slow5_set_press

NAME

slow5_set_press - sets the compression method for a BLOW5 file opened for writing

SYNOPSYS

int slow5_set_press(slow5_file_t *s5p, enum slow5_press_method rec_press, enum slow5_press_method sig_press)

DESCRIPTION

slow5_set_press() sets the record compression and signal compression in a BLOW5 file s5p to rec_press and sig_press, respectively. s5p should have been opened for writing (mode “w”) using slow5_open() and must be a binary SLOW5 (BLOW5) file. slow5_set_press() must be called immediately after calling slow5_open().

rec_press can be one of the following:

• SLOW5_COMPRESS_NONE No compression
• SLOW5_COMPRESS_ZLIB Zlib (default)
• SLOW5_COMPRESS_ZSTD Zstandard

sig_press can be one of the following:

• SLOW5_COMPRESS_NONE No compression
• SLOW5_COMPRESS_SVB_ZD Stream variable byte - zig-zag delta (default)

RETURN VALUE

Upon successful completion, slow5_set_press() returns a non negative integer (>=0). Otherwise, a negative value is returned that indicates the error and slow5_errno is set to indicate the error.

ERRORS

• SLOW5_ERR_ARG      Invalid argument - s5p is NULL.

NOTES

If slow5_set_press() is not explicitly called, the default will be SLOW5_COMPRESS_ZLIB for record compression and SLOW5_COMPRESS_SVB_ZD for signal compression. Default values are recommended for most cases. SLOW5_COMPRESS_ZSTD+SLOW5_COMPRESS_SVB_ZD is similar to VBZ compression from Oxford Nanopore Technologies. If SLOW5_COMPRESS_ZSTD is specified, slow5lib require to be built with zstd support and your programme must be linked with libzstd (-lzstd flag). SLOW5 files compressed with zstd offer smaller file size and better performance compared to the default zlib. However, zlib runtime library is available by default on almost all distributions unlike zstd and thus files compressed with zlib will be more ‘portable’.

EXAMPLES

No record and signal compression:

slow5_file_t *sp = slow5_open(FILE_PATH, "w");
if(sp==NULL){
	fprintf(stderr,"Error opening file!\n");
	exit(EXIT_FAILURE);
}

//set no record compression, no signal compression
if(slow5_set_press(sp, SLOW5_COMPRESS_NONE, SLOW5_COMPRESS_NONE) < 0){ //
	fprintf(stderr,"Error setting compression method!\n");
	exit(EXIT_FAILURE);
}

//... do the rest as in slow5_write example

Compression similar to VBZ:

slow5_file_t *sp = slow5_open(FILE_PATH, "w");
if(sp==NULL){
	fprintf(stderr,"Error opening file!\n");
	exit(EXIT_FAILURE);
}

//set zstd record compression, svb-zd signal compression
if(slow5_set_press(sp, SLOW5_COMPRESS_ZSTD, SLOW5_COMPRESS_SVB_ZD) < 0){ //
	fprintf(stderr,"Error setting compression method!\n");
	exit(EXIT_FAILURE);
}

//... do the rest as in slow5_write example

SEE ALSO

slow5_open(), slow5_write()