io_get_extension

#include <IO.h>

int io_get_extension(
	GapIO  *io,
	int	N,
	char   *seq,
	int	max_seq,
	int    *length,
	int    *complement);

io_get_extension reads the usable 3' cutoff data for reading number N. The cutoff data is stored in seq. The length stored is the smaller of max_seq bytes or the length of the 3' cutoff data. The length of data stored in seq is written to the length pointer. The orientation of the reading is stored in the complement pointer.

The reading annotations are also read to determine which segments are considered usable. The existance of a tag with type IGNS or IGNC, anywhere on the reading, indicates that there is no suitable cutoff data for this reading. length is set to 1 and the function returns 1.

If a tag of type SVEC or CVEC exists within the 3' cutoff data the segment returned consists of that between the 3' cutoff point and the start of the vector tag.

The function returns 0 for success and 1 for failure.

NOTE: The current implementation looks any tags with types IGN? and ?VEC rather than the specific types listed.