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#include <iostream>
#include <string>
#include <fstream>
#include <sstream>
#include <vector>
#include <algorithm>
#include <chrono>
#include <functional>
#include <cmath>
#include <map>
#include <tuple>
#include <cstdlib>
#include <cstdio>
#include <limits>
#include <cassert>
using namespace std;
map<string, int> vertexmap;
uint32_t numlines;
void ParseSplint(string locline, uint32_t & vertexid, ofstream & out)
{
string name;
string splint;
std::tuple<string, string, int64_t> triple;
stringstream ssline(locline);
ssline >> name;
assert((name == "SPLINT") || (name == "SPAN") );
ssline >> splint;
vector<string> contigpair(2);
size_t pos = splint.find("<=>");
contigpair[1] = splint.substr(pos+3);
contigpair[0] = splint.substr(0, pos);
pos = contigpair[0].find(".");
contigpair[0] = contigpair[0].substr(0,pos);
pos = contigpair[1].find(".");
contigpair[1] = contigpair[1].substr(0,pos);
auto ret = vertexmap.insert(make_pair(contigpair[0], vertexid));
if (ret.second) // successfully inserted
++vertexid;
get<0>(triple) = ret.first->first;
ret = vertexmap.insert(make_pair(contigpair[1], vertexid));
if (ret.second) ++vertexid;
get<1>(triple) = ret.first->first;
get<2>(triple) = 1;
out << get<0>(triple) << "\t" << get<1>(triple) << "\t" << get<2>(triple) << "\n";
numlines++;
}
int main(int argc, char* argv[])
{
if(argc < 4)
{
cout << "Usage: ./mer2gr <splint_file> <kmer_file> <span_file" << endl;
return 0;
}
numlines = 0;
uint32_t vertexid = 0;
string locline;
ofstream out("contig_graph.txt");
ifstream input1(argv[1]);
while(getline(input1,locline))
{
ParseSplint(locline, vertexid, out);
}
input1.close();
ifstream input2(argv[2]);
while(getline(input2,locline))
{
ParseSplint(locline, vertexid, out);
}
input2.close();
ifstream input3(argv[3]);
while(getline(input3,locline))
{
ParseSplint(locline, vertexid, out);
}
input3.close();
ofstream dictout("vertex_dict.txt");
int max = 0;
for (auto it = vertexmap.begin(); it != vertexmap.end(); ++it)
{
max = std::max(max, it->second);
dictout << it ->first << endl;
}
cout << (max+1) << "\t" << (max+1) << "\t" << numlines << endl;
dictout.close();
}
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