@nextage/omics-lib 1.0.7 → 1.0.10

package/build/index.d.ts

@@ -1,7 +1,6 @@
 export * from './constants';
 export * from './enums';
-export * from './omics/models';
-export * from './omics/types';
+export * from './omics';
 export * from './interfaces';
 export * from './types';
 export * from './utils';

package/build/index.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,cAAc,aAAa,CAAC;AAC5B,cAAc,SAAS,CAAC;AACxB,cAAc,gBAAgB,CAAC;AAC/B,cAAc,eAAe,CAAC;AAC9B,cAAc,cAAc,CAAC;AAC7B,cAAc,SAAS,CAAC;AACxB,cAAc,SAAS,CAAC"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,cAAc,aAAa,CAAC;AAC5B,cAAc,SAAS,CAAC;AACxB,cAAc,SAAS,CAAC;AACxB,cAAc,cAAc,CAAC;AAC7B,cAAc,SAAS,CAAC;AACxB,cAAc,SAAS,CAAC"}

package/build/index.js

@@ -16,8 +16,7 @@ var __exportStar = (this && this.__exportStar) || function(m, exports) {
 Object.defineProperty(exports, "__esModule", { value: true });
 __exportStar(require("./constants"), exports);
 __exportStar(require("./enums"), exports);
-__exportStar(require("./omics/models"), exports);
-__exportStar(require("./omics/types"), exports);
+__exportStar(require("./omics"), exports);
 __exportStar(require("./interfaces"), exports);
 __exportStar(require("./types"), exports);
 __exportStar(require("./utils"), exports);

package/build/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;AAAA,8CAA4B;AAC5B,0CAAwB;AACxB,iDAA+B;AAC/B,gDAA8B;AAC9B,+CAA6B;AAC7B,0CAAwB;AACxB,0CAAwB"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;AAAA,8CAA4B;AAC5B,0CAAwB;AACxB,0CAAwB;AACxB,+CAA6B;AAC7B,0CAAwB;AACxB,0CAAwB"}

package/build/omics/enums/index.d.ts

@@ -0,0 +1,2 @@
+export * from './tsvfile';
+//# sourceMappingURL=index.d.ts.map

package/build/omics/enums/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/omics/enums/index.ts"],"names":[],"mappings":"AAAA,cAAc,WAAW,CAAC"}

package/build/omics/enums/index.js

@@ -0,0 +1,18 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __exportStar = (this && this.__exportStar) || function(m, exports) {
+    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+__exportStar(require("./tsvfile"), exports);
+//# sourceMappingURL=index.js.map

package/build/omics/enums/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/omics/enums/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;AAAA,4CAA0B"}

package/build/omics/enums/tsvfile.d.ts

@@ -0,0 +1,28 @@
+export declare enum TSVColumns {
+    chromosome = "Chromosome",
+    posistion = "Start_Position",
+    referenceAllele = "Reference_Allele",
+    allele1 = "Tumor_Seq_Allele1",
+    allele2 = "Tumor_Seq_Allele2",
+    gene = "Hugo_Symbol",
+    sampleId = "Sample_ID",
+    variantType = "Variant_Type",
+    variantClassification = "Variant_Classification",
+    consequence = "Consequence",
+    transcriptId = "Transcript_ID",
+    hgvsc = "HGVSc",
+    hgvsp = "HGVSp",
+    hgvspShort = "HGVSp_Short",
+    proteinPosition = "Protein_position",
+    codons = "Codons",
+    exonNumber = "Exon_Number",
+    diagnosis = "Diagnosis",
+    snomedM = "Snomed-M",
+    snomedT = "Snomed-T",
+    tumorSite = "Tumor_Site",
+    vaf = "VAF",
+    dp = "DP",
+    altReads = "t_alt_count",
+    refReads = "t_ref_count"
+}
+//# sourceMappingURL=tsvfile.d.ts.map

package/build/omics/enums/tsvfile.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"tsvfile.d.ts","sourceRoot":"","sources":["../../../src/omics/enums/tsvfile.ts"],"names":[],"mappings":"AAAA,oBAAY,UAAU;IACtB,UAAU,eAA0B;IACpC,SAAS,mBAA+B;IACxC,eAAe,qBAA2B;IAC1C,OAAO,sBAAoC;IAC3C,OAAO,sBAAoC;IAC3C,IAAI,gBAAiC;IACrC,QAAQ,cAA2B;IACnC,WAAW,iBAA2B;IACtC,qBAAqB,2BAA2B;IAChD,WAAW,gBAA0B;IACrC,YAAY,kBAA2B;IACvC,KAAK,UAA0B;IAC/B,KAAK,UAA0B;IAC/B,UAAU,gBAA2B;IACrC,eAAe,qBAA2B;IAC1C,MAAM,WAA0B;IAChC,UAAU,gBAA2B;IACrC,SAAS,cAA0B;IACnC,OAAO,aAA2B;IAClC,OAAO,aAA2B;IAClC,SAAS,eAA2B;IACpC,GAAG,QAA0B;IAC7B,EAAE,OAA0B;IAC5B,QAAQ,gBAA6B;IACrC,QAAQ,gBAA6B;CACpC"}

package/build/omics/enums/tsvfile.js

@@ -0,0 +1,33 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.TSVColumns = void 0;
+var TSVColumns;
+(function (TSVColumns) {
+    TSVColumns["chromosome"] = "Chromosome";
+    TSVColumns["posistion"] = "Start_Position";
+    TSVColumns["referenceAllele"] = "Reference_Allele";
+    TSVColumns["allele1"] = "Tumor_Seq_Allele1";
+    TSVColumns["allele2"] = "Tumor_Seq_Allele2";
+    TSVColumns["gene"] = "Hugo_Symbol";
+    TSVColumns["sampleId"] = "Sample_ID";
+    TSVColumns["variantType"] = "Variant_Type";
+    TSVColumns["variantClassification"] = "Variant_Classification";
+    TSVColumns["consequence"] = "Consequence";
+    TSVColumns["transcriptId"] = "Transcript_ID";
+    TSVColumns["hgvsc"] = "HGVSc";
+    TSVColumns["hgvsp"] = "HGVSp";
+    TSVColumns["hgvspShort"] = "HGVSp_Short";
+    TSVColumns["proteinPosition"] = "Protein_position";
+    TSVColumns["codons"] = "Codons";
+    TSVColumns["exonNumber"] = "Exon_Number";
+    TSVColumns["diagnosis"] = "Diagnosis";
+    TSVColumns["snomedM"] = "Snomed-M";
+    TSVColumns["snomedT"] = "Snomed-T";
+    TSVColumns["tumorSite"] = "Tumor_Site";
+    TSVColumns["vaf"] = "VAF";
+    TSVColumns["dp"] = "DP";
+    TSVColumns["altReads"] = "t_alt_count";
+    TSVColumns["refReads"] = "t_ref_count";
+})(TSVColumns || (exports.TSVColumns = TSVColumns = {}));
+;
+//# sourceMappingURL=tsvfile.js.map

package/build/omics/enums/tsvfile.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"tsvfile.js","sourceRoot":"","sources":["../../../src/omics/enums/tsvfile.ts"],"names":[],"mappings":";;;AAAA,IAAY,UA0BX;AA1BD,WAAY,UAAU;IACtB,uCAAoC,CAAA;IACpC,0CAAwC,CAAA;IACxC,kDAA0C,CAAA;IAC1C,2CAA2C,CAAA;IAC3C,2CAA2C,CAAA;IAC3C,kCAAqC,CAAA;IACrC,oCAAmC,CAAA;IACnC,0CAAsC,CAAA;IACtC,8DAAgD,CAAA;IAChD,yCAAqC,CAAA;IACrC,4CAAuC,CAAA;IACvC,6BAA+B,CAAA;IAC/B,6BAA+B,CAAA;IAC/B,wCAAqC,CAAA;IACrC,kDAA0C,CAAA;IAC1C,+BAAgC,CAAA;IAChC,wCAAqC,CAAA;IACrC,qCAAmC,CAAA;IACnC,kCAAkC,CAAA;IAClC,kCAAkC,CAAA;IAClC,sCAAoC,CAAA;IACpC,yBAA6B,CAAA;IAC7B,uBAA4B,CAAA;IAC5B,sCAAqC,CAAA;IACrC,sCAAqC,CAAA;AACrC,CAAC,EA1BW,UAAU,0BAAV,UAAU,QA0BrB;AAAA,CAAC"}

package/build/omics/index.d.ts

@@ -0,0 +1,6 @@
+export * from './enums';
+export * from './models';
+export * from './services';
+export * from './types';
+export * from './utils';
+//# sourceMappingURL=index.d.ts.map

package/build/omics/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/omics/index.ts"],"names":[],"mappings":"AAAA,cAAc,SAAS,CAAC;AACxB,cAAc,UAAU,CAAC;AACzB,cAAc,YAAY,CAAC;AAC3B,cAAc,SAAS,CAAC;AACxB,cAAc,SAAS,CAAC"}

package/build/omics/index.js

@@ -0,0 +1,22 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __exportStar = (this && this.__exportStar) || function(m, exports) {
+    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+__exportStar(require("./enums"), exports);
+__exportStar(require("./models"), exports);
+__exportStar(require("./services"), exports);
+__exportStar(require("./types"), exports);
+__exportStar(require("./utils"), exports);
+//# sourceMappingURL=index.js.map

package/build/omics/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/omics/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;AAAA,0CAAwB;AACxB,2CAAyB;AACzB,6CAA2B;AAC3B,0CAAwB;AACxB,0CAAwB"}

package/build/omics/models/genotype.d.ts.map

@@ -1 +1 @@
-{"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,eAAO,MAAM,QAAQ,eAAiE,CAAC"}
+{"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;AAsCD,eAAO,MAAM,QAAQ,eAAiE,CAAC"}

package/build/omics/models/genotype.js

@@ -25,6 +25,9 @@ const schema = new mongoose_1.default.Schema({
         },
     },
 });
+schema.index({ variantId: 1, sampleId: 1 }, { name: 'variantid_sampleid_uidx', unique: true });
+schema.index({ variantId: 1 }, { name: 'variantid_idx' });
+schema.index({ sampleId: 1 }, { name: 'sampled_idx' });
 schema.set('versionKey', 'version');
 schema.plugin(mongoose_update_if_current_1.updateIfCurrentPlugin);
 schema.statics.build = (attrs) => {

package/build/omics/models/genotype.js.map

@@ -1 +1 @@
-{"version":3,"file":"genotype.js","sourceRoot":"","sources":["../../../src/omics/models/genotype.ts"],"names":[],"mappings":";;;;;;AAAA,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,GAAG,CAAC,YAAY,EAAE,SAAS,CAAC,CAAC;AACpC,MAAM,CAAC,MAAM,CAAC,kDAAqB,CAAC,CAAC;AAErC,MAAM,CAAC,OAAO,CAAC,KAAK,GAAG,CAAC,KAAoB,EAAE,EAAE;IAC9C,OAAO,IAAI,gBAAQ,CAAC,KAAK,CAAC,CAAC;AAC7B,CAAC,CAAC;AAEW,QAAA,QAAQ,GAAG,kBAAQ,CAAC,KAAK,CAA6B,UAAU,EAAE,MAAM,CAAC,CAAC"}
+{"version":3,"file":"genotype.js","sourceRoot":"","sources":["../../../src/omics/models/genotype.ts"],"names":[],"mappings":";;;;;;AAAA,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;AAIrE,MAAM,CAAC,GAAG,CAAC,YAAY,EAAE,SAAS,CAAC,CAAC;AACpC,MAAM,CAAC,MAAM,CAAC,kDAAqB,CAAC,CAAC;AAErC,MAAM,CAAC,OAAO,CAAC,KAAK,GAAG,CAAC,KAAoB,EAAE,EAAE;IAC9C,OAAO,IAAI,gBAAQ,CAAC,KAAK,CAAC,CAAC;AAC7B,CAAC,CAAC;AAEW,QAAA,QAAQ,GAAG,kBAAQ,CAAC,KAAK,CAA6B,UAAU,EAAE,MAAM,CAAC,CAAC"}

package/build/omics/models/sample.d.ts.map

@@ -1 +1 @@
-{"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;AAmCD,eAAO,MAAM,MAAM,aAA2D,CAAC"}
+{"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,eAAO,MAAM,MAAM,aAA2D,CAAC"}

package/build/omics/models/sample.js

@@ -13,7 +13,7 @@ const ClinicalSchema = new mongoose_1.default.Schema({
     tumorSite: { type: String }
 }, { _id: false });
 const schema = new mongoose_1.default.Schema({
-    biobankSampleId: { type: String, required: true, unique: true },
+    sampleId: { type: String, required: true, unique: true },
     sequencingSampleId: { type: String, required: true, unique: true },
     clinical: { type: ClinicalSchema },
     createdAt: { type: Date },
@@ -32,5 +32,8 @@ schema.plugin(mongoose_update_if_current_1.updateIfCurrentPlugin);
 schema.statics.build = (attrs) => {
     return new exports.Sample(attrs);
 };
+schema.index({ sampleId: 1 }, { name: 'sampleid_uidx', unique: true });
+schema.index({ sequencingSampleId: 1 }, { name: 'seqsampleid_idx' });
 exports.Sample = mongoose_1.default.model('Sample', schema);
+// indice unico
 //# sourceMappingURL=sample.js.map

package/build/omics/models/sample.js.map

@@ -1 +1 @@
-{"version":3,"file":"sample.js","sourceRoot":"","sources":["../../../src/omics/models/sample.ts"],"names":[],"mappings":";;;;;;AAAA,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,eAAe,EAAK,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,MAAM,CAAC,OAAO,CAAC,KAAK,GAAG,CAAC,KAAkB,EAAE,EAAE;IAC5C,OAAO,IAAI,cAAM,CAAC,KAAK,CAAC,CAAC;AAC3B,CAAC,CAAC;AAEW,QAAA,MAAM,GAAG,kBAAQ,CAAC,KAAK,CAAyB,QAAQ,EAAE,MAAM,CAAC,CAAC"}
+{"version":3,"file":"sample.js","sourceRoot":"","sources":["../../../src/omics/models/sample.ts"],"names":[],"mappings":";;;;;;AAAA,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,MAAM,CAAC,OAAO,CAAC,KAAK,GAAG,CAAC,KAAkB,EAAE,EAAE;IAC5C,OAAO,IAAI,cAAM,CAAC,KAAK,CAAC,CAAC;AAC3B,CAAC,CAAC;AAEF,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;AAExD,QAAA,MAAM,GAAG,kBAAQ,CAAC,KAAK,CAAyB,QAAQ,EAAE,MAAM,CAAC,CAAC;AAE/E,eAAe"}

package/build/omics/models/variant.d.ts.map

@@ -1 +1 @@
-{"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;AA4CD,eAAO,MAAM,OAAO,cAA8D,CAAC"}
+{"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,eAAO,MAAM,OAAO,cAA8D,CAAC"}

package/build/omics/models/variant.js

@@ -12,12 +12,13 @@ const AnnotationSchema = new mongoose_1.default.Schema({
     transcript: { type: String },
     hgvsc: { type: String },
     hgvsp: { type: String },
+    hgvspShort: { type: String },
     proteinPosition: { type: String },
     codons: { type: String },
     exon: { type: String }
 }, { _id: false });
 const schema = new mongoose_1.default.Schema({
-    variantId: { type: String, required: true, unique: true },
+    variantId: { type: String, required: true },
     chrom: { type: String },
     pos: { type: Number },
     ref: { type: String },
@@ -36,6 +37,9 @@ const schema = new mongoose_1.default.Schema({
         },
     },
 });
+schema.index({ variantId: 1 }, { name: 'variantid_uidx', unique: true });
+schema.index({ chrom: 1, pos: 1 }, { name: 'chrom_pos_idx' });
+schema.index({ 'annotations.gene': 1 }, { name: 'annotation_gene_idx' });
 schema.set('versionKey', 'version');
 schema.plugin(mongoose_update_if_current_1.updateIfCurrentPlugin);
 schema.statics.build = (attrs) => {

package/build/omics/models/variant.js.map

@@ -1 +1 @@
-{"version":3,"file":"variant.js","sourceRoot":"","sources":["../../../src/omics/models/variant.ts"],"names":[],"mappings":";;;;;;AAAA,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,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,MAAM,EAAE,IAAI,EAAE;IAC9D,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,GAAG,CAAC,YAAY,EAAE,SAAS,CAAC,CAAC;AACpC,MAAM,CAAC,MAAM,CAAC,kDAAqB,CAAC,CAAC;AAErC,MAAM,CAAC,OAAO,CAAC,KAAK,GAAG,CAAC,KAAmB,EAAE,EAAE;IAC7C,OAAO,IAAI,eAAO,CAAC,KAAK,CAAC,CAAC;AAC5B,CAAC,CAAC;AAEW,QAAA,OAAO,GAAG,kBAAQ,CAAC,KAAK,CAA2B,SAAS,EAAE,MAAM,CAAC,CAAC"}
+{"version":3,"file":"variant.js","sourceRoot":"","sources":["../../../src/omics/models/variant.ts"],"names":[],"mappings":";;;;;;AAAA,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,MAAM,CAAC,OAAO,CAAC,KAAK,GAAG,CAAC,KAAmB,EAAE,EAAE;IAC7C,OAAO,IAAI,eAAO,CAAC,KAAK,CAAC,CAAC;AAC5B,CAAC,CAAC;AAEW,QAAA,OAAO,GAAG,kBAAQ,CAAC,KAAK,CAA2B,SAAS,EAAE,MAAM,CAAC,CAAC"}

package/build/omics/services/index.d.ts

@@ -0,0 +1,2 @@
+export * from './tsv-parser';
+//# sourceMappingURL=index.d.ts.map

package/build/omics/services/index.d.ts.map

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

package/build/omics/services/index.js

@@ -0,0 +1,18 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __exportStar = (this && this.__exportStar) || function(m, exports) {
+    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+__exportStar(require("./tsv-parser"), exports);
+//# sourceMappingURL=index.js.map

package/build/omics/services/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/omics/services/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;AAAA,+CAA6B"}

package/build/omics/services/tsv-parser.d.ts

@@ -0,0 +1,51 @@
+import { GenotypeAttrs } from '../models/genotype';
+import { SampleAttrs } from '../models/sample';
+import { VariantAttrs } from '../models/variant';
+export declare class TSVParser {
+    private readonly variantOps;
+    private readonly sampleOps;
+    private readonly genotypeOps;
+    private readonly bulkSize;
+    constructor(bulkSize?: number);
+    /**
+     *
+     * @param file
+     */
+    parse(file: string): Promise<void>;
+    /**
+     *
+     * @param row
+     */
+    parseRow(row: any): Promise<void>;
+    /**
+     *
+     */
+    checkBulkSize(): Promise<void>;
+    /**
+     *
+     * @param vaf
+     * @returns
+     */
+    computeGT(vaf?: number): string | undefined;
+    /**
+     *
+     * @param altReads
+     * @param refReads
+     * @returns
+     */
+    computeVAF(altReads: number, refReads: number): {
+        dp?: number;
+        vaf?: number;
+    };
+    /**
+     *
+     * @param row
+     * @returns
+     */
+    mapRowToDocument(row: Record<string, string>): {
+        variant: VariantAttrs;
+        sample: SampleAttrs;
+        genotype: GenotypeAttrs;
+    };
+}
+//# sourceMappingURL=tsv-parser.d.ts.map

package/build/omics/services/tsv-parser.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"tsv-parser.d.ts","sourceRoot":"","sources":["../../../src/omics/services/tsv-parser.ts"],"names":[],"mappings":"AAKA,OAAO,EAAY,aAAa,EAAE,MAAoB,oBAAoB,CAAC;AAC3E,OAAO,EAAU,WAAW,EAAE,MAAwB,kBAAkB,CAAC;AACzE,OAAO,EAAW,YAAY,EAAE,MAAsB,mBAAmB,CAAC;AAI1E,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,QAAQ,CAAY;gBAEzB,QAAQ,GAAE,MAAa;IAKnC;;;OAGG;IACG,KAAK,CAAC,IAAI,EAAE,MAAM;IAyBxB;;;OAGG;IACG,QAAQ,CAAC,GAAG,EAAE,GAAG;IAgCvB;;OAEG;IACG,aAAa;IAcnB;;;;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"}

package/build/omics/services/tsv-parser.js

@@ -0,0 +1,187 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.TSVParser = void 0;
+const node_fs_1 = __importDefault(require("node:fs"));
+const node_readline_1 = __importDefault(require("node:readline"));
+const genotype_1 = require("../models/genotype");
+const sample_1 = require("../models/sample");
+const variant_1 = require("../models/variant");
+const tsvfile_1 = require("../enums/tsvfile");
+const utils_1 = require("../utils");
+class TSVParser {
+    constructor(bulkSize = 5000) {
+        this.variantOps = [];
+        this.sampleOps = [];
+        this.genotypeOps = [];
+        this.bulkSize = bulkSize;
+    }
+    /**
+     *
+     * @param file
+     */
+    async parse(file) {
+        const stream = node_fs_1.default.createReadStream(file);
+        const rl = node_readline_1.default.createInterface({ input: stream });
+        let header = [];
+        for await (const line of rl) {
+            if (!header.length) {
+                header = line.split('\t');
+                continue;
+            }
+            const values = line.split('\t');
+            const row = {};
+            header.forEach((h, i) => row[h] = values[i]);
+            await this.parseRow(row);
+            await this.checkBulkSize();
+        }
+    }
+    /**
+     *
+     * @param row
+     */
+    async parseRow(row) {
+        const { variant, sample, genotype } = this.mapRowToDocument(row);
+        this.variantOps.push({
+            updateOne: {
+                filter: { variantId: variant.variantId },
+                update: { $setOnInsert: variant },
+                upsert: true
+            }
+        });
+        this.sampleOps.push({
+            updateOne: {
+                filter: { sampleId: sample.sampleId },
+                update: { $setOnInsert: sample },
+                upsert: true
+            }
+        });
+        this.genotypeOps.push({
+            updateOne: {
+                filter: {
+                    variantId: genotype.variantId,
+                    sampleId: genotype.sampleId
+                },
+                update: { $set: genotype },
+                upsert: true
+            }
+        });
+    }
+    /**
+     *
+     */
+    async checkBulkSize() {
+        if (this.variantOps.length >= this.bulkSize) {
+            await variant_1.Variant.bulkWrite(this.variantOps);
+            await sample_1.Sample.bulkWrite(this.sampleOps);
+            await genotype_1.Genotype.bulkWrite(this.genotypeOps);
+            this.variantOps.length = 0;
+            this.sampleOps.length = 0;
+            this.genotypeOps.length = 0;
+        }
+    }
+    /**
+     *
+     * @param vaf
+     * @returns
+     */
+    computeGT(vaf) {
+        if (vaf === undefined)
+            return undefined;
+        if (vaf < 0.2)
+            return '0/0';
+        if (vaf < 0.8)
+            return '0/1';
+        return '1/1';
+    }
+    /**
+     *
+     * @param altReads
+     * @param refReads
+     * @returns
+     */
+    computeVAF(altReads, refReads) {
+        let vaf;
+        let dp;
+        if (!Number.isNaN(altReads) && !Number.isNaN(refReads)) {
+            dp = altReads + refReads;
+            if (dp > 0)
+                vaf = altReads / dp;
+        }
+        return { vaf, dp };
+    }
+    /**
+     *
+     * @param row
+     * @returns
+     */
+    mapRowToDocument(row) {
+        const chrom = row[tsvfile_1.TSVColumns.chromosome];
+        const pos = Number(row[tsvfile_1.TSVColumns.posistion]);
+        const ref = row[tsvfile_1.TSVColumns.referenceAllele];
+        const allele1 = row[tsvfile_1.TSVColumns.allele1];
+        const allele2 = row[tsvfile_1.TSVColumns.allele2];
+        const gene = row[tsvfile_1.TSVColumns.gene];
+        if (!chrom || !pos || !ref || !allele2)
+            throw new Error('Invalid variant row');
+        const variantId = (0, utils_1.computeVariantId)(chrom, pos, ref, allele2);
+        const sampleId = row[tsvfile_1.TSVColumns.sampleId];
+        const sequencingSampleId = (0, utils_1.extractSequencingId)(sampleId);
+        if (!sampleId)
+            throw new Error('Missing sample ID');
+        // const altReads    = Number(row['t_alt_count']);
+        // const refReads    = Number(row['t_ref_count']);
+        // const { dp, vaf } = this.computeVAF(altReads, refReads);
+        const vaf = Number.parseFloat(row[tsvfile_1.TSVColumns.vaf]);
+        const dp = Number.parseInt(row[tsvfile_1.TSVColumns.dp]);
+        const gt = this.computeGT(vaf);
+        const variant = {
+            variantId,
+            chrom,
+            pos,
+            ref,
+            alt: [allele2],
+            type: row[tsvfile_1.TSVColumns.variantType],
+            classification: row[tsvfile_1.TSVColumns.variantClassification],
+            annotations: {
+                gene,
+                consequence: row[tsvfile_1.TSVColumns.consequence],
+                transcript: row[tsvfile_1.TSVColumns.transcriptId],
+                hgvsc: row[tsvfile_1.TSVColumns.hgvsc],
+                hgvsp: row[tsvfile_1.TSVColumns.hgvsp],
+                hgvspShort: row[tsvfile_1.TSVColumns.hgvspShort],
+                proteinPosition: row[tsvfile_1.TSVColumns.proteinPosition],
+                codons: row[tsvfile_1.TSVColumns.codons],
+                exon: row[tsvfile_1.TSVColumns.exonNumber]
+            }
+        };
+        const sample = {
+            sampleId,
+            sequencingSampleId,
+            clinical: {
+                diagnosis: row[tsvfile_1.TSVColumns.diagnosis],
+                snomedM: row[tsvfile_1.TSVColumns.snomedM],
+                snomedT: row[tsvfile_1.TSVColumns.snomedT],
+                tumorSite: row[tsvfile_1.TSVColumns.tumorSite]
+            }
+        };
+        const genotype = {
+            variantId,
+            sampleId,
+            sequencingSampleId,
+            alleles: [allele1, allele2],
+            VAF: vaf,
+            DP: dp,
+            GT: gt
+        };
+        return {
+            variant,
+            sample,
+            genotype
+        };
+    }
+}
+exports.TSVParser = TSVParser;
+//# sourceMappingURL=tsv-parser.js.map

package/build/omics/services/tsv-parser.js.map

@@ -0,0 +1 @@
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package/build/omics/types/genotype.d.ts

@@ -2,10 +2,10 @@ import { BaseDBItem } from '../../types';
 export interface IGenotype extends BaseDBItem {
     variantId: string;
     sampleId: string;
-    sequencingSampleId: string;
-    GT: string;
-    VAF: number;
-    DP: number;
+    sequencingSampleId?: string;
+    GT?: string;
+    VAF?: number;
+    DP?: number;
     alleles: string[];
 }
 //# sourceMappingURL=genotype.d.ts.map

package/build/omics/types/genotype.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"genotype.d.ts","sourceRoot":"","sources":["../../../src/omics/types/genotype.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,aAAa,CAAA;AAExC,MAAM,WAAW,SAAU,SAAQ,UAAU;IAC3C,SAAS,EAAW,MAAM,CAAC;IAC3B,QAAQ,EAAY,MAAM,CAAC;IAC3B,kBAAkB,EAAE,MAAM,CAAC;IAC3B,EAAE,EAAkB,MAAM,CAAC;IAC3B,GAAG,EAAiB,MAAM,CAAC;IAC3B,EAAE,EAAkB,MAAM,CAAC;IAC3B,OAAO,EAAa,MAAM,EAAE,CAAC;CAC9B"}
+{"version":3,"file":"genotype.d.ts","sourceRoot":"","sources":["../../../src/omics/types/genotype.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,aAAa,CAAA;AAExC,MAAM,WAAW,SAAU,SAAQ,UAAU;IAC3C,SAAS,EAAY,MAAM,CAAC;IAC5B,QAAQ,EAAa,MAAM,CAAC;IAC5B,kBAAkB,CAAC,EAAE,MAAM,CAAC;IAC5B,EAAE,CAAC,EAAkB,MAAM,CAAC;IAC5B,GAAG,CAAC,EAAiB,MAAM,CAAC;IAC5B,EAAE,CAAC,EAAkB,MAAM,CAAC;IAC5B,OAAO,EAAc,MAAM,EAAE,CAAC;CAC/B"}

package/build/omics/types/sample.d.ts

@@ -1,7 +1,7 @@
 import { BaseDBItem } from '../../types';
 export interface ISample extends BaseDBItem {
-    biobankSampleId: string;
-    sequencingSampleId: string;
+    sampleId: string;
+    sequencingSampleId?: string;
     clinical: SampleClinicalData;
 }
 export interface SampleClinicalData {

package/build/omics/types/sample.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"sample.d.ts","sourceRoot":"","sources":["../../../src/omics/types/sample.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,aAAa,CAAA;AAExC,MAAM,WAAW,OAAQ,SAAQ,UAAU;IACzC,eAAe,EAAK,MAAM,CAAC;IAC3B,kBAAkB,EAAE,MAAM,CAAC;IAC3B,QAAQ,EAAY,kBAAkB,CAAC;CACxC;AAED,MAAM,WAAW,kBAAkB;IACjC,SAAS,EAAE,MAAM,CAAC;IAClB,OAAO,EAAI,MAAM,CAAC;IAClB,OAAO,EAAI,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;CACnB"}
+{"version":3,"file":"sample.d.ts","sourceRoot":"","sources":["../../../src/omics/types/sample.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,aAAa,CAAA;AAExC,MAAM,WAAW,OAAQ,SAAQ,UAAU;IACzC,QAAQ,EAAa,MAAM,CAAC;IAC5B,kBAAkB,CAAC,EAAE,MAAM,CAAC;IAC5B,QAAQ,EAAa,kBAAkB,CAAC;CACzC;AAED,MAAM,WAAW,kBAAkB;IACjC,SAAS,EAAE,MAAM,CAAC;IAClB,OAAO,EAAI,MAAM,CAAC;IAClB,OAAO,EAAI,MAAM,CAAC;IAClB,SAAS,EAAE,MAAM,CAAC;CACnB"}

package/build/omics/types/variant.d.ts

@@ -15,6 +15,7 @@ export interface VariantAnnotation {
     transcript: string;
     hgvsc: string;
     hgvsp: string;
+    hgvspShort: string;
     proteinPosition: string;
     codons: string;
     exon: string;

package/build/omics/types/variant.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"variant.d.ts","sourceRoot":"","sources":["../../../src/omics/types/variant.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,aAAa,CAAA;AAExC,MAAM,WAAW,QAAS,SAAQ,UAAU;IAC1C,SAAS,EAAO,MAAM,CAAC;IACvB,KAAK,EAAW,MAAM,CAAC;IACvB,GAAG,EAAa,MAAM,CAAC;IACvB,GAAG,EAAa,MAAM,CAAC;IACvB,GAAG,EAAa,MAAM,EAAE,CAAC;IACzB,IAAI,EAAY,MAAM,CAAC;IACvB,cAAc,EAAE,MAAM,CAAC;IACvB,WAAW,EAAK,iBAAiB,CAAC;CACnC;AAED,MAAM,WAAW,iBAAiB;IAChC,IAAI,EAAa,MAAM,CAAC;IACxB,WAAW,EAAM,MAAM,CAAC;IACxB,UAAU,EAAO,MAAM,CAAC;IACxB,KAAK,EAAY,MAAM,CAAC;IACxB,KAAK,EAAY,MAAM,CAAC;IACxB,eAAe,EAAE,MAAM,CAAC;IACxB,MAAM,EAAW,MAAM,CAAC;IACxB,IAAI,EAAa,MAAM,CAAC;CACzB"}
+{"version":3,"file":"variant.d.ts","sourceRoot":"","sources":["../../../src/omics/types/variant.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,aAAa,CAAA;AAExC,MAAM,WAAW,QAAS,SAAQ,UAAU;IAC1C,SAAS,EAAO,MAAM,CAAC;IACvB,KAAK,EAAW,MAAM,CAAC;IACvB,GAAG,EAAa,MAAM,CAAC;IACvB,GAAG,EAAa,MAAM,CAAC;IACvB,GAAG,EAAa,MAAM,EAAE,CAAC;IACzB,IAAI,EAAY,MAAM,CAAC;IACvB,cAAc,EAAE,MAAM,CAAC;IACvB,WAAW,EAAK,iBAAiB,CAAC;CACnC;AAED,MAAM,WAAW,iBAAiB;IAChC,IAAI,EAAa,MAAM,CAAC;IACxB,WAAW,EAAM,MAAM,CAAC;IACxB,UAAU,EAAO,MAAM,CAAC;IACxB,KAAK,EAAY,MAAM,CAAC;IACxB,KAAK,EAAY,MAAM,CAAC;IACxB,UAAU,EAAO,MAAM,CAAC;IACxB,eAAe,EAAE,MAAM,CAAC;IACxB,MAAM,EAAW,MAAM,CAAC;IACxB,IAAI,EAAa,MAAM,CAAC;CACzB"}

package/build/omics/utils.d.ts

@@ -0,0 +1,3 @@
+export declare function extractSequencingId(sampleId: string): string | undefined;
+export declare function computeVariantId(chr: string, pos: number, ref: string, alt: string): string;
+//# sourceMappingURL=utils.d.ts.map

package/build/omics/utils.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"utils.d.ts","sourceRoot":"","sources":["../../src/omics/utils.ts"],"names":[],"mappings":"AAAA,wBAAgB,mBAAmB,CAAC,QAAQ,EAAE,MAAM,sBAOnD;AAED,wBAAgB,gBAAgB,CAAC,GAAG,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,EAAE,GAAG,EAAE,MAAM,UAGlF"}

package/build/omics/utils.js

@@ -0,0 +1,14 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.extractSequencingId = extractSequencingId;
+exports.computeVariantId = computeVariantId;
+function extractSequencingId(sampleId) {
+    const match = sampleId.match(/BB[0-9]+-(.*)/);
+    if (!match)
+        return;
+    return match[1];
+}
+function computeVariantId(chr, pos, ref, alt) {
+    return `${chr}-${pos}-${ref}-${alt}`;
+}
+//# sourceMappingURL=utils.js.map

package/build/omics/utils.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"utils.js","sourceRoot":"","sources":["../../src/omics/utils.ts"],"names":[],"mappings":";;AAAA,kDAOC;AAED,4CAGC;AAZD,SAAgB,mBAAmB,CAAC,QAAgB;IAElD,MAAM,KAAK,GAAG,QAAQ,CAAC,KAAK,CAAC,eAAe,CAAC,CAAC;IAE9C,IAAI,CAAC,KAAK;QACR,OAAO;IACT,OAAO,KAAK,CAAC,CAAC,CAAC,CAAC;AAClB,CAAC;AAED,SAAgB,gBAAgB,CAAC,GAAW,EAAE,GAAW,EAAE,GAAW,EAAE,GAAW;IAEjF,OAAO,GAAG,GAAG,IAAI,GAAG,IAAI,GAAG,IAAI,GAAG,EAAE,CAAC;AACvC,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@nextage/omics-lib",
-  "version": "1.0.7",
+  "version": "1.0.10",
   "main": "./build/index.js",
   "types": "./build/index.d.ts",
   "files": [