Change the name of OutputTools to MappingWriter. (072fa11b) · 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 feature_barcode_matrix.cc ksw.cc output_tools.cc chromap.cc
		cpp_source=sequence_batch.cc index.cc candidate_processor.cc feature_barcode_matrix.cc ksw.cc mapping_writer.cc chromap.cc
		src_dir=src
		objs_dir=objs
		objs+=$(patsubst %.cc,$(objs_dir)/%.o,$(cpp_source))

src/chromap.cc

+16 −16

Original line number	Diff line number	Diff line
		@@ -500,7 +500,7 @@ void Chromap<MappingRecord>::PostProcessingInLowMemory(
		temp_mapping_file_handles_.emplace_back(temp_mapping_file_handle);
		SortOutputMappings(num_reference_sequences, mappings_on_diff_ref_seqs_);
		// double output_temp_mapping_start_time = Chromap<>::GetRealTime();
		output_tools_.OutputTempMapping(temp_mapping_file_handle.file_path,
		mapping_writer_.OutputTempMapping(temp_mapping_file_handle.file_path,
		num_reference_sequences,
		mappings_on_diff_ref_seqs_);
		// std::cerr << "Output temp mappings in " << Chromap<>::GetRealTime() -
		@@ -637,7 +637,7 @@ void Chromap<MappingRecord>::PostProcessingInLowMemory(
		if (Tn5_shift_) {
		last_mapping.Tn5Shift();
		}
		output_tools_.AppendMapping(last_rid, reference, last_mapping);
		mapping_writer_.AppendMapping(last_rid, reference, last_mapping);
		++num_mappings_passing_filters;
		//}
		}
		@@ -708,7 +708,7 @@ void Chromap<MappingRecord>::PostProcessingInLowMemory(
		if (Tn5_shift_) {
		last_mapping.Tn5Shift();
		}
		output_tools_.AppendMapping(last_rid, reference, last_mapping);
		mapping_writer_.AppendMapping(last_rid, reference, last_mapping);
		++num_mappings_passing_filters;
		//}
		}
		@@ -877,12 +877,12 @@ void Chromap<MappingRecord>::MapPairedEndReads() {

		// Initialize output tools
		if (mapping_output_format_ == MAPPINGFORMAT_PAIRS) {
		output_tools_.SetPairsCustomRidRank(pairs_custom_rid_rank_);
		mapping_writer_.SetPairsCustomRidRank(pairs_custom_rid_rank_);
		}

		output_tools_.InitializeMappingOutput(
		mapping_writer_.InitializeMappingOutput(
		barcode_length_, mapping_output_file_path_, mapping_output_format_);
		output_tools_.OutputHeader(num_reference_sequences, reference);
		mapping_writer_.OutputHeader(num_reference_sequences, reference);

		CandidateProcessor candidate_processor(min_num_seeds_required_for_mapping_,
		max_seed_frequencies_);
		@@ -930,7 +930,7 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		barcode_batch_for_loading.SwapSequenceBatch(barcode_batch);
		// TODO(Haowen): simplify this condition check.
		if (num_loaded_pairs > 0) {
		output_tools_.SetBarcodeLength(barcode_batch.GetSequenceLengthAt(0));
		mapping_writer_.SetBarcodeLength(barcode_batch.GetSequenceLengthAt(0));
		}
		}

		@@ -958,7 +958,7 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		}
		}

		#pragma omp parallel default(none) shared(output_mappings_not_in_whitelist_, barcode_whitelist_file_path_, trim_adapters_, window_size_, custom_rid_order_path_, split_alignment_, error_threshold_, max_seed_frequencies_, max_num_best_mappings_, max_insert_size_, num_threads_, num_reads_, low_memory_mode_, num_reference_sequences, reference, index, read_batch1, read_batch2, barcode_batch, read_batch1_for_loading, read_batch2_for_loading, barcode_batch_for_loading, candidate_processor, output_tools_, std::cerr, num_loaded_pairs_for_loading, num_loaded_pairs, mappings_on_diff_ref_seqs_for_diff_threads, mappings_on_diff_ref_seqs_for_diff_threads_for_saving, mappings_on_diff_ref_seqs_, mapping_output_file_path_, num_mappings_in_mem, max_num_mappings_in_mem, temp_mapping_file_handles_, mm_to_candidates_cache, mm_history1, mm_history2) num_threads(num_threads_) reduction(+:num_candidates_, num_mappings_, num_mapped_reads_, num_uniquely_mapped_reads_, num_barcode_in_whitelist_, num_corrected_barcode_)
		#pragma omp parallel default(none) shared(output_mappings_not_in_whitelist_, barcode_whitelist_file_path_, trim_adapters_, window_size_, custom_rid_order_path_, split_alignment_, error_threshold_, max_seed_frequencies_, max_num_best_mappings_, max_insert_size_, num_threads_, num_reads_, low_memory_mode_, num_reference_sequences, reference, index, read_batch1, read_batch2, barcode_batch, read_batch1_for_loading, read_batch2_for_loading, barcode_batch_for_loading, candidate_processor, mapping_writer_, std::cerr, num_loaded_pairs_for_loading, num_loaded_pairs, mappings_on_diff_ref_seqs_for_diff_threads, mappings_on_diff_ref_seqs_for_diff_threads_for_saving, mappings_on_diff_ref_seqs_, mapping_output_file_path_, num_mappings_in_mem, max_num_mappings_in_mem, temp_mapping_file_handles_, mm_to_candidates_cache, mm_history1, mm_history2) num_threads(num_threads_) reduction(+:num_candidates_, num_mappings_, num_mapped_reads_, num_uniquely_mapped_reads_, num_barcode_in_whitelist_, num_corrected_barcode_)
		{
		thread_num_candidates = 0;
		thread_num_mappings = 0;
		@@ -1261,7 +1261,7 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		temp_mapping_file_handles_.emplace_back(temp_mapping_file_handle);
		SortOutputMappings(num_reference_sequences,
		mappings_on_diff_ref_seqs_);
		output_tools_.OutputTempMapping(
		mapping_writer_.OutputTempMapping(
		temp_mapping_file_handle.file_path, num_reference_sequences,
		mappings_on_diff_ref_seqs_);
		num_mappings_in_mem = 0;
		@@ -1361,7 +1361,7 @@ void Chromap<MappingRecord>::MapPairedEndReads() {
		//}
		}

		output_tools_.FinalizeMappingOutput();
		mapping_writer_.FinalizeMappingOutput();

		reference.FinalizeLoading();

		@@ -1381,7 +1381,7 @@ void Chromap<MappingRecord>::OutputMappingsInVector(
		if (mapq >= mapq_threshold) {
		// if (allocate_multi_mappings_ \|\| (only_output_unique_mappings_ &&
		// is_unique == 1)) {
		output_tools_.AppendMapping(ri, reference, *it);
		mapping_writer_.AppendMapping(ri, reference, *it);
		++num_mappings_passing_filters;
		//}
		}
		@@ -2213,9 +2213,9 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		}
		}

		output_tools_.InitializeMappingOutput(
		mapping_writer_.InitializeMappingOutput(
		barcode_length_, mapping_output_file_path_, mapping_output_format_);
		output_tools_.OutputHeader(num_reference_sequences, reference);
		mapping_writer_.OutputHeader(num_reference_sequences, reference);

		mm_cache mm_to_candidates_cache(2000003);
		mm_to_candidates_cache.SetKmerLength(kmer_size_);
		@@ -2250,7 +2250,7 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		barcode_batch_for_loading.SwapSequenceBatch(barcode_batch);
		// TODO(Haowen): simplify this condition check.
		if (num_loaded_reads > 0) {
		output_tools_.SetBarcodeLength(barcode_batch.GetSequenceLengthAt(0));
		mapping_writer_.SetBarcodeLength(barcode_batch.GetSequenceLengthAt(0));
		}
		}

		@@ -2279,7 +2279,7 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		num_threads_ / num_reference_sequences);
		}
		}
		#pragma omp parallel default(none) shared(barcode_whitelist_file_path_, output_mappings_not_in_whitelist_, window_size_, custom_rid_order_path_, error_threshold_, max_num_best_mappings_, max_seed_frequencies_, num_threads_, num_reads_, mm_history, reference, index, read_batch, barcode_batch, read_batch_for_loading, barcode_batch_for_loading, std::cerr, num_loaded_reads_for_loading, num_loaded_reads, num_reference_sequences, mappings_on_diff_ref_seqs_for_diff_threads, mappings_on_diff_ref_seqs_for_diff_threads_for_saving, mm_to_candidates_cache, output_tools_, candidate_processor) num_threads(num_threads_) reduction(+:num_candidates_, num_mappings_, num_mapped_reads_, num_uniquely_mapped_reads_, num_barcode_in_whitelist_, num_corrected_barcode_)
		#pragma omp parallel default(none) shared(barcode_whitelist_file_path_, output_mappings_not_in_whitelist_, window_size_, custom_rid_order_path_, error_threshold_, max_num_best_mappings_, max_seed_frequencies_, num_threads_, num_reads_, mm_history, reference, index, read_batch, barcode_batch, read_batch_for_loading, barcode_batch_for_loading, std::cerr, num_loaded_reads_for_loading, num_loaded_reads, num_reference_sequences, mappings_on_diff_ref_seqs_for_diff_threads, mappings_on_diff_ref_seqs_for_diff_threads_for_saving, mm_to_candidates_cache, mapping_writer_, candidate_processor) num_threads(num_threads_) reduction(+:num_candidates_, num_mappings_, num_mapped_reads_, num_uniquely_mapped_reads_, num_barcode_in_whitelist_, num_corrected_barcode_)
		{
		thread_num_candidates = 0;
		thread_num_mappings = 0;
		@@ -2479,7 +2479,7 @@ void Chromap<MappingRecord>::MapSingleEndReads() {
		OutputMappings(num_reference_sequences, reference, mappings);
		}

		output_tools_.FinalizeMappingOutput();
		mapping_writer_.FinalizeMappingOutput();
		reference.FinalizeLoading();
		std::cerr << "Total time: " << GetRealTime() - real_start_time << "s.\n";
		}

src/chromap.h

+3 −3

Original line number	Diff line number	Diff line
		@@ -14,7 +14,7 @@
		#include "ksort.h"
		#include "mapping_metadata.h"
		#include "mapping_parameters.h"
		#include "output_tools.h"
		#include "mapping_writer.h"
		#include "paired_end_mapping_metadata.h"
		#include "sequence_batch.h"
		#include "temp_mapping.h"
		@@ -124,7 +124,7 @@ class Chromap {
		ParseReadFormat(mapping_parameters.read_format);
		if (mapping_parameters.barcode_translate_table_path.length() > 0) {
		std::string tmp = mapping_parameters.barcode_translate_table_path;
		output_tools_.SetBarcodeTranslateTable(tmp);
		mapping_writer_.SetBarcodeTranslateTable(tmp);
		}
		}

		@@ -479,7 +479,7 @@ class Chromap {
		std::vector<std::vector<uint32_t> > tree_extras_on_diff_ref_seqs_; // max
		// (max_level, # nodes)
		std::vector<std::pair<int, uint32_t> > tree_info_on_diff_ref_seqs_;
		OutputTools<MappingRecord> output_tools_;
		MappingWriter<MappingRecord> mapping_writer_;
		// For mapping stats.
		uint64_t num_candidates_ = 0;
		uint64_t num_mappings_ = 0;

src/output_tools.cc→src/mapping_writer.cc

+47 −44

Original line number	Diff line number	Diff line
		#include "output_tools.h"
		#include "mapping_writer.h"

		namespace chromap {

		// Specialization for BED format.
		template <>
		void OutputTools<MappingWithBarcode>::OutputHeader(
		void MappingWriter<MappingWithBarcode>::OutputHeader(
		uint32_t num_reference_sequences, const SequenceBatch &reference) {}

		template <>
		void OutputTools<MappingWithBarcode>::AppendMapping(
		void MappingWriter<MappingWithBarcode>::AppendMapping(
		uint32_t rid, const SequenceBatch &reference,
		const MappingWithBarcode &mapping) {
		if (mapping_output_format_ == MAPPINGFORMAT_BED) {
		std::string strand = mapping.IsPositiveStrand() ? "+" : "-";
		const char *reference_sequence_name = reference.GetSequenceNameAt(rid);
		uint32_t mapping_end_position = mapping.GetEndPosition();
		this->AppendMappingOutput(
		std::string(reference_sequence_name) + "\t" +
		std::to_string(mapping.GetStartPosition()) + "\t" +
		std::to_string(mapping_end_position) + "\t" +
		barcode_translator_.Translate(mapping.cell_barcode_, cell_barcode_length_) +
		this->AppendMappingOutput(std::string(reference_sequence_name) + "\t" +
		std::to_string(mapping.GetStartPosition()) +
		"\t" + std::to_string(mapping_end_position) +
		"\t" +
		barcode_translator_.Translate(
		mapping.cell_barcode_, cell_barcode_length_) +
		"\t" + std::to_string(mapping.num_dups_) + "\n");
		} else {
		std::string strand = mapping.IsPositiveStrand() ? "+" : "-";
		@@ -34,11 +35,11 @@ void OutputTools<MappingWithBarcode>::AppendMapping(
		}

		template <>
		void OutputTools<MappingWithoutBarcode>::OutputHeader(
		void MappingWriter<MappingWithoutBarcode>::OutputHeader(
		uint32_t num_reference_sequences, const SequenceBatch &reference) {}

		template <>
		void OutputTools<MappingWithoutBarcode>::AppendMapping(
		void MappingWriter<MappingWithoutBarcode>::AppendMapping(
		uint32_t rid, const SequenceBatch &reference,
		const MappingWithoutBarcode &mapping) {
		if (mapping_output_format_ == MAPPINGFORMAT_BED) {
		@@ -64,11 +65,11 @@ void OutputTools<MappingWithoutBarcode>::AppendMapping(

		// Specialization for BEDPE format.
		template <>
		void OutputTools<PairedEndMappingWithoutBarcode>::OutputHeader(
		void MappingWriter<PairedEndMappingWithoutBarcode>::OutputHeader(
		uint32_t num_reference_sequences, const SequenceBatch &reference) {}

		template <>
		void OutputTools<PairedEndMappingWithoutBarcode>::AppendMapping(
		void MappingWriter<PairedEndMappingWithoutBarcode>::AppendMapping(
		uint32_t rid, const SequenceBatch &reference,
		const PairedEndMappingWithoutBarcode &mapping) {
		if (mapping_output_format_ == MAPPINGFORMAT_BED) {
		@@ -114,23 +115,24 @@ void OutputTools<PairedEndMappingWithoutBarcode>::AppendMapping(
		}

		template <>
		void OutputTools<PairedEndMappingWithBarcode>::OutputHeader(
		void MappingWriter<PairedEndMappingWithBarcode>::OutputHeader(
		uint32_t num_reference_sequences, const SequenceBatch &reference) {}

		template <>
		void OutputTools<PairedEndMappingWithBarcode>::AppendMapping(
		void MappingWriter<PairedEndMappingWithBarcode>::AppendMapping(
		uint32_t rid, const SequenceBatch &reference,
		const PairedEndMappingWithBarcode &mapping) {
		if (mapping_output_format_ == MAPPINGFORMAT_BED) {
		std::string strand = mapping.IsPositiveStrand() ? "+" : "-";
		const char *reference_sequence_name = reference.GetSequenceNameAt(rid);
		uint32_t mapping_end_position = mapping.GetEndPosition();
		this->AppendMappingOutput(
		std::string(reference_sequence_name) + "\t" +
		std::to_string(mapping.GetStartPosition()) + "\t" +
		std::to_string(mapping_end_position) + "\t" +
		barcode_translator_.Translate(mapping.cell_barcode_, cell_barcode_length_) + "\t" +
		std::to_string(mapping.num_dups_) + "\n");
		this->AppendMappingOutput(std::string(reference_sequence_name) + "\t" +
		std::to_string(mapping.GetStartPosition()) +
		"\t" + std::to_string(mapping_end_position) +
		"\t" +
		barcode_translator_.Translate(
		mapping.cell_barcode_, cell_barcode_length_) +
		"\t" + std::to_string(mapping.num_dups_) + "\n");
		} else {
		bool positive_strand = mapping.IsPositiveStrand();
		uint32_t positive_read_end =
		@@ -166,11 +168,11 @@ void OutputTools<PairedEndMappingWithBarcode>::AppendMapping(

		// Specialization for PAF format.
		template <>
		void OutputTools<PAFMapping>::OutputHeader(uint32_t num_reference_sequences,
		void MappingWriter<PAFMapping>::OutputHeader(uint32_t num_reference_sequences,
		const SequenceBatch &reference) {}

		template <>
		void OutputTools<PAFMapping>::AppendMapping(uint32_t rid,
		void MappingWriter<PAFMapping>::AppendMapping(uint32_t rid,
		const SequenceBatch &reference,
		const PAFMapping &mapping) {
		const char *reference_sequence_name = reference.GetSequenceNameAt(rid);
		@@ -191,7 +193,7 @@ void OutputTools<PAFMapping>::AppendMapping(uint32_t rid,
		}

		template <>
		void OutputTools<PAFMapping>::OutputTempMapping(
		void MappingWriter<PAFMapping>::OutputTempMapping(
		const std::string &temp_mapping_output_file_path,
		uint32_t num_reference_sequences,
		const std::vector<std::vector<PAFMapping> > &mappings) {
		@@ -215,11 +217,11 @@ void OutputTools<PAFMapping>::OutputTempMapping(

		// Specialization for PairedPAF format.
		template <>
		void OutputTools<PairedPAFMapping>::OutputHeader(
		void MappingWriter<PairedPAFMapping>::OutputHeader(
		uint32_t num_reference_sequences, const SequenceBatch &reference) {}

		template <>
		void OutputTools<PairedPAFMapping>::OutputTempMapping(
		void MappingWriter<PairedPAFMapping>::OutputTempMapping(
		const std::string &temp_mapping_output_file_path,
		uint32_t num_reference_sequences,
		const std::vector<std::vector<PairedPAFMapping> > &mappings) {
		@@ -242,7 +244,7 @@ void OutputTools<PairedPAFMapping>::OutputTempMapping(
		}

		template <>
		void OutputTools<PairedPAFMapping>::AppendMapping(
		void MappingWriter<PairedPAFMapping>::AppendMapping(
		uint32_t rid, const SequenceBatch &reference,
		const PairedPAFMapping &mapping) {
		bool positive_strand = mapping.IsPositiveStrand();
		@@ -305,7 +307,7 @@ void OutputTools<PairedPAFMapping>::AppendMapping(

		// Specialization for SAM format.
		template <>
		void OutputTools<SAMMapping>::OutputHeader(uint32_t num_reference_sequences,
		void MappingWriter<SAMMapping>::OutputHeader(uint32_t num_reference_sequences,
		const SequenceBatch &reference) {
		for (uint32_t rid = 0; rid < num_reference_sequences; ++rid) {
		const char *reference_sequence_name = reference.GetSequenceNameAt(rid);
		@@ -317,7 +319,7 @@ void OutputTools<SAMMapping>::OutputHeader(uint32_t num_reference_sequences,
		}

		template <>
		void OutputTools<SAMMapping>::AppendMapping(uint32_t rid,
		void MappingWriter<SAMMapping>::AppendMapping(uint32_t rid,
		const SequenceBatch &reference,
		const SAMMapping &mapping) {
		// const char *reference_sequence_name = reference.GetSequenceNameAt(rid);
		@@ -338,14 +340,15 @@ void OutputTools<SAMMapping>::AppendMapping(uint32_t rid,
		mapping.GenerateIntTagString("NM", mapping.NM_) +
		"\tMD:Z:" + mapping.MD_);
		if (cell_barcode_length_ > 0) {
		this->AppendMappingOutput(
		"\tCB:Z:" + barcode_translator_.Translate(mapping.cell_barcode_, cell_barcode_length_));
		this->AppendMappingOutput("\tCB:Z:" +
		barcode_translator_.Translate(
		mapping.cell_barcode_, cell_barcode_length_));
		}
		this->AppendMappingOutput("\n");
		}

		template <>
		void OutputTools<SAMMapping>::OutputTempMapping(
		void MappingWriter<SAMMapping>::OutputTempMapping(
		const std::string &temp_mapping_output_file_path,
		uint32_t num_reference_sequences,
		const std::vector<std::vector<SAMMapping> > &mappings) {
		@@ -369,7 +372,7 @@ void OutputTools<SAMMapping>::OutputTempMapping(

		// Specialization for pairs format.
		template <>
		void OutputTools<PairsMapping>::OutputHeader(uint32_t num_reference_sequences,
		void MappingWriter<PairsMapping>::OutputHeader(uint32_t num_reference_sequences,
		const SequenceBatch &reference) {
		std::vector<uint32_t> rid_order;
		rid_order.resize(num_reference_sequences);
		@@ -391,7 +394,7 @@ void OutputTools<PairsMapping>::OutputHeader(uint32_t num_reference_sequences,
		}

		template <>
		void OutputTools<PairsMapping>::AppendMapping(uint32_t rid,
		void MappingWriter<PairsMapping>::AppendMapping(uint32_t rid,
		const SequenceBatch &reference,
		const PairsMapping &mapping) {
		const char *reference_sequence_name1 =
		@@ -408,7 +411,7 @@ void OutputTools<PairsMapping>::AppendMapping(uint32_t rid,
		}

		template <>
		void OutputTools<PairsMapping>::OutputTempMapping(
		void MappingWriter<PairsMapping>::OutputTempMapping(
		const std::string &temp_mapping_output_file_path,
		uint32_t num_reference_sequences,
		const std::vector<std::vector<PairsMapping> > &mappings) {

src/output_tools.h→src/mapping_writer.h

+35 −35

Original line number	Diff line number	Diff line
		#ifndef OUTPUTTOOLS_H_
		#define OUTPUTTOOLS_H_
		#ifndef MAPPING_WRITER_H_
		#define MAPPING_WRITER_H_

		#include <assert.h>

		@@ -28,10 +28,10 @@ bool ReadIdLess(const std::pair<uint32_t, MappingRecord> &a,
		}

		template <typename MappingRecord>
		class OutputTools {
		class MappingWriter {
		public:
		OutputTools() {}
		~OutputTools() {}
		MappingWriter() {}
		~MappingWriter() {}

		// Output the mappings in a temp file.
		inline void OutputTempMapping(
		@@ -114,106 +114,106 @@ class OutputTools {

		// Specialization for BED format.
		template <>
		void OutputTools<MappingWithBarcode>::OutputHeader(
		void MappingWriter<MappingWithBarcode>::OutputHeader(
		uint32_t num_reference_sequences, const SequenceBatch &reference);

		template <>
		void OutputTools<MappingWithBarcode>::AppendMapping(
		void MappingWriter<MappingWithBarcode>::AppendMapping(
		uint32_t rid, const SequenceBatch &reference,
		const MappingWithBarcode &mapping);

		template <>
		void OutputTools<MappingWithoutBarcode>::OutputHeader(
		void MappingWriter<MappingWithoutBarcode>::OutputHeader(
		uint32_t num_reference_sequences, const SequenceBatch &reference);

		template <>
		void OutputTools<MappingWithoutBarcode>::AppendMapping(
		void MappingWriter<MappingWithoutBarcode>::AppendMapping(
		uint32_t rid, const SequenceBatch &reference,
		const MappingWithoutBarcode &mapping);

		// Specialization for BEDPE format.
		template <>
		void OutputTools<PairedEndMappingWithoutBarcode>::OutputHeader(
		void MappingWriter<PairedEndMappingWithoutBarcode>::OutputHeader(
		uint32_t num_reference_sequences, const SequenceBatch &reference);

		template <>
		void OutputTools<PairedEndMappingWithoutBarcode>::AppendMapping(
		void MappingWriter<PairedEndMappingWithoutBarcode>::AppendMapping(
		uint32_t rid, const SequenceBatch &reference,
		const PairedEndMappingWithoutBarcode &mapping);

		template <>
		void OutputTools<PairedEndMappingWithBarcode>::OutputHeader(
		void MappingWriter<PairedEndMappingWithBarcode>::OutputHeader(
		uint32_t num_reference_sequences, const SequenceBatch &reference);

		template <>
		void OutputTools<PairedEndMappingWithBarcode>::AppendMapping(
		void MappingWriter<PairedEndMappingWithBarcode>::AppendMapping(
		uint32_t rid, const SequenceBatch &reference,
		const PairedEndMappingWithBarcode &mapping);

		// Specialization for PAF format.
		template <>
		void OutputTools<PAFMapping>::OutputHeader(uint32_t num_reference_sequences,
		void MappingWriter<PAFMapping>::OutputHeader(uint32_t num_reference_sequences,
		const SequenceBatch &reference);

		template <>
		void OutputTools<PAFMapping>::AppendMapping(uint32_t rid,
		void MappingWriter<PAFMapping>::AppendMapping(uint32_t rid,
		const SequenceBatch &reference,
		const PAFMapping &mapping);

		template <>
		void OutputTools<PAFMapping>::OutputTempMapping(
		void MappingWriter<PAFMapping>::OutputTempMapping(
		const std::string &temp_mapping_output_file_path,
		uint32_t num_reference_sequences,
		const std::vector<std::vector<PAFMapping> > &mappings);

		// Specialization for PairedPAF format.
		template <>
		void OutputTools<PairedPAFMapping>::OutputHeader(
		void MappingWriter<PairedPAFMapping>::OutputHeader(
		uint32_t num_reference_sequences, const SequenceBatch &reference);

		template <>
		void OutputTools<PairedPAFMapping>::OutputTempMapping(
		void MappingWriter<PairedPAFMapping>::OutputTempMapping(
		const std::string &temp_mapping_output_file_path,
		uint32_t num_reference_sequences,
		const std::vector<std::vector<PairedPAFMapping> > &mappings);

		template <>
		void OutputTools<PairedPAFMapping>::AppendMapping(
		void MappingWriter<PairedPAFMapping>::AppendMapping(
		uint32_t rid, const SequenceBatch &reference,
		const PairedPAFMapping &mapping);

		// Specialization for SAM format.
		template <>
		void OutputTools<SAMMapping>::OutputHeader(uint32_t num_reference_sequences,
		void MappingWriter<SAMMapping>::OutputHeader(uint32_t num_reference_sequences,
		const SequenceBatch &reference);

		template <>
		void OutputTools<SAMMapping>::AppendMapping(uint32_t rid,
		void MappingWriter<SAMMapping>::AppendMapping(uint32_t rid,
		const SequenceBatch &reference,
		const SAMMapping &mapping);

		template <>
		void OutputTools<SAMMapping>::OutputTempMapping(
		void MappingWriter<SAMMapping>::OutputTempMapping(
		const std::string &temp_mapping_output_file_path,
		uint32_t num_reference_sequences,
		const std::vector<std::vector<SAMMapping> > &mappings);

		// Specialization for pairs format.
		template <>
		void OutputTools<PairsMapping>::OutputHeader(uint32_t num_reference_sequences,
		void MappingWriter<PairsMapping>::OutputHeader(uint32_t num_reference_sequences,
		const SequenceBatch &reference);

		template <>
		void OutputTools<PairsMapping>::AppendMapping(uint32_t rid,
		void MappingWriter<PairsMapping>::AppendMapping(uint32_t rid,
		const SequenceBatch &reference,
		const PairsMapping &mapping);

		template <>
		void OutputTools<PairsMapping>::OutputTempMapping(
		void MappingWriter<PairsMapping>::OutputTempMapping(
		const std::string &temp_mapping_output_file_path,
		uint32_t num_reference_sequences,
		const std::vector<std::vector<PairsMapping> > &mappings);

		} // namespace chromap

		#endif // OUTPUTTOOLS_H_
		#endif // MAPPING_WRITER_H_

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