Merge remote-tracking branch 'origin/li_dev' (5c533895) · Commits · github_fork / Chromap

src/chromap.cc

+6 −4

Original line number	Diff line number	Diff line
		@@ -706,7 +706,8 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		if (mm_to_candidates_cache.Query(minimizers2, positive_candidates2, negative_candidates2, repetitive_seed_length2, read_batch2.GetSequenceLengthAt(pair_index)) == -1)
		index.GenerateCandidates(error_threshold_, minimizers2, &repetitive_seed_length2, &positive_hits2, &negative_hits2, &positive_candidates2, &negative_candidates2);
		uint32_t current_num_candidates2 = positive_candidates2.size() + negative_candidates2.size();
		if (pair_index < num_loaded_pairs / num_threads_ \|\| num_reads_ < 2 * 5000000) {
		if (pair_index < num_loaded_pairs / 2
		&& (pair_index < num_loaded_pairs / num_threads_ \|\| num_reads_ < 2 * 5000000)) {
		mm_history1[pair_index].minimizers = minimizers1;
		mm_history1[pair_index].positive_candidates = positive_candidates1;
		mm_history1[pair_index].negative_candidates = negative_candidates1;
		@@ -863,7 +864,7 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		// }
		// }
		//}
		for (uint32_t pair_index = 0; pair_index < num_loaded_pairs; ++pair_index) {
		for (uint32_t pair_index = 0; pair_index < num_loaded_pairs / 2; ++pair_index) {
		if (num_reads_ >= 2 * 5000000 && pair_index >= num_loaded_pairs / num_threads_)
		break;
		mm_to_candidates_cache.Update(mm_history1[pair_index].minimizers, mm_history1[pair_index].positive_candidates, mm_history1[pair_index].negative_candidates, mm_history1[pair_index].repetitive_seed_length);
		@@ -1500,7 +1501,8 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		// positive_candidates.size() + negative_candidates.size()) ;
		//if (positive_hits.size() + negative_hits.size() > minimizers.size() * 100)
		}
		if (read_index < num_loaded_reads / num_threads_ \|\| num_reads_ < 5000000) {
		if (read_index < num_loaded_reads / 2
		&& (read_index < num_loaded_reads / num_threads_ \|\| num_reads_ < 5000000)) {
		mm_history[read_index].minimizers = minimizers;
		mm_history[read_index].positive_candidates = positive_candidates;
		mm_history[read_index].negative_candidates = negative_candidates;
		@@ -1529,7 +1531,7 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		}
		}
		}
		for (uint32_t read_index = 0; read_index < num_loaded_reads ; ++read_index) {
		for (uint32_t read_index = 0; read_index < num_loaded_reads / 2; ++read_index) {
		if ( num_reads_ >= 5000000 && read_index >= num_loaded_reads / num_threads_)
		break;
		mm_to_candidates_cache.Update(mm_history[read_index].minimizers, mm_history[read_index].positive_candidates, mm_history[read_index].negative_candidates, mm_history[read_index].repetitive_seed_length);

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