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());
}
}
void hal::validateSequence(const Sequence* sequence)
{
// Verify that the DNA sequence doesn't contain funny characters
DNAIteratorConstPtr dnaIt = sequence->getDNAIterator();
hal_size_t length = sequence->getSequenceLength();
for (hal_size_t i = 0; i < length; ++i)
{
char c = dnaIt->getChar();
if (isNucleotide(c) == false)
{
stringstream ss;
ss << "Non-nucleotide character discoverd at position "
<< i << " of sequence " << sequence->getName() << ": " << c;
throw hal_exception(ss.str());
}
}
// Check the top segments
if (sequence->getGenome()->getParent() != NULL)
{
hal_size_t totalTopLength = 0;
TopSegmentIteratorConstPtr topIt = sequence->getTopSegmentIterator();
hal_size_t numTopSegments = sequence->getNumTopSegments();
for (hal_size_t i = 0; i < numTopSegments; ++i)
{
const TopSegment* topSegment = topIt->getTopSegment();
validateTopSegment(topSegment);
totalTopLength += topSegment->getLength();
topIt->toRight();
}
if (totalTopLength != length)
{
stringstream ss;
ss << "Sequence " << sequence->getName() << " has length " << length
<< " but its top segments add up to " << totalTopLength;
throw hal_exception(ss.str());
}
}
// Check the bottom segments
if (sequence->getGenome()->getNumChildren() > 0)
{
hal_size_t totalBottomLength = 0;
BottomSegmentIteratorConstPtr bottomIt =
sequence->getBottomSegmentIterator();
hal_size_t numBottomSegments = sequence->getNumBottomSegments();
for (hal_size_t i = 0; i < numBottomSegments; ++i)
{
const BottomSegment* bottomSegment = bottomIt->getBottomSegment();
validateBottomSegment(bottomSegment);
totalBottomLength += bottomSegment->getLength();
bottomIt->toRight();
}
if (totalBottomLength != length)
{
stringstream ss;
ss << "Sequence " << sequence->getName() << " has length " << length
<< " but its bottom segments add up to " << totalBottomLength;
throw hal_exception(ss.str());
}
}
}