More encapsulation for mapping metadata. (fc69224c) · Commits · github_fork / Chromap

src/chromap.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -28,7 +28,7 @@
		#include "temp_mapping.h"
		#include "utils.h"

		#define CHROMAP_VERSION "0.2.3-r420"
		#define CHROMAP_VERSION "0.2.3-r424"

		namespace chromap {

src/draft_mapping_generator.cc

+10 −11

Original line number	Diff line number	Diff line
		@@ -88,9 +88,6 @@ bool DraftMappingGenerator::
		const std::vector<Candidate> &negative_candidates =
		mapping_metadata.negative_candidates_;

		const std::vector<std::pair<uint64_t, uint64_t>> &minimizers =
		mapping_metadata.minimizers_;

		std::vector<DraftMapping> &positive_mappings =
		mapping_metadata.positive_mappings_;
		std::vector<DraftMapping> &negative_mappings =
		@@ -101,14 +98,14 @@ bool DraftMappingGenerator::
		Direction all_minimizer_candidate_direction = kPositive;

		for (uint32_t i = 0; i < positive_candidates.size(); ++i) {
		if (positive_candidates[i].count == minimizers.size()) {
		if (positive_candidates[i].count == mapping_metadata.GetNumMinimizers()) {
		all_minimizer_candidate_index = i;
		++num_all_minimizer_candidates;
		}
		}

		for (uint32_t i = 0; i < negative_candidates.size(); ++i) {
		if (negative_candidates[i].count == minimizers.size()) {
		if (negative_candidates[i].count == mapping_metadata.GetNumMinimizers()) {
		all_minimizer_candidate_index = i;
		all_minimizer_candidate_direction = kNegative;
		++num_all_minimizer_candidates;
		@@ -123,18 +120,20 @@ bool DraftMappingGenerator::
		mapping_metadata.SetNumBestMappings(1);
		mapping_metadata.SetNumSecondBestMappings(0);

		uint32_t rid = 0;
		uint32_t position = 0;
		const uint32_t read_length = read_batch.GetSequenceLengthAt(read_index);
		const std::vector<Candidate> &candidates =
		all_minimizer_candidate_direction == kPositive ? positive_candidates
		: negative_candidates;

		const uint32_t rid =
		candidates[all_minimizer_candidate_index].GetReferenceSequenceIndex();

		uint32_t position = 0;

		if (all_minimizer_candidate_direction == kPositive) {
		rid = positive_candidates[all_minimizer_candidate_index]
		.GetReferenceSequenceIndex();
		position = positive_candidates[all_minimizer_candidate_index]
		.GetReferenceSequencePosition();
		} else {
		rid = negative_candidates[all_minimizer_candidate_index]
		.GetReferenceSequenceIndex();
		position = negative_candidates[all_minimizer_candidate_index]
		.GetReferenceSequencePosition() -
		read_length + 1;

src/mapping_metadata.h

+4 −0

Original line number	Diff line number	Diff line
		@@ -28,6 +28,10 @@ class MappingMetadata {
		repetitive_seed_length_ = 0;
		}

		inline size_t GetNumMinimizers() const {
		return minimizers_.size();
		}

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

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