diff --git a/src/rock.cpp b/src/rock.cpp old mode 100644 new mode 100755 index a09488e3ec4cfbb05f25aedb302b73444eb072d2..bfaf0c74b59fb9cdc9a63d6b7d91ff4d36be844b --- a/src/rock.cpp +++ b/src/rock.cpp @@ -45,7 +45,23 @@ void printRUsage() { } #endif +// method used for debug only +void printFastqQualThreshold(const FasqQualThreshold& q) { + cout<<"nucl_score_threshold="<<q.nucl_score_threshold<<endl; + cout<<"min_correct_k_mers_in_read="<<q.min_correct_k_mers_in_read<<endl; + cout<<"k="<<q.k<<endl; +} + +// function used for debugging purpose only +void printCMSparams(const CMSparams& p) { + cout<<"CMSparams content:"<<endl; + cout<<"lambda="<<p.lambda<<endl; + cout<<"kappa="<<p.kappa<<endl; + cout<<"kappa_prime="<<p.kappa_prime<<endl; + cout<<"filter_size="<<p.filter_size<<endl; + cout<<"filter_PE_separately="<<p.filter_PE_separately<<endl; +} int main(int argc,char * argv[]) { @@ -58,7 +74,9 @@ int main(int argc,char * argv[]) { main_parms.initFromMainOptsArgs(argc,argv); int f_id=main_parms.get_f_id(); CMSparams parms=main_parms.getCMSparams(); + printCMSparams(parms); FasqQualThreshold qual_thres=main_parms.getQualThresholds(); + printFastqQualThreshold(qual_thres); std::vector<IO_fq_files> single_files=main_parms.get_single_files(); vector<PE_files> v_PE_files=main_parms.get_PE_files();