void hal::validateDuplications(const Genome* genome)
{
const Genome* parent = genome->getParent();
if (parent == NULL)
{
return;
}
TopSegmentIteratorConstPtr topIt = genome->getTopSegmentIterator();
TopSegmentIteratorConstPtr endIt = genome->getTopSegmentEndIterator();
vector<unsigned char> pcount(parent->getNumBottomSegments(), 0);
for (; topIt != endIt; topIt->toRight())
{
if (topIt->hasParent())
{
if (pcount[topIt->getTopSegment()->getParentIndex()] < 250)
{
++pcount[topIt->getTopSegment()->getParentIndex()];
}
}
}
for (topIt = genome->getTopSegmentIterator(); topIt != endIt; topIt->toRight())
{
if (topIt->hasParent())
{
size_t count = pcount[topIt->getTopSegment()->getParentIndex()];
assert(count > 0);
{
if (topIt->hasNextParalogy() == false && count > 1)
{
stringstream ss;
ss << "Top Segment " << topIt->getTopSegment()->getArrayIndex()
<< " in genome " << genome->getName() << " is not marked as a"
<< " duplication but it shares its parent "
<< topIt->getTopSegment()->getArrayIndex() << " with at least "
<< count - 1 << " other segments in the same genome";
throw hal_exception(ss.str());
}
}
}
}
}
void SummarizeMutations::subsAndGapInserts(
GappedTopSegmentIteratorConstPtr gappedTop, MutationsStats& stats)
{
assert(gappedTop->getReversed() == false);
hal_size_t numGaps = gappedTop->getNumGaps();
if (numGaps > 0)
{
stats._gapInsertionLength.add(gappedTop->getNumGapBases(), numGaps);
}
string parent, child;
TopSegmentIteratorConstPtr l = gappedTop->getLeft();
TopSegmentIteratorConstPtr r = gappedTop->getRight();
BottomSegmentIteratorConstPtr p =
l->getTopSegment()->getGenome()->getParent()->getBottomSegmentIterator();
for (TopSegmentIteratorConstPtr i = l->copy();
i->getTopSegment()->getArrayIndex() <=
r->getTopSegment()->getArrayIndex();
i->toRight())
{
if (i->hasParent())
{
p->toParent(i);
i->getString(child);
p->getString(parent);
assert(child.length() == parent.length());
for (size_t j = 0; j < child.length(); ++j)
{
if (isTransition(child[j], parent[j]))
{
++stats._transitions;
++stats._subs;
}
else if (isTransversion(child[j], parent[j]))
{
++stats._transversions;
++stats._subs;
}
else if (isSubstitution(child[j], parent[j]))
{
++stats._subs;
}
else if (!isMissingData(child[j]) && !isMissingData(parent[j]))
{
++stats._matches;
}
}
}
}
}
void DefaultGappedBottomSegmentIterator::toRightNextUngapped(
TopSegmentIteratorConstPtr ts) const
{
while (ts->hasParent() == false &&
ts->getLength() <= _gapThreshold)
{
if ((!ts->getReversed() && ts->getTopSegment()->isLast()) ||
(ts->getReversed() && ts->getTopSegment()->isFirst()))
{
break;
}
ts->toRight();
}
}
