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| bl_gff_index_add(3) | FreeBSD Library Functions Manual | bl_gff_index_add(3) |
LIBRARY
#include <biolibc/gff-index.h> -lbiolibc -lxtend
SYNOPSIS
int bl_gff_index_add(bl_gff_index_t *gi, bl_gff_t *feature)ARGUMENTS
gi Pointer to gff_index_t object to which a record will be added feature Pointer to GFF feature to be indexed
DESCRIPTION
The gff_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_gff_read(3), which records the file position of each GFF feature it reads.bl_gff_index_add_pos(3) adds a GFF feature with file position file_pos to the index. Features of interest, perhaps only genes or only exons, can be added to the index on-the fly while reading through a GFF file with bl_gff_read(3).
The index can later be searched or traversed forward or backward to quickly find the location of a feature and reposition a FILE pointer to it using fseek(3). This system eliminates the need to inhale large numbers of GFF features into memory.
RETURN VALUES
BL_GFF_INDEX_OK on success, BL_GFF_MALLOC_FAILED if memory could not be allocatedEXAMPLES
bl_gff_index_t gi;
bl_gff_t feature;
if ( bl_gff_read(&feature, gff_stream, BL_GFF_FIELD_ALL) == BL_READ_OK )
{
if ( bl_gff_index_add(&gi, &feature) != BL_GFF_INDEX_OK )
fprintf(stderr, "Error addind to GFF index.n");
}
SEE ALSO
bl_gff_index_seek_reverse(3), bl_gff_read(3)
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