//
// Main
//
int overlapLongMain(int argc, char** argv)
{
parseOverlapLongOptions(argc, argv);
// Open output file
std::ostream* pASQGWriter = createWriter(opt::outFile);
// Build and write the ASQG header
ASQG::HeaderRecord headerRecord;
headerRecord.setOverlapTag(opt::minOverlap);
headerRecord.setErrorRateTag(opt::errorRate);
headerRecord.setInputFileTag(opt::readsFile);
headerRecord.setTransitiveTag(true);
headerRecord.write(*pASQGWriter);
// Determine which index files to use. If a target file was provided,
// use the index of the target reads
std::string indexPrefix;
if(!opt::targetFile.empty())
indexPrefix = stripFilename(opt::targetFile);
else
indexPrefix = stripFilename(opt::readsFile);
BWT* pBWT = new BWT(indexPrefix + BWT_EXT, opt::sampleRate);
SampledSuffixArray* pSSA = new SampledSuffixArray(indexPrefix + SAI_EXT, SSA_FT_SAI);
Timer* pTimer = new Timer(PROGRAM_IDENT);
pBWT->printInfo();
// Read the sequence file and write vertex records for each
// Also store the read names in a vector of strings
ReadTable reads;
SeqReader* pReader = new SeqReader(opt::readsFile, SRF_NO_VALIDATION);
SeqRecord record;
while(pReader->get(record))
{
reads.addRead(record.toSeqItem());
ASQG::VertexRecord vr(record.id, record.seq.toString());
vr.write(*pASQGWriter);
if(reads.getCount() % 100000 == 0)
printf("Read %zu sequences\n", reads.getCount());
}
delete pReader;
pReader = NULL;
BWTIndexSet index;
index.pBWT = pBWT;
index.pSSA = pSSA;
index.pReadTable = &reads;
// Make a prefix for the temporary hits files
size_t n_reads = reads.getCount();
omp_set_num_threads(opt::numThreads);
#pragma omp parallel for
for(size_t read_idx = 0; read_idx < n_reads; ++read_idx)
{
const SeqItem& curr_read = reads.getRead(read_idx);
printf("read %s %zubp\n", curr_read.id.c_str(), curr_read.seq.length());
SequenceOverlapPairVector sopv =
KmerOverlaps::retrieveMatches(curr_read.seq.toString(),
opt::seedLength,
opt::minOverlap,
1 - opt::errorRate,
100,
index);
printf("Found %zu matches\n", sopv.size());
for(size_t i = 0; i < sopv.size(); ++i)
{
std::string match_id = reads.getRead(sopv[i].match_idx).id;
// We only want to output each edge once so skip this overlap
// if the matched read has a lexicographically lower ID
if(curr_read.id > match_id)
continue;
std::string ao = ascii_overlap(sopv[i].sequence[0], sopv[i].sequence[1], sopv[i].overlap, 50);
printf("\t%s\t[%d %d] ID=%s OL=%d PI:%.2lf C=%s\n", ao.c_str(),
sopv[i].overlap.match[0].start,
sopv[i].overlap.match[0].end,
match_id.c_str(),
sopv[i].overlap.getOverlapLength(),
sopv[i].overlap.getPercentIdentity(),
sopv[i].overlap.cigar.c_str());
// Convert to ASQG
SeqCoord sc1(sopv[i].overlap.match[0].start, sopv[i].overlap.match[0].end, sopv[i].overlap.length[0]);
SeqCoord sc2(sopv[i].overlap.match[1].start, sopv[i].overlap.match[1].end, sopv[i].overlap.length[1]);
// KmerOverlaps returns the coordinates of the overlap after flipping the reads
// to ensure the strand matches. The ASQG file wants the coordinate of the original
// sequencing strand. Flip here if necessary
if(sopv[i].is_reversed)
sc2.flip();
// Convert the SequenceOverlap the ASQG's overlap format
Overlap ovr(curr_read.id, sc1, match_id, sc2, sopv[i].is_reversed, -1);
ASQG::EdgeRecord er(ovr);
er.setCigarTag(sopv[i].overlap.cigar);
er.setPercentIdentityTag(sopv[i].overlap.getPercentIdentity());
#pragma omp critical
{
er.write(*pASQGWriter);
}
}
}
// Cleanup
delete pReader;
delete pBWT;
delete pSSA;
delete pASQGWriter;
delete pTimer;
if(opt::numThreads > 1)
pthread_exit(NULL);
return 0;
}
//
// Main
//
int overlapMain(int argc, char** argv)
{
parseOverlapOptions(argc, argv);
// Prepare the output ASQG file
assert(opt::outputType == OT_ASQG);
// Open output file
std::ostream* pASQGWriter = createWriter(opt::outFile);
// Build and write the ASQG header
ASQG::HeaderRecord headerRecord;
headerRecord.setOverlapTag(opt::minOverlap);
headerRecord.setErrorRateTag(opt::errorRate);
headerRecord.setInputFileTag(opt::readsFile);
headerRecord.setContainmentTag(true); // containments are always present
headerRecord.setTransitiveTag(!opt::bIrreducibleOnly);
headerRecord.write(*pASQGWriter);
// Compute the overlap hits
StringVector hitsFilenames;
// Determine which index files to use. If a target file was provided,
// use the index of the target reads
std::string indexPrefix;
if(!opt::prefix.empty())
indexPrefix = opt::prefix;
else
{
if(!opt::targetFile.empty())
indexPrefix = stripFilename(opt::targetFile);
else
indexPrefix = stripFilename(opt::readsFile);
}
BWT* pBWT = new BWT(indexPrefix + BWT_EXT, opt::sampleRate);
BWT* pRBWT = new BWT(indexPrefix + RBWT_EXT, opt::sampleRate);
OverlapAlgorithm* pOverlapper = new OverlapAlgorithm(pBWT, pRBWT,
opt::errorRate, opt::seedLength,
opt::seedStride, opt::bIrreducibleOnly);
pOverlapper->setExactModeOverlap(opt::errorRate <= 0.0001);
pOverlapper->setExactModeIrreducible(opt::errorRate <= 0.0001);
Timer* pTimer = new Timer(PROGRAM_IDENT);
pBWT->printInfo();
// Make a prefix for the temporary hits files
std::string outPrefix;
outPrefix = stripFilename(opt::readsFile);
if(!opt::targetFile.empty())
{
outPrefix.append(1, '.');
outPrefix.append(stripFilename(opt::targetFile));
}
if(opt::numThreads <= 1)
{
printf("[%s] starting serial-mode overlap computation\n", PROGRAM_IDENT);
computeHitsSerial(outPrefix, opt::readsFile, pOverlapper, opt::minOverlap, hitsFilenames, pASQGWriter);
}
else
{
printf("[%s] starting parallel-mode overlap computation with %d threads\n", PROGRAM_IDENT, opt::numThreads);
computeHitsParallel(opt::numThreads, outPrefix, opt::readsFile, pOverlapper, opt::minOverlap, hitsFilenames, pASQGWriter);
}
// Get the number of strings in the BWT, this is used to pre-allocated the read table
delete pOverlapper;
delete pBWT;
delete pRBWT;
// Parse the hits files and write the overlaps to the ASQG file
convertHitsToASQG(indexPrefix, hitsFilenames, pASQGWriter);
// Cleanup
delete pASQGWriter;
delete pTimer;
if(opt::numThreads > 1)
pthread_exit(NULL);
return 0;
}