Commit 41f684a7 authored by Haowen Zhang's avatar Haowen Zhang
Browse files

Declare specialization in header.

parent bfdc5f41

src/output_tools.cc

+4 −0
Original line number Diff line number Diff line
@@ -163,6 +163,7 @@ void OutputTools<PairedEndMappingWithBarcode>::AppendMapping( 
  }

}



// Specialization for PAF format.

template <>

void OutputTools<PAFMapping>::OutputHeader(uint32_t num_reference_sequences,

                                           const SequenceBatch &reference) {}
@@ -211,6 +212,7 @@ void OutputTools<PAFMapping>::OutputTempMapping( 
  fclose(temp_mapping_output_file);

}



// Specialization for PairedPAF format.

template <>

void OutputTools<PairedPAFMapping>::OutputHeader(

    uint32_t num_reference_sequences, const SequenceBatch &reference) {}
@@ -296,6 +298,7 @@ void OutputTools<PairedPAFMapping>::AppendMapping( 
  }

}



// Specialization for SAM format.

template <>

void OutputTools<SAMMapping>::OutputHeader(uint32_t num_reference_sequences,

                                           const SequenceBatch &reference) {
@@ -358,6 +361,7 @@ void OutputTools<SAMMapping>::OutputTempMapping( 
  fclose(temp_mapping_output_file);

}



// Specialization for pairs format.

template <>

void OutputTools<PairsMapping>::OutputHeader(uint32_t num_reference_sequences,

                                             const SequenceBatch &reference) {

src/output_tools.h

+102 −0
Original line number Diff line number Diff line
@@ -1223,6 +1223,108 @@ class OutputTools { 
  FILE *matrix_output_file_;

};



// Specialization for BED format.

template <>

void OutputTools<MappingWithBarcode>::OutputHeader(

    uint32_t num_reference_sequences, const SequenceBatch &reference);



template <>

void OutputTools<MappingWithBarcode>::AppendMapping(

    uint32_t rid, const SequenceBatch &reference,

    const MappingWithBarcode &mapping);



template <>

void OutputTools<MappingWithoutBarcode>::OutputHeader(

    uint32_t num_reference_sequences, const SequenceBatch &reference);



template <>

void OutputTools<MappingWithoutBarcode>::AppendMapping(

    uint32_t rid, const SequenceBatch &reference,

    const MappingWithoutBarcode &mapping);



// Specialization for BEDPE format.

template <>

void OutputTools<PairedEndMappingWithoutBarcode>::OutputHeader(

    uint32_t num_reference_sequences, const SequenceBatch &reference);



template <>

void OutputTools<PairedEndMappingWithoutBarcode>::AppendMapping(

    uint32_t rid, const SequenceBatch &reference,

    const PairedEndMappingWithoutBarcode &mapping);



template <>

void OutputTools<PairedEndMappingWithBarcode>::OutputHeader(

    uint32_t num_reference_sequences, const SequenceBatch &reference);



template <>

void OutputTools<PairedEndMappingWithBarcode>::AppendMapping(

    uint32_t rid, const SequenceBatch &reference,

    const PairedEndMappingWithBarcode &mapping);



// Specialization for PAF format.

template <>

void OutputTools<PAFMapping>::OutputHeader(uint32_t num_reference_sequences,

                                           const SequenceBatch &reference);



template <>

void OutputTools<PAFMapping>::AppendMapping(uint32_t rid,

                                            const SequenceBatch &reference,

                                            const PAFMapping &mapping);



template <>

void OutputTools<PAFMapping>::OutputTempMapping(

    const std::string &temp_mapping_output_file_path,

    uint32_t num_reference_sequences,

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



// Specialization for PairedPAF format.

template <>

void OutputTools<PairedPAFMapping>::OutputHeader(

    uint32_t num_reference_sequences, const SequenceBatch &reference);



template <>

void OutputTools<PairedPAFMapping>::OutputTempMapping(

    const std::string &temp_mapping_output_file_path,

    uint32_t num_reference_sequences,

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



template <>

void OutputTools<PairedPAFMapping>::AppendMapping(

    uint32_t rid, const SequenceBatch &reference,

    const PairedPAFMapping &mapping);



// Specialization for SAM format.

template <>

void OutputTools<SAMMapping>::OutputHeader(uint32_t num_reference_sequences,

                                           const SequenceBatch &reference);



template <>

void OutputTools<SAMMapping>::AppendMapping(uint32_t rid,

                                            const SequenceBatch &reference,

                                            const SAMMapping &mapping);



template <>

void OutputTools<SAMMapping>::OutputTempMapping(

    const std::string &temp_mapping_output_file_path,

    uint32_t num_reference_sequences,

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



// Specialization for pairs format.

template <>

void OutputTools<PairsMapping>::OutputHeader(uint32_t num_reference_sequences,

                                             const SequenceBatch &reference);



template <>

void OutputTools<PairsMapping>::AppendMapping(uint32_t rid,

                                              const SequenceBatch &reference,

                                              const PairsMapping &mapping);



template <>

void OutputTools<PairsMapping>::OutputTempMapping(

    const std::string &temp_mapping_output_file_path,

    uint32_t num_reference_sequences,

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



}  // namespace chromap



#endif  // OUTPUTTOOLS_H_

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