bl_sam_fopen(3) Library Functions Manual bl_sam_fopen(3) 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 sam- tools_args is not NULL or "", data will be piped through "samtools view" with the given samtools_args as arguments. The flag --with-header is al- ways 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) bl_sam_fopen(3)
NAME | LIBRARY | SYNOPSIS | ARGUMENTS | DESCRIPTION | RETURN VALUES | SEE ALSO
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