bl_sam_write(3)

NAME
bl_sam_write() - Write a SAM object to a file stream

LIBRARY
#include <biolibc/sam.h>
-lbiolibc -lxtend

SYNOPSIS
int     bl_sam_write(bl_sam_t *alignment, FILE *sam_stream,
sam_field_mask_t field_mask)

ARGUMENTS
sam_stream  A FILE stream to which to write the line
alignment   Pointer to a bl_sam_t structure
field_mask  Bit mask indicating which fields to store in alignment

DESCRIPTION
Write an alignment (line) to a SAM stream. If field_mask is not BL_SAM_FIELD_ALL, fields not indicated by a 1 in the bit mask are written as an appropriate placeholder such as '.' rather than stored in alignment. Possible mask values are: BL_SAM_FIELD_ALL BL_SAM_FIELD_QNAME BL_SAM_FIELD_FLAG BL_SAM_FIELD_RNAME BL_SAM_FIELD_POS BL_SAM_FIELD_MAPQ BL_SAM_FIELD_CIGAR BL_SAM_FIELD_RNEXT BL_SAM_FIELD_PNEXT BL_SAM_FIELD_TLEN BL_SAM_FIELD_SEQ BL_SAM_FIELD_QUAL

RETURN VALUES
Number of items written (per fprintf() output)

SEE ALSO
bl_sam_read(3)