NAME

bl_sam_fopen() - Open a SAM/BAM/CRAM file

LIBRARY

#include <xtend/file.h>
-lxtend

SYNOPSIS

FILE    *bl_sam_fopen(const char *filename, const char *mode,
char *samtools_args)

ARGUMENTS

filename:       Name of the file to be opened
mode:           "r" or "w", passed to fopen() or popen()
samtools_args   Flags to pass to samtools view

DESCRIPTION

Open a raw SAM file using fopen() or a compressed SAM file, or BAM or CRAM file using popen(). If the file extension is .bam or .cram, or samtools_args is not NULL or "", data will be piped through "samtools view" with the given samtools_args as arguments. The flag --with-header is always added for consistency with the case of reading a raw SAM file without piping through samtools. Programs that don't want the header can filter it out by other means, such as bl_sam_skip_header(3).

bl_sam_fopen() must be used in conjunction with bl_sam_fclose() to ensure that fclose() or pclose() is called where appropriate.

RETURN VALUES

A pointer to the FILE structure or NULL if open failed

SEE ALSO

fopen(3), popen(3), gzip(1), bzip2(1), xz(1)