Revert "Merge branch 'master' of github.com:haowenz/chromap" (5e717302) · Commits · github_fork / Chromap

src/chromap.cc

+1 −14

Original line number	Diff line number	Diff line
		@@ -20,7 +20,6 @@ struct _mm_history {
		std::vector<std::pair<uint64_t, uint64_t> > minimizers;
		std::vector<Candidate> positive_candidates;
		std::vector<Candidate> negative_candidates;
		uint32_t repetitive_seed_length;
		};

		template <typename MappingRecord>
		@@ -490,7 +489,7 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		SequenceBatch read_batch1_for_loading(read_batch_size_);
		SequenceBatch read_batch2_for_loading(read_batch_size_);
		SequenceBatch barcode_batch_for_loading(read_batch_size_);
		mm_cache mm_to_candidates_cache(2000003);
		mm_cache mm_to_candidates_cache(1000003);
		mm_to_candidates_cache.SetKmerLength(kmer_size_);
		struct _mm_history *mm_history1 = new struct _mm_history[read_batch_size_];
		struct _mm_history *mm_history2 = new struct _mm_history[read_batch_size_];
		@@ -1223,18 +1222,6 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		SequenceBatch read_batch_for_loading(read_batch_size_);
		SequenceBatch barcode_batch(read_batch_size_);
		SequenceBatch barcode_batch_for_loading(read_batch_size_);
		mm_cache mm_to_candidates_cache(2000003);
		mm_to_candidates_cache.SetKmerLength(kmer_size_);
		struct _mm_history *mm_history = new struct _mm_history[read_batch_size_];
		read_batch_for_loading.InitializeLoading(read_file1_path_);
		if (!is_bulk_data_) {
		barcode_batch_for_loading.InitializeLoading(barcode_file_path_);
		}
		double real_start_mapping_time = Chromap<>::GetRealTime();
		uint32_t num_loaded_reads_for_loading = 0;
		uint32_t num_loaded_reads = LoadSingleEndReadsWithBarcodes(&read_batch_for_loading, &barcode_batch_for_loading);
		read_batch_for_loading.SwapSequenceBatch(read_batch);
		barcode_batch_for_loading.SwapSequenceBatch(barcode_batch);
		mappings_on_diff_ref_seqs_.reserve(num_reference_sequences);
		deduped_mappings_on_diff_ref_seqs_.reserve(num_reference_sequences);
		for (uint32_t i = 0; i < num_reference_sequences; ++i) {

src/mmcache.hpp

+2 −6

Original line number	Diff line number	Diff line
		@@ -14,7 +14,6 @@ struct _mm_cache_entry {
		int weight;
		unsigned short finger_print_cnt[FINGER_PRINT_SIZE];
		int finger_print_cnt_sum;
		uint32_t repetitive_seed_length;
		};

		class mm_cache {
		@@ -85,7 +84,7 @@ class mm_cache {
		}

		// Return the hash entry index. -1 if failed.
		int Query(const std::vector<std::pair<uint64_t, uint64_t> > &minimizers, std::vector<Candidate> &pos_candidates, std::vector<Candidate> &neg_candidates, uint32_t &repetitive_seed_length, uint32_t read_len) {
		int Query(const std::vector<std::pair<uint64_t, uint64_t> > &minimizers, std::vector<Candidate> &pos_candidates, std::vector<Candidate> &neg_candidates, uint32_t read_len) {
		int i;
		int msize = minimizers.size();
		uint64_t h = 0;
		@@ -96,7 +95,6 @@ class mm_cache {
		if (direction == 1) {
		pos_candidates = cache[hidx].positive_candidates;
		neg_candidates = cache[hidx].negative_candidates;
		repetitive_seed_length = cache[hidx].repetitive_seed_length;
		int size = pos_candidates.size();
		int shift = (int)minimizers[0].second >> 1;
		for (i = 0; i < size; ++i)
		@@ -118,14 +116,13 @@ class mm_cache {
		neg_candidates = cache[hidx].positive_candidates;
		for (i = 0; i < size; ++i)
		neg_candidates[i].position = cache[hidx].positive_candidates[i].position - shift + read_len - 1;
		repetitive_seed_length = cache[hidx].repetitive_seed_length;
		return hidx;
		} else {
		return -1;
		}
		}

		void Update(const std::vector<std::pair<uint64_t, uint64_t> > &minimizers, std::vector<Candidate> &pos_candidates, std::vector<Candidate> &neg_candidates, uint32_t repetitive_seed_length) {
		void Update(const std::vector<std::pair<uint64_t, uint64_t> > &minimizers, std::vector<Candidate> &pos_candidates, std::vector<Candidate> &neg_candidates) {
		int i;
		int msize = minimizers.size();

		@@ -170,7 +167,6 @@ class mm_cache {
		std::vector<Candidate>().swap(cache[hidx].negative_candidates);
		cache[hidx].positive_candidates = pos_candidates;
		cache[hidx].negative_candidates = neg_candidates;
		cache[hidx].repetitive_seed_length = repetitive_seed_length;

		// adjust the candidate position.
		int size = cache[hidx].positive_candidates.size();

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