void convertHitsToASQG(const std::string& indexPrefix, const StringVector& hitsFilenames, std::ostream* pASQGWriter)
{
// Load the suffix array index and the reverse suffix array index
// Note these are not the full suffix arrays
SuffixArray* pFwdSAI = new SuffixArray(indexPrefix + SAI_EXT);
SuffixArray* pRevSAI = new SuffixArray(indexPrefix + RSAI_EXT);
// Load the ReadInfoTable for the queries to look up the ID and lengths of the hits
ReadInfoTable* pQueryRIT = new ReadInfoTable(opt::readsFile);
// If the target file is not the query file, load its ReadInfoTable
ReadInfoTable* pTargetRIT;
if(!opt::targetFile.empty() && opt::targetFile != opt::readsFile)
pTargetRIT = new ReadInfoTable(opt::targetFile);
else
pTargetRIT = pQueryRIT;
bool bIsSelfCompare = pTargetRIT == pQueryRIT;
// Convert the hits to overlaps and write them to the asqg file as initial edges
for(StringVector::const_iterator iter = hitsFilenames.begin(); iter != hitsFilenames.end(); ++iter)
{
printf("[%s] parsing file %s\n", PROGRAM_IDENT, iter->c_str());
std::istream* pReader = createReader(*iter);
// Read each hit sequentially, converting it to an overlap
std::string line;
while(getline(*pReader, line))
{
size_t readIdx;
size_t totalEntries;
bool isSubstring;
OverlapVector ov;
OverlapCommon::parseHitsString(line, pQueryRIT, pTargetRIT, pFwdSAI, pRevSAI, bIsSelfCompare, readIdx, totalEntries, ov, isSubstring);
for(OverlapVector::iterator iter = ov.begin(); iter != ov.end(); ++iter)
{
ASQG::EdgeRecord edgeRecord(*iter);
edgeRecord.write(*pASQGWriter);
}
}
delete pReader;
// delete the hits file
unlink(iter->c_str());
}
// Deallocate data
if(pTargetRIT != pQueryRIT)
delete pTargetRIT;
delete pFwdSAI;
delete pRevSAI;
delete pQueryRIT;
}
StringGraph* SGUtil::loadASQG(const std::string& filename, const unsigned int minOverlap,
bool allowContainments)
{
// Initialize graph
StringGraph* pGraph = new StringGraph;
std::istream* pReader = createReader(filename);
int stage = 0;
int line = 0;
std::string recordLine;
while(getline(*pReader, recordLine))
{
ASQG::RecordType rt = ASQG::getRecordType(recordLine);
switch(rt)
{
case ASQG::RT_HEADER:
{
if(stage != 0)
{
std::cerr << "Error: Unexpected header record found at line " << line << "\n";
exit(EXIT_FAILURE);
}
ASQG::HeaderRecord headerRecord(recordLine);
const SQG::IntTag& overlapTag = headerRecord.getOverlapTag();
if(overlapTag.isInitialized())
pGraph->setMinOverlap(overlapTag.get());
else
pGraph->setMinOverlap(0);
const SQG::FloatTag& errorRateTag = headerRecord.getErrorRateTag();
if(errorRateTag.isInitialized())
pGraph->setErrorRate(errorRateTag.get());
const SQG::IntTag& containmentTag = headerRecord.getContainmentTag();
if(containmentTag.isInitialized())
pGraph->setContainmentFlag(containmentTag.get());
else
pGraph->setContainmentFlag(true); // conservatively assume containments are present
const SQG::IntTag& transitiveTag = headerRecord.getTransitiveTag();
if(!transitiveTag.isInitialized())
{
std::cerr << "Warning: ASQG does not have transitive tag\n";
pGraph->setTransitiveFlag(true);
}
else
{
pGraph->setTransitiveFlag(transitiveTag.get());
}
break;
}
case ASQG::RT_VERTEX:
{
// progress the stage if we are done the header
if(stage == 0)
stage = 1;
if(stage != 1)
{
std::cerr << "Error: Unexpected vertex record found at line " << line << "\n";
exit(EXIT_FAILURE);
}
ASQG::VertexRecord vertexRecord(recordLine);
const SQG::IntTag& ssTag = vertexRecord.getSubstringTag();
Vertex* pVertex = new(pGraph->getVertexAllocator()) Vertex(vertexRecord.getID(), vertexRecord.getSeq());
if(ssTag.isInitialized() && ssTag.get() == 1)
{
// Vertex is a substring of some other vertex, mark it as contained
pVertex->setContained(true);
pGraph->setContainmentFlag(true);
}
pGraph->addVertex(pVertex);
break;
}
case ASQG::RT_EDGE:
{
if(stage == 1)
stage = 2;
if(stage != 2)
{
std::cerr << "Error: Unexpected edge record found at line " << line << "\n";
exit(EXIT_FAILURE);
}
ASQG::EdgeRecord edgeRecord(recordLine);
const Overlap& ovr = edgeRecord.getOverlap();
// Add the edge to the graph
if(ovr.match.getMinOverlapLength() >= (int)minOverlap)
SGAlgorithms::createEdgesFromOverlap(pGraph, ovr, allowContainments);
break;
}
}
++line;
}
// Remove any duplicate edges
SGDuplicateVisitor dupVisit;
pGraph->visit(dupVisit);
SGGraphStatsVisitor statsVisit;
pGraph->visit(statsVisit);
// Remove identical vertices
// This is much cheaper to do than remove via
// SGContainRemove as no remodelling needs to occur
/*
SGIdenticalRemoveVisitor irv;
pGraph->visit(irv);
// Remove substring vertices
while(pGraph->hasContainment())
{
SGContainRemoveVisitor crv;
pGraph->visit(crv);
}
*/
delete pReader;
return pGraph;
}