hal-grpc-server/halBlockViz.proto at master · ComparativeGenomicsToolkit/hal-grpc-server · GitHub

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syntax = "proto3";
package hal;

service BlockViz {
    rpc GetBlocksInTargetRange (BlockRequest) returns (stream BlockResults);
    rpc GetPossibleCoalescenceLimits (Alignment) returns (stream Genome);
    rpc GetGenomes (Alignment) returns (stream Genome);
    rpc GetChroms (GenomeRequest) returns (stream Chromosome);
    rpc GetDNA (DNARequest) returns (DNAResponse);
    rpc GetMaxLODQueryLength (Alignment) returns (MaxQueryLengthResponse);
    rpc GetGenomeMetadata (GenomeRequest) returns (stream Metadata);
}

message MaxQueryLengthResponse {
    uint64 maxSize = 1;
}

message DNARequest {
    string alignmentName = 1;
    string genome = 2;
    uint64 start = 3;
    uint64 end = 4;
}

message DNAResponse {
    string dna = 1;
}

message GenomeRequest {
    string alignmentName = 1;
    string genome = 2;
}

message Alignment {
    string name = 1;
}

message BlockRequest {
    string alignmentName = 1;
    string qSpecies = 2;
    string tSpecies = 3;
    string tChrom = 4;
    uint64 tStart = 5;
    uint64 tEnd = 6;
    bool tReversed = 7;
    enum SeqMode {
        HAL_NO_SEQUENCE = 0;
        HAL_LOD0_SEQUENCE = 1;
        HAL_FORCE_LOD0_SEQUENCE = 2;
    }
    SeqMode seqMode = 8;
    enum DupMode {
        HAL_NO_DUPS = 0;
        HAL_QUERY_DUPS = 1;
        HAL_QUERY_AND_TARGET_DUPS = 2;
    }
    DupMode dupMode = 9;
    bool mapBackAdjacencies = 10;
    string coalescenceLimit = 11;
}

message BlockResults {
    repeated Block mappedBlocks = 1;
    repeated TargetDupe targetDupeBlocks = 2;
}

message Block {
    string qChrom = 1;
    uint64 tStart = 2;
    uint64 qStart = 3;
    uint64 size = 4;
    enum Strand {
        PLUS = 0;
        MINUS = 1;
    }
    Strand strand = 5;
    string qSequence = 6;
    string tSequence = 7;
}

message TargetDupe {
    uint64 id = 1;
    string qChrom = 2;
    message TargetRange {
        int64 tStart = 1;
        int64 size = 2;
    }
    repeated TargetRange tRange = 3;
}

message Genome {
    string name = 1;
    uint64 numChroms = 2;
    string parentName = 3;
    double parentBranchLength = 4;
}

message Chromosome {
    string name = 1;
    uint64 length = 2;
}

message Metadata {
    string key = 1;
    string value = 2;
}