Refactor VerifyCandidates. (05705cec) · Commits · github_fork / Chromap

src/chromap.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -27,7 +27,7 @@
		#include "temp_mapping.h"
		#include "utils.h"

		#define CHROMAP_VERSION "0.2.3-r409"
		#define CHROMAP_VERSION "0.2.3-r410"

		namespace chromap {

src/mapping_generator.h

+10 −19

Original line number	Diff line number	Diff line
		@@ -139,15 +139,11 @@ template <typename MappingRecord>
		void MappingGenerator<MappingRecord>::VerifyCandidates(
		const SequenceBatch &read_batch, uint32_t read_index,
		const SequenceBatch &reference, MappingMetadata &mapping_metadata) {
		int &min_num_errors = mapping_metadata.min_num_errors_;
		int &num_best_mappings = mapping_metadata.num_best_mappings_;
		int &second_min_num_errors = mapping_metadata.second_min_num_errors_;
		int &num_second_best_mappings = mapping_metadata.num_second_best_mappings_;

		min_num_errors = mapping_parameters_.error_threshold + 1;
		num_best_mappings = 0;
		second_min_num_errors = mapping_parameters_.error_threshold + 1;
		num_second_best_mappings = 0;
		mapping_metadata.SetMinNumErrors(mapping_parameters_.error_threshold + 1);
		mapping_metadata.SetNumBestMappings(0);
		mapping_metadata.SetSecondMinNumErrors(mapping_parameters_.error_threshold +
		1);
		mapping_metadata.SetNumSecondBestMappings(0);

		// Directly obtain the non-split mapping in ideal case and return without
		// running actual verification.
		@@ -173,13 +169,8 @@ void MappingGenerator<MappingRecord>::VerifyCandidates(
		return;
		}

		const size_t num_positive_candidates =
		mapping_metadata.positive_candidates_.size();
		const size_t num_negative_candidates =
		mapping_metadata.negative_candidates_.size();

		// For non-split alignments, use SIMD when possible.
		if (num_positive_candidates < (size_t)NUM_VPU_LANES_) {
		if (mapping_metadata.GetNumPositiveCandidates() < (size_t)NUM_VPU_LANES_) {
		VerifyCandidatesOnOneDirection(kPositive, read_index, read_batch, reference,
		mapping_metadata);
		} else {
		@@ -187,7 +178,7 @@ void MappingGenerator<MappingRecord>::VerifyCandidates(
		reference, mapping_metadata);
		}

		if (num_negative_candidates < (size_t)NUM_VPU_LANES_) {
		if (mapping_metadata.GetNumNegativeCandidates() < (size_t)NUM_VPU_LANES_) {
		VerifyCandidatesOnOneDirection(kNegative, read_index, read_batch, reference,
		mapping_metadata);
		} else {
		@@ -279,9 +270,9 @@ bool MappingGenerator<MappingRecord>::
		return false;
		}

		mapping_metadata.min_num_errors_ = 0;
		mapping_metadata.num_best_mappings_ = 1;
		mapping_metadata.num_second_best_mappings_ = 0;
		mapping_metadata.SetMinNumErrors(0);
		mapping_metadata.SetNumBestMappings(1);
		mapping_metadata.SetNumSecondBestMappings(0);

		uint32_t rid = 0;
		uint32_t position = 0;

src/mapping_metadata.h

+8 −0

Original line number	Diff line number	Diff line
		@@ -25,6 +25,14 @@ class MappingMetadata {
		repetitive_seed_length_ = 0;
		}

		inline size_t GetNumPositiveCandidates() const {
		return positive_candidates_.size();
		}

		inline size_t GetNumNegativeCandidates() const {
		return negative_candidates_.size();
		}

		inline size_t GetNumCandidates() const {
		return positive_candidates_.size() + negative_candidates_.size();
		}

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