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DBGSplitter.cpp
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DBGSplitter.cpp
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#include <fstream>
#include <cstring>
#include <string>
#include <vector>
#include <iostream>
#include <algorithm>
#include <unordered_set>
#include "sparsepp/spp.h"
#include <cstdint>
using spp::sparse_hash_map;
using namespace std;
string intToString(uint64_t n){
if(n<1000){
return to_string(n);
}
string end(to_string(n%1000));
if(end.size()==3){
return intToString(n/1000)+","+end;
}
if(end.size()==2){
return intToString(n/1000)+",0"+end;
}
return intToString(n/1000)+",00"+end;
}
char revCompChar(char c) {
switch (c) {
case 'A': return 'T';
case 'C': return 'G';
case 'G': return 'C';
}
return 'A';
}
string revComp(const string& s){
string rc(s.size(),0);
for (int i((int)s.length() - 1); i >= 0; i--){
rc[s.size()-1-i] = revCompChar(s[i]);
}
return rc;
}
string getCanonical(const string& str){
return (min(str,revComp(str)));
}
uint64_t str2num(const string& str){
uint64_t res(0);
for(unsigned int i(0);i<str.size();i++){
res<<=2;
switch (str[i]){
case 'A':res+=0;break;
case 'C':res+=1;break;
case 'G':res+=2;break;
default:res+=3;break;
}
}
return res;
}
uint32_t xs(uint32_t& y){
y^=(y<<13); y^=(y>>17);y=(y^=(y<<15)); return y;
}
string min_accordingtoXS(const string& seq1,const string& seq2){
uint32_t u1(str2num(seq1)),u2(str2num(seq2));
if(xs(u1)<xs(u2)){
return seq1;
}
return seq2;
}
int main(int argc, char ** argv){
if(argc<4){
cout<<"[unitig file] [k value] [m value]"<<endl;
exit(0);
}
string inputUnitig(argv[1]);
unsigned int k(stoi(argv[2]));
unsigned int m(stoi(argv[3]));
srand (time(NULL));
string ref, useless;
ifstream inUnitigs(inputUnitig);
if( not inUnitigs.good()){
cout<<"Problem with files opening"<<endl;
exit(1);
}
string super_minimizer,kmer,minimizer,mmer;
while(not inUnitigs.eof()){
getline(inUnitigs,useless);
getline(inUnitigs,ref);
//FOREACH UNITIG
if(not ref.empty() and not useless.empty()){
super_minimizer=kmer=minimizer=mmer="";
unsigned int last_position(0);
//FOREACH KMER
unsigned int i(0);
for(;i+k<=ref.size();++i){
kmer=getCanonical(ref.substr(i,k));
minimizer=(getCanonical(kmer.substr(0,m)));
//COMPUTE KMER MINIMIZER
for(unsigned int j(1);j+m<=kmer.size();++j){
mmer=getCanonical(kmer.substr(j,m));
minimizer=min_accordingtoXS(minimizer,mmer);
}
if(super_minimizer==""){
super_minimizer=minimizer;
}else{
if(super_minimizer!=minimizer){
//~ cerr<<super_minimizer<<" "<<minimizer<<endl;
cout<<">\n"<<ref.substr(last_position,i-last_position+k-1)<<"\n";
last_position=i;
super_minimizer=minimizer;
}
}
}
if(i-last_position+k-1!=0){
cout<<">\n"<<ref.substr(last_position,i-last_position+k-1)<<"\n";
}
}
}
}