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feat: message members explicitely optional for protobufs #431

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Aug 6, 2024
Merged

feat: message members explicitely optional for protobufs #431

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34 changes: 17 additions & 17 deletions protos/varfish/v1/seqvars/output.proto
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Original file line number Diff line number Diff line change
Expand Up @@ -15,13 +15,13 @@ message OutputHeader {
// Versions for each used database or software.
repeated VersionEntry versions = 2;
// The used query settings.
varfish.v1.seqvars.query.CaseQuery query = 3;
optional varfish.v1.seqvars.query.CaseQuery query = 3;
// Case UUID.
string case_uuid = 4;
// Resources used.
ResourcesUsed resources = 5;
optional ResourcesUsed resources = 5;
// Statistics about results.
OutputStatistics statistics = 6;
optional OutputStatistics statistics = 6;
// Information about the variant scores in the output.
repeated VariantScoreColumn variant_score_columns = 7;
}
Expand Down Expand Up @@ -69,9 +69,9 @@ message VersionEntry {
// Query resource requirements.
message ResourcesUsed {
// Start time.
google.protobuf.Timestamp start_time = 1;
optional google.protobuf.Timestamp start_time = 1;
// End time.
google.protobuf.Timestamp end_time = 2;
optional google.protobuf.Timestamp end_time = 2;
// RAM usage in bytes.
uint64 memory_used = 3;
}
Expand Down Expand Up @@ -101,9 +101,9 @@ message OutputRecord {
// Case UUID.
string case_uuid = 2;
// The description.
VcfVariant vcf_variant = 3;
optional VcfVariant vcf_variant = 3;
// The variant annotation payload.
VariantAnnotation variant_annotation = 4;
optional VariantAnnotation variant_annotation = 4;
}

// Store a sequnce variant in VCF representation.
Expand All @@ -125,11 +125,11 @@ message VcfVariant {
// Store the variant annotation payload (always for a single gene).
message VariantAnnotation {
// Gene-related annotation.
GeneRelatedAnnotation gene = 1;
optional GeneRelatedAnnotation gene = 1;
// Variant-related annotation.
VariantRelatedAnnotation variant = 2;
optional VariantRelatedAnnotation variant = 2;
// Call-related annotation.
CallRelatedAnnotation call = 3;
optional CallRelatedAnnotation call = 3;
}

/*
Expand All @@ -139,7 +139,7 @@ message VariantAnnotation {
// Store gene-related annotation (always for a single gene).
message GeneRelatedAnnotation {
// Gene ID information.
GeneIdentity identity = 1;
optional GeneIdentity identity = 1;
// Gene-related consequences, if any (none if intergenic).
optional GeneRelatedConsequences consequences = 2;
// Gene-related phenotype information, if any.
Expand Down Expand Up @@ -277,15 +277,15 @@ message VariantRelatedAnnotation {
// Population frequency information.
message FrequencyAnnotation {
// gnomAD-exomes filter
NuclearFrequency gnomad_exomes = 1;
optional NuclearFrequency gnomad_exomes = 1;
// gnomAD-genomes filter
NuclearFrequency gnomad_genomes = 2;
optional NuclearFrequency gnomad_genomes = 2;
// gnomAD-MT filter
GnomadMitochondrialFrequency gnomad_mtdna = 3;
optional GnomadMitochondrialFrequency gnomad_mtdna = 3;
// HelixMtDb filter
HelixMtDbFrequency helixmtdb = 4;
optional HelixMtDbFrequency helixmtdb = 4;
// In-house filter
NuclearFrequency inhouse = 5;
optional NuclearFrequency inhouse = 5;
}

// gnomAD and in-house frequency information.
Expand Down Expand Up @@ -379,7 +379,7 @@ message ScoreEntry {
// Key.
string key = 1;
// Value.
google.protobuf.Value value = 2;
optional google.protobuf.Value value = 2;
}

/*
Expand Down
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