LIBRARY

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

SYNOPSIS

int bl_sam_write(bl_sam_t *sam_alignment, FILE *sam_stream, sam_field_mask_t field_mask)

ARGUMENTS

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

LIBRARY

SYNOPSIS

ARGUMENTS

DESCRIPTION

RETURN VALUES

SEE ALSO