LIBRARY

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

SYNOPSIS

int bl_bed_gff_cmp(bl_bed_t *bed_feature, bl_gff_t *gff_feature, bl_overlap_t *overlap)

ARGUMENTS

bed_feature     Pointer to the bl_bed_t structure to compare
gff_feature     Pointer to the bl_gff_t structure to compare
overlap         Pointer to the bl_overlap_t structure to receive
comparison results

DESCRIPTION

Compare the position of a BED feature to that of a GFF feature. Return 0 if the features overlap, < 0 if the BED feature is upstream of the GFF feature, > 0 if the BED feature is downstream of the GFF feature.

If the features overlap, populate the bl_overlap_t structure pointed to by overlap. The structure contains the lengths of the two features, the start and end positions of the overlapping region, and the length of the overlap. Positions in overlap are 1-based and inclusive at both ends (like most bioinformatics formats and unlike BED).

RETURN VALUES

A value < 0 if the BED feature is upstream of the GFF feature A value > 0 if the BED feature is downstream of the GFF feature 0 if the BED feature overlaps the GFF feature

EXAMPLES

if ( bl_bed_gff_cmp(&bed_feature, &gff_feature, *overlap) == 0 )

SEE ALSO

bl_bed_read(3), bl_gff_read(3)