Clean up the code. (16de1d2d) · Commits · github_fork / Chromap

src/chromap.cc

+317 −319

File changed.

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src/chromap.h

+17 −10

Original line number	Diff line number	Diff line
		@@ -9,7 +9,6 @@
		#include <tuple>
		#include <vector>

		#include "alignment.h"
		#include "candidate_processor.h"
		#include "cxxopts.hpp"
		#include "feature_barcode_matrix.h"
		@@ -27,7 +26,7 @@
		#include "temp_mapping.h"
		#include "utils.h"

		#define CHROMAP_VERSION "0.1.6-r310"
		#define CHROMAP_VERSION "0.1.6-r346"

		namespace chromap {

		@@ -73,8 +72,6 @@ class Chromap {
		void MapPairedEndReads();

		private:
		uint32_t SampleInputBarcodesAndExamineLength();

		uint32_t LoadSingleEndReadsWithBarcodes(SequenceBatch &read_batch,
		SequenceBatch &barcode_batch);

		@@ -91,6 +88,8 @@ class Chromap {
		const SequenceBatch &read_batch1,
		const SequenceBatch &read_batch2);

		uint32_t SampleInputBarcodesAndExamineLength();

		void LoadBarcodeWhitelist();

		void ComputeBarcodeAbundance(uint64_t max_num_sample_barcodes);
		@@ -106,6 +105,8 @@ class Chromap {

		void OutputMappingStatistics();

		void ParseReadFormat(const std::string &read_format);

		void GenerateCustomizedRidRank(const std::string &rid_order_path,
		uint32_t num_reference_sequences,
		const SequenceBatch &reference,
		@@ -114,40 +115,46 @@ class Chromap {
		// TODO: generate reranked candidates directly.
		void RerankCandidatesRid(std::vector<Candidate> &candidates);

		void ParseReadFormat(const std::string &read_format);

		// Parameters
		const IndexParameters index_parameters_;
		const MappingParameters mapping_parameters_;

		// Default batch size, # reads for single-end reads, # read pairs for
		// paired-end reads.
		const uint32_t read_batch_size_ = 500000;

		// 0-start, 1-end (includsive), 2-strand(-1:minus, 1:plus)
		int barcode_format_[3];
		int read1_format_[3];
		int read2_format_[3];

		std::vector<int> custom_rid_rank_;
		std::vector<int> pairs_custom_rid_rank_;

		khash_t(k64_seq) * barcode_whitelist_lookup_table_;

		// For identical read dedupe
		khash_t(k64_seq) * barcode_lookup_table_;
		std::vector<khash_t(k128) *> read_lookup_tables_;
		// For mapping

		// For mapping.
		const int min_unique_mapping_mapq_ = 4;

		// For mapping stats.
		uint64_t num_candidates_ = 0;
		uint64_t num_mappings_ = 0;
		uint64_t num_mapped_reads_ = 0;
		uint64_t num_uniquely_mapped_reads_ = 0;
		uint64_t num_reads_ = 0;
		uint64_t num_duplicated_reads_ = 0; // # identical reads
		// For barcode stats
		// # identical reads.
		uint64_t num_duplicated_reads_ = 0;

		// For barcode stats.
		const uint64_t initial_num_sample_barcodes_ = 20000000;
		uint64_t num_sample_barcodes_ = 0;
		uint64_t num_barcode_in_whitelist_ = 0;
		uint64_t num_corrected_barcode_ = 0;
		uint32_t barcode_length_ = 0;
		bool skip_barcode_check_ = false;
		};

		template <typename MappingRecord>

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