BioHDF version 0.3 alpha
Scalable NGS Data Storage Based on HDF5
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Basic BioHDF data structures. More...
Defines | |
#define | BIOHDF_API |
Platform-specific library prefix. | |
#define | BIOHDF_MAX_STRING_SIZE 4096 |
The max string size in some fixed data structures. | |
#define | BIOHDF_DEFAULT_COMPRESSION_LEVEL 5 |
The default compression level (zlib compression) | |
#define | BIOHDF_DEFAULT_CHUNK_SIZE 1024 |
The default HDF5 chunk size for all datasets (KB) | |
#define | BIOHDF_TYPE_ATTR_NAME "BIOHDF_TYPE" |
The name of the BioHDF type attribute. | |
Enumerations | |
enum | biohdf_string_storage_scheme { FIXED_LENGTH_STRING, VARIABLE_LENGTH_STRING, HYBRID_STRING } |
The BioHDF string storage scheme. More... | |
enum | biohdf_open_mode { READ_ONLY = 0, READ_WRITE } |
Modes for opening collections. More... | |
enum | compression_level { NO_COMPRESSION = 0, GZIP_1 = 1, GZIP_2 = 2, GZIP_3 = 3, GZIP_4 = 4, GZIP_5 = 5, GZIP_6 = 6, GZIP_7 = 7, GZIP_8 = 8, GZIP_9 = 9 } |
GZIP compression level. More... |
Basic BioHDF data structures.
#define BIOHDF_API |
Platform-specific library prefix.
extern "C", __declspec(dllexport), etc.
enum biohdf_open_mode |
The BioHDF string storage scheme.
BioHDF can use several storage schemes to hold string data. The default is variable length storage since there is no risk of data truncation. However, there are performance advantages (in both size and I/O speed) to using the fixed-length scheme (assuming your strings are roughly uniform in length). Unfortunately, profiling is required to determine which scheme will work best in a given situation.
NOTE: The hybrid type is unimplemented at this time. It should eventually combine the flexibility of the variable-length scheme with the performance benefits of the fixed-length scheme.
enum compression_level |
GZIP compression level.
The same compression level is used for all data in the collection.