GenomicsDB Protobuf Documentation

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genomicsdb_callsets_mapping.proto

CallsetMappingPB

Field	Type	Label	Description
callsets	SampleIDToTileDBIDMap	repeated

SampleIDToTileDBIDMap

Field	Type	Label	Description
sample_name	string	required
row_idx	int64	required
idx_in_file	int64	required
stream_name	string	optional
filename	string	optional

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genomicsdb_coordinates.proto

ContigInterval

Field	Type	Label	Description
contig	string	required
begin	int64	optional
end	int64	optional

ContigPosition

Field	Type	Label	Description
contig	string	required
position	int64	required

GenomicsDBColumn

Field	Type	Label	Description
tiledb_column	int64	optional
contig_position	ContigPosition	optional

GenomicsDBColumnInterval

Field	Type	Label	Description
tiledb_column_interval	TileDBColumnInterval	optional
contig_interval	ContigInterval	optional

GenomicsDBColumnOrInterval

Field	Type	Label	Description
column	GenomicsDBColumn	optional
column_interval	GenomicsDBColumnInterval	optional

TileDBColumnInterval

Field	Type	Label	Description
begin	int64	required
end	int64	required

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genomicsdb_export_config.proto

AnnotationSource

Field	Type	Label	Description
filename	string	required
data_source	string	required
attributes	string	repeated
is_vcf	bool	optional	Default: true
file_chromosomes	string	repeated

ExportConfiguration

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

GenomicsDBColumnOrIntervalList

Field	Type	Label	Description
column_or_interval_list	GenomicsDBColumnOrInterval	repeated

QueryConfiguration

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

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

RowRange

Field	Type	Label	Description
low	int64	required
high	int64	required

RowRangeList

Field	Type	Label	Description
range_list	RowRange	repeated

SparkConfig

Field	Type	Label	Description
query_block_size	int64	optional
query_block_size_margin	int64	optional

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genomicsdb_import_config.proto

ImportConfiguration

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

Partition

Field	Type	Label	Description
begin	GenomicsDBColumn	required
workspace	string	optional
array_name	string	optional
generate_array_name_from_partition_bounds	bool	optional
vcf_output_filename	string	optional
vcf_header_filename	string	optional
end	GenomicsDBColumn	optional

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genomicsdb_vid_mapping.proto

Chromosome

Field	Type	Label	Description
name	string	required
length	int64	required
tiledb_column_offset	int64	required

FieldLengthDescriptorComponentPB

Field	Type	Label	Description
variable_length_descriptor	string	optional
fixed_length	int32	optional

GenomicsDBFieldInfo

Field	Type	Label	Description
name	string	required
type	string	repeated
vcf_field_class	string	repeated
vcf_type	string	optional
length	FieldLengthDescriptorComponentPB	repeated
vcf_delimiter	string	repeated
VCF_field_combine_operation	string	optional
vcf_name	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	optional	Default: false

VidMappingPB

Field	Type	Label	Description
fields	GenomicsDBFieldInfo	repeated
contigs	Chromosome	repeated

Scalar Value Types

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