RearrangementPtr HDF5Sequence::getRearrangement(hal_index_t position,
hal_size_t gapLengthThreshold,
double nThreshold,
bool atomic) const
{
TopSegmentIteratorConstPtr top = getTopSegmentIterator(position);
DefaultRearrangement* rea = new DefaultRearrangement(getGenome(),
gapLengthThreshold,
nThreshold,
atomic);
rea->identifyFromLeftBreakpoint(top);
return RearrangementPtr(rea);
}
RearrangementPtr HDF5Genome::getRearrangement(hal_index_t position,
hal_size_t gapLengthThreshold,
double nThreshold,
bool atomic) const
{
assert(position >= 0 && position < (hal_index_t)getNumTopSegments());
TopSegmentIteratorConstPtr top = getTopSegmentIterator(position);
DefaultRearrangement* rea = new DefaultRearrangement(this,
gapLengthThreshold,
nThreshold,
atomic);
rea->identifyFromLeftBreakpoint(top);
return RearrangementPtr(rea);
}
