NAME

bl_gff3_sam_cmp() - Compare SAM/GFF3 positions

LIBRARY

#include <gff3.h>
-lbiolibc -lxtend

SYNOPSIS

int     bl_gff3_sam_cmp(bl_gff3_t *feature, bl_sam_t *alignment)

ARGUMENTS

feature     Pointer to a bl_gff3_t object
alignment   Pointer to a bl_sam_t object

DESCRIPTION

Compare the positions of a GFF feature and a SAM alignment and return a status value much like strcmp(). 0 is returned if the feature and alignment overlap. A value < 0 is returned if the feature is entirely "before" the alignment, i.e. it is on an earlier chromosome according to bl_chrom_name_cmp(3), or on the same chromosome at a lower position. A value > 0 is returned if the feature is entirely "after" the alignment, i.e. on a later chromosome or same chromosome and higher position.

This function is mainly intended for programs that sweep properly sorted GFF and SAM files locating overlaps in a single pass.

A converse function, bl_sam_gff3_cmp(3) is also provided so that the programmer can choose the more intuitive interface.

RETURN VALUES

A value < 0 if the the feature is entirely before the alignment A value > 0 if the the feature is entirely after the alignment 0 if the feature and the alignment overlap

SEE ALSO

bl_gff3_sam_cmp(3), bl_chrom_name_cmp(3)