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@namespace("org.gel.models.report.avro")
/**
This protocol defines the Commons for GEL models
*/
protocol CommonRequest {

    /*
Types of files:

* `BAM`: alignment
* `gVCF`: genomic VCF for variants
* `VCF_small`: VCF file for SNV and indel
* `VCF_somatic_small`: VCF file for somatic SNV and indel
* `VCF_CNV`: VCF file for copy number variants
* `VCF_somatic_CNV`: VCF file somatic for copy number variants
* `VCF_SV`: VCF file for structural variants only
* `VCF_somatic_SV`: VCF file for somatic structural variants only
* `VCF_SV_CNV`: VCF file for CNV and SVs
* `SVG`: an SVG for example of a pedigree
* `ANN`: a Json File for the annotation file from openCBschema/IDLs/variantAnnotation.avdl
* `BigWig`: a bigwig file with the genome coverage
* `MD5Sum`: a MD5Sum file
* `ROH`: a BED file with Regions of homozygosity
* `OTHER`: other unspecified file type
* `PARTITION`: Canvas output of coverage in high density areas
* `VARIANT_FREQUENCIES`: b-allele frequencies
* `COVERAGE`: whole genome coverage metrics in JSON format
    **/
    enum FileType {
        BAM,
        gVCF,
        VCF_small,
        VCF_somatic_small,
        VCF_CNV,
        VCF_somatic_CNV,
        VCF_SV,
        VCF_somatic_SV,
        VCF_SV_CNV,
        SVG,
        ANN,
        BigWig,
        MD5Sum,
        ROH,
        OTHER,
        PARTITION,
        VARIANT_FREQUENCIES,
        COVERAGE
        }

    /**
    This defines a file
    This record is uniquely defined by the sample identfier and an URI
    Currently sample identifier can be a single string or a list of strings if multiple samples are associated with the same file
    **/
    record File {
        /**
        Unique identifier(s) of the sample. For example in a multisample vcf this would have an array of all the sample identifiers
        */
        union {null, array} sampleId;

        /**
        URI path of the file
        */
        string uriFile;

        /**
        The type of the file
        */
        FileType fileType;

        /**
        The MD5 checksum
        */
        union {null, string} md5Sum;

    }

    /**
    Family history for secondary findings.
    Arrays of strings describing discrete family history phenotypes.
    Usually: `EndocrineTumours`, `colorectal`, `BreastOvarian` and `HDOrStroke` but can be others
    */
    record OtherFamilyHistory {
        /**
        Relevant Maternal family history
        */
        union {null, array} maternalFamilyHistory;
        /**
        Relevant Maternal family history
        */
        union {null, array} paternalFamilyHistory;
    }

    /**
    The Genomics England program
    */
    enum Program {
        cancer,
        rare_disease
    }

    /**
    Some flags relevant to the interpretation of a case
    */
    enum InterpretationFlags {
        mixed_chemistries,
        mixedLab_preparation,
        low_tumour_purity,
        uniparental_isodisomy,
        uniparental_heterodisomy,
        unusual_karyotype,
        high_cnv_count,
        high_estimate_human_contamination_fraction,
        mixed_recruiting_gmc,
        suspected_mosaicism,
        low_quality_sample,
        ffpe_tumour_sample,
        ff_nano_tumour_sample,
        missing_values_for_proband_in_reported_variant,
        reissued,
        supplementary_report_errors,
        internal_use_only,
        high_priority,
        suspected_increased_number_of_false_positive_heterozygous_loss_calls,
        suspected_poor_quality_cnv_calls,
        cnv_calls_assumed_xx_karyo,
        cnv_calls_assumed_xy_karyo,
        other
    }

    /**
    A given interpretation flag together with an optional description
    */
    record InterpretationFlag{
        /**
        The interpretation flag
        */
        InterpretationFlags  interpretationFlag;
        /**
        The description for the flag
        */
        union {null, string} additionalDescription;
    }

    /**
    Interpretation flags at the participant level
    */
    record ParticipantInterpretationFlags{
        /**
        The interpretation flag
        */
        InterpretationFlags  interpretationFlag;
        /**
        The description for the flag
        */
        union {null, string} additionalDescription;
        /**
        Sample Id fron which this flag was reported
        */
        string SampleId;
        /**
        Participant Id as appeared in the pedigree
        */
        union {null, string} participantId;

    }


}