| 623 | } |
| 624 | |
| 625 | ExitCodes main_(int, const char **) override |
| 626 | { |
| 627 | /////////////////////////////////// |
| 628 | // Prepare Parameters |
| 629 | /////////////////////////////////// |
| 630 | StringList file_list = getStringList_("in"); |
| 631 | String tr_file = getStringOption_("tr"); |
| 632 | |
| 633 | //tr_file input file type |
| 634 | FileTypes::Type tr_type = FileTypes::nameToType(getStringOption_("tr_type")); |
| 635 | if (tr_type == FileTypes::UNKNOWN) |
| 636 | { |
| 637 | tr_type = FileHandler::getType(tr_file); |
| 638 | writeDebug_(String("Input file type (-tr): ") + FileTypes::typeToName(tr_type), 2); |
| 639 | } |
| 640 | |
| 641 | if (tr_type == FileTypes::UNKNOWN) |
| 642 | { |
| 643 | writeLogError_("Error: Could not determine input file type for '-tr' !"); |
| 644 | return PARSE_ERROR; |
| 645 | } |
| 646 | |
| 647 | String out = getStringOption_("out_features"); |
| 648 | String out_tsv = getStringOption_("out_tsv"); |
| 649 | String out_osw = getStringOption_("out_osw"); |
| 650 | |
| 651 | String out_qc = getStringOption_("out_qc"); |
| 652 | |
| 653 | |
| 654 | String irt_tr_file = getStringOption_("tr_irt"); |
| 655 | String nonlinear_irt_tr_file = getStringOption_("tr_irt_nonlinear"); |
| 656 | String trafo_in = getStringOption_("rt_norm"); |
| 657 | String swath_windows_file = getStringOption_("swath_windows_file"); |
| 658 | |
| 659 | String out_chrom = getStringOption_("out_chrom"); |
| 660 | bool split_file = getFlag_("split_file_input"); |
| 661 | bool use_emg_score = getFlag_("use_elution_model_score"); |
| 662 | bool force = getFlag_("force"); |
| 663 | bool sonar = getFlag_("sonar"); |
| 664 | bool pasef = getFlag_("pasef"); |
| 665 | bool sort_swath_maps = getFlag_("sort_swath_maps"); |
| 666 | bool use_ms1_traces = getStringOption_("enable_ms1") == "true"; |
| 667 | bool enable_uis_scoring = getStringOption_("enable_ipf") == "true"; |
| 668 | int batchSize = (int)getIntOption_("batchSize"); |
| 669 | int outer_loop_threads = (int)getIntOption_("outer_loop_threads"); |
| 670 | int ms1_isotopes = (int)getIntOption_("ms1_isotopes"); |
| 671 | Size debug_level = (Size)getIntOption_("debug"); |
| 672 | |
| 673 | double min_rsq = getDoubleOption_("min_rsq"); |
| 674 | double min_coverage = getDoubleOption_("min_coverage"); |
| 675 | |
| 676 | Param debug_params = getParam_().copy("Debugging:", true); |
| 677 | |
| 678 | String readoptions = getStringOption_("readOptions"); |
| 679 | String mz_correction_function = getStringOption_("mz_correction_function"); |
| 680 | |
| 681 | // make sure tmp is a directory with proper separator at the end (downstream methods simply do path + filename) |
| 682 | // (do not use QDir::separator(), since its platform specific (/ or \) while absolutePath() will always use '/') |
nothing calls this directly
no test coverage detected