Implement a minimizer class and its generator. (22f52653) · Commits · github_fork / Chromap

Makefile

+1 −1

Original line number	Diff line number	Diff line
		@@ -2,7 +2,7 @@ CXX=g++
		CXXFLAGS=-std=c++11 -Wall -O3 -fopenmp -msse4.1
		LDFLAGS=-lm -lz

		cpp_source=sequence_batch.cc index.cc candidate_processor.cc alignment.cc feature_barcode_matrix.cc ksw.cc draft_mapping_generator.cc mapping_generator.cc mapping_writer.cc chromap.cc chromap_driver.cc
		cpp_source=sequence_batch.cc index.cc minimizer_generator.cc candidate_processor.cc alignment.cc feature_barcode_matrix.cc ksw.cc draft_mapping_generator.cc mapping_generator.cc mapping_writer.cc chromap.cc chromap_driver.cc
		src_dir=src
		objs_dir=objs
		objs+=$(patsubst %.cc,$(objs_dir)/%.o,$(cpp_source))

src/alignment.cc

+2 −2

Original line number	Diff line number	Diff line
		@@ -21,12 +21,12 @@ int GetLongestMatchLength(const char pattern, const char text,
		return max_match;
		}

		int AdjustGapBeginning(Direction mapping_direction, const char *ref,
		int AdjustGapBeginning(const Strand mapping_strand, const char *ref,
		const char read, int gap_beginning, int read_end,
		int ref_start_position, int ref_end_position,
		int n_cigar, uint32_t *cigar) {
		int i, j;
		if (mapping_direction == kPositive) {
		if (mapping_strand == kPositive) {
		if (*gap_beginning <= 0) {
		return ref_start_position;
		}

src/alignment.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -13,7 +13,7 @@ int GetLongestMatchLength(const char pattern, const char text,

		// Return newly adjusted reference start/end position for kPositive/kNegative
		// mappings.
		int AdjustGapBeginning(Direction mapping_direction, const char *ref,
		int AdjustGapBeginning(const Strand mapping_strand, const char *ref,
		const char read, int gap_beginning, int read_end,
		int ref_start_position, int ref_end_position,
		int n_cigar, uint32_t *cigar);

src/candidate_processor.cc

+15 −17

Original line number	Diff line number	Diff line
		@@ -12,8 +12,7 @@ namespace chromap {
		void CandidateProcessor::GenerateCandidates(
		int error_threshold, const Index &index,
		MappingMetadata &mapping_metadata) const {
		const std::vector<std::pair<uint64_t, uint64_t>> &minimizers =
		mapping_metadata.minimizers_;
		const std::vector<Minimizer> &minimizers = mapping_metadata.minimizers_;
		std::vector<uint64_t> &positive_hits = mapping_metadata.positive_hits_;
		std::vector<uint64_t> &negative_hits = mapping_metadata.negative_hits_;
		std::vector<Candidate> &positive_candidates =
		@@ -51,11 +50,11 @@ void CandidateProcessor::GenerateCandidates(
		}

		// std::cerr << "Normal positive gen on one dir\n";
		GenerateCandidatesOnOneDirection(error_threshold, num_required_seeds,
		GenerateCandidatesOnOneStrand(error_threshold, num_required_seeds,
		minimizers.size(), positive_hits,
		positive_candidates);
		// std::cerr << "Normal negative gen on one dir\n";
		GenerateCandidatesOnOneDirection(error_threshold, num_required_seeds,
		GenerateCandidatesOnOneStrand(error_threshold, num_required_seeds,
		minimizers.size(), negative_hits,
		negative_candidates);
		// fprintf(stderr, "p+n: %d\n", positive_candidates->size() +
		@@ -75,7 +74,7 @@ int CandidateProcessor::SupplementCandidates(
		int ret = 0;

		for (int mate = 0; mate <= 1; ++mate) {
		std::vector<std::pair<uint64_t, uint64_t>> *minimizers;
		std::vector<Minimizer> *minimizers;
		std::vector<uint64_t> *positive_hits;
		std::vector<uint64_t> *negative_hits;
		std::vector<Candidate> *positive_candidates;
		@@ -256,22 +255,21 @@ void CandidateProcessor::ReduceCandidatesForPairedEndRead(

		int CandidateProcessor::GenerateCandidatesFromRepetitiveReadWithMateInfo(
		int error_threshold, const Index &index,
		const std::vector<std::pair<uint64_t, uint64_t>> &minimizers,
		uint32_t &repetitive_seed_length, std::vector<uint64_t> &hits,
		std::vector<Candidate> &candidates,
		const std::vector<Candidate> &mate_candidates, const Direction direction,
		const std::vector<Minimizer> &minimizers, uint32_t &repetitive_seed_length,
		std::vector<uint64_t> &hits, std::vector<Candidate> &candidates,
		const std::vector<Candidate> &mate_candidates, const Strand strand,
		uint32_t search_range) const {
		int max_seed_count = index.CollectSeedHitsFromRepetitiveReadWithMateInfo(
		error_threshold, minimizers, repetitive_seed_length, hits,
		mate_candidates, direction, search_range,
		mate_candidates, strand, search_range,
		min_num_seeds_required_for_mapping_, max_seed_frequencies_[0]);

		GenerateCandidatesOnOneDirection(error_threshold, /num_seeds_required=/1,
		GenerateCandidatesOnOneStrand(error_threshold, /num_seeds_required=/1,
		minimizers.size(), hits, candidates);
		return max_seed_count;
		}

		void CandidateProcessor::GenerateCandidatesOnOneDirection(
		void CandidateProcessor::GenerateCandidatesOnOneStrand(
		int error_threshold, int num_seeds_required, uint32_t num_minimizers,
		std::vector<uint64_t> &hits, std::vector<Candidate> &candidates) const {
		hits.emplace_back(UINT64_MAX);

src/candidate_processor.h

+8 −5

Original line number	Diff line number	Diff line
		@@ -13,6 +13,7 @@
		#include "mapping_metadata.h"
		#include "paired_end_mapping_metadata.h"
		#include "sequence_batch.h"
		#include "utils.h"

		namespace chromap {

		@@ -39,16 +40,18 @@ class CandidateProcessor {
		PairedEndMappingMetadata &paired_end_mapping_metadata) const;

		private:
		void GenerateCandidatesOnOneDirection(
		int error_threshold, int num_seeds_required, uint32_t num_minimizers,
		std::vector<uint64_t> &hits, std::vector<Candidate> &candidates) const;
		void GenerateCandidatesOnOneStrand(int error_threshold,
		int num_seeds_required,
		uint32_t num_minimizers,
		std::vector<uint64_t> &hits,
		std::vector<Candidate> &candidates) const;

		int GenerateCandidatesFromRepetitiveReadWithMateInfo(
		int error_threshold, const Index &index,
		const std::vector<std::pair<uint64_t, uint64_t> > &minimizers,
		const std::vector<Minimizer> &minimizers,
		uint32_t &repetitive_seed_length, std::vector<uint64_t> &hits,
		std::vector<Candidate> &candidates,
		const std::vector<Candidate> &mate_candidates, const Direction direction,
		const std::vector<Candidate> &mate_candidates, const Strand strand,
		uint32_t search_range) const;

		void MergeCandidates(int error_threshold, std::vector<Candidate> &c1,

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