LIBRARY

#include <sam.h>
-lbiolibc -lxtend

SYNOPSIS

int     bl_sam_gff_cmp(bl_sam_t *alignment, bl_gff_t *feature)

ARGUMENTS

alignment   Pointer to a bl_sam_t object
feature     Pointer to a bl_gff_t object

DESCRIPTION

Compare the positions of a SAM alignment and a GFF feature and return a status value much like strcmp(). 0 is returned if the alignment and feature overlap. A value < 0 is returned if the alignment is entirely "before" the feature, 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 alignment is entirely "after" the feature, 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_gff_sam_cmp(3) is also provided so that the programmer can choose the more intuitive interface.

RETURN VALUES

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

SEE ALSO

bl_gff_sam_cmp(3), bl_chrom_name_cmp(3)