slow5_open

NAME

slow5_open - opens a SLOW5 file

SYNOPSYS

slow5_file_t *slow5_open(const char *pathname, const char *mode)

DESCRIPTION

The slow_open() function opens a SLOW5 file (ASCII or binary) pointed by the argument pathname, parses and populates the SLOW5 header. slow_open() determines if the file is SLOW5 ASCII or SLOW5 Binary from extension of the argument pathname (.slow5 for SLOW5 ASCII and .blow5 for SLOW5 binary).

Currently, the argument mode points to a string which can be one of the following:

• r Open a SLOW5 file for reading.
• w Open a SLOW5 file for writing. Creates a new file if the file does not exit. An existing file is truncated to zero.
• a Open a SLOW5 file for appending (writing at end of file). The file must already exist. If it does not exist, slow_open() will fail. If pathname is a BLOW5 file, the existing SLOW5 EOF marker is overwritten.

An open slow5 file should be closed at the end using slow5_close() function.

RETURN VALUE

Upon successful completion, slow_open() returns a slow5_file_t pointer. Otherwise, NULL is returned and slow5_errno is set to indicate the error.

ERRORS

• SLOW5_ERR_ARG      Invalid argument - pathname or mode provided was NULL.
• SLOW5_ERR_IO      File I/O error, for instance, fopen, ftello or fileno failed.
• SLOW5_ERR_UNK      Wrong file extension, that is neither .slow5 nor .blow5
• SLOW5_ERR_HDRPARSE      Parsing and populating the header failed.
• SLOW5_ERR_MEM      Memory allocation failed.
• SLOW5_ERR_TRUNC      End of file (EOF) reached prematurely.
• SLOW5_ERR_MAGIC      Invalid magic number.
• SLOW5_ERR_VERSION      File version is incompatible with this library version.
• SLOW5_ERR_PRESS      Initialisation of compression/decompression buffers failed.
• SLOW5_ERR_OTH      Other error.

NOTES

Internally uses fopen(). If mode is r, the stream is positioned at the beginning of the data records when slow_open() returns. If mode is w, the stream is positioned at the end of the file. If mode is a, the stream is positioned at the end of the file for .slow5; and 5 bytes before the end of the file for .blow5 such that the existing SLOW5 EOF marker is overwritten.

EXAMPLES

#include <stdio.h>
#include <stdlib.h>
#include <slow5/slow5.h>

#define FILE_PATH "examples/example.slow5"

int main(){

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

    //...

    slow5_close(sp);

}

SEE ALSO

slow5_close()