| 2476 | } |
| 2477 | |
| 2478 | bool getELANDinfo(std::string line,std::string &chr1,std::string &chr2,std::string &orient1,std::string &orient2,int &left,int &right, int &insertSize) { |
| 2479 | if (! line.length()) |
| 2480 | return false; |
| 2481 | |
| 2482 | std::vector<std::string> strs = split(line, '\t'); |
| 2483 | if (strs.size()>=14) { |
| 2484 | chr1=strs[11]; |
| 2485 | chr2=strs[12]; |
| 2486 | processChrName(chr1); |
| 2487 | processChrName(chr2); |
| 2488 | |
| 2489 | orient1 = strs[8]; |
| 2490 | orient2 =strs[10]; |
| 2491 | |
| 2492 | left = atoi(strs[7].c_str()); |
| 2493 | right = atoi(strs[9].c_str()); |
| 2494 | |
| 2495 | insertSize=atoi(strs[13].c_str()); |
| 2496 | |
| 2497 | if (chr1.compare(chr2)!=0) {//Can be avoided, TODO { |
| 2498 | insertSize=0; |
| 2499 | return false; |
| 2500 | } |
| 2501 | } else { |
| 2502 | return false; |
| 2503 | } |
| 2504 | strs.clear(); |
| 2505 | return true; |
| 2506 | } |
| 2507 | |
| 2508 | bool getSAMinfo(const char* line, std::string &chr1, std::string &chr2, char& orient1, char& orient2, int &left,int &right, int &insert_size) { |
| 2509 | if (!*line) { |
no test coverage detected