bl_gff3_sam_cmp(3) Library Functions Manual bl_gff3_sam_cmp(3) 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 align- ment 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 pro- grammer 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) bl_gff3_sam_cmp(3)
NAME | LIBRARY | SYNOPSIS | ARGUMENTS | DESCRIPTION | RETURN VALUES | SEE ALSO
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