gzIndex.h File Reference

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <zlib.h>
#include <iostream>
#include <fstream>

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Classes
struct	point
struct	access

Macros
#define	local   static
#define	SPAN   1048576L /* desired distance between access points */
#define	WINSIZE   32768U /* sliding window size */
#define	CHUNK   16384 /* file input buffer size */

Functions
void	freeGzIndex (struct access *index)
void	serializeGzIndex (struct access *index, string outputFile)
struct access *	deserializeGzIndex (struct access *index, string inputFile)
int	buildGzIndex (string gzFile, off_t span, struct access **built)
int	buildGzIndex_Stream (FILE *in, off_t span, struct access **built)
int	extract (string gzFile, struct access *index, off_t offset, unsigned char *buf, int len)
int	extract_Stream (FILE *in, struct access *index, off_t offset, unsigned char *buf, int len)
string	extractFastqReadFromOffset (FILE *in, struct access *index, off_t offset)

Macro Definition Documentation

CHUNK

#define CHUNK   16384 /* file input buffer size */

Definition at line 73 of file gzIndex.h.

local

#define local   static

Definition at line 69 of file gzIndex.h.

SPAN

#define SPAN   1048576L /* desired distance between access points */

Definition at line 71 of file gzIndex.h.

WINSIZE

#define WINSIZE   32768U /* sliding window size */

Definition at line 72 of file gzIndex.h.

Function Documentation

buildGzIndex()

int buildGzIndex	(	string	gzFile,
		off_t	span,
		struct access **	built
	)

Index a given gzip file.

Parameters

gzFile	gzip file to build the index for
span	build access points every span bits of uncompressed output
built	structure where to store the index

Exceptions

ios_base::failure

thrown if gzFile could not be open

Returns

the number of access points on success (>=1), Z_MEM_ERROR for out of memory, Z_DATA_ERROR for an error in the input file, or Z_ERRNO for a file read error. On success, *built points to the resulting index.

buildGzIndex_Stream()

int buildGzIndex_Stream	(	FILE *	in,
		off_t	span,
		struct access **	built
	)

Index a given gzip file.

Parameters

FILE	open on the desired gzip file to build the index for
span	build access points every span bits of uncompressed output
built	structure where to store the index

Returns

the number of access points on success (>=1), Z_MEM_ERROR for out of memory, Z_DATA_ERROR for an error in the input file, or Z_ERRNO for a file read error. On success, *built points to the resulting index.

deserializeGzIndex()

struct access* deserializeGzIndex	(	struct access *	index,
		string	inputFile
	)

Deserialize a gzip index from a file.

Parameters

index	index to fill
inputFile	file where the index is stored

Exceptions

ios_base::failure

thrown if inputFile could not be open

Returns

the index populated with the contents of the file

extract()

int extract	(	string	gzFile,
		struct access *	index,
		off_t	offset,
		unsigned char *	buf,
		int	len
	)

Extract data starting from a given offset off the uncompressed file, using the index.

Parameters

gzFile	gzip to extract data from
index	the index of the gzip file
offset	offset to start extracting data from
buf	buffer where to store the extracted data
len	number of bytes to extract

Exceptions

ios_base::failure

thrown if gzFile could not be open

Returns

bytes read or negative for error (Z_DATA_ERROR or Z_MEM_ERROR)

extract_Stream()

int extract_Stream	(	FILE *	in,
		struct access *	index,
		off_t	offset,
		unsigned char *	buf,
		int	len
	)

Extract data starting from a given offset off the uncompressed file, using the index.

Parameters

in	FILE open on the desired gzip file
index	the index of the gzip file
offset	offset to start extracting data from
buf	buffer where to store the extracted data
len	number of bytes to extract

Returns

bytes read or negative for error (Z_DATA_ERROR or Z_MEM_ERROR)

extractFastqReadFromOffset()

string extractFastqReadFromOffset	(	FILE *	in,
		struct access *	index,
		off_t	offset
	)

Extract the fastq format read at the specified offset.

Parameters

in	FILE open on the desired gzip file
index	the index of the gzip file
offset	offset off the read to extract

Returns

the extracted read in fastq format

freeGzIndex()

void freeGzIndex

(

struct access *

index

)

Deallocate an index built by build_index()

Parameters

index

index to deallocate

serializeGzIndex()

void serializeGzIndex	(	struct access *	index,
		string	outputFile
	)

Serialize the gzip index into a file.

Parameters

index	index to serialize
outputFile	file where to store the index

Exceptions

ios_base::failure

thrown if outputFile could not be open