# GenomicsDB Protobuf Documentation
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<a name="genomicsdb_callsets_mapping-proto"></a>
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## genomicsdb_callsets_mapping.proto



<a name="-CallsetMappingPB"></a>

### CallsetMappingPB



| Field | Type | Label | Description |
| ----- | ---- | ----- | ----------- |
| callsets | [SampleIDToTileDBIDMap](#SampleIDToTileDBIDMap) | repeated |  |






<a name="-SampleIDToTileDBIDMap"></a>

### SampleIDToTileDBIDMap



| Field | Type | Label | Description |
| ----- | ---- | ----- | ----------- |
| sample_name | [string](#string) | required |  |
| row_idx | [int64](#int64) | required |  |
| idx_in_file | [int64](#int64) | required |  |
| stream_name | [string](#string) | optional |  |
| filename | [string](#string) | optional |  |





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<a name="genomicsdb_coordinates-proto"></a>
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## genomicsdb_coordinates.proto



<a name="-ContigInterval"></a>

### ContigInterval



| Field | Type | Label | Description |
| ----- | ---- | ----- | ----------- |
| contig | [string](#string) | required |  |
| begin | [int64](#int64) | optional |  |
| end | [int64](#int64) | optional |  |






<a name="-ContigPosition"></a>

### ContigPosition



| Field | Type | Label | Description |
| ----- | ---- | ----- | ----------- |
| contig | [string](#string) | required |  |
| position | [int64](#int64) | required |  |






<a name="-GenomicsDBColumn"></a>

### GenomicsDBColumn



| Field | Type | Label | Description |
| ----- | ---- | ----- | ----------- |
| tiledb_column | [int64](#int64) | optional |  |
| contig_position | [ContigPosition](#ContigPosition) | optional |  |






<a name="-GenomicsDBColumnInterval"></a>

### GenomicsDBColumnInterval



| Field | Type | Label | Description |
| ----- | ---- | ----- | ----------- |
| tiledb_column_interval | [TileDBColumnInterval](#TileDBColumnInterval) | optional |  |
| contig_interval | [ContigInterval](#ContigInterval) | optional |  |






<a name="-GenomicsDBColumnOrInterval"></a>

### GenomicsDBColumnOrInterval



| Field | Type | Label | Description |
| ----- | ---- | ----- | ----------- |
| column | [GenomicsDBColumn](#GenomicsDBColumn) | optional |  |
| column_interval | [GenomicsDBColumnInterval](#GenomicsDBColumnInterval) | optional |  |






<a name="-TileDBColumnInterval"></a>

### TileDBColumnInterval



| Field | Type | Label | Description |
| ----- | ---- | ----- | ----------- |
| begin | [int64](#int64) | required |  |
| end | [int64](#int64) | required |  |





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<a name="genomicsdb_export_config-proto"></a>
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## genomicsdb_export_config.proto



<a name="genomicsdb_pb-AnnotationSource"></a>

### AnnotationSource



| Field | Type | Label | Description |
| ----- | ---- | ----- | ----------- |
| filename | [string](#string) | required |  |
| data_source | [string](#string) | required |  |
| attributes | [string](#string) | repeated |  |
| is_vcf | [bool](#bool) | optional |  Default: true |
| file_chromosomes | [string](#string) | repeated |  |






<a name="genomicsdb_pb-ExportConfiguration"></a>

### ExportConfiguration



| Field | Type | Label | Description |
| ----- | ---- | ----- | ----------- |
| workspace | [string](#string) | required |  |
| reference_genome | [string](#string) | optional |  |
| array_name | [string](#string) | optional |  |
| generate_array_name_from_partition_bounds | [bool](#bool) | optional |  Default: true |
| query_column_ranges | [GenomicsDBColumnOrIntervalList](#genomicsdb_pb-GenomicsDBColumnOrIntervalList) | repeated | Only one of the following two fields must be defined query_contig_intervals is recommended for use |
| query_contig_intervals | [ContigInterval](#ContigInterval) | repeated |  |
| query_row_ranges | [RowRangeList](#genomicsdb_pb-RowRangeList) | repeated | Only one of the following two fields must be defined |
| query_sample_names | [string](#string) | repeated |  |
| attributes | [string](#string) | repeated |  |
| query_filter | [string](#string) | optional | QueryConfiguration - END |
| vcf_header_filename | [string](#string) | optional |  |
| vcf_output_filename | [string](#string) | optional |  |
| vcf_output_format | [string](#string) | optional |  |
| vid_mapping_file | [string](#string) | optional |  |
| vid_mapping | [VidMappingPB](#VidMappingPB) | optional |  |
| callset_mapping_file | [string](#string) | optional |  |
| callset_mapping | [CallsetMappingPB](#CallsetMappingPB) | optional |  |
| max_diploid_alt_alleles_that_can_be_genotyped | [uint32](#uint32) | optional | Other configuration |
| max_genotype_count | [uint32](#uint32) | optional |  |
| index_output_VCF | [bool](#bool) | optional |  |
| produce_GT_field | [bool](#bool) | optional |  |
| produce_FILTER_field | [bool](#bool) | optional |  |
| sites_only_query | [bool](#bool) | optional |  |
| produce_GT_with_min_PL_value_for_spanning_deletions | [bool](#bool) | optional |  |
| scan_full | [bool](#bool) | optional |  |
| segment_size | [uint32](#uint32) | optional |  Default: 10485760 |
| combined_vcf_records_buffer_size_limit | [uint32](#uint32) | optional |  |
| enable_shared_posixfs_optimizations | [bool](#bool) | optional |  Default: false |
| bypass_intersecting_intervals_phase | [bool](#bool) | optional |  Default: false |
| spark_config | [SparkConfig](#genomicsdb_pb-SparkConfig) | optional |  |
| annotation_source | [AnnotationSource](#genomicsdb_pb-AnnotationSource) | repeated |  |
| annotation_buffer_size | [uint32](#uint32) | optional |  Default: 10240 |






<a name="genomicsdb_pb-GenomicsDBColumnOrIntervalList"></a>

### GenomicsDBColumnOrIntervalList



| Field | Type | Label | Description |
| ----- | ---- | ----- | ----------- |
| column_or_interval_list | [GenomicsDBColumnOrInterval](#GenomicsDBColumnOrInterval) | repeated |  |






<a name="genomicsdb_pb-QueryConfiguration"></a>

### QueryConfiguration
Simple query configuration for GenomicsDB::query_variant_calls
for the class initialized with ExportConfiguration below


| Field | Type | Label | Description |
| ----- | ---- | ----- | ----------- |
| array_name | [string](#string) | optional |  |
| generate_array_name_from_partition_bounds | [bool](#bool) | optional |  Default: true |
| query_column_ranges | [GenomicsDBColumnOrIntervalList](#genomicsdb_pb-GenomicsDBColumnOrIntervalList) | repeated | Only one of the following two fields must be defined query_contig_intervals is recommended for use |
| query_contig_intervals | [ContigInterval](#ContigInterval) | repeated |  |
| query_row_ranges | [RowRangeList](#genomicsdb_pb-RowRangeList) | repeated | Only one of the following two fields must be defined |
| query_sample_names | [string](#string) | repeated |  |
| attributes | [string](#string) | repeated |  |
| query_filter | [string](#string) | optional |  |






<a name="genomicsdb_pb-RowRange"></a>

### RowRange



| Field | Type | Label | Description |
| ----- | ---- | ----- | ----------- |
| low | [int64](#int64) | required |  |
| high | [int64](#int64) | required |  |






<a name="genomicsdb_pb-RowRangeList"></a>

### RowRangeList



| Field | Type | Label | Description |
| ----- | ---- | ----- | ----------- |
| range_list | [RowRange](#genomicsdb_pb-RowRange) | repeated |  |






<a name="genomicsdb_pb-SparkConfig"></a>

### SparkConfig



| Field | Type | Label | Description |
| ----- | ---- | ----- | ----------- |
| query_block_size | [int64](#int64) | optional |  |
| query_block_size_margin | [int64](#int64) | optional |  |





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<a name="genomicsdb_import_config-proto"></a>
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## genomicsdb_import_config.proto



<a name="genomicsdb_pb-ImportConfiguration"></a>

### ImportConfiguration



| Field | Type | Label | Description |
| ----- | ---- | ----- | ----------- |
| size_per_column_partition | [int64](#int64) | required |  Default: 16384 |
| row_based_partitioning | [bool](#bool) | optional |  Default: false |
| produce_combined_vcf | [bool](#bool) | optional |  Default: false |
| produce_tiledb_array | [bool](#bool) | optional |  Default: true |
| column_partitions | [Partition](#genomicsdb_pb-Partition) | repeated |  |
| vid_mapping_file | [string](#string) | optional |  |
| vid_mapping | [VidMappingPB](#VidMappingPB) | optional |  |
| callset_mapping_file | [string](#string) | optional |  |
| callset_mapping | [CallsetMappingPB](#CallsetMappingPB) | optional |  |
| treat_deletions_as_intervals | [bool](#bool) | optional |  Default: true |
| num_parallel_vcf_files | [int32](#int32) | optional |  Default: 1 |
| delete_and_create_tiledb_array | [bool](#bool) | optional |  Default: false |
| do_ping_pong_buffering | [bool](#bool) | optional |  Default: true |
| offload_vcf_output_processing | [bool](#bool) | optional |  Default: true |
| discard_vcf_index | [bool](#bool) | optional |  Default: true |
| segment_size | [int64](#int64) | optional |  Default: 10485760 |
| compress_tiledb_array | [bool](#bool) | optional |  Default: true |
| num_cells_per_tile | [int64](#int64) | optional |  Default: 1000 |
| fail_if_updating | [bool](#bool) | optional |  Default: false |
| tiledb_compression_type | [int32](#int32) | optional |  Default: 1 |
| tiledb_compression_level | [int32](#int32) | optional |  Default: -1 |
| consolidate_tiledb_array_after_load | [bool](#bool) | optional |  Default: false |
| disable_synced_writes | [bool](#bool) | optional |  Default: true |
| ignore_cells_not_in_partition | [bool](#bool) | optional |  |
| lb_callset_row_idx | [int64](#int64) | optional |  Default: 0 |
| ub_callset_row_idx | [int64](#int64) | optional |  |
| enable_shared_posixfs_optimizations | [bool](#bool) | optional |  Default: false |
| disable_delta_encode_for_offsets | [bool](#bool) | optional |  Default: false |
| disable_delta_encode_for_coords | [bool](#bool) | optional |  Default: false |
| enable_bit_shuffle_gt | [bool](#bool) | optional |  Default: false |
| enable_lz4_compression_gt | [bool](#bool) | optional |  Default: false |
| reference_genome | [string](#string) | optional |  |
| vcf_header_filename | [string](#string) | optional |  |






<a name="genomicsdb_pb-Partition"></a>

### Partition



| Field | Type | Label | Description |
| ----- | ---- | ----- | ----------- |
| begin | [GenomicsDBColumn](#GenomicsDBColumn) | required |  |
| workspace | [string](#string) | optional |  |
| array_name | [string](#string) | optional |  |
| generate_array_name_from_partition_bounds | [bool](#bool) | optional |  |
| vcf_output_filename | [string](#string) | optional |  |
| vcf_header_filename | [string](#string) | optional |  |
| end | [GenomicsDBColumn](#GenomicsDBColumn) | optional |  |





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<a name="genomicsdb_vid_mapping-proto"></a>
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## genomicsdb_vid_mapping.proto



<a name="-Chromosome"></a>

### Chromosome



| Field | Type | Label | Description |
| ----- | ---- | ----- | ----------- |
| name | [string](#string) | required |  |
| length | [int64](#int64) | required |  |
| tiledb_column_offset | [int64](#int64) | required |  |






<a name="-FieldLengthDescriptorComponentPB"></a>

### FieldLengthDescriptorComponentPB



| Field | Type | Label | Description |
| ----- | ---- | ----- | ----------- |
| variable_length_descriptor | [string](#string) | optional |  |
| fixed_length | [int32](#int32) | optional |  |






<a name="-GenomicsDBFieldInfo"></a>

### GenomicsDBFieldInfo



| Field | Type | Label | Description |
| ----- | ---- | ----- | ----------- |
| name | [string](#string) | required |  |
| type | [string](#string) | repeated |  |
| vcf_field_class | [string](#string) | repeated |  |
| vcf_type | [string](#string) | optional |  |
| length | [FieldLengthDescriptorComponentPB](#FieldLengthDescriptorComponentPB) | repeated |  |
| vcf_delimiter | [string](#string) | repeated |  |
| VCF_field_combine_operation | [string](#string) | optional |  |
| vcf_name | [string](#string) | optional | useful when multiple fields of different types/length with the same name (FILTER, FORMAT, INFO) are defined in the VCF header |
| disable_remap_missing_with_non_ref | [bool](#bool) | optional |  Default: false |






<a name="-VidMappingPB"></a>

### VidMappingPB



| Field | Type | Label | Description |
| ----- | ---- | ----- | ----------- |
| fields | [GenomicsDBFieldInfo](#GenomicsDBFieldInfo) | repeated |  |
| contigs | [Chromosome](#Chromosome) | repeated |  |





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## Scalar Value Types

| .proto Type | Notes | C++ | Java | Python | Go |
| ----------- | ----- | --- | ---- | ------ | -- |
| <a name="double" /> double |  | double | double | float | float64 |
| <a name="float" /> float |  | float | float | float | float32 |
| <a name="int32" /> int32 | Uses variable-length encoding. Inefficient for encoding negative numbers – if your field is likely to have negative values, use sint32 instead. | int32 | int | int | int32 |
| <a name="int64" /> int64 | Uses variable-length encoding. Inefficient for encoding negative numbers – if your field is likely to have negative values, use sint64 instead. | int64 | long | int/long | int64 |
| <a name="uint32" /> uint32 | Uses variable-length encoding. | uint32 | int | int/long | uint32 |
| <a name="uint64" /> uint64 | Uses variable-length encoding. | uint64 | long | int/long | uint64 |
| <a name="sint32" /> sint32 | Uses variable-length encoding. Signed int value. These more efficiently encode negative numbers than regular int32s. | int32 | int | int | int32 |
| <a name="sint64" /> sint64 | Uses variable-length encoding. Signed int value. These more efficiently encode negative numbers than regular int64s. | int64 | long | int/long | int64 |
| <a name="fixed32" /> fixed32 | Always four bytes. More efficient than uint32 if values are often greater than 2^28. | uint32 | int | int | uint32 |
| <a name="fixed64" /> fixed64 | Always eight bytes. More efficient than uint64 if values are often greater than 2^56. | uint64 | long | int/long | uint64 |
| <a name="sfixed32" /> sfixed32 | Always four bytes. | int32 | int | int | int32 |
| <a name="sfixed64" /> sfixed64 | Always eight bytes. | int64 | long | int/long | int64 |
| <a name="bool" /> bool |  | bool | boolean | boolean | bool |
| <a name="string" /> string | A string must always contain UTF-8 encoded or 7-bit ASCII text. | string | String | str/unicode | string |
| <a name="bytes" /> bytes | May contain any arbitrary sequence of bytes. | string | ByteString | str | []byte |