def liftover(self, intersecting_region):
<EOL>if not self.intersects(intersecting_region):<EOL><INDENT>raise RetrotransposonError("<STR_LIT>" + str(intersecting_region) +<EOL>"<STR_LIT>" +<EOL>"<STR_LIT>" + str(self) + "<STR_LIT>" +<EOL>"<STR_LIT>")<EOL><DEDENT>if self.pairwise_alignment is not None:<EOL><INDENT>return self.pairwise_alignment.liftover(self.chrom, self.repeat_name(),<EOL>intersecting_region.start,<EOL>intersecting_region.end,<EOL>trim=True)<EOL><DEDENT>return self.liftover_coordinates(intersecting_region)<EOL>
Lift a region that overlaps the genomic occurrence of the retrotransposon
to consensus sequence co-ordinates. This method will behave differently
depending on whether this retrotransposon occurrance contains a full
alignment or not. If it does, the alignment is used to do the liftover and
an exact result is provided. If it does not, the coordinates are used to
do the liftover, padding either the genomic region or consensus sequence
(whichever is shorter) with equally spaced gaps to make the size of both
match.

:param intersecting_region: a region that intersects this occurrence.
:return: list of GenomicInterval objects. This is a list because a genomic
         deletion of part of the retrotransposon can fragment the
         intersecting region and result in more than one returned interval.