Commit c10a4c30 authored by Li's avatar Li Committed by Haowen Zhang
Browse files

Fix several issues in the output format of single-end data.

parent 9ca20e7e

src/chromap.cc

+39 −14
Original line number Diff line number Diff line
@@ -2778,9 +2778,12 @@ void Chromap<MappingRecord>::MapSingleEndReads() { 
  static uint64_t thread_num_mappings = 0;

  static uint64_t thread_num_mapped_reads = 0;

  static uint64_t thread_num_uniquely_mapped_reads = 0;

  static uint64_t thread_num_barcode_in_whitelist = 0;

  static uint64_t thread_num_corrected_barcode = 0;

#pragma omp threadprivate(thread_num_candidates, thread_num_mappings, \

                          thread_num_mapped_reads,                    \

                          thread_num_uniquely_mapped_reads)

                          thread_num_uniquely_mapped_reads, thread_num_barcode_in_whitelist, \

                          thread_num_corrected_barcode)

  double real_start_mapping_time = Chromap<>::GetRealTime();

  for (size_t read_file_index = 0; read_file_index < read_file1_paths_.size();

       ++read_file_index) {
@@ -2827,12 +2830,14 @@ void Chromap<MappingRecord>::MapSingleEndReads() { 
            num_threads_ / num_reference_sequences);

      }

    }

#pragma omp parallel default(none) shared(window_size_, custom_rid_order_path_, error_threshold_, max_num_best_mappings_, 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) num_threads(num_threads_) reduction(+:num_candidates_, num_mappings_, num_mapped_reads_, num_uniquely_mapped_reads_)

#pragma omp parallel default(none) shared(window_size_, custom_rid_order_path_, error_threshold_, max_num_best_mappings_, 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) 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;

      thread_num_mapped_reads = 0;

      thread_num_uniquely_mapped_reads = 0;

      thread_num_barcode_in_whitelist = 0;

      thread_num_corrected_barcode = 0;

      MappingMetadata mapping_metadata;

#pragma omp single

      {
@@ -2849,6 +2854,18 @@ void Chromap<MappingRecord>::MapSingleEndReads() { 
#pragma omp taskloop num_tasks(num_threads_ *num_threads_)

          for (uint32_t read_index = 0; read_index < num_loaded_reads;

               ++read_index) {

            

            bool current_barcode_is_whitelisted = true;

            if (!barcode_whitelist_file_path_.empty()) {

              current_barcode_is_whitelisted = CorrectBarcodeAt(

                  read_index, barcode_batch, thread_num_barcode_in_whitelist,

                  thread_num_corrected_barcode);

            }

            

            if (!(current_barcode_is_whitelisted ||

                output_mappings_not_in_whitelist_)) 

              continue;



            read_batch.PrepareNegativeSequenceAt(read_index);



            mapping_metadata.PrepareForMappingNextRead(
@@ -2956,6 +2973,8 @@ void Chromap<MappingRecord>::MapSingleEndReads() { 
        }

      }  // end of openmp single

      {

        num_barcode_in_whitelist_ += thread_num_barcode_in_whitelist;

        num_corrected_barcode_ += thread_num_corrected_barcode;

        num_candidates_ += thread_num_candidates;

        num_mappings_ += thread_num_mappings;

        num_mapped_reads_ += thread_num_mapped_reads;
@@ -2968,12 +2987,19 @@ void Chromap<MappingRecord>::MapSingleEndReads() { 
    }

  }



  delete[] mm_history;

  OutputMappingStatistics();

  std::cerr << "Mapped all reads in "

            << Chromap<>::GetRealTime() - real_start_mapping_time << "s.\n";

  OutputMappingStatistics(num_reference_sequences, mappings_on_diff_ref_seqs_,

                          mappings_on_diff_ref_seqs_);

  

  delete[] mm_history;

  

  OutputMappingStatistics();

  if (!is_bulk_data_) {

    OutputBarcodeStatistics();

  }



  index.Destroy();

  //OutputMappingStatistics(num_reference_sequences, mappings_on_diff_ref_seqs_,

  //                        mappings_on_diff_ref_seqs_);



  if (Tn5_shift_) {

    ApplyTn5ShiftOnSingleEndMapping(num_reference_sequences,
@@ -3015,14 +3041,14 @@ void Chromap<MappingRecord>::MapSingleEndReads() { 


template <typename MappingRecord>

void Chromap<MappingRecord>::EmplaceBackMappingRecord(

    uint32_t read_id, uint32_t barcode, uint32_t fragment_start_position,

    uint32_t read_id, uint64_t barcode, uint32_t fragment_start_position,

    uint16_t fragment_length, uint8_t mapq, uint8_t direction,

    uint8_t is_unique, uint8_t num_dups,

    std::vector<MappingRecord> *mappings_on_diff_ref_seqs) {}



template <>

void Chromap<MappingWithoutBarcode>::EmplaceBackMappingRecord(

    uint32_t read_id, uint32_t barcode, uint32_t fragment_start_position,

    uint32_t read_id, uint64_t barcode, uint32_t fragment_start_position,

    uint16_t fragment_length, uint8_t mapq, uint8_t direction,

    uint8_t is_unique, uint8_t num_dups,

    std::vector<MappingWithoutBarcode> *mappings_on_diff_ref_seqs) {
@@ -3033,7 +3059,7 @@ void Chromap<MappingWithoutBarcode>::EmplaceBackMappingRecord( 


template <>

void Chromap<MappingWithBarcode>::EmplaceBackMappingRecord(

    uint32_t read_id, uint32_t barcode, uint32_t fragment_start_position,

    uint32_t read_id, uint64_t barcode, uint32_t fragment_start_position,

    uint16_t fragment_length, uint8_t mapq, uint8_t direction,

    uint8_t is_unique, uint8_t num_dups,

    std::vector<MappingWithBarcode> *mappings_on_diff_ref_seqs) {
@@ -3045,7 +3071,7 @@ void Chromap<MappingWithBarcode>::EmplaceBackMappingRecord( 
template <typename MappingRecord>

void Chromap<MappingRecord>::EmplaceBackMappingRecord(

    uint32_t read_id, const char *read_name, uint16_t read_length,

    uint32_t barcode, uint32_t fragment_start_position,

    uint64_t barcode, uint32_t fragment_start_position,

    uint16_t fragment_length, uint8_t mapq, uint8_t direction,

    uint8_t is_unique, uint8_t num_dups,

    std::vector<MappingRecord> *mappings_on_diff_ref_seqs) {}
@@ -3053,7 +3079,7 @@ void Chromap<MappingRecord>::EmplaceBackMappingRecord( 
template <>

void Chromap<PAFMapping>::EmplaceBackMappingRecord(

    uint32_t read_id, const char *read_name, uint16_t read_length,

    uint32_t barcode, uint32_t fragment_start_position,

    uint64_t barcode, uint32_t fragment_start_position,

    uint16_t fragment_length, uint8_t mapq, uint8_t direction,

    uint8_t is_unique, uint8_t num_dups,

    std::vector<PAFMapping> *mappings_on_diff_ref_seqs) {
@@ -3064,7 +3090,7 @@ void Chromap<PAFMapping>::EmplaceBackMappingRecord( 


template <typename MappingRecord>

void Chromap<MappingRecord>::EmplaceBackMappingRecord(

    uint32_t read_id, const char *read_name, uint32_t cell_barcode,

    uint32_t read_id, const char *read_name, uint64_t cell_barcode,

    uint8_t num_dups, int64_t position, int rid, int flag, uint8_t direction,

    uint8_t is_unique, uint8_t mapq, uint32_t NM, int n_cigar, uint32_t *cigar,

    std::string &MD_tag, const char *read, const char *read_qual,
@@ -3072,7 +3098,7 @@ void Chromap<MappingRecord>::EmplaceBackMappingRecord( 


template <>

void Chromap<SAMMapping>::EmplaceBackMappingRecord(

    uint32_t read_id, const char *read_name, uint32_t cell_barcode,

    uint32_t read_id, const char *read_name, uint64_t cell_barcode,

    uint8_t num_dups, int64_t position, int rid, int flag, uint8_t direction,

    uint8_t is_unique, uint8_t mapq, uint32_t NM, int n_cigar, uint32_t *cigar,

    std::string &MD_tag, const char *read, const char *read_qual,
@@ -3490,7 +3516,6 @@ void Chromap<MappingRecord>::ProcessBestMappingsForSingleEndRead( 
            ref_end_position - ref_start_position + 1, min_num_errors,

            num_best_mappings, second_min_num_errors, num_second_best_mappings,

            error_threshold_, read_length);



        if (mapping_output_format_ == MAPPINGFORMAT_SAM) {

          uint16_t flag = mapping_direction == kPositive ? 0 : BAM_FREVERSE;

          if (num_best_mappings_reported >= 1) {

src/chromap.h

+3 −3
Original line number Diff line number Diff line
@@ -366,18 +366,18 @@ class Chromap { 
      int &num_best_mappings_reported,

      std::vector<std::vector<MappingRecord> > &mappings_on_diff_ref_seqs);

  void EmplaceBackMappingRecord(

      uint32_t read_id, uint32_t barcode, uint32_t fragment_start_position,

      uint32_t read_id, uint64_t barcode, uint32_t fragment_start_position,

      uint16_t fragment_length, uint8_t mapq, uint8_t direction,

      uint8_t is_unique, uint8_t num_dups,

      std::vector<MappingRecord> *mappings_on_diff_ref_seqs);

  void EmplaceBackMappingRecord(

      uint32_t read_id, const char *read_name, uint16_t read_length,

      uint32_t barcode, uint32_t fragment_start_position,

      uint64_t barcode, uint32_t fragment_start_position,

      uint16_t fragment_length, uint8_t mapq, uint8_t direction,

      uint8_t is_unique, uint8_t num_dups,

      std::vector<MappingRecord> *mappings_on_diff_ref_seqs);

  void EmplaceBackMappingRecord(

      uint32_t read_id, const char *read_name, uint32_t cell_barcode,

      uint32_t read_id, const char *read_name, uint64_t cell_barcode,

      uint8_t num_dups, int64_t position, int rid, int flag, uint8_t direction,

      uint8_t is_unique, uint8_t mapq, uint32_t NM, int n_cigar,

      uint32_t *cigar, std::string &MD_tag, const char *read,

src/output_tools.cc

+2 −1
Original line number Diff line number Diff line
@@ -19,7 +19,8 @@ void OutputTools<MappingWithBarcode>::AppendMapping( 
        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_) + "\n");

        barcode_translator.Translate(mapping.cell_barcode_, cell_barcode_length_) + 

        "\t" + std::to_string(mapping.num_dups_) + "\n");

  } else {

    std::string strand = mapping.IsPositiveStrand() ? "+" : "-";

    const char *reference_sequence_name = reference.GetSequenceNameAt(rid);

src/output_tools.h

+3 −3
Original line number Diff line number Diff line
@@ -96,11 +96,11 @@ public: 
      ProcessTranslateFileLine(file_line); 

    }

    

    mask = 0;

    for (int i = 0; i < from_bc_length; ++i)

    mask = (1ull<<(2*from_bc_length)) - 1;

    /*for (int i = 0; i < from_bc_length; ++i)

    {

      mask |= (3ull << (2*i));

    }

    }*/

  }

  

  std::string Translate(uint64_t bc, uint32_t bc_length) {

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