| 446 | } |
| 447 | |
| 448 | bool Options::shallDetectAdapter(bool isR2) { |
| 449 | if(!adapter.enabled) |
| 450 | return false; |
| 451 | |
| 452 | if(isR2) { |
| 453 | return isPaired() && adapter.detectAdapterForPE && adapter.sequenceR2 == "auto"; |
| 454 | } else { |
| 455 | if(isPaired()) |
| 456 | return adapter.detectAdapterForPE && adapter.sequence == "auto"; |
| 457 | else |
| 458 | return adapter.sequence == "auto"; |
| 459 | } |
| 460 | } |
| 461 | |
| 462 | void Options::initIndexFiltering(string blacklistFile1, string blacklistFile2, int threshold) { |
| 463 | if(blacklistFile1.empty() && blacklistFile2.empty()) |