bl_gff3_read(3) Library Functions Manual bl_gff3_read(3) 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 be- ing passed to this function. bl_gff3_read() will allocate memory for string fields as needed. The ob- ject 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 '.'. Pos- sible 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 else- where 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); SEE ALSO bl_gff3_write(3) bl_gff3_read(3)
NAME | LIBRARY | SYNOPSIS | ARGUMENTS | DESCRIPTION | RETURN VALUES | EXAMPLES | SEE ALSO
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