Commit 42a1dbb4 authored by Haowen Zhang's avatar Haowen Zhang
Browse files

Keep one OutputTools class.

parent 4316fba0

Makefile

+1 −1
Original line number Diff line number Diff line 
cpp_source=sequence_batch.cc index.cc ksw.cc chromap.cc

cpp_source=sequence_batch.cc index.cc ksw.cc output_tools.cc chromap.cc

src_dir=src

objs_dir=objs

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

src/chromap.cc

+28 −75
Original line number Diff line number Diff line
@@ -419,7 +419,7 @@ uint32_t Chromap<PairedEndMappingWithBarcode>::CallPeaks( 
        peaks_on_diff_ref_seqs_[ri].emplace_back(

            Peak{peak_start_position, peak_length, peak_count});

        tree_extras_on_diff_ref_seqs_[ri].emplace_back(0);

        output_tools_->OutputPeaks(peak_start_position, peak_length, ri,

        output_tools_.OutputPeaks(peak_start_position, peak_length, ri,

                                  reference);

        ++peak_count;

        peak_length = 0;
@@ -442,7 +442,7 @@ void Chromap<PairedEndMappingWithBarcode>::OutputFeatureMatrix( 
    uint32_t num_sequences, const SequenceBatch &reference) {

  uint32_t num_peaks = 0;

  if (cell_by_bin_) {

    output_tools_->OutputPeaks(bin_size_, num_sequences, reference);

    output_tools_.OutputPeaks(bin_size_, num_sequences, reference);

    for (uint32_t i = 0; i < num_sequences; ++i) {

      uint32_t ref_seq_length = reference.GetSequenceLengthAt(i);

      num_peaks += ref_seq_length / bin_size_;
@@ -474,7 +474,7 @@ void Chromap<PairedEndMappingWithBarcode>::OutputFeatureMatrix( 
        kh_value(barcode_index_table_, barcode_index_table_iterator) =

            barcode_index;

        ++barcode_index;

        output_tools_->AppendBarcodeOutput(barcode_key);

        output_tools_.AppendBarcodeOutput(barcode_key);

      }

    }

  }
@@ -521,7 +521,7 @@ void Chromap<PairedEndMappingWithBarcode>::OutputFeatureMatrix( 
            << Chromap<>::GetRealTime() - real_start_time << "s.\n";

  // Output matrix

  real_start_time = GetRealTime();

  output_tools_->WriteMatrixOutputHead(num_peaks, kh_size(barcode_index_table_),

  output_tools_.WriteMatrixOutputHead(num_peaks, kh_size(barcode_index_table_),

                                      kh_size(matrix));

  uint64_t key;

  uint32_t value;
@@ -534,7 +534,7 @@ void Chromap<PairedEndMappingWithBarcode>::OutputFeatureMatrix( 
  kh_destroy(kmatrix, matrix);

  std::sort(feature_matrix.begin(), feature_matrix.end());

  for (size_t i = 0; i < feature_matrix.size(); ++i) {

    output_tools_->AppendMatrixOutput((uint32_t)feature_matrix[i].first,

    output_tools_.AppendMatrixOutput((uint32_t)feature_matrix[i].first,

                                     (uint32_t)(feature_matrix[i].first >> 32),

                                     feature_matrix[i].second);

  }
@@ -944,7 +944,7 @@ 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,

    output_tools_.OutputTempMapping(temp_mapping_file_handle.file_path,

                                    num_reference_sequences,

                                    mappings_on_diff_ref_seqs_);

    // std::cerr << "Output temp mappings in " << Chromap<>::GetRealTime() -
@@ -1077,7 +1077,7 @@ void Chromap<MappingRecord>::PostProcessingInLowMemory( 
              // last_mapping.negative_alignment_length -= 5;

              last_mapping.Tn5Shift();

            }

            output_tools_->AppendMapping(last_rid, reference, last_mapping);

            output_tools_.AppendMapping(last_rid, reference, last_mapping);

            ++num_mappings_passing_filters;

            //}

          }
@@ -1150,7 +1150,7 @@ void Chromap<MappingRecord>::PostProcessingInLowMemory( 
      // last_mapping.negative_alignment_length -= 5;

      last_mapping.Tn5Shift();

    }

    output_tools_->AppendMapping(last_rid, reference, last_mapping);

    output_tools_.AppendMapping(last_rid, reference, last_mapping);

    ++num_mappings_passing_filters;

    //}

  }
@@ -1309,36 +1309,13 @@ void Chromap<MappingRecord>::MapPairedEndReads() { 
  }



  // Initialize output tools

  switch (mapping_output_format_) {

    case MAPPINGFORMAT_BED:

      output_tools_ = std::unique_ptr<BEDPEOutputTools<MappingRecord>>(

          new BEDPEOutputTools<MappingRecord>);

      break;

    case MAPPINGFORMAT_TAGALIGN:

      output_tools_ = std::unique_ptr<PairedTagAlignOutputTools<MappingRecord>>(

          new PairedTagAlignOutputTools<MappingRecord>);

      break;

    case MAPPINGFORMAT_PAF:

      output_tools_ = std::unique_ptr<PairedPAFOutputTools<MappingRecord>>(

          new PairedPAFOutputTools<MappingRecord>);

      break;

    case MAPPINGFORMAT_SAM:

      output_tools_ = std::unique_ptr<SAMOutputTools<MappingRecord>>(

          new SAMOutputTools<MappingRecord>);

      break;

    case MAPPINGFORMAT_PAIRS:

      output_tools_ = std::unique_ptr<PairsOutputTools<MappingRecord>>(

          new PairsOutputTools<MappingRecord>);

      output_tools_->SetPairsCustomRidRank(pairs_custom_rid_rank_);

      break;

    default:

      chromap::Chromap<>::ExitWithMessage("Unknown mapping output format!");

      break;

  if (mapping_output_format_ == MAPPINGFORMAT_PAIRS) {

    output_tools_.SetPairsCustomRidRank(pairs_custom_rid_rank_);

  }



  output_tools_->InitializeMappingOutput(barcode_length_,

                                         mapping_output_file_path_);

  output_tools_->OutputHeader(num_reference_sequences, reference);

  output_tools_.InitializeMappingOutput(

      barcode_length_, mapping_output_file_path_, mapping_output_format_);

  output_tools_.OutputHeader(num_reference_sequences, reference);



  uint32_t num_mappings_in_mem = 0;

  uint64_t max_num_mappings_in_mem =
@@ -1906,7 +1883,7 @@ 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(

              output_tools_.OutputTempMapping(

                  temp_mapping_file_handle.file_path, num_reference_sequences,

                  mappings_on_diff_ref_seqs_);

              num_mappings_in_mem = 0;
@@ -1975,12 +1952,12 @@ void Chromap<MappingRecord>::MapPairedEndReads() { 
      OutputMappings(num_reference_sequences, reference, mappings);

    }

    if (!is_bulk_data_ && !matrix_output_prefix_.empty()) {

      output_tools_->InitializeMatrixOutput(matrix_output_prefix_);

      output_tools_.InitializeMatrixOutput(matrix_output_prefix_);

      OutputFeatureMatrix(num_reference_sequences, reference);

      output_tools_->FinalizeMatrixOutput();

      output_tools_.FinalizeMatrixOutput();

    }

  }

  output_tools_->FinalizeMappingOutput();

  output_tools_.FinalizeMappingOutput();

  reference.FinalizeLoading();

  std::cerr << "Total time: " << Chromap<>::GetRealTime() - real_start_time

            << "s.\n";
@@ -1999,7 +1976,7 @@ 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);

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

        ++num_mappings_passing_filters;

        //}

      }
@@ -2863,34 +2840,10 @@ void Chromap<MappingRecord>::MapSingleEndReads() { 
    }

  }



  switch (mapping_output_format_) {

    case MAPPINGFORMAT_BED:

      output_tools_ = std::unique_ptr<BEDOutputTools<MappingRecord>>(

          new BEDOutputTools<MappingRecord>);

      break;

    case MAPPINGFORMAT_TAGALIGN:

      output_tools_ = std::unique_ptr<TagAlignOutputTools<MappingRecord>>(

          new TagAlignOutputTools<MappingRecord>);

      break;

    case MAPPINGFORMAT_PAF:

      output_tools_ = std::unique_ptr<PAFOutputTools<MappingRecord>>(

          new PAFOutputTools<MappingRecord>);

      break;

    case MAPPINGFORMAT_SAM:

      output_tools_ = std::unique_ptr<SAMOutputTools<MappingRecord>>(

          new SAMOutputTools<MappingRecord>);

      break;

    case MAPPINGFORMAT_PAIRS:

      chromap::Chromap<>::ExitWithMessage("No support for single-end HiC!");

      break;

    default:

      chromap::Chromap<>::ExitWithMessage("Unknown mapping output format!");

      break;

  }

  output_tools_.InitializeMappingOutput(

      barcode_length_, mapping_output_file_path_, mapping_output_format_);

  output_tools_.OutputHeader(num_reference_sequences, reference);



  output_tools_->InitializeMappingOutput(barcode_length_,

                                         mapping_output_file_path_);

  output_tools_->OutputHeader(num_reference_sequences, reference);

  mm_cache mm_to_candidates_cache(2000003);

  mm_to_candidates_cache.SetKmerLength(kmer_size_);

  struct _mm_history *mm_history = new struct _mm_history[read_batch_size_];
@@ -3138,7 +3091,7 @@ void Chromap<MappingRecord>::MapSingleEndReads() { 
                               : mappings_on_diff_ref_seqs_;

    OutputMappings(num_reference_sequences, reference, mappings);

  }

  output_tools_->FinalizeMappingOutput();

  output_tools_.FinalizeMappingOutput();

  reference.FinalizeLoading();

  std::cerr << "Total time: " << Chromap<>::GetRealTime() - real_start_time

            << "s.\n";

src/chromap.h

+1 −10
Original line number Diff line number Diff line
@@ -45,15 +45,6 @@ struct Peak { 
  uint32_t index;

};



enum MappingOutputFormat {

  MAPPINGFORMAT_UNKNOWN,

  MAPPINGFORMAT_BED,

  MAPPINGFORMAT_TAGALIGN,

  MAPPINGFORMAT_PAF,

  MAPPINGFORMAT_SAM,

  MAPPINGFORMAT_PAIRS

};



KHASH_MAP_INIT_INT64(k128, uint128_t);

KHASH_MAP_INIT_INT64(k64_seq, uint64_t);

KHASH_SET_INIT_INT(k32_set);
@@ -674,7 +665,7 @@ 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_;

  std::unique_ptr<OutputTools<MappingRecord> > output_tools_;

  OutputTools<MappingRecord> output_tools_;

  // For mapping stats.

  uint64_t num_candidates_ = 0;

  uint64_t num_mappings_ = 0;

src/output_tools.cc

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src/output_tools.h

+43 −490

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