Merge branch 'refactor' (567fc3ed) · Commits · github_fork / Chromap

Makefile

+1 −1

Original line number	Diff line number	Diff line
		cpp_source=sequence_batch.cc index.cc ksw.cc chromap.cc
		cpp_source=sequence_batch.cc index.cc ksw.cc output_tools.cc chromap.cc
		src_dir=src
		objs_dir=objs
		objs+=$(patsubst %.cc,$(objs_dir)/%.o,$(cpp_source))

src/chromap.cc

+3846 −2105

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src/chromap.h

+486 −102

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src/index.cc

+325 −177

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src/index.h

+57 −34

Original line number	Diff line number	Diff line
		#ifndef INDEX_H_
		#define INDEX_H_

		#include <queue>
		#include <string>
		#include <vector>
		#include <queue>

		#include "khash.h"
		#include "sequence_batch.h"
		@@ -35,16 +35,27 @@ struct mmHit {
		uint32_t mi;
		uint64_t position;
		bool operator<(const mmHit &h) const {
		return position > h.position; // the inversed direction is to make a min-heap
		return position >
		h.position; // the inversed direction is to make a min-heap
		}
		};

		class Index {
		public:
		Index(int min_num_seeds_required_for_mapping, const std::vector<int> &max_seed_frequencies, const std::string &index_file_path) : min_num_seeds_required_for_mapping_(min_num_seeds_required_for_mapping), max_seed_frequencies_(max_seed_frequencies), index_file_path_(index_file_path) { // for read mapping
		Index(int min_num_seeds_required_for_mapping,
		const std::vector<int> &max_seed_frequencies,
		const std::string &index_file_path)
		: min_num_seeds_required_for_mapping_(min_num_seeds_required_for_mapping),
		max_seed_frequencies_(max_seed_frequencies),
		index_file_path_(index_file_path) { // for read mapping
		lookup_table_ = kh_init(k64);
		}
		Index(int kmer_size, int window_size, int num_threads, const std::string &index_file_path) : kmer_size_(kmer_size), window_size_(window_size), num_threads_(num_threads), index_file_path_(index_file_path) { // for index construction
		Index(int kmer_size, int window_size, int num_threads,
		const std::string &index_file_path)
		: kmer_size_(kmer_size),
		window_size_(window_size),
		num_threads_(num_threads),
		index_file_path_(index_file_path) { // for index construction
		lookup_table_ = kh_init(k64);
		}
		~Index() {
		@@ -57,31 +68,43 @@ class Index {
		lookup_table_ = NULL;
		std::vector<uint64_t>().swap(occurrence_table_);
		}
		khash_t(k64) const * GetLookupTable() const {
		return lookup_table_;
		}
		int GetKmerSize() const {
		return kmer_size_;
		}
		int GetWindowSize() const {
		return window_size_;
		}
		uint32_t GetLookupTableSize() const {
		return kh_size(lookup_table_);
		}
		khash_t(k64) const *GetLookupTable() const { return lookup_table_; }
		int GetKmerSize() const { return kmer_size_; }
		int GetWindowSize() const { return window_size_; }
		uint32_t GetLookupTableSize() const { return kh_size(lookup_table_); }
		std::vector<uint64_t> const &GetOccurrenceTable() const {
		return occurrence_table_;
		}
		void Statistics(uint32_t num_sequences, const SequenceBatch &reference);
		void CheckIndex(uint32_t num_sequences, const SequenceBatch &reference);
		void GenerateMinimizerSketch(const SequenceBatch &sequence_batch, uint32_t sequence_index, std::vector<std::pair<uint64_t, uint64_t> > *minimizers);
		void GenerateMinimizerSketch(
		const SequenceBatch &sequence_batch, uint32_t sequence_index,
		std::vector<std::pair<uint64_t, uint64_t> > *minimizers);
		void Construct(uint32_t num_sequences, const SequenceBatch &reference);
		void Save();
		void Load();
		void GenerateCandidatesOnOneDirection(int error_threshold, int num_seeds_required, uint32_t num_minimizers, std::vector<uint64_t> hits, std::vector<Candidate> candidates) const;
		void GenerateCandidates(int error_threshold, const std::vector<std::pair<uint64_t, uint64_t> > &minimizers, uint32_t repetitive_seed_length, std::vector<uint64_t> positive_hits, std::vector<uint64_t> negative_hits, std::vector<Candidate> positive_candidates, std::vector<Candidate> *negative_candidates) const;
		int GenerateCandidatesFromRepetitiveReadWithMateInfo(int error_threshold, const std::vector<std::pair<uint64_t, uint64_t> > &minimizers, uint32_t repetitive_seed_length, std::vector<uint64_t> hits, std::vector<Candidate> candidates, std::vector<Candidate> mate_candidates, Direction direction, uint32_t range) const;
		int CollectCandidates(int max_seed_frequency, int repetitive_seed_frequency, const std::vector<std::pair<uint64_t, uint64_t> > &minimizers, uint32_t repetitive_seed_length, std::vector<uint64_t> positive_hits, std::vector<uint64_t> *negative_hits, bool use_heap) const;
		void GenerateCandidatesOnOneDirection(
		int error_threshold, int num_seeds_required, uint32_t num_minimizers,
		std::vector<uint64_t> hits, std::vector<Candidate> candidates) const;
		void GenerateCandidates(
		int error_threshold,
		const std::vector<std::pair<uint64_t, uint64_t> > &minimizers,
		uint32_t repetitive_seed_length, std::vector<uint64_t> positive_hits,
		std::vector<uint64_t> *negative_hits,
		std::vector<Candidate> *positive_candidates,
		std::vector<Candidate> *negative_candidates) const;
		int GenerateCandidatesFromRepetitiveReadWithMateInfo(
		int error_threshold,
		const std::vector<std::pair<uint64_t, uint64_t> > &minimizers,
		uint32_t repetitive_seed_length, std::vector<uint64_t> hits,
		std::vector<Candidate> *candidates,
		std::vector<Candidate> *mate_candidates, Direction direction,
		uint32_t range) const;
		int CollectCandidates(
		int max_seed_frequency, int repetitive_seed_frequency,
		const std::vector<std::pair<uint64_t, uint64_t> > &minimizers,
		uint32_t repetitive_seed_length, std::vector<uint64_t> positive_hits,
		std::vector<uint64_t> *negative_hits, bool use_heap) const;
		inline static uint64_t Hash64(uint64_t key, const uint64_t mask) {
		key = (~key + (key << 21)) & mask; // key = (key << 21) - key - 1;
		key = key ^ key >> 24;

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