@nextage/omics-lib 1.0.11 → 1.0.13
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/enums.d.ts
CHANGED
package/build/enums.js
CHANGED
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@@ -57,7 +57,7 @@ var FileContentTypes;
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57
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FileContentTypes["txt"] = "txt";
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FileContentTypes["xml"] = "xml";
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FileContentTypes["csv"] = "csv";
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60
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-
FileContentTypes["tsv"] = "
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60
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+
FileContentTypes["tsv"] = "tsv";
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FileContentTypes["xls"] = "xsl";
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FileContentTypes["xlsx"] = "xslx";
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})(FileContentTypes || (exports.FileContentTypes = FileContentTypes = {}));
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@@ -1 +1 @@
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1
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-
{"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;
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1
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+
{"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;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"}
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@@ -37,6 +37,7 @@ class TSVParser {
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await this.parseRow(row);
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await this.checkBulkSize();
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}
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await this.saveData();
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}
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/**
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*
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@@ -73,12 +74,23 @@ class TSVParser {
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*
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*/
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async checkBulkSize() {
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-
if (this.variantOps.length >= this.bulkSize)
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if (this.variantOps.length >= this.bulkSize)
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await this.saveData();
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}
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/**
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*
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*/
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async saveData() {
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84
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if (this.variantOps.length) {
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await variant_1.Variant.bulkWrite(this.variantOps);
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78
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-
await sample_1.Sample.bulkWrite(this.sampleOps);
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79
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-
await genotype_1.Genotype.bulkWrite(this.genotypeOps);
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this.variantOps.length = 0;
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87
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}
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if (this.sampleOps.length) {
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await sample_1.Sample.bulkWrite(this.sampleOps);
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this.sampleOps.length = 0;
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}
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if (this.genotypeOps.length) {
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await genotype_1.Genotype.bulkWrite(this.genotypeOps);
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this.genotypeOps.length = 0;
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}
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}
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"tsv-parser.js","sourceRoot":"","sources":["../../../src/omics/services/tsv-parser.ts"],"names":[],"mappings":";;;;;;AAEA,sDAAgE;AAChE,kEAAsE;AAEtE,iDAA2E;AAC3E,6CAAyE;AACzE,+CAA0E;AAC1E,8CAAyE;AACzE,oCAAiE;AAEjE,MAAa,SAAS;IAQpB,YAAY,WAAmB,IAAI;QANlB,eAAU,GAA4C,EAAE,CAAC;QACzD,cAAS,GAA6C,EAAE,CAAC;QACzD,gBAAW,GAA2C,EAAE,CAAC;QAMxE,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;IAC1B,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;
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1
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{"version":3,"file":"tsv-parser.js","sourceRoot":"","sources":["../../../src/omics/services/tsv-parser.ts"],"names":[],"mappings":";;;;;;AAEA,sDAAgE;AAChE,kEAAsE;AAEtE,iDAA2E;AAC3E,6CAAyE;AACzE,+CAA0E;AAC1E,8CAAyE;AACzE,oCAAiE;AAEjE,MAAa,SAAS;IAQpB,YAAY,WAAmB,IAAI;QANlB,eAAU,GAA4C,EAAE,CAAC;QACzD,cAAS,GAA6C,EAAE,CAAC;QACzD,gBAAW,GAA2C,EAAE,CAAC;QAMxE,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;IAC1B,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,iBAAO,CAAC,SAAS,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;YACxC,IAAI,CAAC,UAAU,CAAC,MAAM,GAAI,CAAC,CAAC;QAC9B,CAAC;QAED,IAAI,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,CAAC;YAC1B,MAAM,eAAM,CAAC,SAAS,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;YACtC,IAAI,CAAC,SAAS,CAAC,MAAM,GAAK,CAAC,CAAC;QAC9B,CAAC;QAED,IAAI,IAAI,CAAC,WAAW,CAAC,MAAM,EAAE,CAAC;YAC5B,MAAM,mBAAQ,CAAC,SAAS,CAAC,IAAI,CAAC,WAAW,CAAC,CAAA;YAC1C,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,CAAA;QAEvC,IAAI,GAAG,GAAG,GAAG;YAAE,OAAO,KAAK,CAAA;QAC3B,IAAI,GAAG,GAAG,GAAG;YAAE,OAAO,KAAK,CAAA;QAE3B,OAAO,KAAK,CAAA;IACd,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;YAC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