Commit 51d51df0 authored by Haowen Zhang's avatar Haowen Zhang
Browse files

Introduce DraftMappingGenerator.

parent 9d474b4f

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 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))

src/chromap.h

+11 −6
Original line number Diff line number Diff line
@@ -11,6 +11,7 @@ 


#include "candidate_processor.h"

#include "cxxopts.hpp"

#include "draft_mapping_generator.h"

#include "feature_barcode_matrix.h"

#include "index.h"

#include "index_parameters.h"
@@ -216,6 +217,8 @@ void Chromap::MapSingleEndReads() { 
  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_);
@@ -291,7 +294,7 @@ void Chromap::MapSingleEndReads() { 
            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;
@@ -368,8 +371,8 @@ void Chromap::MapSingleEndReads() { 
                  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();
@@ -593,6 +596,8 @@ void Chromap::MapPairedEndReads() { 
  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_);
@@ -670,7 +675,7 @@ void Chromap::MapPairedEndReads() { 
      }

    }



#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;
@@ -844,7 +849,7 @@ void Chromap::MapPairedEndReads() { 
                            .negative_candidates_);

                  }



                  mapping_generator.VerifyCandidates(

                  draft_mapping_generator.GenerateDraftMappings(

                      read_batch1, pair_index, reference,

                      paired_end_mapping_metadata.mapping_metadata1_);
@@ -852,7 +857,7 @@ void Chromap::MapPairedEndReads() { 
                      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_);

src/draft_mapping_generator.cc

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src/draft_mapping_generator.h

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#ifndef DRAFT_MAPPING_GENERATOR_H_

#define DRAFT_MAPPING_GENERATOR_H_



#include <cstdint>



#include "draft_mapping.h"

#include "mapping_metadata.h"

#include "mapping_parameters.h"

#include "sequence_batch.h"

#include "utils.h"



namespace chromap {



class DraftMappingGenerator {

 public:

  DraftMappingGenerator() = delete;



  DraftMappingGenerator(const MappingParameters &mapping_parameters)

      : error_threshold_(mapping_parameters.error_threshold),

        split_alignment_(mapping_parameters.split_alignment),

        num_vpu_lanes_(mapping_parameters.GetNumVPULanes()),

        mapping_output_format_(mapping_parameters.mapping_output_format) {}



  ~DraftMappingGenerator() = default;



  void GenerateDraftMappings(const SequenceBatch &read_batch,

                             uint32_t read_index,

                             const SequenceBatch &reference,

                             MappingMetadata &mapping_metadata);



 private:

  // Return true if the candidate position is valid on the reference with rid.

  // Note only the position is checked and the input rid is not checked in this

  // function. So the input rid must be valid.

  bool IsValidCandidate(uint32_t rid, uint32_t position, uint32_t read_length,

                        const SequenceBatch &reference);



  // Return true when there is one non-split mapping generated and the mapping

  // is supported by all the minimizers.

  bool DirectlyGenerateOneNonSplitMappingSupportedByAllMinimizers(

      const SequenceBatch &read_batch, uint32_t read_index,

      const SequenceBatch &reference, MappingMetadata &mapping_metadata);



  void GenerateDraftMappingsOnOneDirectionUsingSIMD(

      Direction candidate_direction, uint32_t read_index,

      const SequenceBatch &read_batch, const SequenceBatch &reference,

      MappingMetadata &mapping_metadata);



  void GenerateDraftMappingsOnOneDirection(Direction candidate_direction,

                                           uint32_t read_index,

                                           const SequenceBatch &read_batch,

                                           const SequenceBatch &reference,

                                           MappingMetadata &mapping_metadata);



  const int error_threshold_;

  const bool split_alignment_;

  const int num_vpu_lanes_;

  const MappingOutputFormat mapping_output_format_;

};



}  // namespace chromap



#endif  // DRAFT_MAPPING_GENERATOR_H_

src/mapping_generator.h

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