NAME

bl_gff3_read() - Read a GFF3 feature

LIBRARY

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

SYNOPSIS

int     bl_gff3_read(bl_gff3_t *feature, FILE *gff3_stream,
gff3_field_mask_t field_mask)

ARGUMENTS

feature         Pointer to a bl_gff3_t structure
gff3_stream      A FILE stream from which to read the line
field_mask      Bit mask indicating which fields to store in feature

DESCRIPTION

Read next feature (line) from a GFF file.

feature must be initialized using BL_GFF3_INIT or bl_gff3_init() before being passed to this function.

bl_gff3_read() will allocate memory for string fields as needed. The object should be passed to bl_gff3_free() as soon as possible after the data are no longer needed.

If passed an object that is not in an initialized state, bl_gff3_read() will free and initialize it before repopulating it with a new feature.

If field_mask is not BL_GFF3_FIELD_ALL, fields not indicated by a 1 in the bit mask are discarded rather than stored in feature. That field in the structure is then populated with an appropriate marker, such as '.'. Possible mask values are:

BL_GFF3_FIELD_ALL BL_GFF3_FIELD_SEQID BL_GFF3_FIELD_SOURCE BL_GFF3_FIELD_TYPE BL_GFF3_FIELD_START BL_GFF3_FIELD_END BL_GFF3_FIELD_SCORE BL_GFF3_FIELD_STRAND BL_GFF3_FIELD_PHASE BL_GFF3_FIELD_ATTRIBUTES

RETURN VALUES

BL_READ_OK on successful read BL_READ_EOF if EOF is encountered after a complete feature BL_READ_TRUNCATED if EOF or bad data is encountered elsewhere

EXAMPLES

bl_gff3_skip_header(stdin);
bl_gff3_init(&feature);
bl_gff3_read(&feature, stdin, BL_GFF3_FIELD_ALL);
bl_gff3_read(&feature, gff3_stream,


    BL_GFF3_FIELD_SEQID|BL_GFF3_FIELD_START|BL_GFF3_FIELD_END);