Introduce DraftMappingGenerator.

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 mapping_generator.cc mapping_writer.cc chromap.cc chromap_driver.cc

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

src_dir=src

objs_dir=objs

objs+=$(patsubst %.cc,$(objs_dir)/%.o,$(cpp_source))

#include "candidate_processor.h"

#include "cxxopts.hpp"

#include "draft_mapping_generator.h"

#include "feature_barcode_matrix.h"

#include "index.h"

#include "index_parameters.h"

  MappingProcessor<MappingRecord> mapping_processor(mapping_parameters_,

                                                    min_unique_mapping_mapq_);

  DraftMappingGenerator draft_mapping_generator(mapping_parameters_);

  MappingGenerator<MappingRecord> mapping_generator(mapping_parameters_,

                                                    pairs_custom_rid_rank_);

            mapping_parameters_.num_threads / num_reference_sequences);

      }

    }

#pragma omp parallel shared(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, mappings_on_diff_ref_seqs, temp_mapping_file_handles, mm_to_candidates_cache, mapping_writer, candidate_processor, mapping_processor, mapping_generator, num_mappings_in_mem, max_num_mappings_in_mem) num_threads(mapping_parameters_.num_threads) reduction(+:num_candidates_, num_mappings_, num_mapped_reads_, num_uniquely_mapped_reads_, num_barcode_in_whitelist_, num_corrected_barcode_)

#pragma omp parallel shared(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, mappings_on_diff_ref_seqs, temp_mapping_file_handles, mm_to_candidates_cache, mapping_writer, candidate_processor, mapping_processor, draft_mapping_generator, mapping_generator, num_mappings_in_mem, max_num_mappings_in_mem) num_threads(mapping_parameters_.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;

                  mapping_metadata.GetNumCandidates();

              if (current_num_candidates > 0) {

                thread_num_candidates += current_num_candidates;

                mapping_generator.VerifyCandidates(read_batch, read_index,

                                                   reference, mapping_metadata);

                draft_mapping_generator.GenerateDraftMappings(

                    read_batch, read_index, reference, mapping_metadata);

                const size_t current_num_draft_mappings =

                    mapping_metadata.GetNumDraftMappings();

  MappingProcessor<MappingRecord> mapping_processor(mapping_parameters_,

                                                    min_unique_mapping_mapq_);

  DraftMappingGenerator draft_mapping_generator(mapping_parameters_);

  MappingGenerator<MappingRecord> mapping_generator(mapping_parameters_,

                                                    pairs_custom_rid_rank_);

      }

    }

#pragma omp parallel shared(num_reads_, 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_processor, mapping_generator, 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, num_mappings_in_mem, max_num_mappings_in_mem, temp_mapping_file_handles, mm_to_candidates_cache, mm_history1, mm_history2) num_threads(mapping_parameters_.num_threads) reduction(+:num_candidates_, num_mappings_, num_mapped_reads_, num_uniquely_mapped_reads_, num_barcode_in_whitelist_, num_corrected_barcode_)

#pragma omp parallel shared(num_reads_, 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_processor, draft_mapping_generator, mapping_generator, 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, num_mappings_in_mem, max_num_mappings_in_mem, temp_mapping_file_handles, mm_to_candidates_cache, mm_history1, mm_history2) num_threads(mapping_parameters_.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;

                            .negative_candidates_);

                  }

                  mapping_generator.VerifyCandidates(

                  draft_mapping_generator.GenerateDraftMappings(

                      read_batch1, pair_index, reference,

                      paired_end_mapping_metadata.mapping_metadata1_);

                      paired_end_mapping_metadata.mapping_metadata1_

                          .GetNumDraftMappings();

                  mapping_generator.VerifyCandidates(

                  draft_mapping_generator.GenerateDraftMappings(

                      read_batch2, pair_index, reference,

                      paired_end_mapping_metadata.mapping_metadata2_);