAS,oBAAoB,CAC3B,OAAkC,EAClC,QAAiB,EACjB,WAAgD;IAEhD,IAAI,CAAC,OAAO,CAAC,QAAQ,EAAE,CAAC;QACtB,OAAO,EAAE,CAAA;IACX,CAAC;IACD,IAAI,OAAO,CAAC,IAAI,KAAK,MAAM,EAAE,CAAC;QAC5B,MAAM,cAAc,GAAkB,EAAE,CAAA;QACxC,MAAM,YAAY,GAAG,eAAe,CAAC,OAAO,CAAC,CAAA;QAC7C,IAAI,OAAO,GAAG,CAAC,CAAA;QACf,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,QAAQ,CAAC,EAAE,CAAC;YACpD,MAAM,QAAQ,GAAG,uBAAuB,CAAC,KAAK,EAAE,QAAQ,EAAE,WAAW,CAAC,CAAA;YACtE,IAAI,KAAK,CAAC,IAAI,KAAK,KAAK,EAAE,CAAC;gBACzB,KAAK,MAAM,GAAG,IAAI,YAAY,CAAC,OAAO,CAAC,EAAE,CAAC;oBACxC,2DAA2D;oBAC3D,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAgB,CAAA;oBAClE,IAAI,MAAM,CAAC,MAAM,IAAI,CAAC,EAAE,CAAC;wBACvB,yBAAyB;wBACzB,MAAM,IAAI,KAAK,CACb,mBAAmB,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,EAAE,CACrD,CAAA;oBACH,CAAC;oBACD,MAAM,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,GAAG,CAAC,GAAG,GAAG,CAAC,CAAA;oBAC7B,MAAM,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,GAAG,CAAC,GAAG,CAAA;oBACvB,MAAM,CAAC,CAAC,CAAC,CAAC,KAAK,GAAG,GAAG,CAAC,KAAK,CAAC,QAAQ,EAAE,CAAA;oBACtC,MAAM,CAAC,CAAC,CAAC,CAAC,IAAI,GAAG,GAAG,CAAC,IAAI,CAAA,CAAC,mBAAmB;oBAC7C,cAAc,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;gBAC7B,CAAC;gBACD,OAAO,EAAE,CAAA;YACX,CAAC;iBAAM,CAAC;gBACN,cAAc,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;YAC/B,CAAC;QACH,CAAC;QACD,OAAO,cAAc,CAAA;IACvB,CAAC;IACD,OAAO,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CACnD,uBAAuB,CAAC,KAAK,EAAE,QAAQ,EAAE,WAAW,CAAC,CACtD,CAAA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|
@@ -137,7 +137,7 @@ describe('annotationFeatureToGFF3', () => {
|
|
|
137
137
|
const [mrna] = children;
|
|
138
138
|
const cds10001 = mrna.child_features.filter((child) => {
|
|
139
139
|
const id = child[0].attributes?.ID;
|
|
140
|
-
return id
|
|
140
|
+
return id?.[0] === 'cds10001';
|
|
141
141
|
});
|
|
142
142
|
assert.deepEqual(cds10001.length, 2);
|
|
143
143
|
const cds1_1 = cds10001[0][0];
|
|
@@ -158,7 +158,7 @@ describe('annotationFeatureToGFF3', () => {
|
|
|
158
158
|
assert.deepEqual(cds1_1.child_features[0][0].phase, null);
|
|
159
159
|
const cds10004 = mrna.child_features.filter((child) => {
|
|
160
160
|
const id = child[0].attributes?.ID;
|
|
161
|
-
return id
|
|
161
|
+
return id?.[0] === 'cds10004';
|
|
162
162
|
});
|
|
163
163
|
assert.deepEqual(cds10004.length, 2);
|
|
164
164
|
const cds4_1 = cds10004[0][0];
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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