added functions for debug

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();