Ah yes, you’re right it should be only in the summary

From: forus [mailto:notifications@github.com]
Sent: maandag 10 maart 2014 12:04
To: thehyve/transmart-core-db
Cc: Jan Hudecek
Subject: Re: [transmart-core-db] Vcf implementation (#20)


In grails-app/domain/org/transmartproject/db/dataquery/highdim/vcf/DeVariantSubjectDetailCoreDb.groovy:

> +    String chr

> +    Long pos

> +    String rsId

> +    String ref

> +    String alt

> +    String quality

> +    String filter

> +    String info

> +    String format

> +    String variant

> +

> +    Map<String, String> additionalInfo

> +    List<String> alternativeAlleles

> +

> +    static belongsTo = [dataset: DeVariantDatasetCoreDb,

> +            assay:  DeSubjectSampleMapping]          //TODO: implement constraint on dataset

I do not understand the gorm mapping between DeVariantSubjectDetailCoreDb and DeSubjectSampleMapping. Do you have assay_id column in de_variant_subject_detail table? I have not found any notion of such column in perl scripts which are used for data upload (https://github.com/j-hudecek/tranSMART-ETL/tree/master/Postgres/GPL%201.0/VCF).

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