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| Original file line number | Diff line number | Diff line change |
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| #include "Util.h" | ||
| #include "Parameters.h" | ||
| #include "Matcher.h" | ||
| #include "Debug.h" | ||
| #include "DBReader.h" | ||
| #include "DBWriter.h" | ||
| #include "IndexReader.h" | ||
| #include "MemoryMapped.h" | ||
| #include "NcbiTaxonomy.h" | ||
| #include "MappingReader.h" | ||
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| #define ZSTD_STATIC_LINKING_ONLY | ||
| #include <zstd.h> | ||
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| #include <map> | ||
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| #ifdef OPENMP | ||
| #include <omp.h> | ||
| #endif | ||
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| int pairaln(int argc, const char **argv, const Command& command) { | ||
| Parameters &par = Parameters::getInstance(); | ||
| par.parseParameters(argc, argv, command, true, 0, 0); | ||
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| const bool sameDB = par.db1.compare(par.db2) == 0 ? true : false; | ||
| const bool touch = (par.preloadMode != Parameters::PRELOAD_MODE_MMAP); | ||
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| std::string db2NoIndexName = PrefilteringIndexReader::dbPathWithoutIndex(par.db2); | ||
| MappingReader* mapping = new MappingReader(db2NoIndexName); | ||
| const int dbaccessMode = (DBReader<unsigned int>::USE_INDEX | DBReader<unsigned int>::USE_DATA); | ||
| IndexReader qDbr(par.db1, par.threads, IndexReader::SRC_SEQUENCES, (touch) ? (IndexReader::PRELOAD_INDEX | IndexReader::PRELOAD_DATA) : 0, dbaccessMode); | ||
| IndexReader *tDbr; | ||
| if (sameDB) { | ||
| tDbr = &qDbr; | ||
| } else { | ||
| tDbr = new IndexReader(par.db2, par.threads, IndexReader::SRC_SEQUENCES, (touch) ? (IndexReader::PRELOAD_INDEX | IndexReader::PRELOAD_DATA) : 0, dbaccessMode); | ||
| } | ||
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| DBReader<unsigned int> alnDbr(par.db3.c_str(), par.db3Index.c_str(), par.threads, DBReader<unsigned int>::USE_INDEX|DBReader<unsigned int>::USE_DATA); | ||
| alnDbr.open(DBReader<unsigned int>::NOSORT); | ||
| if(alnDbr.getSize() % 2 != 0){ | ||
| Debug(Debug::ERROR) << "Alignment database does not seem to be paired\n"; | ||
| EXIT(EXIT_FAILURE); | ||
| } | ||
| size_t localThreads = 1; | ||
| #ifdef OPENMP | ||
| localThreads = std::max(std::min((size_t)par.threads, alnDbr.getSize()), (size_t)1); | ||
| #endif | ||
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| DBWriter resultWriter(par.db4.c_str(), par.db4Index.c_str(), localThreads, par.compressed, Parameters::DBTYPE_ALIGNMENT_RES); | ||
| resultWriter.open(); | ||
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| Debug::Progress progress(alnDbr.getSize()); | ||
| #pragma omp parallel num_threads(localThreads) | ||
| { | ||
| unsigned int thread_idx = 0; | ||
| #ifdef OPENMP | ||
| thread_idx = static_cast<unsigned int>(omp_get_thread_num()); | ||
| #endif | ||
| char buffer[1024 + 32768*4]; | ||
| std::string result; | ||
| result.reserve(1024 * 1024); | ||
| std::vector<Matcher::result_t> resultA; | ||
| resultA.reserve(100000); | ||
| std::vector<Matcher::result_t> resultB; | ||
| resultB.reserve(100000); | ||
| std::unordered_map<unsigned int, Matcher::result_t *> findPair; | ||
| std::string outputA; | ||
| outputA.reserve(100000); | ||
| std::string outputB; | ||
| outputB.reserve(100000); | ||
| #pragma omp for schedule(static, 2) | ||
| for (size_t i = 0; i < alnDbr.getSize(); i+=2) { | ||
| progress.updateProgress(); | ||
| progress.updateProgress(); | ||
| resultA.clear(); | ||
| resultB.clear(); | ||
| outputA.clear(); | ||
| outputB.clear(); | ||
| Matcher::readAlignmentResults(resultA, alnDbr.getData(i, thread_idx), true); | ||
| Matcher::readAlignmentResults(resultB, alnDbr.getData(i+1, thread_idx), true); | ||
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| for (size_t resIdx = 0; resIdx < resultA.size(); ++resIdx) { | ||
| unsigned int taxon = mapping->lookup(resultA[resIdx].dbKey); | ||
| if(findPair.find(taxon) == findPair.end()){ | ||
| findPair.insert({taxon, &resultA[resIdx]}); | ||
| } | ||
| } | ||
| // find pairs | ||
| for (size_t resIdx = 0; resIdx < resultB.size(); ++resIdx) { | ||
| unsigned int taxon = mapping->lookup(resultB[resIdx].dbKey); | ||
| // found pair! | ||
| if(findPair.find(taxon) != findPair.end()) { | ||
| bool hasBacktrace = (resultB[resIdx].backtrace.size() > 0); | ||
| size_t len = Matcher::resultToBuffer(buffer, *findPair[taxon], hasBacktrace, false, false); | ||
| outputA.append(buffer, len); | ||
| len = Matcher::resultToBuffer(buffer, resultB[resIdx], hasBacktrace, false, false); | ||
| outputB.append(buffer, len); | ||
| findPair.erase (taxon); | ||
| } | ||
| } | ||
| resultWriter.writeData(outputA.c_str(), outputA.length(), alnDbr.getDbKey(i), thread_idx); | ||
| resultWriter.writeData(outputB.c_str(), outputB.length(), alnDbr.getDbKey(i+1), thread_idx); | ||
| } | ||
| } | ||
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| resultWriter.close(); | ||
| // clean up | ||
| delete mapping; | ||
| alnDbr.close(); | ||
| if (sameDB == false) { | ||
| delete tDbr; | ||
| } | ||
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| return 0; | ||
| } | ||
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