LIBRARY

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

SYNOPSIS

int bl_bed_read(bl_bed_t *bed_feature, bed_field_mask_t field_mask, FILE *bed_stream)

ARGUMENTS

bed_stream      A FILE stream from which to read the line
bed_feature     Pointer to a bl_bed_t structure
field_mask      Bit mask indicating which fields to store in bed_feature

DESCRIPTION

Read next entry (line) from a BED file. The line must have at least the first 3 fields (chrom, start, and end). It may have up to 12 fields, all of which must be in the correct order according to the BED specification.

If field_mask is not BL_BED_FIELD_ALL, fields not indicated by a 1 in the bit mask are discarded rather than stored in bed_feature. Possible mask values are:

BL_BED_FIELD_ALL BL_BED_FIELD_NAME BL_BED_FIELD_SCORE BL_BED_FIELD_STRAND BL_BED_FIELD_THICK BL_BED_FIELD_RGB BL_BED_FIELD_BLOCK

The chrom, start, and end fields are required and therefore have no corresponding mask bits. The thickStart and thickEnd fields must occur together or not at all, so only a single bit BL_BED_FIELD_THICK selects both of them. Likewise, blockCount, blockSizes and blockStarts must all be present or omitted, so BL_BED_FIELD_BLOCK masks all three.

RETURN VALUES

BL_READ_OK on successful read BL_READ_EOF if EOF is encountered at the start of a line BL_READ_TRUNCATED if EOF or bad data is encountered elsewhere

EXAMPLES