Commit 1519d2a3 authored by Haowen Zhang's avatar Haowen Zhang
Browse files

Make mapping_writer a local variable. 

Have to make barcode_translate_table_path a member variable and set it
for mapping_writer.
parent 3ecd8904

src/chromap.cc

+44 −29
Original line number Diff line number Diff line
@@ -534,10 +534,12 @@ template <typename MappingRecord> 
void Chromap<MappingRecord>::ProcessAndOutputMappingsInLowMemory(

    uint32_t num_mappings_in_mem, uint32_t num_reference_sequences,

    const SequenceBatch &reference,

    const MappingProcessor<MappingRecord> &mapping_processor) {

    const MappingProcessor<MappingRecord> &mapping_processor,

    MappingWriter<MappingRecord> &mapping_writer) {

  // First, process the mappings in the memory and save them on disk.

  if (num_mappings_in_mem > 0) {

    OutputTempMappings(num_reference_sequences, mapping_processor);

    OutputTempMappings(num_reference_sequences, mapping_processor,

                       mapping_writer);

    num_mappings_in_mem = 0;

  }
@@ -656,7 +658,7 @@ void Chromap<MappingRecord>::ProcessAndOutputMappingsInLowMemory( 
          if (Tn5_shift_) {

            last_mapping.Tn5Shift();

          }

          mapping_writer_.AppendMapping(last_rid, reference, last_mapping);

          mapping_writer.AppendMapping(last_rid, reference, last_mapping);

          ++num_mappings_passing_filters;

        }
@@ -694,7 +696,7 @@ void Chromap<MappingRecord>::ProcessAndOutputMappingsInLowMemory( 
    if (Tn5_shift_) {

      last_mapping.Tn5Shift();

    }

    mapping_writer_.AppendMapping(last_rid, reference, last_mapping);

    mapping_writer.AppendMapping(last_rid, reference, last_mapping);

    ++num_mappings_passing_filters;

  }
@@ -857,14 +859,18 @@ void Chromap<MappingRecord>::MapPairedEndReads() { 
    }

  }



  MappingWriter<MappingRecord> mapping_writer;

  if (!barcode_translate_table_path_.empty()) {

    mapping_writer.SetBarcodeTranslateTable(barcode_translate_table_path_);

  }

  // Initialize output tools

  if (mapping_output_format_ == MAPPINGFORMAT_PAIRS) {

    mapping_writer_.SetPairsCustomRidRank(pairs_custom_rid_rank_);

    mapping_writer.SetPairsCustomRidRank(pairs_custom_rid_rank_);

  }



  mapping_writer_.InitializeMappingOutput(

  mapping_writer.InitializeMappingOutput(

      barcode_length_, mapping_output_file_path_, mapping_output_format_);

  mapping_writer_.OutputHeader(num_reference_sequences, reference);

  mapping_writer.OutputHeader(num_reference_sequences, reference);



  CandidateProcessor candidate_processor(min_num_seeds_required_for_mapping_,

                                         max_seed_frequencies_);
@@ -922,7 +928,7 @@ void Chromap<MappingRecord>::MapPairedEndReads() { 
      barcode_batch_for_loading.SwapSequenceBatch(barcode_batch);

      // TODO(Haowen): simplify this condition check.

      if (num_loaded_pairs > 0) {

        mapping_writer_.SetBarcodeLength(barcode_batch.GetSequenceLengthAt(0));

        mapping_writer.SetBarcodeLength(barcode_batch.GetSequenceLengthAt(0));

      }

    }
@@ -950,7 +956,7 @@ 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, 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_, 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_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_, 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;
@@ -1245,7 +1251,8 @@ void Chromap<MappingRecord>::MapPairedEndReads() { 
                mappings_on_diff_ref_seqs_for_diff_threads_for_saving);

            if (low_memory_mode_ &&

                num_mappings_in_mem > max_num_mappings_in_mem) {

              OutputTempMappings(num_reference_sequences, mapping_processor);

              OutputTempMappings(num_reference_sequences, mapping_processor,

                                 mapping_writer);

              num_mappings_in_mem = 0;

            }

          }  // end of omp task to handle output
@@ -1284,7 +1291,7 @@ void Chromap<MappingRecord>::MapPairedEndReads() { 
  if (low_memory_mode_) {

    ProcessAndOutputMappingsInLowMemory(num_mappings_in_mem,

                                        num_reference_sequences, reference,

                                        mapping_processor);

                                        mapping_processor, mapping_writer);

  } else {

    // OutputMappingStatistics(num_reference_sequences,

    // mappings_on_diff_ref_seqs_, mappings_on_diff_ref_seqs_);
@@ -1319,7 +1326,7 @@ void Chromap<MappingRecord>::MapPairedEndReads() { 
                                           mappings_on_diff_ref_seqs_);

    }

    OutputMappings(num_reference_sequences, reference,

                   mappings_on_diff_ref_seqs_);

                   mappings_on_diff_ref_seqs_, mapping_writer);



    // Temporarily disable feature matrix output. Do not delete the following

    // commented code.
@@ -1342,7 +1349,7 @@ void Chromap<MappingRecord>::MapPairedEndReads() { 
    //}

  }



  mapping_writer_.FinalizeMappingOutput();

  mapping_writer.FinalizeMappingOutput();



  reference.FinalizeLoading();
@@ -1352,7 +1359,8 @@ void Chromap<MappingRecord>::MapPairedEndReads() { 
template <typename MappingRecord>

void Chromap<MappingRecord>::OutputTempMappings(

    uint32_t num_reference_sequences,

    const MappingProcessor<MappingRecord> &mapping_processor) {

    const MappingProcessor<MappingRecord> &mapping_processor,

    MappingWriter<MappingRecord> &mapping_writer) {

  TempMappingFileHandle<MappingRecord> temp_mapping_file_handle;

  temp_mapping_file_handle.file_path =

      mapping_output_file_path_ + ".temp" +
@@ -1362,7 +1370,7 @@ void Chromap<MappingRecord>::OutputTempMappings( 
  mapping_processor.SortOutputMappings(num_reference_sequences,

                                       mappings_on_diff_ref_seqs_);



  mapping_writer_.OutputTempMapping(temp_mapping_file_handle.file_path,

  mapping_writer.OutputTempMapping(temp_mapping_file_handle.file_path,

                                   num_reference_sequences,

                                   mappings_on_diff_ref_seqs_);
@@ -1375,7 +1383,8 @@ template <typename MappingRecord> 
void Chromap<MappingRecord>::OutputMappingsInVector(

    uint8_t mapq_threshold, uint32_t num_reference_sequences,

    const SequenceBatch &reference,

    const std::vector<std::vector<MappingRecord>> &mappings) {

    const std::vector<std::vector<MappingRecord>> &mappings,

    MappingWriter<MappingRecord> &mapping_writer) {

  uint64_t num_mappings_passing_filters = 0;

  for (uint32_t ri = 0; ri < num_reference_sequences; ++ri) {

    for (auto it = mappings[ri].begin(); it != mappings[ri].end(); ++it) {
@@ -1384,7 +1393,7 @@ void Chromap<MappingRecord>::OutputMappingsInVector( 
      if (mapq >= mapq_threshold) {

        // if (allocate_multi_mappings_ || (only_output_unique_mappings_ &&

        // is_unique == 1)) {

        mapping_writer_.AppendMapping(ri, reference, *it);

        mapping_writer.AppendMapping(ri, reference, *it);

        ++num_mappings_passing_filters;

        //}

      }
@@ -1397,11 +1406,12 @@ void Chromap<MappingRecord>::OutputMappingsInVector( 
template <typename MappingRecord>

void Chromap<MappingRecord>::OutputMappings(

    uint32_t num_reference_sequences, const SequenceBatch &reference,

    const std::vector<std::vector<MappingRecord>> &mappings) {

    const std::vector<std::vector<MappingRecord>> &mappings,

    MappingWriter<MappingRecord> &mapping_writer) {

  // if (only_output_unique_mappings_ && mapq_threshold_ < 4)

  //  mapq_threshold_ = 4;

  OutputMappingsInVector(mapq_threshold_, num_reference_sequences, reference,

                         mappings);

                         mappings, mapping_writer);

}



template <typename MappingRecord>
@@ -1461,9 +1471,13 @@ void Chromap<MappingRecord>::MapSingleEndReads() { 
      max_insert_size_, min_read_length_, drop_repetitive_reads_, is_bulk_data_,

      split_alignment_, mapping_output_format_, pairs_custom_rid_rank_);



  mapping_writer_.InitializeMappingOutput(

  MappingWriter<MappingRecord> mapping_writer;

  if (!barcode_translate_table_path_.empty()) {

    mapping_writer.SetBarcodeTranslateTable(barcode_translate_table_path_);

  }

  mapping_writer.InitializeMappingOutput(

      barcode_length_, mapping_output_file_path_, mapping_output_format_);

  mapping_writer_.OutputHeader(num_reference_sequences, reference);

  mapping_writer.OutputHeader(num_reference_sequences, reference);



  uint32_t num_mappings_in_mem = 0;

  uint64_t max_num_mappings_in_mem =
@@ -1507,7 +1521,7 @@ void Chromap<MappingRecord>::MapSingleEndReads() { 
      barcode_batch_for_loading.SwapSequenceBatch(barcode_batch);

      // TODO(Haowen): simplify this condition check.

      if (num_loaded_reads > 0) {

        mapping_writer_.SetBarcodeLength(barcode_batch.GetSequenceLengthAt(0));

        mapping_writer.SetBarcodeLength(barcode_batch.GetSequenceLengthAt(0));

      }

    }
@@ -1533,7 +1547,7 @@ 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, mapping_writer_, candidate_processor, mapping_processor, mapping_generator, low_memory_mode_, num_mappings_in_mem, max_num_mappings_in_mem) 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, mapping_processor, mapping_generator, low_memory_mode_, num_mappings_in_mem, max_num_mappings_in_mem) 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;
@@ -1671,7 +1685,8 @@ void Chromap<MappingRecord>::MapSingleEndReads() { 
                mappings_on_diff_ref_seqs_for_diff_threads_for_saving);

            if (low_memory_mode_ &&

                num_mappings_in_mem > max_num_mappings_in_mem) {

              OutputTempMappings(num_reference_sequences, mapping_processor);

              OutputTempMappings(num_reference_sequences, mapping_processor,

                                 mapping_writer);

              num_mappings_in_mem = 0;

            }

          }
@@ -1709,7 +1724,7 @@ void Chromap<MappingRecord>::MapSingleEndReads() { 
  if (low_memory_mode_) {

    ProcessAndOutputMappingsInLowMemory(num_mappings_in_mem,

                                        num_reference_sequences, reference,

                                        mapping_processor);

                                        mapping_processor, mapping_writer);

  } else {

    if (Tn5_shift_) {

      mapping_processor.ApplyTn5ShiftOnMappings(num_reference_sequences,
@@ -1742,10 +1757,10 @@ void Chromap<MappingRecord>::MapSingleEndReads() { 
                                           mappings_on_diff_ref_seqs_);

    }

    OutputMappings(num_reference_sequences, reference,

                   mappings_on_diff_ref_seqs_);

                   mappings_on_diff_ref_seqs_, mapping_writer);

  }



  mapping_writer_.FinalizeMappingOutput();

  mapping_writer.FinalizeMappingOutput();

  reference.FinalizeLoading();

  std::cerr << "Total time: " << GetRealTime() - real_start_time << "s.\n";

}

src/chromap.h

+11 −9
Original line number Diff line number Diff line
@@ -102,6 +102,8 @@ class Chromap { 
        custom_rid_order_path_(mapping_parameters.custom_rid_order_path),

        pairs_custom_rid_order_path_(

            mapping_parameters.pairs_custom_rid_order_path),

        barcode_translate_table_path_(

            mapping_parameters.barcode_translate_table_path),

        skip_barcode_check_(mapping_parameters.skip_barcode_check) {

    barcode_lookup_table_ = kh_init(k64_seq);

    barcode_whitelist_lookup_table_ = kh_init(k64_seq);
@@ -115,10 +117,6 @@ 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;

      mapping_writer_.SetBarcodeTranslateTable(tmp);

    }

  }



  ~Chromap() {
@@ -179,7 +177,8 @@ class Chromap { 
  void ProcessAndOutputMappingsInLowMemory(

      uint32_t num_mappings_in_mem, uint32_t num_reference_sequences,

      const SequenceBatch &reference,

      const MappingProcessor<MappingRecord> &mapping_processor);

      const MappingProcessor<MappingRecord> &mapping_processor,

      MappingWriter<MappingRecord> &mapping_writer);



  uint32_t MoveMappingsInBuffersToMappingContainer(

      uint32_t num_reference_sequences,
@@ -197,16 +196,19 @@ class Chromap { 


  void OutputTempMappings(

      uint32_t num_reference_sequences,

      const MappingProcessor<MappingRecord> &mapping_processor);

      const MappingProcessor<MappingRecord> &mapping_processor,

      MappingWriter<MappingRecord> &mapping_writer);



  void OutputMappingsInVector(

      uint8_t mapq_threshold, uint32_t num_reference_sequences,

      const SequenceBatch &reference,

      const std::vector<std::vector<MappingRecord> > &mappings);

      const std::vector<std::vector<MappingRecord> > &mappings,

      MappingWriter<MappingRecord> &mapping_writer);



  void OutputMappings(uint32_t num_reference_sequences,

                      const SequenceBatch &reference,

                      const std::vector<std::vector<MappingRecord> > &mappings);

                      const std::vector<std::vector<MappingRecord> > &mappings,

                      MappingWriter<MappingRecord> &mapping_writer);



  void GenerateCustomizedRidRank(const std::string &rid_order_path,

                                 const SequenceBatch &reference,
@@ -278,6 +280,7 @@ class Chromap { 
  std::string pairs_custom_rid_order_path_;

  std::vector<int> custom_rid_rank_;

  std::vector<int> pairs_custom_rid_rank_;

  std::string barcode_translate_table_path_;

  // khash_t(k32_set)* barcode_whitelist_lookup_table_;

  khash_t(k64_seq) * barcode_whitelist_lookup_table_;

  // For identical read dedupe
@@ -288,7 +291,6 @@ class Chromap { 
  int min_unique_mapping_mapq_ = 4;

  std::vector<TempMappingFileHandle<MappingRecord> > temp_mapping_file_handles_;

  std::vector<std::vector<MappingRecord> > mappings_on_diff_ref_seqs_;

  MappingWriter<MappingRecord> mapping_writer_;

  // For mapping stats.

  uint64_t num_candidates_ = 0;

  uint64_t num_mappings_ = 0;

src/mapping_writer.h

+1 −1
Original line number Diff line number Diff line
@@ -90,7 +90,7 @@ class MappingWriter { 
    custom_rid_rank_ = custom_rid_rank;

  }



  inline void SetBarcodeTranslateTable(std::string &file) {

  inline void SetBarcodeTranslateTable(const std::string &file) {

    barcode_translator_.SetTranslateTable(file);

  }

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