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#include<cstdio>
#include<cstring>
#include<cstdlib>
#include<string>
#include<fstream>
#include<iostream>
#include "utils.h"
using namespace std;
bool verbose = true;
int gap;
bool hasQ;
void buildIndex(char* readF, int gap, bool hasQ) {
int nPos;
READ_INT_TYPE nReads;
bool success;
string line;
char idxF[STRLEN];
char buf[sizeof(nReads) + sizeof(gap) + sizeof(nPos)];
streampos startPos;
sprintf(idxF, "%s.ridx", readF);
ifstream fin(readF);
if (!fin.is_open()) { fprintf(stderr, "Cannot open %s! It may not exist.\n", readF); exit(-1); }
ofstream fout(idxF, ios::binary);
startPos = fout.tellp();
memset(buf, 0, sizeof(buf));
fout.write((char*)buf, sizeof(buf));
nReads = 0; nPos = 0;
do {
streampos pos = fin.tellg();
success = true;
success = ((bool)getline(fin, line));
if (!success) continue;
success = ((bool)getline(fin, line));
if (!success) continue;
if (hasQ) {
success = ((bool)getline(fin, line));
if (!success) continue;
success = ((bool)getline(fin, line));
if (!success) continue;
}
if (nReads % gap == 0) {
++nPos;
fout.write((char*)&pos, sizeof(pos));
}
++nReads;
if (verbose && nReads % 1000000 == 0) { cout<< "FIN "<< nReads<< endl; }
} while (success);
fout.seekp(startPos);
fout.write((char*)&nReads, sizeof(nReads));
fout.write((char*)&gap, sizeof(gap));
fout.write((char*)&nPos, sizeof(nPos));
fin.close();
fout.close();
if (verbose) { cout<< "Build Index "<< readF<< " is Done!"<< endl; }
}
int main(int argc, char* argv[]) {
if (argc < 5) {
printf("Usage : rsem-build-read-index gap hasQ quiet readFile1, readFile2, ...\n");
exit(-1);
}
gap = atoi(argv[1]);
hasQ = atoi(argv[2]);
verbose = !atoi(argv[3]);
for (int i = 4; i < argc; i++) {
buildIndex(argv[i], gap, hasQ);
}
return 0;
}
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