| 14 | bool hasQ; |
| 15 | |
| 16 | void buildIndex(char* readF, int gap, bool hasQ) { |
| 17 | int nPos; |
| 18 | READ_INT_TYPE nReads; |
| 19 | bool success; |
| 20 | string line; |
| 21 | char idxF[STRLEN]; |
| 22 | char buf[sizeof(nReads) + sizeof(gap) + sizeof(nPos)]; |
| 23 | streampos startPos; |
| 24 | |
| 25 | sprintf(idxF, "%s.ridx", readF); |
| 26 | |
| 27 | ifstream fin(readF); |
| 28 | if (!fin.is_open()) { fprintf(stderr, "Cannot open %s! It may not exist.\n", readF); exit(-1); } |
| 29 | ofstream fout(idxF, ios::binary); |
| 30 | |
| 31 | startPos = fout.tellp(); |
| 32 | memset(buf, 0, sizeof(buf)); |
| 33 | fout.write((char*)buf, sizeof(buf)); |
| 34 | |
| 35 | nReads = 0; nPos = 0; |
| 36 | do { |
| 37 | streampos pos = fin.tellg(); |
| 38 | success = true; |
| 39 | |
| 40 | success = (getline(fin, line)); |
| 41 | if (!success) continue; |
| 42 | success = (getline(fin, line)); |
| 43 | if (!success) continue; |
| 44 | |
| 45 | if (hasQ) { |
| 46 | success = (getline(fin, line)); |
| 47 | if (!success) continue; |
| 48 | success = (getline(fin, line)); |
| 49 | if (!success) continue; |
| 50 | } |
| 51 | |
| 52 | if (nReads % gap == 0) { |
| 53 | ++nPos; |
| 54 | fout.write((char*)&pos, sizeof(pos)); |
| 55 | } |
| 56 | ++nReads; |
| 57 | |
| 58 | if (verbose && nReads % 1000000 == 0) { cout<< "FIN "<< nReads<< endl; } |
| 59 | } while (success); |
| 60 | |
| 61 | fout.seekp(startPos); |
| 62 | fout.write((char*)&nReads, sizeof(nReads)); |
| 63 | fout.write((char*)&gap, sizeof(gap)); |
| 64 | fout.write((char*)&nPos, sizeof(nPos)); |
| 65 | |
| 66 | fin.close(); |
| 67 | fout.close(); |
| 68 | |
| 69 | if (verbose) { cout<< "Build Index "<< readF<< " is Done!"<< endl; } |
| 70 | } |
| 71 | |
| 72 | int main(int argc, char* argv[]) { |
| 73 | if (argc < 5) { |