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| bl_sam_read(3) | FreeBSD Library Functions Manual | bl_sam_read(3) |
LIBRARY
#include <biolibc/sam.h> -lbiolibc -lxtend
SYNOPSIS
int bl_sam_read(bl_sam_t *sam_alignment, FILE *sam_stream, sam_field_mask_t field_mask)ARGUMENTS
sam_stream A FILE stream from which to read the line sam_alignment Pointer to a bl_sam_t structure field_mask Bit mask indicating which fields to store in sam_alignment
DESCRIPTION
Read next alignment (line) from a SAM stream.If field_mask is not BL_SAM_FIELD_ALL, fields not indicated by a 1 in the bit mask are discarded rather than stored in sam_alignment. That field in the structure is then populated with an appropriate marker, such as '.'. 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
BL_READ_OK on successful read BL_READ_EOF if EOF is encountered after a complete feature BL_READ_TRUNCATED if EOF or bad data is encountered elsewhereEXAMPLES
bl_sam_read(stdin, &sam_alignment, BL_SAM_FIELD_ALL);
bl_sam_read(sam_stream, &sam_alignment,
BL_SAM_FIELD_QNAME|BL_SAM_FIELD_POS|BL_SAM_FIELD_TLEN);
SEE ALSO
bl_sam_write(3)
Visit the GSP FreeBSD Man Page Interface.
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