<commit_before>syntax = "proto3";

option java_package = "org.monarchinitiative.exomiser.core.proto";
option java_outer_classname = "AlleleProto";
//option java_multiple_files = true;

message AlleleKey {
    int32 chr = 1;
    int32 position = 2;
    string ref = 3;
    string alt = 4;
}

message AlleleProperties {
    string rs_id = 1;
    map<string, float> properties = 2;
}<commit_msg>Add AlleleProto.ClinVar to allele.proto<commit_after>syntax = "proto3";

option java_package = "org.monarchinitiative.exomiser.core.proto";
option java_outer_classname = "AlleleProto";
//option java_multiple_files = true;

message AlleleKey {
    int32 chr = 1;
    int32 position = 2;
    string ref = 3;
    string alt = 4;
}

message AlleleProperties {
    string rs_id = 1;
    map<string, float> properties = 2;
    ClinVar clinVar = 3;

    message ClinVar {
        enum ClinSig {
            //default
            NOT_PROVIDED = 0;
            // ACMG/AMP-based
            BENIGN = 1;
            BENIGN_OR_LIKELY_BENIGN = 2;
            LIKELY_BENIGN = 3;
            UNCERTAIN_SIGNIFICANCE = 4;
            LIKELY_PATHOGENIC = 5;
            PATHOGENIC_OR_LIKELY_PATHOGENIC = 6;
            PATHOGENIC = 7;
            CONFLICTING_PATHOGENICITY_INTERPRETATIONS = 8;
            //Non-ACMG-based
            AFFECTS = 9;
            ASSOCIATION = 10;
            DRUG_RESPONSE = 11;
            OTHER = 12;
            PROTECTIVE = 13;
            RISK_FACTOR = 14;
        }

        string alleleId = 1;
        ClinSig primaryInterpretation = 2;
        repeated ClinSig secondaryInterpretations = 3;
        string reviewStatus = 4;
        map<string, ClinSig> includedAlleles = 5;
    }
}
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