@apollo-annotation/shared 0.3.4 → 0.3.6
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/AddAssemblyAndFeaturesFromFileChange.d.ts +1 -1
- package/dist/Changes/AddAssemblyFromExternalChange.d.ts +1 -1
- package/dist/Changes/AddAssemblyFromFileChange.d.ts +1 -1
- package/dist/Changes/AddAssemblyFromFileChange.js +3 -3
- package/dist/Changes/AddAssemblyFromFileChange.js.map +1 -1
- package/dist/Changes/AddFeatureChange.d.ts +2 -2
- package/dist/Changes/AddFeatureChange.js +1 -0
- package/dist/Changes/AddFeatureChange.js.map +1 -1
- package/dist/Changes/AddFeaturesFromFileChange.d.ts +1 -1
- package/dist/Changes/AddRefSeqAliasesChange.d.ts +1 -1
- package/dist/Changes/DeleteAssemblyChange.d.ts +1 -1
- package/dist/Changes/DeleteFeatureChange.d.ts +3 -3
- package/dist/Changes/DeleteUserChange.d.ts +1 -1
- package/dist/Changes/FeatureAttributeChange.d.ts +1 -1
- package/dist/Changes/FromFileBaseChange.d.ts +3 -3
- package/dist/Changes/FromFileBaseChange.js.map +1 -1
- package/dist/Changes/ImportJBrowseConfigChange.d.ts +1 -1
- package/dist/Changes/LocationEndChange.d.ts +1 -1
- package/dist/Changes/LocationStartChange.d.ts +1 -1
- package/dist/Changes/StrandChange.d.ts +1 -1
- package/dist/Changes/TypeChange.d.ts +1 -1
- package/dist/Changes/UserChange.d.ts +1 -1
- package/dist/Checks/CDSCheck.d.ts +2 -1
- package/dist/Checks/CDSCheck.js +98 -30
- package/dist/Checks/CDSCheck.js.map +1 -1
- package/dist/GFF3/annotationFeatureToGFF3.d.ts +2 -2
- package/dist/GFF3/annotationFeatureToGFF3.js +2 -0
- package/dist/GFF3/annotationFeatureToGFF3.js.map +1 -1
- package/dist/GFF3/annotationFeatureToGFF3.test.js +1 -1
- package/dist/GFF3/annotationFeatureToGFF3.test.js.map +1 -1
- package/dist/GFF3/gff3ToAnnotationFeature.d.ts +2 -2
- package/dist/GFF3/gff3ToAnnotationFeature.js +9 -2
- package/dist/GFF3/gff3ToAnnotationFeature.js.map +1 -1
- package/dist/GFF3/gff3ToAnnotationFeature.test.d.ts +1 -1
- package/dist/GFF3/gff3ToAnnotationFeature.test.js +1 -1
- package/dist/GFF3/gff3ToAnnotationFeature.test.js.map +1 -1
- package/dist/GFF3/gffReservedKeys.d.ts +7 -0
- package/dist/GFF3/gffReservedKeys.js +21 -1
- package/dist/GFF3/gffReservedKeys.js.map +1 -1
- package/dist/Messages.d.ts +2 -2
- package/dist/Operations/GetAssembliesOperation.d.ts +1 -1
- package/dist/Operations/GetFeaturesOperation.d.ts +1 -1
- package/dist/Validations/CoreValidation.d.ts +2 -2
- package/dist/Validations/CoreValidation.js +1 -1
- package/dist/Validations/CoreValidation.js.map +1 -1
- package/dist/Validations/ParentChildValidation.d.ts +5 -5
- package/dist/Validations/ParentChildValidation.js.map +1 -1
- package/dist/Validations/Validation.d.ts +5 -5
- package/dist/Validations/ValidationSet.d.ts +4 -4
- package/dist/Validations/ValidationSet.js.map +1 -1
- package/dist/tsconfig.tsbuildinfo +1 -1
- package/package.json +4 -4
- package/src/Changes/AddAssemblyAndFeaturesFromFileChange.ts +6 -6
- package/src/Changes/AddAssemblyFromExternalChange.ts +5 -5
- package/src/Changes/AddAssemblyFromFileChange.ts +8 -8
- package/src/Changes/AddFeatureChange.ts +7 -6
- package/src/Changes/AddFeaturesFromFileChange.ts +6 -6
- package/src/Changes/AddRefSeqAliasesChange.ts +6 -6
- package/src/Changes/DeleteAssemblyChange.ts +4 -4
- package/src/Changes/DeleteFeatureChange.ts +7 -7
- package/src/Changes/DeleteUserChange.ts +5 -5
- package/src/Changes/FeatureAttributeChange.ts +6 -6
- package/src/Changes/FromFileBaseChange.ts +6 -3
- package/src/Changes/ImportJBrowseConfigChange.ts +4 -4
- package/src/Changes/LocationEndChange.ts +6 -6
- package/src/Changes/LocationStartChange.ts +6 -6
- package/src/Changes/StrandChange.ts +6 -6
- package/src/Changes/TypeChange.ts +6 -6
- package/src/Changes/UserChange.ts +5 -5
- package/src/Checks/CDSCheck.ts +113 -32
- package/src/GFF3/annotationFeatureToGFF3.test.ts +4 -2
- package/src/GFF3/annotationFeatureToGFF3.ts +6 -4
- package/src/GFF3/gff3ToAnnotationFeature.test.ts +3 -3
- package/src/GFF3/gff3ToAnnotationFeature.ts +11 -2
- package/src/GFF3/gffReservedKeys.ts +25 -0
- package/src/Messages.ts +2 -2
- package/src/Operations/GetAssembliesOperation.ts +3 -3
- package/src/Operations/GetFeaturesOperation.ts +4 -4
- package/src/Validations/CoreValidation.ts +4 -3
- package/src/Validations/ParentChildValidation.ts +7 -6
- package/src/Validations/Validation.ts +5 -5
- package/src/Validations/ValidationSet.ts +8 -4
- package/test_data/example01.json +3 -3
- package/test_data/example02.json +3 -3
- package/test_data/example04.json +3 -3
- package/test_data/gene_representations.gff3 +686 -1686
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@@ -1,4 +1,4 @@
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import { ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
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import { type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type SerializedAssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
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import { FromFileBaseChange } from './FromFileBaseChange';
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export interface SerializedAddAssemblyAndFeaturesFromFileChangeBase extends SerializedAssemblySpecificChange {
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typeName: 'AddAssemblyAndFeaturesFromFileChange';
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import { AssemblySpecificChange, ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
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import { AssemblySpecificChange, type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type SerializedAssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
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export interface SerializedAddAssemblyFromExternalChangeBase extends SerializedAssemblySpecificChange {
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typeName: 'AddAssemblyFromExternalChange';
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}
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import { ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
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import { type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type SerializedAssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
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import { FromFileBaseChange } from './FromFileBaseChange';
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export interface SerializedAddAssemblyFromFileChangeBase extends SerializedAssemblySpecificChange {
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typeName: 'AddAssemblyFromFileChange';
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@@ -47,17 +47,17 @@ class AddAssemblyFromFileChange extends FromFileBaseChange_1.FromFileBaseChange
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const faDoc = await fileModel.findById(faId);
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const faChecksum = faDoc?.checksum;
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if (!faChecksum) {
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throw new Error(`No checksum for file document ${faDoc}`);
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throw new Error(`No checksum for file document ${faDoc?.id}`);
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}
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const faiDoc = await fileModel.findById(faiId);
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const faiChecksum = faiDoc?.checksum;
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if (!faiChecksum) {
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throw new Error(`No checksum for file document ${faiDoc}`);
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throw new Error(`No checksum for file document ${faiDoc?.id}`);
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}
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const gziDoc = await fileModel.findById(gziId);
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const gziChecksum = gziDoc?.checksum;
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if (!gziChecksum) {
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throw new Error(`No checksum for file document ${gziDoc}`);
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throw new Error(`No checksum for file document ${gziDoc?.id}`);
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}
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const fasta = filesService.getFileHandle(faDoc);
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const fai = filesService.getFileHandle(faiDoc);
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|
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@@ -1,5 +1,5 @@
|
|
|
1
|
-
import { ChangeOptions, ClientDataStore, FeatureChange, LocalGFF3DataStore, SerializedFeatureChange, ServerDataStore } from '@apollo-annotation/common';
|
|
2
|
-
import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
|
|
1
|
+
import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
|
|
2
|
+
import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
|
|
3
3
|
import { DeleteFeatureChange } from './DeleteFeatureChange';
|
|
4
4
|
interface SerializedAddFeatureChangeBase extends SerializedFeatureChange {
|
|
5
5
|
typeName: 'AddFeatureChange';
|
|
@@ -93,6 +93,7 @@ class AddFeatureChange extends common_1.FeatureChange {
|
|
|
93
93
|
}
|
|
94
94
|
attributes = {
|
|
95
95
|
_id: [parentFeature._id.toString()],
|
|
96
|
+
// eslint-disable-next-line unicorn/prefer-structured-clone
|
|
96
97
|
...JSON.parse(JSON.stringify(attributes)),
|
|
97
98
|
};
|
|
98
99
|
parentFeature.attributes = attributes;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"AddFeatureChange.js","sourceRoot":"","sources":["../../src/Changes/AddFeatureChange.ts"],"names":[],"mappings":";;;
|
|
1
|
+
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@@ -1,4 +1,4 @@
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-
import { ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
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import { type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type SerializedAssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
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2
2
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import { FromFileBaseChange } from './FromFileBaseChange';
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export interface SerializedAddFeaturesFromFileChangeBase extends SerializedAssemblySpecificChange {
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typeName: 'AddFeaturesFromFileChange';
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@@ -1,4 +1,4 @@
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-
import { AssemblySpecificChange, Change, ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
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import { AssemblySpecificChange, type Change, type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type SerializedAssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
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2
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export interface SerializedRefSeqAliases {
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refName: string;
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aliases: string[];
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@@ -1,4 +1,4 @@
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-
import { AssemblySpecificChange, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
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import { AssemblySpecificChange, type ClientDataStore, type LocalGFF3DataStore, type SerializedAssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
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export interface SerializedDeleteAssemblyChange extends SerializedAssemblySpecificChange {
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typeName: 'DeleteAssemblyChange';
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}
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@@ -1,6 +1,6 @@
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1
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-
import { ChangeOptions, ClientDataStore, FeatureChange, LocalGFF3DataStore, SerializedFeatureChange, ServerDataStore } from '@apollo-annotation/common';
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2
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-
import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
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3
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-
import { Feature } from '@apollo-annotation/schemas';
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1
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import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
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2
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+
import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
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3
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import { type Feature } from '@apollo-annotation/schemas';
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4
4
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import { AddFeatureChange } from './AddFeatureChange';
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5
5
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interface SerializedDeleteFeatureChangeBase extends SerializedFeatureChange {
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6
6
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typeName: 'DeleteFeatureChange';
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@@ -1,4 +1,4 @@
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1
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-
import { Change, ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedChange, ServerDataStore } from '@apollo-annotation/common';
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1
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+
import { Change, type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type SerializedChange, type ServerDataStore } from '@apollo-annotation/common';
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2
2
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export interface SerializedDeleteUserChangeBase extends SerializedChange {
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3
3
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typeName: 'DeleteUserChange';
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4
4
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userId: string;
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@@ -1,4 +1,4 @@
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1
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-
import { ChangeOptions, ClientDataStore, FeatureChange, LocalGFF3DataStore, SerializedFeatureChange, ServerDataStore } from '@apollo-annotation/common';
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1
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+
import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
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2
2
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interface SerializedFeatureAttributeChangeBase extends SerializedFeatureChange {
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3
3
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typeName: 'FeatureAttributeChange';
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4
4
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}
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@@ -1,6 +1,6 @@
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1
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-
import { AssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
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2
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-
import { FileDocument } from '@apollo-annotation/schemas';
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3
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-
import { GFF3Feature } from '@gmod/gff';
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1
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+
import { AssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
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2
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+
import { type FileDocument } from '@apollo-annotation/schemas';
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3
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+
import { type GFF3Feature } from '@gmod/gff';
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4
4
|
export declare abstract class FromFileBaseChange extends AssemblySpecificChange {
|
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5
5
|
addRefSeqIntoDb(fileDoc: FileDocument, assembly: string, backend: ServerDataStore): Promise<void>;
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6
6
|
private refSeqCache;
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@@ -1 +1 @@
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1
|
-
{"version":3,"file":"FromFileBaseChange.js","sourceRoot":"","sources":["../../src/Changes/FromFileBaseChange.ts"],"names":[],"mappings":";;;AAAA,8DAA8D;AAC9D,4DAA4D;AAC5D,+DAA+D;AAC/D,sDAAsD;AACtD,0DAA0D;AAC1D,sDAGkC;
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1
|
+
{"version":3,"file":"FromFileBaseChange.js","sourceRoot":"","sources":["../../src/Changes/FromFileBaseChange.ts"],"names":[],"mappings":";;;AAAA,8DAA8D;AAC9D,4DAA4D;AAC5D,+DAA+D;AAC/D,sDAAsD;AACtD,0DAA0D;AAC1D,sDAGkC;AAOlC,kCAAiD;AAEjD,MAAsB,kBAAmB,SAAQ,+BAAsB;IACrE,KAAK,CAAC,eAAe,CACnB,OAAqB,EACrB,QAAgB,EAChB,OAAwB;QAExB,MAAM,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;QACvB,MAAM,EAAE,YAAY,EAAE,gBAAgB,EAAE,WAAW,EAAE,IAAI,EAAE,GAAG,OAAO,CAAA;QACrE,MAAM,EAAE,UAAU,EAAE,GAAG,OAAO,CAAC,GAAG,CAAA;QAClC,MAAM,eAAe,GAAG,UAAU,IAAI,MAAM,CAAC,UAAU,CAAC,CAAA;QACxD,IAAI,UAAU,GAAG,CAAC,CAAA;QAClB,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,IAAI,SAAqC,CAAA;QACzC,IAAI,gBAAgB,GAAG,OAAO,CAAC,IAAI,KAAK,aAAa,CAAA;QAErD,uDAAuD;QACvD,MAAM,cAAc,GAAG,YAAY,CAAC,aAAa,CAAC,OAAO,CAAC,CAAA;QAC1D,IAAI,cAAc,GAAG,EAAE,CAAA;QACvB,IAAI,cAAc,GAAG,EAAE,CAAA;QACvB,IAAI,oBAAoB,GAAG,IAAI,CAAA;QAC/B,IAAI,cAAc,GAAG,KAAK,CAAA;QAC1B,MAAM,CAAC,KAAK,EAAE,CAAC,0BAA0B,CAAC,CAAA;QAC1C,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,IAAI,KAAK,EAAE,MAAM,IAAI,IAAI,cAAc,EAAE,CAAC;YACxC,MAAM,KAAK,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAA;YAC7B,oBAAoB,GAAG,CAAC,KAAK,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;YAC5C,2HAA2H;YAC3H,MAAM,KAAK,GAAG,KAAK,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;YAClC,IAAI,cAAc,EAAE,CAAC;gBACnB,KAAK,CAAC,CAAC,CAAC,GAAG,GAAG,cAAc,GAAG,KAAK,CAAC,CAAC,CAAC,EAAE,CAAA;gBACzC,cAAc,GAAG,EAAE,CAAA;YACrB,CAAC;YACD,IAAI,oBAAoB,EAAE,CAAC;gBACzB,cAAc,GAAG,KAAK,CAAC,GAAG,EAAE,IAAI,EAAE,CAAA;YACpC,CAAC;YACD,IAAI,KAAK,EAAE,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;gBAC/B,SAAS,EAAE,CAAA;gBACX,IAAI,SAAS,GAAG,SAAS,KAAK,CAAC,EAAE,CAAC;oBAChC,MAAM,CAAC,KAAK,EAAE,CAAC,aAAa,SAAS,QAAQ,CAAC,CAAA;gBAChD,CAAC;gBACD,0EAA0E;gBAC1E,IAAI,CAAC,gBAAgB,EAAE,CAAC;oBACtB,IAAI,IAAI,CAAC,IAAI,EAAE,KAAK,SAAS,EAAE,CAAC;wBAC9B,gBAAgB,GAAG,IAAI,CAAA;oBACzB,CAAC;oBACD,SAAQ;gBACV,CAAC;gBACD,MAAM,cAAc,GAAG,mBAAmB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBACrD,8DAA8D;gBAC9D,IAAI,cAAc,EAAE,CAAC;oBACnB,cAAc,GAAG,IAAI,CAAA;oBACrB,MAAM,CAAC,KAAK,EAAE,CACZ,wCAAwC,cAAc,CAAC,CAAC,CAAC,GAAG,CAC7D,CAAA;oBAED,mGAAmG;oBACnG,IAAI,cAAc,KAAK,EAAE,EAAE,CAAC;wBAC1B,IAAI,CAAC,SAAS,EAAE,CAAC;4BACf,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;wBAC7C,CAAC;wBACD,SAAS,IAAI,cAAc,CAAC,MAAM,CAAA;wBAClC,iGAAiG;wBACjG,MAAM,gBAAgB,CAAC,MAAM,CAAC;4BAC5B;gCACE,MAAM,EAAE,SAAS,CAAC,GAAG;gCACrB,CAAC,EAAE,UAAU;gCACb,QAAQ,EAAE,cAAc;gCACxB,IAAI;gCACJ,MAAM,EAAE,CAAC,CAAC;6BACX;yBACF,CAAC,CAAA;wBACF,cAAc,GAAG,EAAE,CAAA;oBACrB,CAAC;oBACD,MAAM,SAAS,EAAE,SAAS,CAAC,EAAE,MAAM,EAAE,SAAS,EAAE,CAAC,CAAA;oBACjD,iEAAiE;oBACjE,SAAS,GAAG,CAAC,CAAA;oBACb,UAAU,GAAG,CAAC,CAAA;oBAEd,MAAM,IAAI,GAAG,cAAc,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;oBACrC,MAAM,WAAW,GAAG,cAAc,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAA;oBAErE,iGAAiG;oBACjG,MAAM,CAAC,YAAY,CAAC,GAAG,MAAM,WAAW,CAAC,MAAM,CAAC;wBAC9C;4BACE,IAAI;4BACJ,WAAW;4BACX,QAAQ;4BACR,MAAM,EAAE,CAAC;4BACT,GAAG,CAAC,eAAe,CAAC,CAAC,CAAC,EAAE,SAAS,EAAE,eAAe,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC;4BAC5D,IAAI;4BACJ,MAAM,EAAE,CAAC,CAAC;yBACX;qBACF,CAAC,CAAA;oBACF,MAAM,CAAC,KAAK,EAAE,CACZ,qBAAqB,IAAI,YAAY,WAAW,aAAa,YAAY,CAAC,GAAG,GAAG,CACjF,CAAA;oBACD,SAAS,GAAG,YAAY,CAAA;gBAC1B,CAAC;qBAAM,IAAI,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;oBAC3B,IAAI,CAAC,SAAS,EAAE,CAAC;wBACf,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;oBAC7C,CAAC;oBACD,MAAM,EAAE,GAAG,EAAE,SAAS,EAAE,GAAG,SAAS,CAAA;oBACpC,cAAc,IAAI,IAAI,CAAC,UAAU,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;oBAC5C,4DAA4D;oBAC5D,OAAO,cAAc,CAAC,MAAM,IAAI,SAAS,EAAE,CAAC;wBAC1C,MAAM,QAAQ,GAAG,cAAc,CAAC,KAAK,CAAC,CAAC,EAAE,SAAS,CAAC,CAAA;wBACnD,SAAS,IAAI,QAAQ,CAAC,MAAM,CAAA;wBAC5B,iGAAiG;wBACjG,MAAM,gBAAgB,CAAC,MAAM,CAAC;4BAC5B,EAAE,MAAM,EAAE,GAAG,EAAE,CAAC,EAAE,UAAU,EAAE,QAAQ,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC,CAAC,EAAE;yBAC3D,CAAC,CAAA;wBACF,UAAU,EAAE,CAAA;wBACZ,yBAAyB;wBACzB,cAAc,GAAG,cAAc,CAAC,KAAK,CAAC,SAAS,CAAC,CAAA;oBAClD,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QACD,IAAI,CAAC,cAAc,EAAE,CAAC;YACpB,MAAM,IAAI,KAAK,CAAC,sCAAsC,CAAC,CAAA;QACzD,CAAC;QAED,IAAI,cAAc,IAAI,oBAAoB,EAAE,CAAC;YAC3C,IAAI,CAAC,SAAS,EAAE,CAAC;gBACf,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;YAC7C,CAAC;YACD,yEAAyE;YACzE,IAAI,oBAAoB,EAAE,CAAC;gBACzB,cAAc,IAAI,cAAc,CAAA;YAClC,CAAC;YACD,SAAS,IAAI,cAAc,CAAC,MAAM,CAAA;YAClC,MAAM,CAAC,OAAO,EAAE,CACd,4CAA4C,SAAS,CAAC,GAAG,YAAY,UAAU,oCAAoC,SAAS,OAAO,cAAc,GAAG,CACrJ,CAAA;YACD,MAAM,CAAC,KAAK,EAAE,CACZ,gCAAgC,UAAU,QAAQ,SAAS,CAAC,GAAG,GAAG,CACnE,CAAA;YACD,iGAAiG;YACjG,MAAM,gBAAgB,CAAC,MAAM,CAAC;gBAC5B;oBACE,MAAM,EAAE,SAAS,CAAC,GAAG;oBACrB,CAAC,EAAE,UAAU;oBACb,QAAQ,EAAE,cAAc;oBACxB,IAAI;oBACJ,MAAM,EAAE,CAAC,CAAC;iBACX;aACF,CAAC,CAAA;YACF,MAAM,SAAS,CAAC,SAAS,CAAC,EAAE,MAAM,EAAE,SAAS,EAAE,CAAC,CAAA;QAClD,CAAC;IACH,CAAC;IAEO,WAAW,GAAG,IAAI,GAAG,EAA0B,CAAA;IAEvD,KAAK,CAAC,sBAAsB,CAAC,OAAwB;QACnD,MAAM,EAAE,YAAY,EAAE,WAAW,EAAE,GAAG,OAAO,CAAA;QAC7C,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;QACjC,MAAM,CAAC,KAAK,EAAE,CAAC,6CAA6C,QAAQ,EAAE,CAAC,CAAA;QAEvE,MAAM,OAAO,GAAqB,MAAM,WAAW;aAChD,IAAI,CAAC,EAAE,QAAQ,EAAE,CAAC;aAClB,IAAI,EAAE,CAAA;QAET,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;YAC7B,MAAM,YAAY,CAAC,UAAU,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,GAAG,EAAE,CAAC,CAAA;QACvD,CAAC;IACH,CAAC;IAED,KAAK,CAAC,gBAAgB,CAAC,WAAwB,EAAE,OAAwB;QACvE,MAAM,EAAE,YAAY,EAAE,WAAW,EAAE,IAAI,EAAE,GAAG,OAAO,CAAA;QACnD,MAAM,EAAE,QAAQ,EAAE,WAAW,EAAE,GAAG,IAAI,CAAA;QAEtC,MAAM,CAAC,EAAE,MAAM,EAAE,OAAO,EAAE,CAAC,GAAG,WAAW,CAAA;QACzC,IAAI,CAAC,OAAO,EAAE,CAAC;YACb,MAAM,IAAI,KAAK,CACb,qCAAqC,IAAI,CAAC,SAAS,CAAC,WAAW,CAAC,EAAE,CACnE,CAAA;QACH,CAAC;QACD,IAAI,SAAS,GAAG,WAAW,CAAC,GAAG,CAAC,OAAO,CAAC,CAAA;QACxC,IAAI,CAAC,SAAS,EAAE,CAAC;YACf,SAAS;gBACP,CAAC,MAAM,WAAW,CAAC,OAAO,CAAC,EAAE,QAAQ,EAAE,IAAI,EAAE,OAAO,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC;oBAC/D,SAAS,CAAA;YACX,IAAI,SAAS,EAAE,CAAC;gBACd,WAAW,CAAC,GAAG,CAAC,OAAO,EAAE,SAAS,CAAC,CAAA;YACrC,CAAC;QACH,CAAC;QACD,IAAI,CAAC,SAAS,EAAE,CAAC;YACf,MAAM,IAAI,KAAK,CACb,qCAAqC,QAAQ,iBAAiB,OAAO,aAAa,CACnF,CAAA;QACH,CAAC;QACD,wCAAwC;QACxC,MAAM,UAAU,GAAa,EAAE,CAAA;QAE/B,MAAM,UAAU,GAAG,IAAA,8BAAuB,EACxC,WAAW,EACX,SAAS,CAAC,GAAG,EACb,UAAU,CACX,CAAA;QAED,iBAAiB;QACjB,iGAAiG;QACjG,MAAM,YAAY,CAAC,MAAM,CAAC;YACxB,EAAE,MAAM,EAAE,UAAU,EAAE,GAAG,UAAU,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC,CAAC,EAAE;SACxD,CAAC,CAAA;IACJ,CAAC;CACF;AA9MD,gDA8MC"}
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@@ -1,4 +1,4 @@
|
|
|
1
|
-
import { Change, ChangeOptions, ClientDataStore, LocalGFF3DataStore, ServerDataStore } from '@apollo-annotation/common';
|
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1
|
+
import { Change, type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type ServerDataStore } from '@apollo-annotation/common';
|
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2
2
|
interface JBrowseAssembly {
|
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3
3
|
sequence: {
|
|
4
4
|
adapter: {
|
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
import { ChangeOptions, ClientDataStore, FeatureChange, LocalGFF3DataStore, SerializedFeatureChange, ServerDataStore } from '@apollo-annotation/common';
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|
1
|
+
import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
|
|
2
2
|
interface SerializedLocationEndChangeBase extends SerializedFeatureChange {
|
|
3
3
|
typeName: 'LocationEndChange';
|
|
4
4
|
}
|
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
import { ChangeOptions, ClientDataStore, FeatureChange, LocalGFF3DataStore, SerializedFeatureChange, ServerDataStore } from '@apollo-annotation/common';
|
|
1
|
+
import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
|
|
2
2
|
interface SerializedLocationStartChangeBase extends SerializedFeatureChange {
|
|
3
3
|
typeName: 'LocationStartChange';
|
|
4
4
|
}
|
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
import { ChangeOptions, ClientDataStore, FeatureChange, LocalGFF3DataStore, SerializedFeatureChange, ServerDataStore } from '@apollo-annotation/common';
|
|
1
|
+
import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
|
|
2
2
|
interface SerializedStrandChangeBase extends SerializedFeatureChange {
|
|
3
3
|
typeName: 'StrandChange';
|
|
4
4
|
}
|
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
import { ChangeOptions, ClientDataStore, FeatureChange, LocalGFF3DataStore, SerializedFeatureChange, ServerDataStore } from '@apollo-annotation/common';
|
|
1
|
+
import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
|
|
2
2
|
interface SerializedTypeChangeBase extends SerializedFeatureChange {
|
|
3
3
|
typeName: 'TypeChange';
|
|
4
4
|
}
|
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
import { Change, ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedChange, ServerDataStore } from '@apollo-annotation/common';
|
|
1
|
+
import { Change, type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type SerializedChange, type ServerDataStore } from '@apollo-annotation/common';
|
|
2
2
|
export interface SerializedUserChangeBase extends SerializedChange {
|
|
3
3
|
typeName: 'UserChange';
|
|
4
4
|
userId: string;
|
|
@@ -1,7 +1,8 @@
|
|
|
1
1
|
import { Check } from '@apollo-annotation/common';
|
|
2
|
-
import { AnnotationFeatureSnapshot, CheckResultSnapshot } from '@apollo-annotation/mst';
|
|
2
|
+
import { type AnnotationFeatureSnapshot, type CheckResultSnapshot } from '@apollo-annotation/mst';
|
|
3
3
|
export declare class CDSCheck extends Check {
|
|
4
4
|
name: string;
|
|
5
|
+
causes: string[];
|
|
5
6
|
version: number;
|
|
6
7
|
default: boolean;
|
|
7
8
|
checkFeature(feature: AnnotationFeatureSnapshot, getSequence: (start: number, end: number) => Promise<string>): Promise<CheckResultSnapshot[]>;
|
package/dist/Checks/CDSCheck.js
CHANGED
|
@@ -11,6 +11,18 @@ var STOP_CODONS;
|
|
|
11
11
|
STOP_CODONS[STOP_CODONS["TAA"] = 1] = "TAA";
|
|
12
12
|
STOP_CODONS[STOP_CODONS["TGA"] = 2] = "TGA";
|
|
13
13
|
})(STOP_CODONS || (STOP_CODONS = {}));
|
|
14
|
+
var START_CODONS;
|
|
15
|
+
(function (START_CODONS) {
|
|
16
|
+
START_CODONS[START_CODONS["ATG"] = 0] = "ATG";
|
|
17
|
+
})(START_CODONS || (START_CODONS = {}));
|
|
18
|
+
const CHECK_NAME = 'CDSCheck';
|
|
19
|
+
var CAUSES;
|
|
20
|
+
(function (CAUSES) {
|
|
21
|
+
CAUSES[CAUSES["InternalStopCodon"] = 0] = "InternalStopCodon";
|
|
22
|
+
CAUSES[CAUSES["MissingStartCodon"] = 1] = "MissingStartCodon";
|
|
23
|
+
CAUSES[CAUSES["MissingStopCodon"] = 2] = "MissingStopCodon";
|
|
24
|
+
CAUSES[CAUSES["MultipleOfThree"] = 3] = "MultipleOfThree";
|
|
25
|
+
})(CAUSES || (CAUSES = {}));
|
|
14
26
|
const iupacComplements = {
|
|
15
27
|
G: 'C',
|
|
16
28
|
A: 'T',
|
|
@@ -46,10 +58,11 @@ function reverseComplement(dna) {
|
|
|
46
58
|
}
|
|
47
59
|
async function getCDSSequence(cdsLocation, strand, getSequence) {
|
|
48
60
|
const sequences = await Promise.all(cdsLocation.map(({ max, min }) => getSequence(min, max)));
|
|
61
|
+
let seq = sequences.join('');
|
|
49
62
|
if (strand === -1) {
|
|
50
|
-
|
|
63
|
+
seq = reverseComplement(seq);
|
|
51
64
|
}
|
|
52
|
-
return
|
|
65
|
+
return seq;
|
|
53
66
|
}
|
|
54
67
|
function splitSequenceInCodons(cds) {
|
|
55
68
|
const codons = [];
|
|
@@ -58,29 +71,49 @@ function splitSequenceInCodons(cds) {
|
|
|
58
71
|
}
|
|
59
72
|
return codons;
|
|
60
73
|
}
|
|
74
|
+
function cmp(pos, max, strand) {
|
|
75
|
+
if (strand === -1) {
|
|
76
|
+
return pos > max;
|
|
77
|
+
}
|
|
78
|
+
return pos < max;
|
|
79
|
+
}
|
|
61
80
|
function getOriginalCodonLocation(cdsLocation, strand, index) {
|
|
62
|
-
|
|
63
|
-
|
|
64
|
-
|
|
65
|
-
|
|
66
|
-
|
|
67
|
-
|
|
68
|
-
|
|
69
|
-
|
|
70
|
-
|
|
71
|
-
|
|
72
|
-
|
|
73
|
-
|
|
74
|
-
|
|
75
|
-
}
|
|
76
|
-
|
|
77
|
-
|
|
78
|
-
|
|
79
|
-
|
|
80
|
-
|
|
81
|
+
// Index 0 is the start codon, so reverse the CDS locations if strand is -1
|
|
82
|
+
const sortedLocation = structuredClone(cdsLocation);
|
|
83
|
+
if (strand === -1) {
|
|
84
|
+
sortedLocation.sort((a, b) => (a.min < b.min ? 1 : -1));
|
|
85
|
+
}
|
|
86
|
+
else {
|
|
87
|
+
sortedLocation.sort((a, b) => (a.min < b.min ? -1 : 1));
|
|
88
|
+
}
|
|
89
|
+
let i = 0;
|
|
90
|
+
let currentStart = undefined;
|
|
91
|
+
let currentEnd = undefined;
|
|
92
|
+
for (let iloc = 0; iloc < sortedLocation.length; iloc++) {
|
|
93
|
+
const loc = sortedLocation[iloc];
|
|
94
|
+
const { phase } = loc;
|
|
95
|
+
// On the reverse strand start iterating from the right and end on the left
|
|
96
|
+
const startAt = strand === -1 ? loc.max - phase : loc.min + phase;
|
|
97
|
+
const endAt = strand === -1 ? loc.min : loc.max;
|
|
98
|
+
for (let pos = startAt; cmp(pos, endAt, strand); pos = strand === -1 ? pos - 3 : pos + 3) {
|
|
99
|
+
currentStart = pos;
|
|
100
|
+
currentEnd = strand === -1 ? currentStart - 3 : currentStart + 3;
|
|
101
|
+
// These if conditions occur if a codon is split between two exons
|
|
102
|
+
if (strand === -1 && currentEnd < loc.min) {
|
|
103
|
+
currentEnd =
|
|
104
|
+
sortedLocation[iloc + 1].max - sortedLocation[iloc + 1].phase;
|
|
105
|
+
}
|
|
106
|
+
else if (currentEnd > loc.max) {
|
|
107
|
+
currentEnd =
|
|
108
|
+
sortedLocation[iloc + 1].min + sortedLocation[iloc + 1].phase;
|
|
109
|
+
}
|
|
110
|
+
if (i === index) {
|
|
111
|
+
return [currentStart, currentEnd].sort((a, b) => a - b);
|
|
112
|
+
}
|
|
113
|
+
i++;
|
|
81
114
|
}
|
|
82
115
|
}
|
|
83
|
-
return;
|
|
116
|
+
return undefined;
|
|
84
117
|
}
|
|
85
118
|
async function checkMRNA(feature, getSequence) {
|
|
86
119
|
const checkResults = [];
|
|
@@ -94,23 +127,45 @@ async function checkMRNA(feature, getSequence) {
|
|
|
94
127
|
const sequence = await getCDSSequence(cdsLocation, strand, getSequence);
|
|
95
128
|
const codons = splitSequenceInCodons(sequence);
|
|
96
129
|
if (sequence.length % 3 === 0) {
|
|
97
|
-
const
|
|
130
|
+
const start_codon = codons.at(0);
|
|
131
|
+
if (start_codon && !(start_codon.toUpperCase() in START_CODONS)) {
|
|
132
|
+
let cdsStart = strand === -1
|
|
133
|
+
? cdsLocation.at(-1)?.max ?? max
|
|
134
|
+
: cdsLocation.at(0)?.min ?? min;
|
|
135
|
+
cdsStart = strand === -1 ? cdsStart - 3 : cdsStart;
|
|
136
|
+
checkResults.push({
|
|
137
|
+
_id: new bson_objectid_1.default().toHexString(),
|
|
138
|
+
name: CHECK_NAME,
|
|
139
|
+
cause: CAUSES[CAUSES.MissingStartCodon],
|
|
140
|
+
ids,
|
|
141
|
+
refSeq: refSeq.toString(),
|
|
142
|
+
start: cdsStart,
|
|
143
|
+
end: cdsStart,
|
|
144
|
+
message: `Unexpected start codon in feature "${_id}": ${start_codon}`,
|
|
145
|
+
});
|
|
146
|
+
}
|
|
147
|
+
const lastCodon = codons.at(-1); // Last codon is supposed to be a stop
|
|
98
148
|
if (lastCodon && !(lastCodon.toUpperCase() in STOP_CODONS)) {
|
|
149
|
+
const cdsEnd = strand === -1
|
|
150
|
+
? cdsLocation.at(0)?.min ?? min
|
|
151
|
+
: cdsLocation.at(-1)?.max ?? max;
|
|
99
152
|
checkResults.push({
|
|
100
153
|
_id: new bson_objectid_1.default().toHexString(),
|
|
101
|
-
name:
|
|
154
|
+
name: CHECK_NAME,
|
|
155
|
+
cause: CAUSES[CAUSES.MissingStopCodon],
|
|
102
156
|
ids,
|
|
103
157
|
refSeq: refSeq.toString(),
|
|
104
|
-
start:
|
|
105
|
-
end:
|
|
106
|
-
message: `Missing stop codon`,
|
|
158
|
+
start: cdsEnd,
|
|
159
|
+
end: cdsEnd,
|
|
160
|
+
message: `Missing stop codon for feature "${_id}"`,
|
|
107
161
|
});
|
|
108
162
|
}
|
|
109
163
|
}
|
|
110
164
|
else {
|
|
111
165
|
checkResults.push({
|
|
112
166
|
_id: new bson_objectid_1.default().toHexString(),
|
|
113
|
-
name:
|
|
167
|
+
name: CHECK_NAME,
|
|
168
|
+
cause: CAUSES[CAUSES.MultipleOfThree],
|
|
114
169
|
ids,
|
|
115
170
|
refSeq: refSeq.toString(),
|
|
116
171
|
start: min,
|
|
@@ -119,12 +174,17 @@ async function checkMRNA(feature, getSequence) {
|
|
|
119
174
|
});
|
|
120
175
|
}
|
|
121
176
|
for (const [idx, codon] of codons.entries()) {
|
|
177
|
+
if (idx === codons.length - 1) {
|
|
178
|
+
// Don't test last codon as it is supposed to be a stop
|
|
179
|
+
break;
|
|
180
|
+
}
|
|
122
181
|
const location = getOriginalCodonLocation(cdsLocation, strand, idx);
|
|
123
182
|
if (location && codon.toUpperCase() in STOP_CODONS) {
|
|
124
183
|
const [codonStart, codonEnd] = location;
|
|
125
184
|
checkResults.push({
|
|
126
185
|
_id: new bson_objectid_1.default().toHexString(),
|
|
127
|
-
name:
|
|
186
|
+
name: CHECK_NAME,
|
|
187
|
+
cause: CAUSES[CAUSES.InternalStopCodon],
|
|
128
188
|
ids,
|
|
129
189
|
refSeq: refSeq.toString(),
|
|
130
190
|
start: codonStart,
|
|
@@ -171,12 +231,20 @@ function getCDSLocations(feature) {
|
|
|
171
231
|
nextPhase = ((3 - ((loc.max - loc.min - phase + 3) % 3)) % 3);
|
|
172
232
|
return { ...loc, phase };
|
|
173
233
|
});
|
|
234
|
+
phasedLocs.sort((a, b) => (a.min < b.min ? -1 : 1));
|
|
174
235
|
cdsLocations.push(phasedLocs);
|
|
175
236
|
}
|
|
237
|
+
if (cdsLocations.length > 1) {
|
|
238
|
+
cdsLocations.sort((a, b) => (a[0].min < b[0].min ? -1 : 1));
|
|
239
|
+
}
|
|
176
240
|
return cdsLocations;
|
|
177
241
|
}
|
|
242
|
+
function getCauses() {
|
|
243
|
+
return Object.values(CAUSES).filter((x) => Number.isNaN(Number(x)));
|
|
244
|
+
}
|
|
178
245
|
class CDSCheck extends common_1.Check {
|
|
179
|
-
name =
|
|
246
|
+
name = CHECK_NAME;
|
|
247
|
+
causes = getCauses();
|
|
180
248
|
version = 1;
|
|
181
249
|
default = true;
|
|
182
250
|
async checkFeature(feature, getSequence) {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"CDSCheck.js","sourceRoot":"","sources":["../../src/Checks/CDSCheck.ts"],"names":[],"mappings":";;;;AAAA,sDAAiD;AAKjD,6CAAkD;AAClD,0EAAoC;AAEpC,IAAK,WAIJ;AAJD,WAAK,WAAW;IACd,2CAAK,CAAA;IACL,2CAAK,CAAA;IACL,2CAAK,CAAA;AACP,CAAC,EAJI,WAAW,KAAX,WAAW,QAIf;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,
|
|
1
|
+
{"version":3,"file":"CDSCheck.js","sourceRoot":"","sources":["../../src/Checks/CDSCheck.ts"],"names":[],"mappings":";;;;AAAA,sDAAiD;AAKjD,6CAAkD;AAClD,0EAAoC;AAEpC,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,MAKJ;AALD,WAAK,MAAM;IACT,6DAAmB,CAAA;IACnB,6DAAmB,CAAA;IACnB,2DAAkB,CAAA;IAClB,yDAAiB,CAAA;AACnB,CAAC,EALI,MAAM,KAAN,MAAM,QAKV;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,GAAgB,eAAe,CAAC,WAAW,CAAC,CAAA;IAChE,IAAI,MAAM,KAAK,CAAC,CAAC,EAAE,CAAC;QAClB,cAAc,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;IACzD,CAAC;SAAM,CAAC;QACN,cAAc,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;IACzD,CAAC;IACD,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,IAAI,YAAY,GAAuB,SAAS,CAAA;IAChD,IAAI,UAAU,GAAuB,SAAS,CAAA;IAC9C,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,IAAI,QAAQ,CAAC,MAAM,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC;YAC9B,MAAM,WAAW,GAAG,MAAM,CAAC,EAAE,CAAC,CAAC,CAAC,CAAA;YAChC,IAAI,WAAW,IAAI,CAAC,CAAC,WAAW,CAAC,WAAW,EAAE,IAAI,YAAY,CAAC,EAAE,CAAC;gBAChE,IAAI,QAAQ,GACV,MAAM,KAAK,CAAC,CAAC;oBACX,CAAC,CAAC,WAAW,CA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|
@@ -1,3 +1,3 @@
|
|
|
1
|
-
import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
|
|
2
|
-
import { GFF3Feature } from '@gmod/gff';
|
|
1
|
+
import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
|
|
2
|
+
import { type GFF3Feature } from '@gmod/gff';
|
|
3
3
|
export declare function annotationFeatureToGFF3(feature: AnnotationFeatureSnapshot, parentId?: string, refSeqNames?: Record<string, string | undefined>): GFF3Feature;
|
|
@@ -4,6 +4,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
|
|
|
4
4
|
exports.annotationFeatureToGFF3 = annotationFeatureToGFF3;
|
|
5
5
|
const util_1 = require("@jbrowse/core/util");
|
|
6
6
|
function annotationFeatureToGFF3(feature, parentId, refSeqNames) {
|
|
7
|
+
// eslint-disable-next-line unicorn/prefer-structured-clone
|
|
7
8
|
const attributes = JSON.parse(JSON.stringify(feature.attributes ?? {}));
|
|
8
9
|
const ontologyTerms = [];
|
|
9
10
|
const source = feature.attributes?.gff_source?.[0] ?? null;
|
|
@@ -103,6 +104,7 @@ function prepareChildFeatures(feature, parentID, refSeqNames) {
|
|
|
103
104
|
const gffChild = annotationFeatureToGFF3(child, parentID, refSeqNames);
|
|
104
105
|
if (child.type === 'CDS') {
|
|
105
106
|
for (const loc of cdsLocations[cds_idx]) {
|
|
107
|
+
// eslint-disable-next-line unicorn/prefer-structured-clone
|
|
106
108
|
const gffCds = JSON.parse(JSON.stringify(gffChild));
|
|
107
109
|
if (gffCds.length != 1) {
|
|
108
110
|
// Do we need this check?
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"annotationFeatureToGFF3.js","sourceRoot":"","sources":["../../src/GFF3/annotationFeatureToGFF3.ts"],"names":[],"mappings":";AAAA,4DAA4D;;AAU5D,
|
|
1
|
+
{"version":3,"file":"annotationFeatureToGFF3.js","sourceRoot":"","sources":["../../src/GFF3/annotationFeatureToGFF3.ts"],"names":[],"mappings":";AAAA,4DAA4D;;AAU5D,0DAqGC;AAvGD,6CAAkD;AAElD,SAAgB,uBAAuB,CACrC,OAAkC,EAClC,QAAiB,EACjB,WAAgD;IAEhD,2DAA2D;IAC3D,MAAM,UAAU,GAAyC,IAAI,CAAC,KAAK,CACjE,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,UAAU,IAAI,EAAE,CAAC,CACzC,CAAA;IACD,MAAM,aAAa,GAAa,EAAE,CAAA;IAClC,MAAM,MAAM,GAAG,OAAO,CAAC,UAAU,EAAE,UAAU,EAAE,CAAC,CAAC,CAAC,IAAI,IAAI,CAAA;IAE1D,OAAO,UAAU,CAAC,UAAU,CAAA;IAC5B,IAAI,QAAQ,EAAE,CAAC;QACb,UAAU,CAAC,MAAM,GAAG,CAAC,QAAQ,CAAC,CAAA;IAChC,CAAC;IACD,IAAI,UAAU,CAAC,MAAM,EAAE,CAAC;QACtB,UAAU,CAAC,EAAE,GAAG,UAAU,CAAC,MAAM,CAAA;QACjC,OAAO,UAAU,CAAC,MAAM,CAAA;IAC1B,CAAC;SAAM,IAAI,OAAO,CAAC,QAAQ,EAAE,CAAC;QAC5B,UAAU,CAAC,EAAE,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;IAC/B,CAAC;IACD,IAAI,UAAU,CAAC,QAAQ,EAAE,CAAC;QACxB,UAAU,CAAC,IAAI,GAAG,UAAU,CAAC,QAAQ,CAAA;QACrC,OAAO,UAAU,CAAC,QAAQ,CAAA;IAC5B,CAAC;IACD,IAAI,UAAU,CAAC,SAAS,EAAE,CAAC;QACzB,UAAU,CAAC,KAAK,GAAG,UAAU,CAAC,SAAS,CAAA;QACvC,OAAO,UAAU,CAAC,SAAS,CAAA;IAC7B,CAAC;IACD,IAAI,UAAU,CAAC,UAAU,EAAE,CAAC;QAC1B,UAAU,CAAC,MAAM,GAAG,UAAU,CAAC,UAAU,CAAA;QACzC,OAAO,UAAU,CAAC,UAAU,CAAA;IAC9B,CAAC;IACD,IAAI,UAAU,CAAC,OAAO,EAAE,CAAC;QACvB,UAAU,CAAC,GAAG,GAAG,UAAU,CAAC,OAAO,CAAA;QACnC,OAAO,UAAU,CAAC,OAAO,CAAA;IAC3B,CAAC;IACD,IAAI,UAAU,CAAC,gBAAgB,EAAE,CAAC;QAChC,UAAU,CAAC,YAAY,GAAG,UAAU,CAAC,gBAAgB,CAAA;QACrD,OAAO,UAAU,CAAC,gBAAgB,CAAA;IACpC,CAAC;IACD,IAAI,UAAU,CAAC,QAAQ,EAAE,CAAC;QACxB,UAAU,CAAC,IAAI,GAAG,UAAU,CAAC,QAAQ,CAAA;QACrC,OAAO,UAAU,CAAC,QAAQ,CAAA;IAC5B,CAAC;IACD,IAAI,UAAU,CAAC,UAAU,EAAE,CAAC;QAC1B,UAAU,CAAC,MAAM,GAAG,UAAU,CAAC,UAAU,CAAA;QACzC,OAAO,UAAU,CAAC,UAAU,CAAA;IAC9B,CAAC;IACD,IAAI,UAAU,CAAC,eAAe,EAAE,CAAC;QAC/B,UAAU,CAAC,WAAW,GAAG,UAAU,CAAC,eAAe,CAAA;QACnD,OAAO,UAAU,CAAC,eAAe,CAAA;IACnC,CAAC;IACD,IAAI,UAAU,CAAC,iBAAiB,EAAE,CAAC;QACjC,aAAa,CAAC,IAAI,CAAC,GAAG,UAAU,CAAC,iBAAiB,CAAC,CAAA;QACnD,OAAO,UAAU,CAAC,iBAAiB,CAAA;IACrC,CAAC;IACD,IAAI,UAAU,CAAC,eAAe,CAAC,EAAE,CAAC;QAChC,aAAa,CAAC,IAAI,CAAC,GAAG,UAAU,CAAC,eAAe,CAAC,CAAC,CAAA;QAClD,OAAO,UAAU,CAAC,eAAe,CAAC,CAAA;IACpC,CAAC;IACD,IAAI,UAAU,CAAC,mBAAmB,CAAC,EAAE,CAAC;QACpC,aAAa,CAAC,IAAI,CAAC,GAAG,UAAU,CAAC,mBAAmB,CAAC,CAAC,CAAA;QACtD,OAAO,UAAU,CAAC,mBAAmB,CAAC,CAAA;IACxC,CAAC;IACD,IAAI,aAAa,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAC7B,UAAU,CAAC,aAAa,GAAG,aAAa,CAAA;IAC1C,CAAC;IAED,MAAM,SAAS,GAAG,OAAO,CAAC,UAAU,EAAE,SAAS,CAAA;IAC/C,IAAI,KAAK,GAAkB,IAAI,CAAA;IAC/B,IAAI,SAAS,IAAI,SAAS,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACtC,IAAI,SAAS,CAAC,CAAC,CAAC,EAAE,CAAC;YACjB,KAAK,GAAG,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAA;YAC5B,IAAI,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC;gBACxB,KAAK,GAAG,IAAI,CAAA;YACd,CAAC;QACH,CAAC;QACD,OAAO,UAAU,CAAC,SAAS,CAAA;IAC7B,CAAC;IAED,MAAM,SAAS,GAAG,CAAC,EAAE,KAAK,EAAE,OAAO,CAAC,GAAG,EAAE,GAAG,EAAE,OAAO,CAAC,GAAG,EAAE,CAAC,CAAA;IAE5D,OAAO,SAAS,CAAC,GAAG,CAAC,CAAC,QAAQ,EAAE,EAAE,CAAC,CAAC;QAClC,KAAK,EAAE,MAAM,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC;QACjC,GAAG,EAAE,MAAM,CAAC,QAAQ,CAAC,GAAG,CAAC;QACzB,MAAM,EAAE,WAAW,CAAC,CAAC,CAAC,WAAW,CAAC,OAAO,CAAC,MAAM,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,MAAM;QAC1E,MAAM;QACN,IAAI,EAAE,OAAO,CAAC,IAAI;QAClB,KAAK;QACL,MAAM,EAAE,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI;QAClE,KAAK,EAAE,IAAI;QACX,UAAU,EAAE,MAAM,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,IAAI;QAClE,gBAAgB,EAAE,EAAE;QACpB,cAAc,EAAE,oBAAoB,CAClC,OAAO,EACP,UAAU,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,EAClB,WAAW,CACZ;KACF,CAAC,CAAC,CAAA;AACL,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;AACH,CAAC;AASD,SAAS,kBAAkB,CACzB,OAAkC;IAElC,IAAI,OAAO,CA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@@ -4,8 +4,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
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4
4
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/* eslint-disable @typescript-eslint/no-floating-promises */
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5
5
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const node_test_1 = require("node:test");
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6
6
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const chai_1 = require("chai");
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7
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-
const gff3ToAnnotationFeature_test_1 = require("./gff3ToAnnotationFeature.test");
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8
7
|
const annotationFeatureToGFF3_1 = require("./annotationFeatureToGFF3");
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8
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+
const gff3ToAnnotationFeature_test_1 = require("./gff3ToAnnotationFeature.test");
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9
9
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(0, node_test_1.describe)('annotationFeatureToGFF3', () => {
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10
10
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(0, node_test_1.it)('Test mandatory columns', () => {
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11
11
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const annotationFeature = (0, gff3ToAnnotationFeature_test_1.readAnnotationFeatureSnapshot)('test_data/gene.json');
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