void subgraph()
{
StringGraph* pGraph = SGUtil::loadASQG(opt::asqgFile, 0, true, opt::maxEdges);
pGraph->printMemSize();
// Remove containments from the graph
SGContainRemoveVisitor containVisit;
std::cout << "Removing contained vertices\n";
while(pGraph->hasContainment())
{
pGraph->visit(containVisit);
}
if (opt::maxOverlap)
{
SGMaximalOverlapVisitor moVisit(-1);
// Remove non-maximal overlap edges
std::cout << "Removing non-maximal overlap edges from graph\n";
pGraph->visit(moVisit);
}
StringGraph* pSubgraph = new StringGraph;
// Set the graph parameters to match the main graph
pSubgraph->setContainmentFlag(pGraph->hasContainment());
pSubgraph->setTransitiveFlag(pGraph->hasTransitive());
pSubgraph->setMinOverlap(pGraph->getMinOverlap());
pSubgraph->setErrorRate(pGraph->getErrorRate());
// Get the root vertex
Vertex* pRootVertex = pGraph->getVertex(opt::rootID);
if(pRootVertex == NULL)
{
std::cout << "Vertex " << opt::rootID << " not found in the graph.\n";
}
else
{
copyVertexToSubgraph(pSubgraph, pRootVertex);
pRootVertex->setColor(GC_BLACK);
// Recursively add neighbors
addNeighborsToSubgraph(pRootVertex, pSubgraph, opt::span);
// Write the subgraph
pSubgraph->writeASQG(opt::outFile);
}
delete pSubgraph;
delete pGraph;
}
// Run the bubble construction process
HaplotypeBuilderReturnCode DeBruijnHaplotypeBuilder::run(StringVector& out_haplotypes)
{
PROFILE_FUNC("GraphCompare::buildVariantStringGraph")
assert(!m_startingKmer.empty());
std::map<std::string, int> kmerCountMap;
// We search until we find the first common vertex in each direction
size_t MIN_TARGET_COUNT = m_parameters.bReferenceMode ? 1 : 2;
size_t MAX_ITERATIONS = 2000;
size_t MAX_SIMULTANEOUS_BRANCHES = 40;
size_t MAX_TOTAL_BRANCHES = 50;
// Tracking stats
size_t max_simul_branches_used = 0;
size_t total_branches = 0;
size_t iterations = 0;
// Initialize the graph
StringGraph* pGraph = new StringGraph;
BuilderExtensionQueue queue;
Vertex* pVertex = new(pGraph->getVertexAllocator()) Vertex(m_startingKmer, m_startingKmer);
pVertex->setColor(GC_BLACK);
pGraph->addVertex(pVertex);
// Add the vertex to the extension queue
queue.push(BuilderExtensionNode(pVertex, ED_SENSE));
queue.push(BuilderExtensionNode(pVertex, ED_ANTISENSE));
std::vector<Vertex*> sense_join_vector;
std::vector<Vertex*> antisense_join_vector;
// Perform the extension. The while conditions are heuristics to avoid searching
// the graph too much
while(!queue.empty() && iterations++ < MAX_ITERATIONS && queue.size() < MAX_SIMULTANEOUS_BRANCHES && total_branches < MAX_TOTAL_BRANCHES)
{
if(queue.size() > max_simul_branches_used)
max_simul_branches_used = queue.size();
BuilderExtensionNode curr = queue.front();
queue.pop();
// Calculate de Bruijn extensions for this node
std::string vertStr = curr.pVertex->getSeq().toString();
AlphaCount64 extensionCounts = BWTAlgorithms::calculateDeBruijnExtensionsSingleIndex(vertStr, m_parameters.variantIndex.pBWT, curr.direction);
std::string extensionsUsed;
for(size_t i = 0; i < DNA_ALPHABET::size; ++i)
{
char b = DNA_ALPHABET::getBase(i);
size_t count = extensionCounts.get(b);
bool acceptExt = count >= m_parameters.minDBGCount;
if(!acceptExt)
continue;
extensionsUsed.push_back(b);
std::string newStr = VariationBuilderCommon::makeDeBruijnVertex(vertStr, b, curr.direction);
kmerCountMap[newStr] = count;
// Create the new vertex and edge in the graph
// Skip if the vertex already exists
if(pGraph->getVertex(newStr) != NULL)
continue;
// Allocate the new vertex and add it to the graph
Vertex* pVertex = new(pGraph->getVertexAllocator()) Vertex(newStr, newStr);
pVertex->setColor(GC_BLACK);
pGraph->addVertex(pVertex);
// Add edges
VariationBuilderCommon::addSameStrandDeBruijnEdges(pGraph, curr.pVertex, pVertex, curr.direction);
// Check if this sequence is present in the FM-index of the target
// If so, it is the join point of the de Bruijn graph and we extend no further.
size_t targetCount = BWTAlgorithms::countSequenceOccurrences(newStr, m_parameters.baseIndex);
if(targetCount >= MIN_TARGET_COUNT)
{
if(curr.direction == ED_SENSE)
sense_join_vector.push_back(pVertex);
else
antisense_join_vector.push_back(pVertex);
}
else
{
// Add the vertex to the extension queue
queue.push(BuilderExtensionNode(pVertex, curr.direction));
}
}
// Update the total number of times we branches the search
if(!extensionsUsed.empty())
total_branches += extensionsUsed.size() - 1;
}
// If the graph construction was successful, walk the graph
// between the endpoints to make a string
// Generate haplotypes between every pair of antisense/sense join vertices
for(size_t i = 0; i < antisense_join_vector.size(); ++i) {
for(size_t j = 0; j < sense_join_vector.size(); ++j) {
SGWalkVector outWalks;
SGSearch::findWalks(antisense_join_vector[i],
sense_join_vector[j],
ED_SENSE,
100000, // max distance to search
10000, // max nodes to search
true, // exhaustive search
outWalks);
for(size_t k = 0; k < outWalks.size(); ++k)
out_haplotypes.push_back(outWalks[k].getString(SGWT_START_TO_END));
}
}
delete pGraph;
return HBRC_OK;
}
