From 8f865ab1ff6df622fe08c0592bb82ce5392ceaab Mon Sep 17 00:00:00 2001
From: Veronique Legrand <vlegrand@pasteur.fr>
Date: Mon, 26 Apr 2021 12:25:56 +0200
Subject: [PATCH] added functions for debug
---
src/rock.cpp | 18 ++++++++++++++++++
1 file changed, 18 insertions(+)
mode change 100644 => 100755 src/rock.cpp
diff --git a/src/rock.cpp b/src/rock.cpp
old mode 100644
new mode 100755
index a09488e..bfaf0c7
--- 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();
--
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