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#ifndef ASSEMBLY_ASSEMBLEALGORITHM_H
#define ASSEMBLY_ASSEMBLEALGORITHM_H 1
#include "DataLayer/FastaWriter.h"
#include <iostream>
#include <climits>
namespace AssemblyAlgorithms {
/** Assemble a contig.
* @return the number of k-mer below the coverage threshold
*/
template <typename Graph>
size_t assembleContig(
Graph* seqCollection, FastaWriter* writer,
BranchRecord& branch, unsigned id)
{
assert(!branch.isActive());
assert(branch.getState() == BS_NOEXT
|| branch.getState() == BS_AMBI_SAME
|| branch.getState() == BS_AMBI_OPP);
// Assemble the contig.
Sequence contig(branch);
size_t kmerCount = branch.calculateBranchMultiplicity();
if (writer != NULL)
writer->WriteSequence(contig, id, kmerCount);
// Remove low-coverage contigs.
float coverage = (float)kmerCount / branch.size();
if (opt::coverage > 0 && coverage < opt::coverage) {
for (BranchRecord::iterator it = branch.begin();
it != branch.end(); ++it)
seqCollection->remove(it->first);
return branch.size();
}
return 0;
}
/** Assemble contigs.
* @return the number of contigs assembled
*/
static inline
size_t assemble(SequenceCollectionHash* seqCollection,
FastaWriter* fileWriter = NULL)
{
typedef SequenceCollectionHash Graph;
typedef graph_traits<Graph>::vertex_descriptor V;
typedef Graph::SymbolSetPair SymbolSetPair;
Timer timer("Assemble");
size_t kmerCount = 0;
unsigned contigID = 0;
size_t assembledKmer = 0;
size_t lowCoverageKmer = 0;
size_t lowCoverageContigs = 0;
for (Graph::iterator iter = seqCollection->begin();
iter != seqCollection->end(); ++iter) {
if (iter->second.deleted())
continue;
kmerCount++;
extDirection dir;
SeqContiguity status = checkSeqContiguity(*iter, dir, true);
if (status == SC_CONTIGUOUS)
continue;
else if(status == SC_ISLAND)
{
BranchRecord currBranch(SENSE);
currBranch.push_back(*iter);
currBranch.terminate(BS_NOEXT);
size_t removed = assembleContig(seqCollection,
fileWriter, currBranch, contigID++);
assembledKmer += currBranch.size();
if (removed > 0) {
lowCoverageContigs++;
lowCoverageKmer += removed;
}
continue;
}
assert(status == SC_ENDPOINT);
BranchRecord currBranch(dir);
currBranch.push_back(*iter);
V currSeq = iter->first;
extendBranch(currBranch, currSeq,
iter->second.getExtension(dir));
assert(currBranch.isActive());
while(currBranch.isActive())
{
SymbolSetPair extRec;
int multiplicity = -1;
bool success = seqCollection->getSeqData(
currSeq, extRec, multiplicity);
assert(success);
(void)success;
processLinearExtensionForBranch(currBranch,
currSeq, extRec, multiplicity, UINT_MAX);
}
if ((opt::ss && currBranch.getDirection() == SENSE)
|| (!opt::ss && currBranch.isCanonical())) {
size_t removed = assembleContig(seqCollection,
fileWriter, currBranch, contigID++);
assembledKmer += currBranch.size();
if (removed > 0) {
lowCoverageContigs++;
lowCoverageKmer += removed;
}
}
seqCollection->pumpNetwork();
}
if (opt::coverage > 0) {
std::cout << "Found " << assembledKmer << " k-mer in " << contigID
<< " contigs before removing low-coverage contigs.\n"
"Removed " << lowCoverageKmer << " k-mer in "
<< lowCoverageContigs << " low-coverage contigs.\n";
tempCounter[3] += lowCoverageContigs;
tempCounter[4] += lowCoverageKmer;
} else {
assert(assembledKmer <= kmerCount);
size_t circularKmer = kmerCount - assembledKmer;
if (circularKmer > 0)
std::cout << "Left " << circularKmer
<< " unassembled k-mer in circular contigs.\n";
std::cout << "Assembled " << assembledKmer << " k-mer in "
<< contigID << " contigs.\n";
if (!opt::db.empty()) {
addToDb("finalAmbgVertices", tempCounter[5]);
//addToDb("finalAmbgEdges", tempCounter[6]);
tempCounter.assign(16,0);
addToDb("assembledKmerNum", assembledKmer);
addToDb("assembledCntg", contigID);
}
}
return contigID;
}
} // namespace AssemblyAlgorithms
#endif
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