Improve memory usage of cache. (7f047e0e) · Commits · github_fork / Chromap

src/chromap.cc

+13 −0

Original line number	Diff line number	Diff line
		@@ -511,6 +511,14 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		mm_history1[pair_index].negative_candidates) ;
		mm_to_candidates_cache.Update(mm_history2[pair_index].minimizers, mm_history2[pair_index].positive_candidates,
		mm_history2[pair_index].negative_candidates) ;
		if (mm_history1[pair_index].positive_candidates.size() < mm_history1[pair_index].positive_candidates.capacity() / 2)
		std::vector<struct _candidate>().swap(mm_history1[pair_index].positive_candidates) ;
		if (mm_history1[pair_index].negative_candidates.size() < mm_history1[pair_index].negative_candidates.capacity() / 2)
		std::vector<struct _candidate>().swap(mm_history1[pair_index].negative_candidates) ;
		if (mm_history2[pair_index].positive_candidates.size() < mm_history2[pair_index].positive_candidates.capacity() / 2)
		std::vector<struct _candidate>().swap(mm_history2[pair_index].positive_candidates) ;
		if (mm_history2[pair_index].negative_candidates.size() < mm_history2[pair_index].negative_candidates.capacity() / 2)
		std::vector<struct _candidate>().swap(mm_history2[pair_index].negative_candidates) ;
		}

		#pragma omp taskwait
		@@ -1037,7 +1045,12 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		for (uint32_t read_index = 0; read_index < num_loaded_reads; ++read_index) {
		mm_to_candidates_cache.Update(mm_history[read_index].minimizers, mm_history[read_index].positive_candidates,
		mm_history[read_index].negative_candidates) ;
		if (mm_history[read_index].positive_candidates.size() < mm_history[read_index].positive_candidates.capacity() / 2)
		std::vector<struct _candidate>().swap(mm_history[read_index].positive_candidates) ;
		if (mm_history[read_index].negative_candidates.size() < mm_history[read_index].negative_candidates.capacity() / 2)
		std::vector<struct _candidate>().swap(mm_history[read_index].negative_candidates) ;
		}
		std::cerr<<"cache memusage: " << mm_to_candidates_cache.GetMemoryBytes() <<"\n" ;
		#pragma omp taskwait
		num_loaded_reads = num_loaded_reads_for_loading;
		read_batch_for_loading.SwapSequenceBatch(read_batch);

src/chromap.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -195,7 +195,7 @@ class Chromap {
		bool output_mapping_in_BED_;
		bool output_mapping_in_TagAlign_;
		bool output_mapping_in_PAF_;
		uint32_t read_batch_size_ = 100000; // default batch size, # reads for single-end reads, # read pairs for paired-end reads
		uint32_t read_batch_size_ = 1000000; // default batch size, # reads for single-end reads, # read pairs for paired-end reads
		std::string reference_file_path_;
		std::string index_file_path_;
		std::string read_file1_path_;

src/mmcache.hpp

+16 −2

Original line number	Diff line number	Diff line
		@@ -152,12 +152,15 @@ public:
		else
		--cache[hidx].weight ;
		// Renew the cache
		if (cache[hidx].weight <= 0)
		if (cache[hidx].weight < 0)
		{
		cache[hidx].weight = 1 ;
		cache[hidx].minimizers.resize(msize) ;
		if (msize == 0)
		{
		cache[hidx].offsets.resize(0) ;
		return ;
		}

		cache[hidx].offsets.resize(msize - 1) ;
		for (i = 0 ; i < msize ; ++i)
		@@ -181,7 +184,18 @@ public:
		}
		}


		int GetMemoryBytes()
		{
		int i, ret = 0 ;
		for (i = 0 ; i < cache_size ; ++i)
		{
		ret += sizeof(cache[i]) + cache[i].minimizers.capacity() * sizeof(uint64_t)
		+ cache[i].offsets.capacity() * sizeof(int)
		+ cache[i].positive_candidates.capacity() * sizeof(struct _candidate)
		+ cache[i].negative_candidates.capacity() * sizeof(struct _candidate) ;
		}
		return ret ;
		}
		} ;

		}

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