diff --git a/src/ROCKparams.cpp b/src/ROCKparams.cpp
index 37960fc34e0ed13c0afbd3551414a706dae201ad..634642d7d37f797429f4d1b72cb7e1c6e12e4df4 100755
--- a/src/ROCKparams.cpp
+++ b/src/ROCKparams.cpp
@@ -300,10 +300,10 @@ int ROCKparams::processInOutFileArgs(const std::vector<string>& v_input_lines,st
PE_files pe;
pe.PE1.in_fq_file=i_name_PE1;
pe.PE1.out_fq_file=o_name_PE1;
- pe.PE1.undef_fq_file=genUndefFilename(i_name_PE1,o_dir_PE1);
+ // pe.PE1.undef_fq_file=genUndefFilename(i_name_PE1,o_dir_PE1);
pe.PE2.in_fq_file=i_name_PE2;
pe.PE2.out_fq_file=o_name_PE2;
- pe.PE2.undef_fq_file=genUndefFilename(i_name_PE2,o_dir_PE2);
+ //pe.PE2.undef_fq_file=genUndefFilename(i_name_PE2,o_dir_PE2);
v_PE_files.push_back(pe);
} else {
@@ -312,7 +312,7 @@ int ROCKparams::processInOutFileArgs(const std::vector<string>& v_input_lines,st
IO_fq_files p;
p.in_fq_file=*it_in;
string o_dir_single=checkDirExists(*it_out);
- p.undef_fq_file=genUndefFilename(*it_in,o_dir_single);
+ // p.undef_fq_file=genUndefFilename(*it_in,o_dir_single);
p.out_fq_file=*it_out;
single_files.push_back(p);
}
diff --git a/src/fqreader.cpp b/src/fqreader.cpp
index 5dc4f3fe40aa797da7c3d1ba286fbcbc37950413..61bab10a668d64a63bd3ae6b24b599d2f5f6294f 100644
--- a/src/fqreader.cpp
+++ b/src/fqreader.cpp
@@ -84,7 +84,7 @@ unsigned long processInputFiles(const std::vector<IO_fq_files>& single_files,\
std::vector<IO_fq_files>::const_iterator it_single;
for (it_single=single_files.begin();it_single!=single_files.end();it_single++) {
FqMainBackend * be_fq=new FqMainBackend(io_sr);
- be_fq->setUndefFile((char *) it_single->undef_fq_file.c_str());
+ //be_fq->setUndefFile((char *) it_single->undef_fq_file.c_str());
be_fq->processFile((char *) it_single->in_fq_file.c_str(),f_id);
be_fq->setOutputFile((char *) it_single->out_fq_file.c_str());
array_be[f_id-1]=be_fq;
@@ -97,12 +97,12 @@ unsigned long processInputFiles(const std::vector<IO_fq_files>& single_files,\
unsigned char f_id1=f_id;
f_id++;
FqAuxBackend * be_fq2=new FqAuxBackend();
- be_fq2->setUndefFile((char *) it_pe->PE2.undef_fq_file.c_str());
+ //be_fq2->setUndefFile((char *) it_pe->PE2.undef_fq_file.c_str());
be_fq2->openFile((char *) (it_pe->PE2.in_fq_file).c_str(),(unsigned char) f_id);
be_fq2->setOutputFile((char *) (it_pe->PE2.out_fq_file).c_str());
be_fq1->setAuxProcessor(be_fq2);
- be_fq1->setUndefFile((char *) it_pe->PE1.undef_fq_file.c_str());
+ //be_fq1->setUndefFile((char *) it_pe->PE1.undef_fq_file.c_str());
be_fq1->processFile((char *) (it_pe->PE1.in_fq_file).c_str(),f_id-1);
be_fq1->setOutputFile((char *) (it_pe->PE1.out_fq_file).c_str());
be_fq2->closeFile();
diff --git a/src/rock.cpp b/src/rock.cpp
index 55673a73dd384e48788f28b22d8c8fa912c1600a..d8f73d63f036895a50181ae5ac7bdd4a78fd7887 100755
--- a/src/rock.cpp
+++ b/src/rock.cpp
@@ -121,10 +121,11 @@ const void printVerboseInfo(const ROCKparams& Rparms,const Filter& filter,const
cout<<setw(40)<<left<<"approx. false positive proba."<<setprecision (6)<<p<<endl;
cout<<setw(40)<<left<<"no. selected reads"<<rc.nb_output_reads<<endl;
for (it_pe=v_PE_files.begin();it_pe!=v_PE_files.end();it_pe++) {
- cout<<setw(40)<<left<<"PE output files"<<it_pe->PE1.out_fq_file<<" "<<it_pe->PE2.out_fq_file<<" "<<it_pe->PE1.undef_fq_file<<" "<<it_pe->PE2.undef_fq_file<<endl;
+ // cout<<setw(40)<<left<<"PE output files"<<it_pe->PE1.out_fq_file<<" "<<it_pe->PE2.out_fq_file<<" "<<it_pe->PE1.undef_fq_file<<" "<<it_pe->PE2.undef_fq_file<<endl;
+ cout<<setw(40)<<left<<"PE output files"<<it_pe->PE1.out_fq_file<<" "<<it_pe->PE2.out_fq_file<<endl;
}
for (it_s=single_files.begin();it_s!=single_files.end();it_s++) {
- cout<<setw(40)<<left<<"SE output files"<<it_s->out_fq_file<<" "<<it_s->undef_fq_file<<endl;
+ cout<<setw(40)<<left<<"SE output files"<<it_s->out_fq_file<<endl;
}
}
diff --git a/src/rock_commons.h b/src/rock_commons.h
index a6fc52d58132393ed2e1b94c666cdefcadb2caa9..f4647d380d8084b9a5335651a010cb4ee646d2c9 100644
--- a/src/rock_commons.h
+++ b/src/rock_commons.h
@@ -61,7 +61,7 @@ const unsigned int Pi_js[k_max_array_in_cms]={4283781797,4283781461,4283738773,4
typedef struct {
std::string in_fq_file;
std::string out_fq_file;
- std::string undef_fq_file;
+ //std::string undef_fq_file;
} IO_fq_files;
typedef struct {
diff --git a/src/unit_test_cms b/src/unit_test_cms
deleted file mode 100755
index 27b3a8364dac9209abcb6410d8a5fb313c7b7b36..0000000000000000000000000000000000000000
Binary files a/src/unit_test_cms and /dev/null differ
diff --git a/src/unit_test_fqreader b/src/unit_test_fqreader
deleted file mode 100755
index 056c2b1304d00ab6a76e4bcae8e3a99ed54f62eb..0000000000000000000000000000000000000000
Binary files a/src/unit_test_fqreader and /dev/null differ
diff --git a/src/unit_test_fqreader.cpp b/src/unit_test_fqreader.cpp
index 6cc5e8884e8bb3fbea1bb6e7f0d54d44cd4b31ee..6702ff53babcd4d168360cd077f0c3ef7445b2b7 100644
--- a/src/unit_test_fqreader.cpp
+++ b/src/unit_test_fqreader.cpp
@@ -54,6 +54,13 @@ void test_processSingleFile() {
k_dim::iterator it_struct;
int cnt_read=0;
+ /*cout<<"sizeof 1rst map when empty:"<<sizeof(srp)<<" "<<sizeof(sr)<<endl;
+ i_dim stuff1;
+ cout<<"sizeof 2np map when empty:"<<sizeof(stuff1)<<endl;
+ k_dim stuff2;
+ cout<<"sizeof vector when empty:"<<sizeof(stuff2)<<endl;
+ cout<<"sizeof(long)"<<sizeof(long)<<endl;
+ cout<<"sizeof(int)"<<sizeof(int)<<endl;*/
for (rit=sr.rbegin(); rit!=sr.rend(); ++rit) { //process map in reverse order (by decreasing scores).
//cout << "score="<<rit->first<<endl;
diff --git a/src/unit_test_fqwriter b/src/unit_test_fqwriter
deleted file mode 100755
index c13adacc2b01f4236a8ba2c702d175fc36616b55..0000000000000000000000000000000000000000
Binary files a/src/unit_test_fqwriter and /dev/null differ
diff --git a/src/unit_test_math_utils b/src/unit_test_math_utils
deleted file mode 100755
index 2b841e519706a85f8914034929fbccc3909d2173..0000000000000000000000000000000000000000
Binary files a/src/unit_test_math_utils and /dev/null differ
diff --git a/src/unit_test_read_utils b/src/unit_test_read_utils
deleted file mode 100755
index fcb34f67c20c3b60f24feb096ea77ae0940c29db..0000000000000000000000000000000000000000
Binary files a/src/unit_test_read_utils and /dev/null differ