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bl_sam_gff3_cmp(3) Library Functions Manual bl_sam_gff3_cmp(3) NAME bl_sam_gff3_cmp() - Compare positions of SAM and GFF3 records LIBRARY #include <sam.h> -lbiolibc -lxtend SYNOPSIS int bl_sam_gff3_cmp(bl_sam_t *alignment, bl_gff3_t *feature) ARGUMENTS alignment Pointer to a bl_sam_t object feature Pointer to a bl_gff3_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_gff3_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 align- ment and the feature overlap SEE ALSO bl_gff3_sam_cmp(3), bl_chrom_name_cmp(3) bl_sam_gff3_cmp(3)
NAME | LIBRARY | SYNOPSIS | ARGUMENTS | DESCRIPTION | RETURN VALUES | SEE ALSO
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