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feat: adding more protobuf files and generated code (#49)
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| Original file line number | Diff line number | Diff line change |
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| syntax = "proto3"; | ||
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| package annonars.cons.base; | ||
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| // List of `Record`s. | ||
| message RecordList { | ||
| // The records in the list. | ||
| repeated Record records = 1; | ||
| } | ||
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| // Protocol buffer for the UCSC conservation record. | ||
| message Record { | ||
| // Chromosome name. | ||
| string chrom = 1; | ||
| // 1-based, inclusive start position. | ||
| int32 start = 2; | ||
| // 1-based, inclusive stop position. | ||
| int32 stop = 3; | ||
| // HGNC identifier. | ||
| string hgnc_id = 4; | ||
| // ENST identifier. | ||
| string enst_id = 5; | ||
| // Exon number (1-based). | ||
| int32 exon_num = 6; | ||
| // Exon count. | ||
| int32 exon_count = 7; | ||
| // Alignment. | ||
| string alignment = 8; | ||
| } |
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| syntax = "proto3"; | ||
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| package annonars.dbsnp.base; | ||
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| // Protocol buffer for the dbSNP VCF record. | ||
| message Record { | ||
| // Chromosome name. | ||
| string chrom = 1; | ||
| // 1-based start position. | ||
| int32 pos = 2; | ||
| // Reference allele. | ||
| string ref_allele = 3; | ||
| /// Alternate allele. | ||
| string alt_allele = 4; | ||
| /// The rs ID. | ||
| int32 rs_id = 5; | ||
| } |
Empty file.
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| Original file line number | Diff line number | Diff line change |
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| // Protocolbuffers definition for RefSeq functional elements. | ||
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| syntax = "proto3"; | ||
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| package annonars.functional.refseq; | ||
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| // Enumeration for `gbkey` field. | ||
| enum Category { | ||
| // unknown | ||
| CATEGORY_UNKNOWN = 0; | ||
| // Miscaellaneous feature. | ||
| CATEGORY_MISC_FEATURE = 1; | ||
| // Miscaellaneous recombination feature. | ||
| CATEGORY_MISC_RECOMB = 2; | ||
| // Miscaellaneous structure. | ||
| CATEGORY_MISC_STRUCTURE = 3; | ||
| // Mobile element. | ||
| CATEGORY_MOBILE_ELEMENT = 4; | ||
| // Protein binding annotation. | ||
| CATEGORY_PROTEIN_BIND = 5; | ||
| // Region. | ||
| CATEGORY_REGION = 6; | ||
| // Regulatory element. | ||
| CATEGORY_REGULATORY = 7; | ||
| // Repeat region | ||
| CATEGORY_REPEAT_REGION = 8; | ||
| // Replication origin. | ||
| CATEGORY_REP_ORIGIN = 9; | ||
| } | ||
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| // Enumeration for `regulatory_class` field. | ||
| enum RegulatoryClass { | ||
| // unknown | ||
| REGULATORY_UNKNOWN = 0; | ||
| // CCAAT signal. | ||
| REGULATORY_CLASS_CAAT_SIGNAL = 1; | ||
| // DNase I hypersensitive site. | ||
| REGULATORY_CLASS_DNASE_I_HYPERSENSITIVE_SITE = 2; | ||
| // Enhancer. | ||
| REGULATORY_CLASS_ENHANCER = 3; | ||
| // Enhancer blocking element. | ||
| REGULATORY_CLASS_ENHANCER_BLOCKING_ELEMENT = 4; | ||
| // Epigenetically modified region. | ||
| REGULATORY_CLASS_EPIGENETICALLY_MODIFIED_REGION = 5; | ||
| // GC signal. | ||
| REGULATORY_CLASS_GC_SIGNAL = 6; | ||
| // Imprinting control region. | ||
| REGULATORY_CLASS_IMPRINTING_CONTROL_REGION = 7; | ||
| // Insulator. | ||
| REGULATORY_CLASS_INSULATOR = 8; | ||
| // Locus control region. | ||
| REGULATORY_CLASS_LOCUS_CONTROL_REGION = 9; | ||
| // Matrix attachment region. | ||
| REGULATORY_CLASS_MATRIX_ATTACHMENT_REGION = 10; | ||
| // Micrococcal nuclease hypersensitive site. | ||
| REGULATORY_CLASS_MICROCOCCAL_NUCLEASE_HYPERSENSITIVE_SITE = 11; | ||
| // Promoter. | ||
| REGULATORY_CLASS_PROMOTER = 12; | ||
| // Replication regulatory region. | ||
| REGULATORY_CLASS_REPLICATION_REGULATORY_REGION = 13; | ||
| // Response element. | ||
| REGULATORY_CLASS_RESPONSE_ELEMENT = 14; | ||
| // Silencer. | ||
| REGULATORY_CLASS_SILENCER = 15; | ||
| // TATA box. | ||
| REGULATORY_CLASS_TATA_BOX = 16; | ||
| // Transcriptional cis regulatory region. | ||
| REGULATORY_CLASS_TRANSCRIPTIONAL_CIS_REGULATORY_REGION = 17; | ||
| } | ||
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| // Message for storing a RefSeq regulatory element. | ||
| message Record { | ||
| // Chromosome | ||
| string chromosome = 1; | ||
| // Start position (1-based) | ||
| int32 start = 2; | ||
| // Stop position (1-based) | ||
| int32 stop = 3; | ||
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| // ID | ||
| string id = 4; | ||
| // Dbxref | ||
| string dbxref = 5; | ||
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| // Category of record. | ||
| Category category = 6; | ||
| // Regulatory class of record. | ||
| optional RegulatoryClass regulatory_class = 7; | ||
| // note | ||
| optional string note = 8; | ||
| // experiment | ||
| optional string experiment = 9; | ||
| // function | ||
| optional string function = 10; | ||
| } | ||
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| // Message for storing multiple Gbxref IDs. | ||
| message DbxrefList { | ||
| // Dbxref IDs. | ||
| repeated string dbxref = 1; | ||
| } |
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| // Protocol buffers for representing ExAC CNV data. | ||
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| syntax = "proto3"; | ||
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| package annonars.gnomad.exac_cnv; | ||
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| // Enumeration for the CNV type. | ||
| enum CnvType { | ||
| // unknown | ||
| CNV_TYPE_UNKNOWN = 0; | ||
| // Deletion. | ||
| CNV_TYPE_DEL = 1; | ||
| // Duplication. | ||
| CNV_TYPE_DUP = 2; | ||
| } | ||
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| // ExAC population. | ||
| enum Population { | ||
| // unknown | ||
| POPULATION_UNKNOWN = 0; | ||
| // African | ||
| POPULATION_AFR = 1; | ||
| // Ad Mixed American | ||
| POPULATION_AMR = 2; | ||
| // East Asian | ||
| POPULATION_EAS = 3; | ||
| // Finnish | ||
| POPULATION_FIN = 4; | ||
| // Non-Finnish European | ||
| POPULATION_NFE = 5; | ||
| // South Asian | ||
| POPULATION_SAS = 6; | ||
| // Other, | ||
| POPULATION_OTHER = 7; | ||
| } | ||
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| // Protocol buffer for the ExAC CNV data. | ||
| // | ||
| // The more specialized fields from the INFO column are stored in separate, optional fields such | ||
| // that we don't end up with a humongous message. | ||
| message Record { | ||
| // Chromosome name. | ||
| string chrom = 1; | ||
| // 1-based start position. | ||
| int32 start = 2; | ||
| // 1-based stop position. | ||
| int32 stop = 3; | ||
| /// The type of the variant. | ||
| CnvType sv_type = 4; | ||
| /// The population. | ||
| Population population = 5; | ||
| } |
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