bool DefaultGappedBottomSegmentIterator::isMissingData(double nThreshold) const
{
if (nThreshold >= 1.0)
{
return false;
}
hal_index_t start = min(_left->getStartPosition(), _right->getEndPosition());
DNAIteratorConstPtr di = _left->getGenome()->getDNAIterator(start);
hal_size_t length = getLength();
size_t maxNs = nThreshold * (double)length;
size_t Ns = 0;
char c;
for (size_t i = 0; i < length; ++i, di->toRight())
{
c = di->getChar();
if (c == 'N' || c == 'n')
{
++Ns;
}
if (Ns > maxNs)
{
return true;
}
if ((length - i) < (maxNs - Ns))
{
break;
}
}
return false;
}
void Genome::copySequence(Genome *dest) const
{
DNAIteratorConstPtr inDna = getDNAIterator();
DNAIteratorPtr outDna = dest->getDNAIterator();
hal_size_t n = getSequenceLength();
assert(n == dest->getSequenceLength());
for (; (hal_size_t)inDna->getArrayIndex() < n; inDna->toRight(),
outDna->toRight())
{
outDna->setChar(inDna->getChar());
}
}