BioHDF version 0.3 alpha
Scalable NGS Data Storage Based on HDF5
Defines | Enumerations
biohdf_api

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...

Detailed Description

Basic BioHDF data structures.


Define Documentation

#define BIOHDF_API

Platform-specific library prefix.

extern "C", __declspec(dllexport), etc.


Enumeration Type Documentation

Modes for opening collections.

Enumerator:
READ_ONLY 

Read-only access (DEFAULT)

READ_WRITE 

Read and write access.

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.

Enumerator:
FIXED_LENGTH_STRING 

All strings are below a given length.

VARIABLE_LENGTH_STRING 

Strings can be any length.

HYBRID_STRING 

UNIMPLEMENTED - DO NOT USE.

GZIP compression level.

The same compression level is used for all data in the collection.

Enumerator:
NO_COMPRESSION 

No compression.

GZIP_1 

compression level 1

GZIP_2 

compression level 2

GZIP_3 

compression level 3

GZIP_4 

compression level 4

GZIP_5 

compression level 5

GZIP_6 

compression level 6

GZIP_7 

compression level 7

GZIP_8 

compression level 8

GZIP_9 

compression level 9

 All Data Structures Variables