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Recover longest orf after fragment elimination (#832)
* recover longest orf after fragment elimination * delete unused variable
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,148 @@ | ||
| #include "Parameters.h" | ||
| #include "DBReader.h" | ||
| #include "DBWriter.h" | ||
| #include "Debug.h" | ||
| #include "Util.h" | ||
| #include "Orf.h" | ||
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| #include <unordered_map> | ||
| #include <unordered_set> | ||
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| #ifdef OPENMP | ||
| #include <omp.h> | ||
| #endif | ||
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| int recoverlongestorf(int argc, const char **argv, const Command &command) { | ||
| Parameters &par = Parameters::getInstance(); | ||
| par.parseParameters(argc, argv, command, true, 0, 0); | ||
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| DBReader<unsigned int> headerReader(par.hdr1.c_str(), par.hdr1Index.c_str(), par.threads, DBReader<unsigned int>::USE_INDEX|DBReader<unsigned int>::USE_DATA); | ||
| headerReader.open(DBReader<unsigned int>::LINEAR_ACCCESS); | ||
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| DBReader<unsigned int> resultReader(par.db2.c_str(), par.db2Index.c_str(), par.threads, DBReader<unsigned int>::USE_INDEX|DBReader<unsigned int>::USE_DATA); | ||
| resultReader.open(DBReader<unsigned int>::LINEAR_ACCCESS); | ||
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| DBWriter writer(par.db3.c_str(), par.db3Index.c_str(), 1, false, Parameters::DBTYPE_OMIT_FILE); | ||
| writer.open(); | ||
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| Debug::Progress progress(resultReader.getSize()); | ||
| std::unordered_map<unsigned int, std::pair<unsigned int, size_t>> contigToLongest; | ||
| #pragma omp parallel | ||
| { | ||
| unsigned int thread_idx = 0; | ||
| #ifdef OPENMP | ||
| thread_idx = static_cast<unsigned int>(omp_get_thread_num()); | ||
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| #endif | ||
| std::unordered_map<unsigned int, std::pair<unsigned int, size_t>> localContigToLongest; | ||
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| #pragma omp for schedule(dynamic, 100) | ||
| for (size_t id = 0; id < headerReader.getSize(); ++id) { | ||
| progress.updateProgress(); | ||
| unsigned int orfKey = headerReader.getDbKey(id); | ||
| char *orfHeader = headerReader.getData(id, thread_idx); | ||
| Orf::SequenceLocation orf = Orf::parseOrfHeader(orfHeader); | ||
| unsigned int contigKey = orf.id; | ||
| size_t orfLen = std::max(orf.from, orf.to) - std::min(orf.from, orf.to) + 1; | ||
| std::unordered_map<unsigned int, std::pair<unsigned int, size_t>>::iterator it = localContigToLongest.find(contigKey); | ||
| if (it != localContigToLongest.end()) { | ||
| std::pair<unsigned int, size_t> orfKeyToLength = it->second; | ||
| if (orfLen > orfKeyToLength.second) { | ||
| it->second = std::make_pair(orfKey, orfLen); | ||
| } | ||
| } else { | ||
| localContigToLongest.emplace(contigKey, std::make_pair(orfKey, orfLen)); | ||
| } | ||
| } | ||
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| #pragma omp critical | ||
| { | ||
| for (auto &entry : localContigToLongest) { | ||
| auto &contigKey = entry.first; | ||
| auto &localData = entry.second; | ||
| auto it = contigToLongest.find(contigKey); | ||
| if (it != contigToLongest.end()) { | ||
| if (localData.second > it->second.second) { | ||
| it->second = localData; | ||
| } | ||
| } else { | ||
| contigToLongest[contigKey] = localData; | ||
| } | ||
| } | ||
| } | ||
| } | ||
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| progress.reset(resultReader.getSize()); | ||
| std::unordered_set<unsigned int> acceptedContigs; | ||
| std::unordered_set<unsigned int> eliminatedContigs; | ||
| #pragma omp parallel | ||
| { | ||
| int thread_idx = 0; | ||
| #ifdef OPENMP | ||
| thread_idx = omp_get_thread_num(); | ||
| #endif | ||
| std::string resultBuffer; | ||
| resultBuffer.reserve(1024 * 1024); | ||
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| std::unordered_set<unsigned int> localAcceptedContigs; | ||
| std::unordered_set<unsigned int> localEliminatedContigs; | ||
| #pragma omp for schedule(dynamic, 5) | ||
| for (size_t i = 0; i < resultReader.getSize(); ++i) { | ||
| progress.updateProgress(); | ||
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| unsigned int key = resultReader.getDbKey(i); | ||
| size_t entryLength = resultReader.getEntryLen(i); | ||
| if (entryLength > 1) { | ||
| size_t id = headerReader.getId(key); | ||
| char *orfHeader = headerReader.getData(id, thread_idx); | ||
| Orf::SequenceLocation orf = Orf::parseOrfHeader(orfHeader); | ||
| unsigned int contigKey = orf.id; | ||
| localAcceptedContigs.emplace(contigKey); | ||
| } | ||
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| size_t id = headerReader.getId(key); | ||
| char *orfHeader = headerReader.getData(id, thread_idx); | ||
| Orf::SequenceLocation orf = Orf::parseOrfHeader(orfHeader); | ||
| unsigned int contigKey = orf.id; | ||
| localEliminatedContigs.emplace(contigKey); | ||
| } | ||
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| #pragma omp critical | ||
| { | ||
| acceptedContigs.insert(localAcceptedContigs.begin(), localAcceptedContigs.end()); | ||
| eliminatedContigs.insert(localEliminatedContigs.begin(), localEliminatedContigs.end()); | ||
| } | ||
| } | ||
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| for (auto it = eliminatedContigs.begin(); it != eliminatedContigs.end(); ) { | ||
| if (acceptedContigs.find(*it) != acceptedContigs.end()) { | ||
| it = eliminatedContigs.erase(it); | ||
| } else { | ||
| ++it; | ||
| } | ||
| } | ||
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| std::string resultBuffer; | ||
| resultBuffer.reserve(1024 * 1024); | ||
| for (auto contigIt = eliminatedContigs.begin(); contigIt != eliminatedContigs.end(); ++contigIt) { | ||
| unsigned int contigKey = *contigIt; | ||
| std::unordered_map<unsigned int, std::pair<unsigned int, size_t>>::iterator it = contigToLongest.find(contigKey); | ||
| if (it != contigToLongest.end()) { | ||
| unsigned int orfKey = it->second.first; | ||
| resultBuffer.append(SSTR(orfKey)); | ||
| resultBuffer.append(1, '\n'); | ||
| writer.writeData(resultBuffer.c_str(), resultBuffer.length(), orfKey, 0, false, false); | ||
| resultBuffer.clear(); | ||
| } else { | ||
| Debug(Debug::ERROR) << "Missing contig " << contigKey << "\n"; | ||
| EXIT(EXIT_FAILURE); | ||
| } | ||
| } | ||
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| writer.close(true); | ||
| FileUtil::remove(writer.getIndexFileName()); | ||
| headerReader.close(); | ||
| resultReader.close(); | ||
|
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||
| return EXIT_SUCCESS; | ||
| } |
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