Commit d26c0d4c authored by Li's avatar Li Committed by Haowen Zhang
Browse files

Code refactoring

parent c1f625c9

src/barcode_translator.h

0 → 100644
+111 −0
Original line number Diff line number Diff line 
#include <cinttypes>

#include <cstring>

#include <functional>

#include <fstream>

#include <iostream>

#include <string>

#include <vector>



#include "khash.h"



namespace chromap {



KHASH_INIT(k64_str, uint64_t, char *, 1, kh_int64_hash_func, kh_int64_hash_equal);



// The class for handling barcode convertion.

class BarcodeTranslator

{

private:

  khash_t(k64_str) *barcode_translate_table;

  int from_bc_length;

  uint64_t mask;



  std::string Seed2Sequence(uint64_t seed, uint32_t seed_length) const {

    std::string sequence;

    sequence.reserve(seed_length);

    uint64_t mask = 3;

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

      sequence.push_back(SequenceBatch::Uint8ToChar(

          (seed >> ((seed_length - 1 - i) * 2)) & mask));

    }

    return sequence;

  }

  

  void ProcessTranslateFileLine(std::string &line) {

    int i;

    int len = line.length();

    std::string to;

    for (i = 0; i < len; ++i) {

      if (line[i] == ',' || line[i] == '\t')

        break;

    }



    to = line.substr(0, i);

    //from = line.substr(i + 1, len - i - 1);

    from_bc_length = len - i - 1;

    uint64_t from_seed = SequenceBatch::GenerateSeedFromSequence(line.c_str(), len, i + 1, from_bc_length);

    

    int khash_return_code;

    khiter_t barcode_translate_table_iter = kh_put(k64_str, barcode_translate_table, from_seed, &khash_return_code);

    kh_value(barcode_translate_table, barcode_translate_table_iter) = strdup(to.c_str());

  }



public:

  BarcodeTranslator() {

    barcode_translate_table = NULL;

    from_bc_length = -1;

  }

  

  ~BarcodeTranslator() {

    if (barcode_translate_table != NULL) {

      khiter_t k ;

      for (k = kh_begin(barcode_translate_table) ; k != kh_end(barcode_translate_table); ++k)

      {

        if (kh_exist(barcode_translate_table, k))

          free(kh_value(barcode_translate_table, k)) ;

      }

      kh_destroy(k64_str, barcode_translate_table);

    }

  }



  void SetTranslateTable(const std::string &file) {

    barcode_translate_table = kh_init(k64_str);

    std::ifstream file_stream(file);

    std::string file_line;

    while (getline(file_stream, file_line)) {

      ProcessTranslateFileLine(file_line); 

    }

    

    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) {

    if (barcode_translate_table == NULL) {

      return Seed2Sequence(bc, bc_length);

    } 



    std::string ret;  

    uint64_t i;

    for (i = 0; i < bc_length / from_bc_length; ++i) {

      uint64_t seed = (bc << (2 * i * from_bc_length)) >> (2 * (bc_length / from_bc_length - 1) * from_bc_length);

      seed &= mask;

      khiter_t barcode_translate_table_iter = kh_get(k64_str, barcode_translate_table, seed);

      if (barcode_translate_table_iter == kh_end(barcode_translate_table)) {

        std::cerr << "Barcode does not exist in the translation table.\n" << std::endl;

        exit(-1);

      }

      std::string bc_to(kh_value(barcode_translate_table, barcode_translate_table_iter));

      if (i == 0) {

        ret = bc_to;

      } else {

        ret += "-" + bc_to;

      }

    }

    return ret;

  }

};

}

src/chromap.cc

+0 −2
Original line number Diff line number Diff line
@@ -2998,8 +2998,6 @@ void Chromap<MappingRecord>::MapSingleEndReads() { 
  }



  index.Destroy();

  //OutputMappingStatistics(num_reference_sequences, mappings_on_diff_ref_seqs_,

  //                        mappings_on_diff_ref_seqs_);



  if (Tn5_shift_) {

    ApplyTn5ShiftOnSingleEndMapping(num_reference_sequences,

src/output_tools.cc

+3 −3
Original line number Diff line number Diff line
@@ -19,7 +19,7 @@ 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_) + 

        barcode_translator_.Translate(mapping.cell_barcode_, cell_barcode_length_) + 

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

  } else {

    std::string strand = mapping.IsPositiveStrand() ? "+" : "-";
@@ -129,7 +129,7 @@ void OutputTools<PairedEndMappingWithBarcode>::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_) + "\t" +

        barcode_translator_.Translate(mapping.cell_barcode_, cell_barcode_length_) + "\t" +

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

  } else {

    bool positive_strand = mapping.IsPositiveStrand();
@@ -339,7 +339,7 @@ void OutputTools<SAMMapping>::AppendMapping(uint32_t rid, 
      "\tMD:Z:" + mapping.MD_);

  if (cell_barcode_length_ > 0) {

    this->AppendMappingOutput(

        "\tCB:Z:" + barcode_translator.Translate(mapping.cell_barcode_, cell_barcode_length_));

        "\tCB:Z:" + barcode_translator_.Translate(mapping.cell_barcode_, cell_barcode_length_));

  }

  this->AppendMappingOutput("\n");

}

src/output_tools.h

+4 −102
Original line number Diff line number Diff line
@@ -18,11 +18,10 @@ 
#include "sam_mapping.h"

#include "sequence_batch.h"

#include "khash.h"

#include "barcode_translator.h"



namespace chromap {



KHASH_INIT(k64_str, uint64_t, char *, 1, kh_int64_hash_func, kh_int64_hash_equal);



enum MappingOutputFormat {

  MAPPINGFORMAT_UNKNOWN,

  MAPPINGFORMAT_BED,
@@ -38,103 +37,6 @@ bool ReadIdLess(const std::pair<uint32_t, MappingRecord> &a, 
  return a.second.read_id_ < b.second.read_id_;

}



// The class for handling barcode convertion.

class BarcodeTranslator

{

private:

  khash_t(k64_str) *barcode_translate_table;

  int from_bc_length;

  uint64_t mask;



  std::string Seed2Sequence(uint64_t seed, uint32_t seed_length) const {

    std::string sequence;

    sequence.reserve(seed_length);

    uint64_t mask = 3;

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

      sequence.push_back(SequenceBatch::Uint8ToChar(

          (seed >> ((seed_length - 1 - i) * 2)) & mask));

    }

    return sequence;

  }

  

  void ProcessTranslateFileLine(std::string &line) {

    int i;

    int len = line.length();

    std::string to;

    for (i = 0; i < len; ++i) {

      if (line[i] == ',' || line[i] == '\t')

        break;

    }



    to = line.substr(0, i);

    //from = line.substr(i + 1, len - i - 1);

    from_bc_length = len - i - 1;

    uint64_t from_seed = SequenceBatch::GenerateSeedFromSequence(line.c_str(), len, i + 1, from_bc_length);

    

    int khash_return_code;

    khiter_t barcode_translate_table_iter = kh_put(k64_str, barcode_translate_table, from_seed, &khash_return_code);

    kh_value(barcode_translate_table, barcode_translate_table_iter) = strdup(to.c_str());

  }



public:

  BarcodeTranslator() {

    barcode_translate_table = NULL;

    from_bc_length = -1;

  }

  

  ~BarcodeTranslator() {

    if (barcode_translate_table != NULL) {

      khiter_t k ;

      for (k = kh_begin(barcode_translate_table) ; k != kh_end(barcode_translate_table); ++k)

      {

        if (kh_exist(barcode_translate_table, k))

          free(kh_value(barcode_translate_table, k)) ;

      }

      kh_destroy(k64_str, barcode_translate_table);

    }

  }



  void SetTranslateTable(const std::string &file) {

    barcode_translate_table = kh_init(k64_str);

    std::ifstream file_stream(file);

    std::string file_line;

    while (getline(file_stream, file_line)) {

      ProcessTranslateFileLine(file_line); 

    }

    

    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) {

    if (barcode_translate_table == NULL) {

      return Seed2Sequence(bc, bc_length);

    } 



    std::string ret;  

    uint64_t i;

    for (i = 0; i < bc_length / from_bc_length; ++i) {

      uint64_t seed = (bc << (2 * i * from_bc_length)) >> (2 * (bc_length / from_bc_length - 1) * from_bc_length);

      seed &= mask;

      khiter_t barcode_translate_table_iter = kh_get(k64_str, barcode_translate_table, seed);

      if (barcode_translate_table_iter == kh_end(barcode_translate_table)) {

        std::cerr << "Barcode does not exist in the translation table.\n" << std::endl;

        exit(-1);

      }

      std::string bc_to(kh_value(barcode_translate_table, barcode_translate_table_iter));

      if (i == 0) {

        ret = bc_to;

      } else {

        ret += "-" + bc_to;

      }

    }

    return ret;

  }

};



template <typename MappingRecord>

class OutputTools {

 public:
@@ -236,7 +138,7 @@ class OutputTools { 


  void AppendBarcodeOutput(uint64_t barcode_key) {

    fprintf(barcode_output_file_, "%s-1\n",

            barcode_translator.Translate(barcode_key, cell_barcode_length_).data());

            barcode_translator_.Translate(barcode_key, cell_barcode_length_).data());

            //Seed2Sequence(barcode_key, cell_barcode_length_).data());

  }
@@ -263,7 +165,7 @@ class OutputTools { 
  }



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

    barcode_translator.SetTranslateTable(file);

    barcode_translator_.SetTranslateTable(file);

  }



  std::vector<int> custom_rid_rank_;  // for pairs
@@ -279,7 +181,7 @@ class OutputTools { 
  FILE *peak_output_file_;

  FILE *barcode_output_file_;

  FILE *matrix_output_file_;

  BarcodeTranslator barcode_translator;

  BarcodeTranslator barcode_translator_;

};



// Specialization for BED format.

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