Func to get candidate rid and position. (818e4b44) · Commits · github_fork / Chromap

src/candidate.h

+14 −5

Original line number	Diff line number	Diff line
		@@ -4,12 +4,21 @@
		namespace chromap {

		struct Candidate {
		uint64_t position;
		uint8_t count;
		// The high 32 bits save the reference sequence index in the reference
		// sequence batch. The low 32 bits save the reference position on that
		// sequence.
		uint64_t position = 0;

		bool operator<(const Candidate &c) const {
		if (count != c.count) {
		return count > c.count;
		// The number of minimizers supports the position.
		uint8_t count = 0;

		inline uint32_t GetReferenceSequenceIndex() const { return (position >> 32); }

		inline uint32_t GetReferenceSequencePosition() const { return position; }

		inline bool operator<(const Candidate &c) const {
		if (count > c.count) {
		return true;
		}

		return position < c.position;

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-r410"
		#define CHROMAP_VERSION "0.2.3-r411"

		namespace chromap {

src/mapping_generator.h

+22 −19

Original line number	Diff line number	Diff line
		@@ -217,18 +217,17 @@ bool MappingGenerator<MappingRecord>::
		return false;
		}

		const std::vector<Candidate> &positive_candidates =
		mapping_metadata.positive_candidates_;
		const std::vector<Candidate> &negative_candidates =
		mapping_metadata.negative_candidates_;

		const bool has_one_candidate =
		(positive_candidates.size() + negative_candidates.size() == 1);
		const bool has_one_candidate = (mapping_metadata.GetNumCandidates() == 1);

		if (!has_one_candidate) {
		return false;
		}

		const std::vector<Candidate> &positive_candidates =
		mapping_metadata.positive_candidates_;
		const std::vector<Candidate> &negative_candidates =
		mapping_metadata.negative_candidates_;

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

		@@ -279,12 +278,15 @@ bool MappingGenerator<MappingRecord>::
		uint32_t read_length = read_batch.GetSequenceLengthAt(read_index);

		if (all_minimizer_candidate_direction == kPositive) {
		rid = positive_candidates[all_minimizer_candidate_index].position >> 32;
		position = positive_candidates[all_minimizer_candidate_index].position;
		rid = positive_candidates[all_minimizer_candidate_index]
		.GetReferenceSequenceIndex();
		position = positive_candidates[all_minimizer_candidate_index]
		.GetReferenceSequencePosition();
		} else {
		rid = negative_candidates[all_minimizer_candidate_index].position >> 32;
		position =
		(uint32_t)negative_candidates[all_minimizer_candidate_index].position -
		rid = negative_candidates[all_minimizer_candidate_index]
		.GetReferenceSequenceIndex();
		position = negative_candidates[all_minimizer_candidate_index]
		.GetReferenceSequencePosition() -
		read_length + 1;
		}

		@@ -334,8 +336,9 @@ void MappingGenerator<MappingRecord>::VerifyCandidatesOnOneDirectionUsingSIMD(
		uint32_t candidate_count_threshold = 0;
		while (candidate_index < num_candidates) {
		if (candidates[candidate_index].count < candidate_count_threshold) break;
		uint32_t rid = candidates[candidate_index].position >> 32;
		uint32_t position = candidates[candidate_index].position;
		uint32_t rid = candidates[candidate_index].GetReferenceSequenceIndex();
		uint32_t position =
		candidates[candidate_index].GetReferenceSequencePosition();
		if (candidate_direction == kNegative) {
		position = position - read_length + 1;
		}
		@@ -457,8 +460,8 @@ void MappingGenerator<MappingRecord>::VerifyCandidatesOnOneDirectionUsingSIMD(
		}

		for (uint32_t ci = 0; ci < valid_candidate_index; ++ci) {
		uint32_t rid = valid_candidates[ci].position >> 32;
		uint32_t position = valid_candidates[ci].position;
		uint32_t rid = valid_candidates[ci].GetReferenceSequenceIndex();
		uint32_t position = valid_candidates[ci].GetReferenceSequencePosition();
		if (candidate_direction == kNegative) {
		position = position - read_length + 1;
		}
		@@ -539,8 +542,8 @@ void MappingGenerator<MappingRecord>::VerifyCandidatesOnOneDirection(

		for (uint32_t ci = 0; ci < candidates.size(); ++ci) {
		if (candidates[ci].count < candidate_count_threshold) break;
		uint32_t rid = candidates[ci].position >> 32;
		uint32_t position = candidates[ci].position;
		uint32_t rid = candidates[ci].GetReferenceSequenceIndex();
		uint32_t position = candidates[ci].GetReferenceSequencePosition();
		if (candidate_direction == kNegative) {
		position = position - read_length + 1;
		}

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