NAME

bl_gff3_index_seek_reverse() - Search backward through GFF3 index

LIBRARY

#include <biolibc/gff3-index.h>
-lbiolibc -lxtend

SYNOPSIS

int     bl_gff3_index_seek_reverse(bl_gff3_index_t *gi, FILE *stream,
bl_gff3_t *feature, int64_t feature_count, int64_t max_nt)

ARGUMENTS

gi              Pointer to the gff3_index_t object used to search
feature         Feature from which search starts
feature_count   Number of indexed features to back up from feature
max_nt          Maximum number of nucleotides to back up

DESCRIPTION

The gff3_index_t class maintains an in-memory index of GFF features, containing the GFF fields SEQ_ID, START, and END, and the offset into the file as reported by ftell(3), or by bl_gff3_read(3), which records the file position of each GFF feature it reads.

bl_gff3_index_seek_reverse(3) moved the FILE pointer stream to feature_count indexed features upstream of feature, or to the most upstream feature within max_nt of feature. A max_nt of 0 indicates no maximum distance, i.e. the search will proceed to feature_count features behind feature or to the beginning of the file, whichever is encontered first.

The max_nt parameter refers to the END of a feature, i.e. bl_gff3_index_seek_reverse() will back up to a feature that overlaps the position of feature minus max_nt. The START position of the feature moved to could be more than max_nt nucleotides behind the START of feature.

Note that this function counts only *indexed* features, i.e. those added to gi by bl_gff3_index_add(3), not all features in the GFF file. An application may only add genes to the index, for example, ignoring exons, etc.

RETURN VALUES

The return value of fseek(), i.e. 0 upon success, -1 on error

EXAMPLES

bl_gff3_index_t  gi;
bl_gff3_t        feature;
long            new_pos;
new_pos = bl_gff3_index_seek_reverse(&gi, &feature, 4, 200000);