bl_sam_read(3) Library Functions Manual bl_sam_read(3) NAME bl_sam_read() - Read one SAM record LIBRARY #include <biolibc/sam.h> -lbiolibc -lxtend SYNOPSIS int bl_sam_read(bl_sam_t *alignment, FILE *sam_stream, sam_field_mask_t field_mask) ARGUMENTS sam_stream A FILE stream from which to read the line alignment Pointer to a bl_sam_t structure field_mask Bit mask indicating which fields to store in 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 alignment. That field in the structure is then populated with an appropriate marker, such as '.'. Pos- sible 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 else- where EXAMPLES bl_sam_read(stdin, &alignment, BL_SAM_FIELD_ALL); bl_sam_read(sam_stream, &alignment, BL_SAM_FIELD_QNAME|BL_SAM_FIELD_POS|BL_SAM_FIELD_TLEN); SEE ALSO bl_sam_write(3) bl_sam_read(3)
NAME | LIBRARY | SYNOPSIS | ARGUMENTS | DESCRIPTION | RETURN VALUES | EXAMPLES | SEE ALSO
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