brute_force.h

////////////////////////////////////////////////////////////////////////////////
// brute_force.h
//   Algorithm header file.
//
// brute force implementation used as a reference for the dynamic minimizer algorithm.
// This version does use a wt_string imported from the DYNAMIC library to store the sequence
//
////////////////////////////////////////////////////////////////////////////////
// author Alexander Petri

#ifndef BRUTE_FORCE_H
#define BRUTE_FORCE_H

#include "main.h"
#include "Variant.h"
#include "B-tree.hh"
#include "dynamic_minimizer.h"
#include "DYNAMIC-master/include/dynamic.hpp"

/*!
* Brute force implementation to compute dynamic minimizers.
* @param minimizerTree:     B-tree holding the final minimizers
* @param dynamic_sequence:  the sequence to be altered
* @param variants:          Vector of variants which are applied to the sequence
* @param k_size:            length of the k-mers
* @param w_size:            window size for the minimizer generations
*/

void brute_force_minimizer_computation(B_tree<int,std::string,7,3>* minimizerTree, dyn::wt_str& dynamic_sequence,std::vector<Variant>& variants,int& k_size,int& w_size){
  int shift=0;
  int original_lenth=dynamic_sequence.size();
  //iterate over the variants to be applied to the sequence (This does only update the sequence)
  for(int i=0;i<variants.size();i++){
    int delta=0;
    int v_pos=variants[i].getVariantPosition();
    int v_originalseqlen=variants[i].getVariantOriginalSeqLen();
    std::string v_sequence=variants[i].getVariantSequence();
    //cout<<"Variation at: "<<v_pos<<", Origlen "<<v_originalseqlen<<", sequence "<<v_sequence<<"\n";
    if(v_pos>0){
      int start=v_pos+shift;
      int end=start+v_originalseqlen;
      if(end>dynamic_sequence.size()){
        end=dynamic_sequence.size();
      }

      dynseq_update_substr(dynamic_sequence, start, end,v_sequence);
    }
    else{
      dynseq_update_substr(dynamic_sequence, 1, v_originalseqlen+1,v_sequence);
    }
    delta=variants[i].getVariantLength()-v_originalseqlen;
    shift+=delta;
    //cout<<"Delta: "<<delta<<"\n";
    //cout<<"Shift: "<<shift<<"\n";
    //cout<<"Intermediate sequence: "<<dynseq_tostring(dynamic_sequence)<<"\n";
  }

  std::string finseq=dynseq_tostring(dynamic_sequence);
  cout<<"Final BF-Sequence: "<<finseq<<"\n";
  //generate the minimizers for the updated sequence
  std::vector<Minimizer> minimizers =get_kmer_minimizers(finseq,k_size,w_size);
  //fill the minimizers into the minimizer tree
  fill_minimizer_tree(minimizerTree,minimizers);

}

#endif