| 2642 | #endif |
| 2643 | |
| 2644 | MateOrientation getMateOrientation(std::string const& matesOrientation) |
| 2645 | { |
| 2646 | if (matesOrientation.compare("0") == 0) { |
| 2647 | return SINGLE_END_SORTED_SAM; |
| 2648 | } |
| 2649 | |
| 2650 | if (matesOrientation.compare("RF") == 0) { |
| 2651 | return ILLUMINA_MATE_PAIRS; |
| 2652 | } |
| 2653 | |
| 2654 | if (matesOrientation.compare("FR") == 0) { |
| 2655 | return ILLUMNINA_PAIRED_END; |
| 2656 | } |
| 2657 | |
| 2658 | if (matesOrientation.compare("FF") == 0 || matesOrientation.compare("RR") == 0 || matesOrientation.compare("FF/RR") == 0 || matesOrientation.compare("RR/FF") == 0) { |
| 2659 | return SOLID_MATE_PAIRS; |
| 2660 | } |
| 2661 | cerr << "Error: you have set an unknown read orientation: \""<<matesOrientation<<"\" ; it does not match 0, RF, FR or FF; please correct your config file.\n"; |
| 2662 | exit(1); |
| 2663 | return SINGLE_END_SORTED_SAM; // instead of UNKNOWN_MATE_ORIENTATION; |
| 2664 | } |
| 2665 | |
| 2666 | InputFormat getInputFormat(std::string const& inputFormat) |
| 2667 | { |
no test coverage detected