Commit 4316fba0 authored by Haowen Zhang's avatar Haowen Zhang
Browse files

Remove an unused function.

parent b51d39fb

src/output_tools.h

+9 −111
Original line number Diff line number Diff line
@@ -918,7 +918,8 @@ inline void TempMappingFileHandle<PAFMapping>::LoadTempMappingBlock( 
        num_mappings_to_load_on_current_rid = block_size;

      }

      // std::cerr << num_mappings_to_load_on_current_rid << " " <<

      // num_loaded_mappings_on_current_rid << " " << num_mappings_on_current_rid

      // num_loaded_mappings_on_current_rid << " " <<

      // num_mappings_on_current_rid

      // << "\n"; std::cerr << mappings.size() << "\n";

      for (size_t mi = 0; mi < num_mappings_to_load_on_current_rid; ++mi) {

        mappings[mi].LoadFromFile(file);
@@ -960,7 +961,8 @@ inline void TempMappingFileHandle<PairedPAFMapping>::LoadTempMappingBlock( 
        num_mappings_to_load_on_current_rid = block_size;

      }

      // std::cerr << num_mappings_to_load_on_current_rid << " " <<

      // num_loaded_mappings_on_current_rid << " " << num_mappings_on_current_rid

      // num_loaded_mappings_on_current_rid << " " <<

      // num_mappings_on_current_rid

      // << "\n"; std::cerr << mappings.size() << "\n";

      for (size_t mi = 0; mi < num_mappings_to_load_on_current_rid; ++mi) {

        mappings[mi].LoadFromFile(file);
@@ -1002,7 +1004,8 @@ inline void TempMappingFileHandle<SAMMapping>::LoadTempMappingBlock( 
        num_mappings_to_load_on_current_rid = block_size;

      }

      // std::cerr << num_mappings_to_load_on_current_rid << " " <<

      // num_loaded_mappings_on_current_rid << " " << num_mappings_on_current_rid

      // num_loaded_mappings_on_current_rid << " " <<

      // num_mappings_on_current_rid

      // << "\n"; std::cerr << mappings.size() << "\n";

      for (size_t mi = 0; mi < num_mappings_to_load_on_current_rid; ++mi) {

        mappings[mi].LoadFromFile(file);
@@ -1044,7 +1047,8 @@ inline void TempMappingFileHandle<PairsMapping>::LoadTempMappingBlock( 
        num_mappings_to_load_on_current_rid = block_size;

      }

      // std::cerr << num_mappings_to_load_on_current_rid << " " <<

      // num_loaded_mappings_on_current_rid << " " << num_mappings_on_current_rid

      // num_loaded_mappings_on_current_rid << " " <<

      // num_mappings_on_current_rid

      // << "\n"; std::cerr << mappings.size() << "\n";

      for (size_t mi = 0; mi < num_mappings_to_load_on_current_rid; ++mi) {

        mappings[mi].LoadFromFile(file);
@@ -1094,27 +1098,7 @@ class OutputTools { 
    }

    fclose(temp_mapping_output_file);

  }

  inline virtual void LoadBinaryTempMapping(

      const std::string &temp_mapping_file_path,

      uint32_t num_reference_sequences,

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

    FILE *temp_mapping_file = fopen(temp_mapping_file_path.c_str(), "rb");

    assert(temp_mapping_file != NULL);

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

      size_t num_mappings = 0;

      fread(&num_mappings, sizeof(size_t), 1, temp_mapping_file);

      if (num_mappings > 0) {

        mappings.emplace_back(std::vector<MappingRecord>(num_mappings));

        // fread(&(mappings[ri].data()), sizeof(MappingRecord), num_mappings,

        // temp_mapping_file);

        fread(mappings[ri].data(), sizeof(MappingRecord), num_mappings,

              temp_mapping_file);

      } else {

        mappings.emplace_back(std::vector<MappingRecord>());

      }

    }

    fclose(temp_mapping_file);

  }



  inline void InitializeMappingOutput(

      uint32_t cell_barcode_length,

      const std::string &mapping_output_file_path) {
@@ -1366,10 +1350,6 @@ class PAFOutputTools : public OutputTools<MappingRecord> { 
      const std::string &temp_mapping_output_file_path,

      uint32_t num_reference_sequences,

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

  inline void LoadBinaryTempMapping(

      const std::string &temp_mapping_file_path,

      uint32_t num_reference_sequences,

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

};



template <>
@@ -1415,31 +1395,6 @@ inline void PAFOutputTools<PAFMapping>::OutputTempMapping( 
  fclose(temp_mapping_output_file);

}



template <>

inline void PAFOutputTools<PAFMapping>::LoadBinaryTempMapping(

    const std::string &temp_mapping_file_path, uint32_t num_reference_sequences,

    std::vector<std::vector<PAFMapping> > &mappings) {

  FILE *temp_mapping_file = fopen(temp_mapping_file_path.c_str(), "rb");

  assert(temp_mapping_file != NULL);

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

    size_t num_mappings = 0;

    fread(&num_mappings, sizeof(size_t), 1, temp_mapping_file);

    if (num_mappings > 0) {

      mappings.emplace_back(std::vector<PAFMapping>(num_mappings));

      for (size_t mi = 0; mi < num_mappings; ++mi) {

        mappings[ri][mi].LoadFromFile(temp_mapping_file);

      }

      // mappings.emplace_back(std::vector<MappingRecord>(num_mappings));

      // fread(&(mappings[ri].data()), sizeof(MappingRecord), num_mappings,

      // temp_mapping_file); fread(mappings[ri].data(), sizeof(MappingRecord),

      // num_mappings, temp_mapping_file);

    } else {

      mappings.emplace_back(std::vector<PAFMapping>());

    }

  }

  fclose(temp_mapping_file);

}



template <>

inline void PAFOutputTools<MappingWithBarcode>::AppendMapping(

    uint32_t rid, const SequenceBatch &reference,
@@ -1595,10 +1550,6 @@ class SAMOutputTools : public OutputTools<MappingRecord> { 
      const std::string &temp_mapping_output_file_path,

      uint32_t num_reference_sequences,

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

  inline void LoadBinaryTempMapping(

      const std::string &temp_mapping_file_path,

      uint32_t num_reference_sequences,

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

};



template <>
@@ -1650,31 +1601,6 @@ inline void SAMOutputTools<SAMMapping>::OutputTempMapping( 
  fclose(temp_mapping_output_file);

}



template <>

inline void SAMOutputTools<SAMMapping>::LoadBinaryTempMapping(

    const std::string &temp_mapping_file_path, uint32_t num_reference_sequences,

    std::vector<std::vector<SAMMapping> > &mappings) {

  FILE *temp_mapping_file = fopen(temp_mapping_file_path.c_str(), "rb");

  assert(temp_mapping_file != NULL);

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

    size_t num_mappings = 0;

    fread(&num_mappings, sizeof(size_t), 1, temp_mapping_file);

    if (num_mappings > 0) {

      mappings.emplace_back(std::vector<SAMMapping>(num_mappings));

      for (size_t mi = 0; mi < num_mappings; ++mi) {

        mappings[ri][mi].LoadFromFile(temp_mapping_file);

      }

      // mappings.emplace_back(std::vector<MappingRecord>(num_mappings));

      // fread(&(mappings[ri].data()), sizeof(MappingRecord), num_mappings,

      // temp_mapping_file); fread(mappings[ri].data(), sizeof(MappingRecord),

      // num_mappings, temp_mapping_file);

    } else {

      mappings.emplace_back(std::vector<SAMMapping>());

    }

  }

  fclose(temp_mapping_file);

}



template <typename MappingRecord>

class PairsOutputTools : public OutputTools<MappingRecord> {

  inline void AppendMapping(uint32_t rid, const SequenceBatch &reference,
@@ -1704,10 +1630,6 @@ class PairsOutputTools : public OutputTools<MappingRecord> { 
      const std::string &temp_mapping_output_file_path,

      uint32_t num_reference_sequences,

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

  inline void LoadBinaryTempMapping(

      const std::string &temp_mapping_file_path,

      uint32_t num_reference_sequences,

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

};



template <>
@@ -1749,29 +1671,5 @@ inline void PairsOutputTools<PairsMapping>::OutputTempMapping( 
  fclose(temp_mapping_output_file);

}



template <>

inline void PairsOutputTools<PairsMapping>::LoadBinaryTempMapping(

    const std::string &temp_mapping_file_path, uint32_t num_reference_sequences,

    std::vector<std::vector<PairsMapping> > &mappings) {

  FILE *temp_mapping_file = fopen(temp_mapping_file_path.c_str(), "rb");

  assert(temp_mapping_file != NULL);

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

    size_t num_mappings = 0;

    fread(&num_mappings, sizeof(size_t), 1, temp_mapping_file);

    if (num_mappings > 0) {

      mappings.emplace_back(std::vector<PairsMapping>(num_mappings));

      for (size_t mi = 0; mi < num_mappings; ++mi) {

        mappings[ri][mi].LoadFromFile(temp_mapping_file);

      }

      // mappings.emplace_back(std::vector<MappingRecord>(num_mappings));

      // fread(&(mappings[ri].data()), sizeof(MappingRecord), num_mappings,

      // temp_mapping_file); fread(mappings[ri].data(), sizeof(MappingRecord),

      // num_mappings, temp_mapping_file);

    } else {

      mappings.emplace_back(std::vector<PairsMapping>());

    }

  }

  fclose(temp_mapping_file);

}

}  // namespace chromap

#endif  // OUTPUTTOOLS_H_

CRA Git | Maintained and supported by SUSTech CRA and CCSE