@nextage/omics-lib 1.0.15 → 1.0.16
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/build/omics/models/genotype.d.ts +1 -1
- package/build/omics/models/genotype.d.ts.map +1 -1
- package/build/omics/models/genotype.js +12 -6
- package/build/omics/models/genotype.js.map +1 -1
- package/build/omics/models/sample.d.ts +1 -1
- package/build/omics/models/sample.d.ts.map +1 -1
- package/build/omics/models/sample.js +11 -5
- package/build/omics/models/sample.js.map +1 -1
- package/build/omics/models/variant.d.ts +1 -1
- package/build/omics/models/variant.d.ts.map +1 -1
- package/build/omics/models/variant.js +11 -6
- package/build/omics/models/variant.js.map +1 -1
- package/build/omics/services/tsv-parser.d.ts +12 -4
- package/build/omics/services/tsv-parser.d.ts.map +1 -1
- package/build/omics/services/tsv-parser.js +7 -7
- package/build/omics/services/tsv-parser.js.map +1 -1
- package/package.json +1 -1
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@@ -15,5 +15,5 @@ export interface GenotypeDoc extends mongoose.Document {
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export interface GenotypeModel extends mongoose.Model<GenotypeDoc> {
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build(attrs: GenotypeAttrs): GenotypeDoc;
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}
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export declare
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export declare function createGenotypeModel(): GenotypeModel;
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//# sourceMappingURL=genotype.d.ts.map
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@@ -1 +1 @@
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-
{"version":3,"file":"genotype.d.ts","sourceRoot":"","sources":["../../../src/omics/models/genotype.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAuB,UAAU,CAAC;AAEjD,OAAO,EAAE,SAAS,EAAE,MAAkB,UAAU,CAAC;AAEjD,MAAM,WAAW,aAAc,SAAQ,SAAS;IAC9C,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,OAAO,CAAC,EAAI,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,WAAY,SAAQ,QAAQ,CAAC,QAAQ;IACpD,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,OAAO,EAAK,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,aAAc,SAAQ,QAAQ,CAAC,KAAK,CAAC,WAAW,CAAC;IAChE,KAAK,CAAC,KAAK,EAAE,aAAa,GAAG,WAAW,CAAC;CAC1C;
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{"version":3,"file":"genotype.d.ts","sourceRoot":"","sources":["../../../src/omics/models/genotype.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAuB,UAAU,CAAC;AAEjD,OAAO,EAAE,SAAS,EAAE,MAAkB,UAAU,CAAC;AAEjD,MAAM,WAAW,aAAc,SAAQ,SAAS;IAC9C,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,OAAO,CAAC,EAAI,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,WAAY,SAAQ,QAAQ,CAAC,QAAQ;IACpD,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,OAAO,EAAK,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,aAAc,SAAQ,QAAQ,CAAC,KAAK,CAAC,WAAW,CAAC;IAChE,KAAK,CAAC,KAAK,EAAE,aAAa,GAAG,WAAW,CAAC;CAC1C;AAgCD,wBAAgB,mBAAmB,kBAQlC"}
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@@ -3,7 +3,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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return (mod && mod.__esModule) ? mod : { "default": mod };
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};
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.
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exports.createGenotypeModel = createGenotypeModel;
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const mongoose_1 = __importDefault(require("mongoose"));
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const mongoose_update_if_current_1 = require("mongoose-update-if-current");
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const schema = new mongoose_1.default.Schema({
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@@ -30,9 +30,15 @@ schema.index({ variantId: 1 }, { name: 'variantid_idx' });
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schema.index({ sampleId: 1 }, { name: 'sampled_idx' });
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schema.set('versionKey', 'version');
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schema.plugin(mongoose_update_if_current_1.updateIfCurrentPlugin);
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function createGenotypeModel() {
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schema.statics.build = (attrs) => {
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return new Genotype(attrs);
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};
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const Genotype = mongoose_1.default.model('Genotype', schema);
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return Genotype;
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}
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// schema.statics.build = (attrs: GenotypeAttrs) => {
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// return new Genotype(attrs);
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// };
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// export const Genotype = mongoose.model<GenotypeDoc, GenotypeModel>('Genotype', schema);
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//# sourceMappingURL=genotype.js.map
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{"version":3,"file":"genotype.js","sourceRoot":"","sources":["../../../src/omics/models/genotype.ts"],"names":[],"mappings":"
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{"version":3,"file":"genotype.js","sourceRoot":"","sources":["../../../src/omics/models/genotype.ts"],"names":[],"mappings":";;;;;AAoDA,kDAQC;AA5DD,wDAAiD;AACjD,2EAAmE;AAqBnE,MAAM,MAAM,GAAG,IAAI,kBAAQ,CAAC,MAAM,CAChC;IACE,SAAS,EAAW,EAAE,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,IAAI,EAAE;IACpD,QAAQ,EAAY,EAAE,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,IAAI,EAAE;IACpD,kBAAkB,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE;IACpC,EAAE,EAAkB,EAAE,IAAI,EAAE,MAAM,EAAE;IACpC,GAAG,EAAiB,EAAE,IAAI,EAAE,MAAM,EAAE;IACpC,EAAE,EAAkB,EAAE,IAAI,EAAE,MAAM,EAAE;IACpC,OAAO,EAAa,EAAE,IAAI,EAAE,CAAC,MAAM,CAAC,EAAE;IACtC,SAAS,EAAW,EAAE,IAAI,EAAE,IAAI,EAAE;IAClC,SAAS,EAAW,EAAE,IAAI,EAAE,IAAI,EAAE;IAClC,SAAS,EAAW,EAAE,IAAI,EAAE,IAAI,EAAE;CACnC,EACD;IACE,MAAM,EAAE;QACN,SAAS,CAAC,GAAG,EAAE,GAAQ;YACrB,GAAG,CAAC,EAAE,GAAG,GAAG,CAAC,GAAG,CAAC;YACjB,OAAO,GAAG,CAAC,GAAG,CAAC;QACjB,CAAC;KACF;CACF,CACF,CAAC;AAEF,MAAM,CAAC,KAAK,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,QAAQ,EAAE,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE,yBAAyB,EAAE,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC;AAC/F,MAAM,CAAC,KAAK,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,EAAe,EAAE,IAAI,EAAE,eAAe,EAAE,CAAC,CAAC;AACvE,MAAM,CAAC,KAAK,CAAC,EAAE,QAAQ,EAAE,CAAC,EAAE,EAAgB,EAAE,IAAI,EAAE,aAAa,EAAE,CAAC,CAAC;AAErE,MAAM,CAAC,GAAG,CAAC,YAAY,EAAE,SAAS,CAAC,CAAC;AACpC,MAAM,CAAC,MAAM,CAAC,kDAAqB,CAAC,CAAC;AAErC,SAAgB,mBAAmB;IAEjC,MAAM,CAAC,OAAO,CAAC,KAAK,GAAG,CAAC,KAAoB,EAAE,EAAE;QAC9C,OAAO,IAAI,QAAQ,CAAC,KAAK,CAAC,CAAC;IAC7B,CAAC,CAAC;IAEF,MAAM,QAAQ,GAAG,kBAAQ,CAAC,KAAK,CAA6B,UAAU,EAAE,MAAM,CAAC,CAAC;IAChF,OAAO,QAAQ,CAAC;AAClB,CAAC;AAED,qDAAqD;AACrD,gCAAgC;AAChC,KAAK;AAEL,0FAA0F"}
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export interface SampleModel extends mongoose.Model<SampleDoc> {
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}
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export declare
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export declare function createSampleModel(): SampleModel;
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//# sourceMappingURL=sample.d.ts.map
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{"version":3,"file":"sample.d.ts","sourceRoot":"","sources":["../../../src/omics/models/sample.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAuB,UAAU,CAAC;AAEjD,OAAO,EAAE,OAAO,EAAE,MAAoB,UAAU,CAAC;AAEjD,MAAM,WAAW,WAAY,SAAQ,OAAO;IAC1C,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,OAAO,CAAC,EAAI,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,SAAU,SAAQ,QAAQ,CAAC,QAAQ;IAClD,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,OAAO,EAAK,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,WAAY,SAAQ,QAAQ,CAAC,KAAK,CAAC,SAAS,CAAC;IAC5D,KAAK,CAAC,KAAK,EAAE,WAAW,GAAG,SAAS,CAAC;CACtC;AAsCD,
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{"version":3,"file":"sample.d.ts","sourceRoot":"","sources":["../../../src/omics/models/sample.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAuB,UAAU,CAAC;AAEjD,OAAO,EAAE,OAAO,EAAE,MAAoB,UAAU,CAAC;AAEjD,MAAM,WAAW,WAAY,SAAQ,OAAO;IAC1C,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,OAAO,CAAC,EAAI,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,SAAU,SAAQ,QAAQ,CAAC,QAAQ;IAClD,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,OAAO,EAAK,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,WAAY,SAAQ,QAAQ,CAAC,KAAK,CAAC,SAAS,CAAC;IAC5D,KAAK,CAAC,KAAK,EAAE,WAAW,GAAG,SAAS,CAAC;CACtC;AAsCD,wBAAgB,iBAAiB,gBAQhC"}
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exports.createSampleModel = createSampleModel;
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const ClinicalSchema = new mongoose_1.default.Schema({
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schema.statics.build = (attrs) => {
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};
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// schema.statics.build = (attrs: SampleAttrs) => {
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// return new Sample(attrs);
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// };
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schema.index({ sampleId: 1 }, { name: 'sampleid_uidx', unique: true });
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schema.index({ sequencingSampleId: 1 }, { name: 'seqsampleid_idx' });
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};
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return Sample;
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}
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// indice unico
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//# sourceMappingURL=sample.js.map
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{"version":3,"file":"sample.js","sourceRoot":"","sources":["../../../src/omics/models/sample.ts"],"names":[],"mappings":"
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{"version":3,"file":"sample.js","sourceRoot":"","sources":["../../../src/omics/models/sample.ts"],"names":[],"mappings":";;;;;AA0DA,8CAQC;AAlED,wDAAiD;AACjD,2EAAmE;AAqBnE,MAAM,cAAc,GAAG,IAAI,kBAAQ,CAAC,MAAM,CAAC;IACzC,SAAS,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE;IAC3B,OAAO,EAAI,EAAE,IAAI,EAAE,MAAM,EAAE;IAC3B,OAAO,EAAI,EAAE,IAAI,EAAE,MAAM,EAAE;IAC3B,SAAS,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE;CAC5B,EAAE,EAAE,GAAG,EAAE,KAAK,EAAE,CAAC,CAAC;AAEnB,MAAM,MAAM,GAAG,IAAI,kBAAQ,CAAC,MAAM,CAChC;IACE,QAAQ,EAAY,EAAE,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE;IAClE,kBAAkB,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE;IAClE,QAAQ,EAAY,EAAE,IAAI,EAAE,cAAc,EAAE;IAC5C,SAAS,EAAW,EAAE,IAAI,EAAE,IAAI,EAAE;IAClC,SAAS,EAAW,EAAE,IAAI,EAAE,IAAI,EAAE;IAClC,SAAS,EAAW,EAAE,IAAI,EAAE,IAAI,EAAE;CACnC,EACD;IACE,MAAM,EAAE;QACN,SAAS,CAAC,GAAG,EAAE,GAAQ;YACrB,GAAG,CAAC,EAAE,GAAG,GAAG,CAAC,GAAG,CAAC;YACjB,OAAO,GAAG,CAAC,GAAG,CAAC;QACjB,CAAC;KACF;CACF,CACF,CAAC;AAEF,MAAM,CAAC,GAAG,CAAC,YAAY,EAAE,SAAS,CAAC,CAAC;AACpC,MAAM,CAAC,MAAM,CAAC,kDAAqB,CAAC,CAAC;AAErC,mDAAmD;AACnD,8BAA8B;AAC9B,KAAK;AAEL,MAAM,CAAC,KAAK,CAAC,EAAE,QAAQ,EAAE,CAAC,EAAE,EAAY,EAAE,IAAI,EAAE,eAAe,EAAE,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC;AACjF,MAAM,CAAC,KAAK,CAAC,EAAE,kBAAkB,EAAE,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE,iBAAiB,EAAE,CAAC,CAAC;AAErE,SAAgB,iBAAiB;IAE/B,MAAM,CAAC,OAAO,CAAC,KAAK,GAAG,CAAC,KAAkB,EAAE,EAAE;QAC5C,OAAO,IAAI,MAAM,CAAC,KAAK,CAAC,CAAC;IAC3B,CAAC,CAAC;IAEF,MAAM,MAAM,GAAG,kBAAQ,CAAC,KAAK,CAAyB,QAAQ,EAAE,MAAM,CAAC,CAAC;IACxE,OAAO,MAAM,CAAC;AAChB,CAAC;AAED,eAAe"}
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{"version":3,"file":"variant.d.ts","sourceRoot":"","sources":["../../../src/omics/models/variant.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAuB,UAAU,CAAC;AAEjD,OAAO,EAAE,QAAQ,EAAE,MAAkB,UAAU,CAAC;AAEhD,MAAM,WAAW,YAAa,SAAQ,QAAQ;IAC5C,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,OAAO,CAAC,EAAI,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,UAAW,SAAQ,QAAQ,CAAC,QAAQ;IACnD,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,OAAO,EAAK,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,YAAa,SAAQ,QAAQ,CAAC,KAAK,CAAC,UAAU,CAAC;IAC9D,KAAK,CAAC,KAAK,EAAE,YAAY,GAAG,UAAU,CAAC;CACxC;AAiDD,
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{"version":3,"file":"variant.d.ts","sourceRoot":"","sources":["../../../src/omics/models/variant.ts"],"names":[],"mappings":"AAAA,OAAO,QAAQ,MAAuB,UAAU,CAAC;AAEjD,OAAO,EAAE,QAAQ,EAAE,MAAkB,UAAU,CAAC;AAEhD,MAAM,WAAW,YAAa,SAAQ,QAAQ;IAC5C,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,OAAO,CAAC,EAAI,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,UAAW,SAAQ,QAAQ,CAAC,QAAQ;IACnD,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,SAAS,CAAC,EAAE,IAAI,CAAC;IACjB,OAAO,EAAK,MAAM,CAAC;CACpB;AAED,MAAM,WAAW,YAAa,SAAQ,QAAQ,CAAC,KAAK,CAAC,UAAU,CAAC;IAC9D,KAAK,CAAC,KAAK,EAAE,YAAY,GAAG,UAAU,CAAC;CACxC;AAiDD,wBAAgB,kBAAkB,iBAQjC"}
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const AnnotationSchema = new mongoose_1.default.Schema({
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|
+
// };
|
|
48
|
+
function createVariantModel() {
|
|
49
|
+
schema.statics.build = (attrs) => {
|
|
50
|
+
return new Variant(attrs);
|
|
51
|
+
};
|
|
52
|
+
const Variant = mongoose_1.default.model('Variant', schema);
|
|
53
|
+
return Variant;
|
|
54
|
+
}
|
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50
55
|
//# sourceMappingURL=variant.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"variant.js","sourceRoot":"","sources":["../../../src/omics/models/variant.ts"],"names":[],"mappings":"
|
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1
|
+
{"version":3,"file":"variant.js","sourceRoot":"","sources":["../../../src/omics/models/variant.ts"],"names":[],"mappings":";;;;;AAqEA,gDAQC;AA7ED,wDAAiD;AACjD,2EAAmE;AAqBnE,MAAM,gBAAgB,GAAG,IAAI,kBAAQ,CAAC,MAAM,CAAC;IAC3C,IAAI,EAAa,EAAE,IAAI,EAAE,MAAM,EAAE;IACjC,WAAW,EAAM,EAAE,IAAI,EAAE,MAAM,EAAE;IACjC,UAAU,EAAO,EAAE,IAAI,EAAE,MAAM,EAAE;IACjC,KAAK,EAAY,EAAE,IAAI,EAAE,MAAM,EAAE;IACjC,KAAK,EAAY,EAAE,IAAI,EAAE,MAAM,EAAE;IACjC,UAAU,EAAO,EAAE,IAAI,EAAE,MAAM,EAAE;IACjC,eAAe,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE;IACjC,MAAM,EAAW,EAAE,IAAI,EAAE,MAAM,EAAE;IACjC,IAAI,EAAa,EAAE,IAAI,EAAE,MAAM,EAAE;CAClC,EAAE,EAAE,GAAG,EAAE,KAAK,EAAE,CAAC,CAAC;AAEnB,MAAM,MAAM,GAAG,IAAI,kBAAQ,CAAC,MAAM,CAChC;IACE,SAAS,EAAO,EAAE,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,IAAI,EAAE;IAChD,KAAK,EAAW,EAAE,IAAI,EAAE,MAAM,EAAE;IAChC,GAAG,EAAa,EAAE,IAAI,EAAE,MAAM,EAAE;IAChC,GAAG,EAAa,EAAE,IAAI,EAAE,MAAM,EAAE;IAChC,GAAG,EAAa,EAAE,IAAI,EAAE,CAAC,MAAM,CAAC,EAAE;IAClC,IAAI,EAAY,EAAE,IAAI,EAAE,MAAM,EAAE;IAChC,cAAc,EAAE,EAAE,IAAI,EAAE,MAAM,EAAE;IAChC,WAAW,EAAK,EAAE,IAAI,EAAE,gBAAgB,EAAE;IAC1C,SAAS,EAAO,EAAE,IAAI,EAAE,IAAI,EAAE;IAC9B,SAAS,EAAO,EAAE,IAAI,EAAE,IAAI,EAAE;IAC9B,SAAS,EAAO,EAAE,IAAI,EAAE,IAAI,EAAE;CAC/B,EACD;IACE,MAAM,EAAE;QACN,SAAS,CAAC,GAAG,EAAE,GAAQ;YACrB,GAAG,CAAC,EAAE,GAAG,GAAG,CAAC,GAAG,CAAC;YACjB,OAAO,GAAG,CAAC,GAAG,CAAC;QACjB,CAAC;KACF;CACF,CACF,CAAC;AAEF,MAAM,CAAC,KAAK,CAAC,EAAE,SAAS,EAAE,CAAC,EAAE,EAAW,EAAE,IAAI,EAAE,gBAAgB,EAAE,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC;AAClF,MAAM,CAAC,KAAK,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE,EAAO,EAAE,IAAI,EAAE,eAAe,EAAE,CAAC,CAAC;AACnE,MAAM,CAAC,KAAK,CAAC,EAAE,kBAAkB,EAAE,CAAC,EAAE,EAAE,EAAE,IAAI,EAAE,qBAAqB,EAAE,CAAC,CAAC;AAEzE,MAAM,CAAC,GAAG,CAAC,YAAY,EAAE,SAAS,CAAC,CAAC;AACpC,MAAM,CAAC,MAAM,CAAC,kDAAqB,CAAC,CAAC;AAErC,oDAAoD;AACpD,+BAA+B;AAC/B,KAAK;AAEL,SAAgB,kBAAkB;IAEhC,MAAM,CAAC,OAAO,CAAC,KAAK,GAAG,CAAC,KAAmB,EAAE,EAAE;QAC7C,OAAO,IAAI,OAAO,CAAC,KAAK,CAAC,CAAC;IAC5B,CAAC,CAAC;IAEF,MAAM,OAAO,GAAG,kBAAQ,CAAC,KAAK,CAA2B,SAAS,EAAE,MAAM,CAAC,CAAC;IAC5E,OAAO,OAAO,CAAC;AACjB,CAAC"}
|
|
@@ -1,12 +1,20 @@
|
|
|
1
|
-
import { GenotypeAttrs } from '../models/genotype';
|
|
2
|
-
import { SampleAttrs } from '../models/sample';
|
|
3
|
-
import { VariantAttrs } from '../models/variant';
|
|
1
|
+
import { GenotypeAttrs, GenotypeModel } from '../models/genotype';
|
|
2
|
+
import { SampleAttrs, SampleModel } from '../models/sample';
|
|
3
|
+
import { VariantAttrs, VariantModel } from '../models/variant';
|
|
4
|
+
export type ParserModels = {
|
|
5
|
+
Variant: VariantModel;
|
|
6
|
+
Sample: SampleModel;
|
|
7
|
+
Genotype: GenotypeModel;
|
|
8
|
+
};
|
|
4
9
|
export declare class TSVParser {
|
|
5
10
|
private readonly variantOps;
|
|
6
11
|
private readonly sampleOps;
|
|
7
12
|
private readonly genotypeOps;
|
|
13
|
+
private readonly Variant;
|
|
14
|
+
private readonly Sample;
|
|
15
|
+
private readonly Genotype;
|
|
8
16
|
private readonly bulkSize;
|
|
9
|
-
constructor(bulkSize?: number);
|
|
17
|
+
constructor({ Variant, Sample, Genotype }: ParserModels, bulkSize?: number);
|
|
10
18
|
/**
|
|
11
19
|
*
|
|
12
20
|
* @param file
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"tsv-parser.d.ts","sourceRoot":"","sources":["../../../src/omics/services/tsv-parser.ts"],"names":[],"mappings":"AAKA,OAAO,
|
|
1
|
+
{"version":3,"file":"tsv-parser.d.ts","sourceRoot":"","sources":["../../../src/omics/services/tsv-parser.ts"],"names":[],"mappings":"AAKA,OAAO,EAAE,aAAa,EAAE,aAAa,EAAE,MAAe,oBAAoB,CAAC;AAC3E,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,MAAmB,kBAAkB,CAAC;AACzE,OAAO,EAAE,YAAY,EAAE,YAAY,EAAE,MAAiB,mBAAmB,CAAC;AAI1E,MAAM,MAAM,YAAY,GAAG;IACzB,OAAO,EAAG,YAAY,CAAC;IACvB,MAAM,EAAI,WAAW,CAAC;IACtB,QAAQ,EAAE,aAAa,CAAC;CACzB,CAAA;AACD,qBAAa,SAAS;IAEpB,OAAO,CAAC,QAAQ,CAAC,UAAU,CAA+C;IAC1E,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgD;IAC1E,OAAO,CAAC,QAAQ,CAAC,WAAW,CAA8C;IAE1E,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAmB;IAC3C,OAAO,CAAC,QAAQ,CAAC,MAAM,CAAmB;IAC1C,OAAO,CAAC,QAAQ,CAAC,QAAQ,CAAmB;IAE5C,OAAO,CAAC,QAAQ,CAAC,QAAQ,CAAY;gBAEzB,EAAE,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,EAAE,YAAY,EAAE,QAAQ,GAAE,MAAa;IAQhF;;;OAGG;IACG,KAAK,CAAC,IAAI,EAAE,MAAM;IA2BxB;;;OAGG;IACG,QAAQ,CAAC,GAAG,EAAE,GAAG;IAgCvB;;OAEG;IACG,aAAa;IAMnB;;OAEG;IACG,QAAQ;IAkBd;;;;OAIG;IACH,SAAS,CAAC,GAAG,CAAC,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS;IAU3C;;;;;OAKG;IACH,UAAU,CAAC,QAAQ,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,GAAG;QAAE,EAAE,CAAC,EAAE,MAAM,CAAC;QAAC,GAAG,CAAC,EAAE,MAAM,CAAA;KAAC;IAgB5E;;;;OAIG;IACH,gBAAgB,CAAC,GAAG,EAAE,MAAM,CAAC,MAAM,EAAC,MAAM,CAAC;;;;;CA2E5C"}
|
|
@@ -6,17 +6,17 @@ Object.defineProperty(exports, "__esModule", { value: true });
|
|
|
6
6
|
exports.TSVParser = void 0;
|
|
7
7
|
const node_fs_1 = __importDefault(require("node:fs"));
|
|
8
8
|
const node_readline_1 = __importDefault(require("node:readline"));
|
|
9
|
-
const genotype_1 = require("../models/genotype");
|
|
10
|
-
const sample_1 = require("../models/sample");
|
|
11
|
-
const variant_1 = require("../models/variant");
|
|
12
9
|
const tsvfile_1 = require("../enums/tsvfile");
|
|
13
10
|
const utils_1 = require("../utils");
|
|
14
11
|
class TSVParser {
|
|
15
|
-
constructor(bulkSize = 5000) {
|
|
12
|
+
constructor({ Variant, Sample, Genotype }, bulkSize = 5000) {
|
|
16
13
|
this.variantOps = [];
|
|
17
14
|
this.sampleOps = [];
|
|
18
15
|
this.genotypeOps = [];
|
|
19
16
|
this.bulkSize = bulkSize;
|
|
17
|
+
this.Variant = Variant;
|
|
18
|
+
this.Sample = Sample;
|
|
19
|
+
this.Genotype = Genotype;
|
|
20
20
|
}
|
|
21
21
|
/**
|
|
22
22
|
*
|
|
@@ -82,15 +82,15 @@ class TSVParser {
|
|
|
82
82
|
*/
|
|
83
83
|
async saveData() {
|
|
84
84
|
if (this.variantOps.length) {
|
|
85
|
-
await
|
|
85
|
+
await this.Variant.bulkWrite(this.variantOps);
|
|
86
86
|
this.variantOps.length = 0;
|
|
87
87
|
}
|
|
88
88
|
if (this.sampleOps.length) {
|
|
89
|
-
await
|
|
89
|
+
await this.Sample.bulkWrite(this.sampleOps);
|
|
90
90
|
this.sampleOps.length = 0;
|
|
91
91
|
}
|
|
92
92
|
if (this.genotypeOps.length) {
|
|
93
|
-
await
|
|
93
|
+
await this.Genotype.bulkWrite(this.genotypeOps);
|
|
94
94
|
this.genotypeOps.length = 0;
|
|
95
95
|
}
|
|
96
96
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"tsv-parser.js","sourceRoot":"","sources":["../../../src/omics/services/tsv-parser.ts"],"names":[],"mappings":";;;;;;AAEA,sDAAgE;AAChE,kEAAsE;
|
|
1
|
+
{"version":3,"file":"tsv-parser.js","sourceRoot":"","sources":["../../../src/omics/services/tsv-parser.ts"],"names":[],"mappings":";;;;;;AAEA,sDAAgE;AAChE,kEAAsE;AAKtE,8CAAyE;AACzE,oCAAiE;AAOjE,MAAa,SAAS;IAYpB,YAAY,EAAE,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAgB,EAAE,WAAmB,IAAI;QAV/D,eAAU,GAA4C,EAAE,CAAC;QACzD,cAAS,GAA6C,EAAE,CAAC;QACzD,gBAAW,GAA2C,EAAE,CAAC;QAUxE,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;QACxB,IAAI,CAAC,OAAO,GAAI,OAAO,CAAC;QACxB,IAAI,CAAC,MAAM,GAAK,MAAM,CAAC;QACvB,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC;IAC3B,CAAC;IAED;;;OAGG;IACH,KAAK,CAAC,KAAK,CAAC,IAAY;QAEtB,MAAM,MAAM,GAAG,iBAAE,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,EAAE,GAAO,uBAAQ,CAAC,eAAe,CAAC,EAAC,KAAK,EAAC,MAAM,EAAC,CAAC,CAAA;QAEvD,IAAI,MAAM,GAAa,EAAE,CAAC;QAE1B,IAAI,KAAK,EAAE,MAAM,IAAI,IAAI,EAAE,EAAE,CAAC;YAE5B,IAAI,CAAC,MAAM,CAAC,MAAM,EAAE,CAAC;gBAEnB,MAAM,GAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;gBACxB,SAAS;YACX,CAAC;YAED,MAAM,MAAM,GAAa,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;YAC1C,MAAM,GAAG,GAAgB,EAAE,CAAC;YAE5B,MAAM,CAAC,OAAO,CAAC,CAAC,CAAC,EAAC,CAAC,EAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC;YAE3C,MAAM,IAAI,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC;YACzB,MAAM,IAAI,CAAC,aAAa,EAAE,CAAC;QAC7B,CAAC;QAED,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAC;IACxB,CAAC;IAED;;;OAGG;IACH,KAAK,CAAC,QAAQ,CAAC,GAAQ;QAErB,MAAM,EAAE,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAC,gBAAgB,CAAC,GAAG,CAAC,CAAA;QAEhE,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC;YACnB,SAAS,EAAE;gBACT,MAAM,EAAE,EAAE,SAAS,EAAK,OAAO,CAAC,SAAS,EAAC;gBAC1C,MAAM,EAAE,EAAE,YAAY,EAAE,OAAO,EAAC;gBAChC,MAAM,EAAE,IAAI;aACb;SACF,CAAC,CAAC;QAEH,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC;YAClB,SAAS,EAAE;gBACT,MAAM,EAAE,EAAE,QAAQ,EAAE,MAAM,CAAC,QAAQ,EAAC;gBACpC,MAAM,EAAE,EAAE,YAAY,EAAK,MAAM,EAAC;gBAClC,MAAM,EAAE,IAAI;aACb;SACF,CAAC,CAAC;QAEH,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC;YACpB,SAAS,EAAE;gBACT,MAAM,EAAE;oBACN,SAAS,EAAE,QAAQ,CAAC,SAAS;oBAC7B,QAAQ,EAAG,QAAQ,CAAC,QAAQ;iBAC7B;gBACD,MAAM,EAAE,EAAE,IAAI,EAAC,QAAQ,EAAE;gBACzB,MAAM,EAAE,IAAI;aACb;SACF,CAAC,CAAC;IACL,CAAC;IAED;;OAEG;IACH,KAAK,CAAC,aAAa;QAEjB,IAAI,IAAI,CAAC,UAAU,CAAC,MAAM,IAAI,IAAI,CAAC,QAAQ;YACzC,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAC;IAC1B,CAAC;IAED;;OAEG;IACH,KAAK,CAAC,QAAQ;QAEZ,IAAI,IAAI,CAAC,UAAU,CAAC,MAAM,EAAE,CAAC;YAC3B,MAAM,IAAI,CAAC,OAAO,CAAC,SAAS,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;YAC9C,IAAI,CAAC,UAAU,CAAC,MAAM,GAAI,CAAC,CAAC;QAC9B,CAAC;QAED,IAAI,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,CAAC;YAC1B,MAAM,IAAI,CAAC,MAAM,CAAC,SAAS,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;YAC5C,IAAI,CAAC,SAAS,CAAC,MAAM,GAAK,CAAC,CAAC;QAC9B,CAAC;QAED,IAAI,IAAI,CAAC,WAAW,CAAC,MAAM,EAAE,CAAC;YAC5B,MAAM,IAAI,CAAC,QAAQ,CAAC,SAAS,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC;YAChD,IAAI,CAAC,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC;QAC9B,CAAC;IACH,CAAC;IAED;;;;OAIG;IACH,SAAS,CAAC,GAAY;QAEpB,IAAI,GAAG,KAAK,SAAS;YAAE,OAAO,SAAS,CAAC;QAExC,IAAI,GAAG,GAAG,GAAG;YAAE,OAAO,KAAK,CAAC;QAC5B,IAAI,GAAG,GAAG,GAAG;YAAE,OAAO,KAAK,CAAC;QAE5B,OAAO,KAAK,CAAC;IACf,CAAC;IAED;;;;;OAKG;IACH,UAAU,CAAC,QAAgB,EAAE,QAAgB;QAE3C,IAAI,GAAuB,CAAC;QAC5B,IAAI,EAAuB,CAAC;QAE5B,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,QAAQ,CAAC,IAAI,CAAC,MAAM,CAAC,KAAK,CAAC,QAAQ,CAAC,EAAE,CAAC;YAEvD,EAAE,GAAG,QAAQ,GAAG,QAAQ,CAAC;YAEzB,IAAI,EAAE,GAAG,CAAC;gBACR,GAAG,GAAG,QAAQ,GAAG,EAAE,CAAC;QACxB,CAAC;QAED,OAAO,EAAE,GAAG,EAAE,EAAE,EAAE,CAAC;IACrB,CAAC;IAED;;;;OAIG;IACH,gBAAgB,CAAC,GAA0B;QAEzC,MAAM,KAAK,GAAK,GAAG,CAAC,oBAAU,CAAC,UAAU,CAAC,CAAC;QAC3C,MAAM,GAAG,GAAO,MAAM,CAAC,GAAG,CAAC,oBAAU,CAAC,SAAS,CAAC,CAAC,CAAC;QAElD,MAAM,GAAG,GAAO,GAAG,CAAC,oBAAU,CAAC,eAAe,CAAC,CAAC;QAChD,MAAM,OAAO,GAAG,GAAG,CAAC,oBAAU,CAAC,OAAO,CAAC,CAAC;QACxC,MAAM,OAAO,GAAG,GAAG,CAAC,oBAAU,CAAC,OAAO,CAAC,CAAC;QACxC,MAAM,IAAI,GAAM,GAAG,CAAC,oBAAU,CAAC,IAAI,CAAC,CAAC;QAErC,IAAI,CAAC,KAAK,IAAI,CAAC,GAAG,IAAI,CAAC,GAAG,IAAI,CAAC,OAAO;YACpC,MAAM,IAAI,KAAK,CAAC,qBAAqB,CAAC,CAAC;QAEzC,MAAM,SAAS,GAAY,IAAA,wBAAgB,EAAC,KAAK,EAAE,GAAG,EAAE,GAAG,EAAE,OAAO,CAAC,CAAC;QACtE,MAAM,QAAQ,GAAa,GAAG,CAAC,oBAAU,CAAC,QAAQ,CAAC,CAAC;QACpD,MAAM,kBAAkB,GAAG,IAAA,2BAAmB,EAAC,QAAQ,CAAC,CAAC;QAEzD,IAAI,CAAC,QAAQ;YACX,MAAM,IAAI,KAAK,CAAC,mBAAmB,CAAC,CAAC;QAEvC,kDAAkD;QAClD,kDAAkD;QAClD,2DAA2D;QAC3D,MAAM,GAAG,GAAG,MAAM,CAAC,UAAU,CAAC,GAAG,CAAC,oBAAU,CAAC,GAAG,CAAC,CAAC,CAAC;QACnD,MAAM,EAAE,GAAI,MAAM,CAAC,QAAQ,CAAC,GAAG,CAAC,oBAAU,CAAC,EAAE,CAAC,CAAC,CAAC;QAChD,MAAM,EAAE,GAAI,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC;QAEhC,MAAM,OAAO,GAAiB;YAC5B,SAAS;YACT,KAAK;YACL,GAAG;YACH,GAAG;YACH,GAAG,EAAE,CAAC,OAAO,CAAC;YACd,IAAI,EAAY,GAAG,CAAC,oBAAU,CAAC,WAAW,CAAC;YAC3C,cAAc,EAAE,GAAG,CAAC,oBAAU,CAAC,qBAAqB,CAAC;YACrD,WAAW,EAAE;gBACX,IAAI;gBACJ,WAAW,EAAM,GAAG,CAAC,oBAAU,CAAC,WAAW,CAAC;gBAC5C,UAAU,EAAO,GAAG,CAAC,oBAAU,CAAC,YAAY,CAAC;gBAC7C,KAAK,EAAY,GAAG,CAAC,oBAAU,CAAC,KAAK,CAAC;gBACtC,KAAK,EAAY,GAAG,CAAC,oBAAU,CAAC,KAAK,CAAC;gBACtC,UAAU,EAAO,GAAG,CAAC,oBAAU,CAAC,UAAU,CAAC;gBAC3C,eAAe,EAAE,GAAG,CAAC,oBAAU,CAAC,eAAe,CAAC;gBAChD,MAAM,EAAW,GAAG,CAAC,oBAAU,CAAC,MAAM,CAAC;gBACvC,IAAI,EAAa,GAAG,CAAC,oBAAU,CAAC,UAAU,CAAC;aAC5C;SACF,CAAC;QAEF,MAAM,MAAM,GAAgB;YAC1B,QAAQ;YACR,kBAAkB;YAClB,QAAQ,EAAE;gBACR,SAAS,EAAE,GAAG,CAAC,oBAAU,CAAC,SAAS,CAAC;gBACpC,OAAO,EAAI,GAAG,CAAC,oBAAU,CAAC,OAAO,CAAC;gBAClC,OAAO,EAAI,GAAG,CAAC,oBAAU,CAAC,OAAO,CAAC;gBAClC,SAAS,EAAE,GAAG,CAAC,oBAAU,CAAC,SAAS,CAAC;aACrC;SACF,CAAC;QAEF,MAAM,QAAQ,GAAkB;YAC9B,SAAS;YACT,QAAQ;YACR,kBAAkB;YAClB,OAAO,EAAE,CAAC,OAAO,EAAE,OAAO,CAAC;YAC3B,GAAG,EAAM,GAAG;YACZ,EAAE,EAAO,EAAE;YACX,EAAE,EAAO,EAAE;SACZ,CAAC;QAEF,OAAO;YACL,OAAO;YACP,MAAM;YACN,QAAQ;SACT,CAAC;IACJ,CAAC;CACF;AA1OD,8BA0OC"}
|