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Added reads splitting with ShortKMerReadMapper
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| Original file line number | Diff line number | Diff line change |
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| //*************************************************************************** | ||
| //* Copyright (c) 2021-2022 Saint Petersburg State University | ||
| //* All Rights Reserved | ||
| //* See file LICENSE for details. | ||
| //*************************************************************************** | ||
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| #include "read_splitting.hpp" | ||
| #include "binning.hpp" | ||
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| #include "modules/alignment/sequence_mapper_notifier.hpp" | ||
| #include "modules/alignment/sequence_mapper.hpp" | ||
| #include "modules/alignment/kmer_sequence_mapper.hpp" | ||
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| #include "io/reads/osequencestream.hpp" | ||
| #include "io/reads/io_helper.hpp" | ||
| #include "io/dataset_support/read_converter.hpp" | ||
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| #include <threadpool/threadpool.hpp> | ||
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| #include <vector> | ||
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| using namespace debruijn_graph; | ||
| using namespace bin_stats; | ||
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| namespace binning { | ||
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| class ReadsPathsToComponentsListener : public debruijn_graph::SequenceMapperListener { | ||
| public: | ||
| ReadsPathsToComponentsListener(const Binning &binning, | ||
| std::vector<io::OFastqPairedStream> &binned_reads_ostreams, | ||
| io::OFastqPairedStream &unbinned_reads_ostream, | ||
| const SoftBinsAssignment &soft_edge_labels, | ||
| const BinningAssignmentStrategy &assignment_strategy, | ||
| const double bin_weight_threshold) | ||
| : binned_reads_ostreams_(binned_reads_ostreams), | ||
| unbinned_reads_ostream_(unbinned_reads_ostream), | ||
| binning_(binning), | ||
| soft_edge_labels_(soft_edge_labels), | ||
| assignment_strategy_(assignment_strategy), | ||
| bin_weight_threshold_(bin_weight_threshold) {} | ||
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| void StartProcessLibrary(size_t threads_count) override { | ||
| binned_reads_.resize(threads_count, BinnedReads(binned_reads_ostreams_.size())); | ||
| unbinned_reads_.resize(threads_count); | ||
| } | ||
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| void MergeBuffer(size_t thread_index) override { | ||
| BinnedReads &reads = binned_reads_[thread_index]; | ||
| ReadVector &unbinned = unbinned_reads_[thread_index]; | ||
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| for (size_t part_id = 0; part_id < binned_reads_ostreams_.size(); ++part_id) { | ||
| io::OFastqPairedStream& paired_ostream = binned_reads_ostreams_[part_id]; | ||
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| for (const auto& paired_read : reads[part_id]) | ||
| paired_ostream << paired_read; | ||
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| reads[part_id].clear(); | ||
| } | ||
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| for (const auto& paired_read : unbinned) | ||
| unbinned_reads_ostream_ << paired_read; | ||
| unbinned.clear(); | ||
| } | ||
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| void ProcessPairedRead(size_t thread_index, | ||
| const io::PairedReadSeq& paired_read, | ||
| const MappingPath<EdgeId>& first_path, | ||
| const MappingPath<EdgeId>& second_path) override { | ||
| BinnedReads &reads = binned_reads_[thread_index]; | ||
| ReadVector &unbinned = unbinned_reads_[thread_index]; | ||
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| if (!first_path.empty() && !second_path.empty()) { | ||
| auto first_read_bins = | ||
| assignment_strategy_.ChooseMajorBins(assignment_strategy_.AssignScaffoldBins(first_path.simple_path(), | ||
| soft_edge_labels_, binning_), | ||
| soft_edge_labels_, binning_); | ||
| auto second_read_bins = | ||
| assignment_strategy_.ChooseMajorBins(assignment_strategy_.AssignScaffoldBins(second_path.simple_path(), | ||
| soft_edge_labels_, binning_), | ||
| soft_edge_labels_, binning_); | ||
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| std::unordered_set<bin_stats::Binning::BinId> read_bins; | ||
| read_bins.insert(first_read_bins.begin(), first_read_bins.end()); | ||
| read_bins.insert(second_read_bins.begin(), second_read_bins.end()); | ||
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| for (auto bin : read_bins) | ||
| reads[bin].push_back(paired_read); | ||
| } else | ||
| unbinned.push_back(paired_read); | ||
| } | ||
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| private: | ||
| using ReadVector = std::vector<io::PairedReadSeq>; | ||
| using BinnedReads = std::vector<ReadVector>; | ||
| // Per thread | ||
| std::vector<BinnedReads> binned_reads_; | ||
| std::vector<ReadVector> unbinned_reads_; | ||
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| std::vector<io::OFastqPairedStream> &binned_reads_ostreams_; | ||
| io::OFastqPairedStream &unbinned_reads_ostream_; | ||
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| const Binning &binning_; | ||
| const SoftBinsAssignment& soft_edge_labels_; | ||
| const BinningAssignmentStrategy& assignment_strategy_; | ||
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| double bin_weight_threshold_; | ||
| }; | ||
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| void SplitAndWriteReads(const debruijn_graph::Graph &graph, | ||
| SequencingLib &lib, | ||
| const Binning &binning, | ||
| const SoftBinsAssignment& edge_soft_labels, | ||
| const BinningAssignmentStrategy& assignment_strategy, | ||
| const std::string &work_dir, | ||
| const std::string &prefix, | ||
| unsigned nthreads, | ||
| const double bin_weight_threshold) { | ||
| if (!io::ReadConverter::LoadLibIfExists(lib)) { | ||
| std::unique_ptr<ThreadPool::ThreadPool> pool; | ||
| if (nthreads > 1) | ||
| pool = std::make_unique<ThreadPool::ThreadPool>(nthreads); | ||
| io::ReadConverter::ConvertToBinary(lib, pool.get()); | ||
| } | ||
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| io::OFastqPairedStream unbinned_reads_ostream(fs::append_path(prefix, "unbinned_1.fastq"), | ||
| fs::append_path(prefix, "unbinned_2.fastq")); | ||
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| std::vector<io::OFastqPairedStream> binned_reads_ostreams; | ||
| for (size_t bin_id = 0; bin_id < binning.bins().size(); ++bin_id) { | ||
| auto bin_label = binning.bin_labels().at(bin_id); | ||
| std::replace(bin_label.begin(), bin_label.end(), '/', '_'); | ||
| const std::pair<std::string, std::string> cur_part_paired_reads_filenames | ||
| {fs::append_path(prefix, bin_label + "_1.fastq"), | ||
| fs::append_path(prefix, bin_label + "_2.fastq")}; | ||
| binned_reads_ostreams.emplace_back(cur_part_paired_reads_filenames.first, | ||
| cur_part_paired_reads_filenames.second); | ||
| } | ||
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| SequenceMapperNotifier notifier; | ||
| auto mapper = alignment::ShortKMerReadMapper(graph, work_dir); | ||
| ReadsPathsToComponentsListener listener(binning, | ||
| binned_reads_ostreams, | ||
| unbinned_reads_ostream, | ||
| edge_soft_labels, | ||
| assignment_strategy, | ||
| bin_weight_threshold); | ||
| notifier.Subscribe(&listener); | ||
| auto paired_streams = paired_binary_readers(lib, /*followed by rc*/ false, 0, | ||
| /*include merged*/true); | ||
| notifier.ProcessLibrary(paired_streams, mapper); | ||
| } | ||
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| } | ||
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