diff --git a/src/CountMinSketch.hpp b/src/CountMinSketch.hpp
index 3216e0871e3c0bc7cfa33844b45867e05b4720a7..d9881a2665e357150be16ca36bc6e4cb78cc77ae 100644
--- a/src/CountMinSketch.hpp
+++ b/src/CountMinSketch.hpp
@@ -148,7 +148,7 @@ private:
 
     inline int isRCovBelowThresPartial(const readNumericValues& read_val, const int& threshold, const int& start=0,const int& stop=0);
 
-    void init(int glambda,int gkappa,int gkappa_prime,int filter_PE_separately=1);
+    void init(int glambda,int gkappa,int gkappa_prime,int filter_PE_separately=0);
 
     // for unit tests.
     friend void test_CMS(int lambda,int kappa,int kappa_prime);
diff --git a/src/ROCKparams.cpp b/src/ROCKparams.cpp
index 95b1907e182c6950c07c1f6179941a1b8b1285cd..ca524b44df9d534e0acbbaa8eaa1c281e5ff8098 100644
--- a/src/ROCKparams.cpp
+++ b/src/ROCKparams.cpp
@@ -24,10 +24,10 @@ void ROCKparams::computeLambda() {
     parms.lambda=tmp/UINT_MAX;
     if (parms.kappa>get_mask<unsigned char>::value) parms.lambda=parms.lambda/sizeof(unsigned short);
 }
-
+/*
 int ROCKparams::getfilterPEMode() {
     return parms.filter_PE_separately;
-}
+}*/
 
 
 void ROCKparams::processMainArgs(int optind, const int argc, char ** argv,std::vector<string>& v_input_lines) {
@@ -279,7 +279,7 @@ void ROCKparams::initFromMainOptsArgs(int argc,char ** argv) {
     //int option_index=0;
 
     // while((i = getopt_long(argc, argv, "i:o:l:k:c:C:g:n:vq:m:",long_options,&option_index)) != -1) {
-    while((i = getopt(argc, argv, "i:o:l:k:c:C:g:n:vq:m:p:")) != -1) {
+    while((i = getopt(argc, argv, "i:o:l:k:c:C:g:n:vq:m:")) != -1) {
         switch(i) {
             case 0:
                 break;
@@ -321,7 +321,7 @@ void ROCKparams::initFromMainOptsArgs(int argc,char ** argv) {
             case 'v':
                 verbose_mode=1;
                 break;
-            case 'p':
+/*            case 'p':
                 if (strlen(optarg)>1) {
                     cout<<"value for -p option must be 0, 1 or 2";
                     usage(EXIT_FAILURE);
@@ -331,7 +331,7 @@ void ROCKparams::initFromMainOptsArgs(int argc,char ** argv) {
                     cout<<"value for -p option must be 0, 1 or 2";
                     usage(EXIT_FAILURE);
                 }
-                break;
+                break;*/
             case 'q':
                 q=atoi(optarg);
                 if (q<0) {
@@ -356,7 +356,7 @@ void ROCKparams::initFromMainOptsArgs(int argc,char ** argv) {
         cout<<"Incompatible options: when PE are processed independently, minimum number of correct k-mers in each end is 1."<<endl;
         usage(EXIT_FAILURE);
     }*/
-    parms.filter_PE_separately=PE_separately;
+    //parms.filter_PE_separately=PE_separately;
     //cout<<PE_as_single<<endl;
     processMainArgs(optind, argc, argv,v_input_lines);
     optArgConsistency(input_file,output_file,g,parms,nb_k_mers,v_input_lines);
diff --git a/src/ROCKparams.h b/src/ROCKparams.h
index f726a9f895513849b501bf3afee5e6ecf6e5dc94..15564013cb0542d2be672426ab758615691501d0 100644
--- a/src/ROCKparams.h
+++ b/src/ROCKparams.h
@@ -79,7 +79,7 @@ class ROCKparams{
 public:
 
     FasqQualThreshold getQualThreshold();
-    int getfilterPEMode();
+    //int getfilterPEMode();
 
     ROCKparams() {
         f_id=0; // to generate id of input/output fastq files. +1=total number of files.
@@ -89,7 +89,7 @@ public:
         parms.kappa=70;
         parms.kappa_prime=5;
         parms.lambda=0;
-        parms.filter_PE_separately=1;
+        //parms.filter_PE_separately=1;
         qual_thres.min_correct_k_mers_in_read=1;
         qual_thres.nucl_score_threshold=10+k_phred_32;
         qual_thres.k=k;
diff --git a/src/rock.cpp b/src/rock.cpp
index 240950011f520897265cd176a800475d60feea0e..a52eecfeffc5e08fa3adbda6f5d3c6d4774b5088 100644
--- a/src/rock.cpp
+++ b/src/rock.cpp
@@ -69,7 +69,7 @@ int main(int argc,char * argv[]) {
     cout<<"processed input args; going to start reading fastq files"<<endl;
     printRUsage();
 #endif
-    processInputFiles(single_files,v_PE_files,map_id_backend,main_parms.getQualThreshold(),&sr,main_parms.getfilterPEMode());
+    processInputFiles(single_files,v_PE_files,map_id_backend,main_parms.getQualThreshold(),&sr,0); // Removing -p option, set default mode to 0 (PE processed as single).
 #ifdef BENCHMARK
     cout<<"finished loading fastq file into sr structure"<<endl;
     cout<<"size of srp structure="<<sizeof(sr)<<endl;
diff --git a/test/rock.sh b/test/rock.sh
index 524608b25262272903a5977c969bd512c211c00c..7c47f03e5d4c5e7d8caf2b31520a9c05e71cb07c 100755
--- a/test/rock.sh
+++ b/test/rock.sh
@@ -55,19 +55,19 @@ mkdir data/fastq.filtered || exit 6
 echo " "
 echo "##################################################################################"
 echo "doing more checks on options and error messages"
-../src/rock -C 500000 -p 0 -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt|grep "Bad value for kappa"  >/dev/null || exit 7
-../src/rock -C 500 -c 600 -p 0 -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt|grep "ERROR lower filter is higher than high filter" >/dev/null || exit 8
-../src/rock -C 500 -c 400 -k 60 -p 0 -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt|grep "Bad value for k" >/dev/null || exit 9
-../src/rock -C 500 -c 400 -k 10 -l 0 -p 0 -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt|grep "Bad value for lambda" >/dev/null || exit 10
-../src/rock -C 500 -c 400 -k 10 -l 500 -p 0 -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt|grep "Not enough RAM on the machine" >/dev/null || exit 11
+../src/rock -C 500000  -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt|grep "Bad value for kappa"  >/dev/null || exit 7
+../src/rock -C 500 -c 600  -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt|grep "ERROR lower filter is higher than high filter" >/dev/null || exit 8
+../src/rock -C 500 -c 400 -k 60  -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt|grep "Bad value for k" >/dev/null || exit 9
+../src/rock -C 500 -c 400 -k 10 -l 0  -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt|grep "Bad value for lambda" >/dev/null || exit 10
+../src/rock -C 500 -c 400 -k 10 -l 500  -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt|grep "Not enough RAM on the machine" >/dev/null || exit 11
 ../src/rock -C 500 -c 400 -k 10 -l 12 -g 25 -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt|grep "options are mutually exclusive" >/dev/null|| exit 12
 ../src/rock -C 500 -c 400 -k 10 -g 10000 -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt|grep "This machine only has" >/dev/null || exit 13
 ../src/rock -C 500 -c 400 -k 10 -l 12 -n 85000000 -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt|grep "options are mutually exclusive">/dev/null || exit 14
-../src/rock -C 500 -c 400 -k 10 -q 3 -m 0 -p 0 -i ${srcdir}/test/data/iofiles.args/extract_klebsiella_long_reads_100.txt|grep "minimum number of valid k-mer for keeping a read must be an integer">/dev/null || exit 15
-../src/rock -C 500 -c 400 -k 10 -q -1 -m 2 -p 0 -i ${srcdir}/test/data/iofiles.args/extract_klebsiella_long_reads_100.txt|grep "q must be">/dev/null || exit 16
-../src/rock -C 500 -c 400 -k 10 -q 4 -m 2 -p 10 -i ${srcdir}/test/data/iofiles.args/extract_klebsiella_long_reads_100.txt|grep "value for -p option must be 0, 1 or 2">/dev/null || exit 17
-../src/rock -C 500 -c 400 -k 10 -q 4 -m 2 -p 1,5 -i ${srcdir}/test/data/iofiles.args/extract_klebsiella_long_reads_100.txt|grep "value for -p option must be 0, 1 or 2">/dev/null || exit 18
-../src/rock -C 500 -c 400 -k 10 -q 4 -m 2 -p -1 -i ${srcdir}/test/data/iofiles.args/extract_klebsiella_long_reads_100.txt|grep "value for -p option must be 0, 1 or 2">/dev/null || exit 17
+../src/rock -C 500 -c 400 -k 10 -q 3 -m 0  -i ${srcdir}/test/data/iofiles.args/extract_klebsiella_long_reads_100.txt|grep "minimum number of valid k-mer for keeping a read must be an integer">/dev/null || exit 15
+../src/rock -C 500 -c 400 -k 10 -q -1 -m 2  -i ${srcdir}/test/data/iofiles.args/extract_klebsiella_long_reads_100.txt|grep "q must be">/dev/null || exit 16
+#../src/rock -C 500 -c 400 -k 10 -q 4 -m 2 -p 10 -i ${srcdir}/test/data/iofiles.args/extract_klebsiella_long_reads_100.txt|grep "value for -p option must be 0, 1 or 2">/dev/null || exit 17
+#../src/rock -C 500 -c 400 -k 10 -q 4 -m 2 -p 1,5 -i ${srcdir}/test/data/iofiles.args/extract_klebsiella_long_reads_100.txt|grep "value for -p option must be 0, 1 or 2">/dev/null || exit 18
+#../src/rock -C 500 -c 400 -k 10 -q 4 -m 2 -p -1 -i ${srcdir}/test/data/iofiles.args/extract_klebsiella_long_reads_100.txt|grep "value for -p option must be 0, 1 or 2">/dev/null || exit 17
 
 #../src/rock -C 500 -c 400 -k 10 -q 2 -m 2 -i ${srcdir}/test/data/iofiles.args/extract_klebsiella_long_reads_100.txt|grep "Incompatible options">/dev/null || exit 161
 
@@ -75,7 +75,7 @@ echo "doing more checks on options and error messages"
 ../src/unit_test_cms CHECK_MEM
 if [ $? = 0 ] ## we have enough memory to run the tests in rock_mem.sh
 then 
-    ${srcdir}/rock_mem.sh ||exit 255
+     ${srcdir}/rock_mem.sh ||exit 255
 fi
 
 # unit tests
diff --git a/test/rock_mem.sh b/test/rock_mem.sh
index d4956a709b561544921272c72143d2ead21d9b0b..446815be61fc0487954bd8d8c2757a22ced1f28f 100755
--- a/test/rock_mem.sh
+++ b/test/rock_mem.sh
@@ -10,7 +10,7 @@ echo "##########################################################################
 echo "testing high filter"
 
 
-../src/rock -C 100 -c 0 -l 2 -p 0 -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt >/dev/null || exit 101
+../src/rock -C 100 -c 0 -l 2  -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt >/dev/null || exit 101
 
 # output files should be the same size, contain the same elements but not in the same order.
 nb_PE1=`grep -c "@" ${srcdir}/data/fastq.raw/klebsiella_100_1.fq`
@@ -34,7 +34,7 @@ test $nb_PE2 -eq $nb_PE2_filtered || exit 105
 echo " "
 echo "##################################################################################"
 echo "testing low filter"
-../src/rock -C 100 -c 99 -l 2 -p 0 -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt >/dev/null || exit 106
+../src/rock -C 100 -c 99 -l 2  -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt >/dev/null || exit 106
 
 [ -f "data/fastq.filtered/SRR1222430_1.filtered.fastq" ] || exit 107
 [ -f "data/fastq.filtered/SRR1222430_2.filtered.fastq" ] || exit 108
@@ -45,11 +45,11 @@ nb_PE2_filtered=`grep -c "@" data/fastq.filtered/SRR1222430_2.filtered.fastq`
 test $nb_PE1_filtered -eq 0 || exit 109
 test $nb_PE2_filtered -eq 0 || exit 110
 
-# test that input fastq file names can be provided in command-line.
+test that input fastq file names can be provided in command-line.
 echo " "
 echo "##################################################################################"
 echo "testing that input fastq file names can be provided in command line."
-../src/rock -C 100 -c 1 -l 2 -p 0 ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq ${srcdir}/data/unit/test_single.fq ${srcdir}/data/unit/test_single2.fq >/dev/null || exit 111
+../src/rock -C 100 -c 1 -l 2  ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq ${srcdir}/data/unit/test_single.fq ${srcdir}/data/unit/test_single2.fq >/dev/null || exit 111
 
 [ -f "klebsiella_100_1.rock.fq" ] || exit 112
 [ -f "klebsiella_100_2.rock.fq" ] || exit 113
@@ -58,7 +58,7 @@ echo "testing that input fastq file names can be provided in command line."
 
 
 
-# checking that output files were sorted in decreasing order of quality score. For that expect to have SRR122430.1.1 as 1rst record in filtered file.
+checking that output files were sorted in decreasing order of quality score. For that expect to have SRR122430.1.1 as 1rst record in filtered file.
 ret=`head -4 "klebsiella_100_1.rock.fq"|grep -c "SRR1222430.1.1"`
 test $ret -eq 2 || exit 116
 
@@ -78,9 +78,9 @@ rm -f "test_single2.undefined.fq" || exit 124
 echo " "
 echo "##################################################################################"
 echo "testing verbose mode"
-../src/rock -C 100 -c 1 -l 2 -p 0 -v ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq ${srcdir}/data/unit/test_single.fq ${srcdir}/data/unit/test_single2.fq|grep "CMS size=" >/dev/null || exit 125
+../src/rock -C 100 -c 1 -l 2  -v ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq ${srcdir}/data/unit/test_single.fq ${srcdir}/data/unit/test_single2.fq|grep "CMS size=" >/dev/null || exit 125
 
-../src/rock -C 100 -c 1 -v -p 0 -n 1000 ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq ${srcdir}/data/unit/test_single.fq ${srcdir}/data/unit/test_single2.fq|grep "expected probability of collision was:" >/dev/null || exit 126
+../src/rock -C 100 -c 1 -v  -n 1000 ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq ${srcdir}/data/unit/test_single.fq ${srcdir}/data/unit/test_single2.fq|grep "expected probability of collision was:" >/dev/null || exit 126
 
 echo "erasing test result files"
 rm -f "klebsiella_100_1.rock.fq" || exit 127
@@ -108,18 +108,18 @@ expected_diff2="> @SRR1222430.37 37 length=251 \
 > A3>333BFA2FF4GBFFDGGCGED?FGEGGHGFFFEEG?AF13@50>///11B13@@1/>//B0?>////<//B/00??@/--:--.;:C000;:0/0009.-9:.00:-.;9/9...-;.--9@--9:////-9-9..////9/;//;9///.9-..--------..99.9.//////;-;--9-.////://9/9.;.-;-99-.//.;////-;?9;...9-9-----9;-.;.;/.-9.;/99=--;"
 
 mkdir tmp
-../src/rock -C 100 -c 1 -l 2 -p 0 -o ${srcdir}/data/iofiles.args/output_files_noNQ_Thres.txt  ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null || exit 140
+../src/rock -C 100 -c 1 -l 2  -o ${srcdir}/data/iofiles.args/output_files_noNQ_Thres.txt  ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null || exit 140
 
-../src/rock -C 100 -c 1 -l 2 -q 2 -p 0 -o ${srcdir}/data/iofiles.args/output_files_NQ_Thres_very_low.txt  ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null || exit 141
+../src/rock -C 100 -c 1 -l 2 -q 2 -o ${srcdir}/data/iofiles.args/output_files_NQ_Thres_very_low.txt  ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null || exit 141
 
 ret1=`diff tmp/klebsiella_100_1_very_low_qual_thres.fq tmp/klebsiella_100_1_no_qual_thres.fq|wc -l`
 test $ret1 -eq 0 || exit 142
 ret2=`diff tmp/klebsiella_100_2_very_low_qual_thres.fq tmp/klebsiella_100_2_no_qual_thres.fq|wc -l`
 test $ret2 -eq 0 || exit 143
 
-../src/rock -C 100 -c 1 -l 2 -q 12 -p 0 -o ${srcdir}/data/iofiles.args/output_files_NQ_Thres_12.txt ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null ||exit 144
+../src/rock -C 100 -c 1 -l 2 -q 12 -o ${srcdir}/data/iofiles.args/output_files_NQ_Thres_12.txt ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null ||exit 144
 
-../src/rock -C 100 -c 1 -l 2 -q 13 -p 0 -o ${srcdir}/data/iofiles.args/output_files_NQ_Thres_13.txt ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null ||exit 145
+../src/rock -C 100 -c 1 -l 2 -q 13 -o ${srcdir}/data/iofiles.args/output_files_NQ_Thres_13.txt ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null ||exit 145
 
 ret1=`diff tmp/klebsiella_100_1_13_qual_thres.fq tmp/klebsiella_100_1_12_qual_thres.fq|grep -c "@SRR1222430.37"`
 test $ret1 -eq  1 || exit 146
@@ -140,9 +140,9 @@ echo "##########################################################################
 echo "testing ROCK with a quality score threshold for nucleotides and minimum number of valid k-mer to keep a read."
 
 mkdir tmp
-../src/rock -C 100 -c 1 -l 2 -p 0 -o ${srcdir}/data/iofiles.args/output_files_noNQ_Thres.txt  ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null || exit 150
+../src/rock -C 100 -c 1 -l 2 -o ${srcdir}/data/iofiles.args/output_files_noNQ_Thres.txt  ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null || exit 150
 
-../src/rock -C 100 -c 1 -l 2 -q 2 -m 5 -p 0 -o ${srcdir}/data/iofiles.args/output_files_NQ_Thres_very_low.txt  ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null || exit 151
+../src/rock -C 100 -c 1 -l 2 -q 2 -m 5 -o ${srcdir}/data/iofiles.args/output_files_NQ_Thres_very_low.txt  ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null || exit 151
 
 ret1=`diff tmp/klebsiella_100_1_very_low_qual_thres.fq tmp/klebsiella_100_1_no_qual_thres.fq|wc -l`
 test $ret1 -eq 0 || exit 152
@@ -159,7 +159,7 @@ ret2=`cat tmp/klebsiella_100_2.undefined.fq|wc -l`
 test $ret1 -eq 0 || exit 156
 test $ret1 -eq 0 || exit 157
 
-../src/rock -C 100 -c 1 -l 2 -q 13 -m 500 -p 0 -o ${srcdir}/data/iofiles.args/output_files_NQ_Thres_13.txt ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null || exit 158
+../src/rock -C 100 -c 1 -l 2 -q 13 -m 500 -o ${srcdir}/data/iofiles.args/output_files_NQ_Thres_13.txt ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null || exit 158
 
 [ -f "tmp/klebsiella_100_1.undefined.fq" ] || exit 159
 [ -f "tmp/klebsiella_100_2.undefined.fq" ] || exit 160
@@ -170,7 +170,7 @@ ret2=`cat tmp/klebsiella_100_2.undefined.fq|wc -l`
 test $ret1 -eq 400 || exit 161
 test $ret1 -eq 400 || exit 162
 
-../src/rock -C 100 -c 1 -l 2 -q 13 -m 300 -p 0 -o ${srcdir}/data/iofiles.args/output_files_NQ_Thres_13.txt ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null || exit 163
+../src/rock -C 100 -c 1 -l 2 -q 13 -m 300 -o ${srcdir}/data/iofiles.args/output_files_NQ_Thres_13.txt ${srcdir}/data/fastq.raw/klebsiella_100_1.fq,${srcdir}/data/fastq.raw/klebsiella_100_2.fq >/dev/null || exit 163
 
 [ -f "tmp/klebsiella_100_1.undefined.fq" ] || exit 164
 [ -f "tmp/klebsiella_100_2.undefined.fq" ] || exit 165
@@ -182,386 +182,386 @@ test $ret1 -eq 136 || exit 166
 test $ret1 -eq 136 || exit 167
 
 echo " "
-echo "##################################################################################"
-echo "testing ROCK with a quality score threshold for nucleotides and PE processed separately with strict filter "
-../src/rock -C 100 -c 1 -l 2 -q 2 -p 1 -o ${srcdir}/data/iofiles.args/output_files_2_PE_separated.txt ${srcdir}/data/fastq.raw/klebsiella_5_1_bad_scores.fq,${srcdir}/data/fastq.raw/klebsiella_5_2_bad_scores.fq >/dev/null || exit 168
-
-[ -f "tmp/klebsiella_5_1_bad_scores.undefined.fq" ] || exit 169
-[ -f "tmp/klebsiella_5_2_bad_scores.undefined.fq" ] || exit 170
-
-ret1=`cat tmp/klebsiella_5_1_bad_scores.undefined.fq|wc -l`
-ret2=`cat tmp/klebsiella_5_2_bad_scores.undefined.fq|wc -l`
-
-test $ret1 -eq 8 || exit 171
-test $ret2 -eq 8 || exit 171
-
-ret1=`grep -c SRR1222430.1 tmp/klebsiella_5_1_bad_scores.undefined.fq`
-ret2=`grep -c SRR1222430.1 tmp/klebsiella_5_2_bad_scores.undefined.fq`
-
-test $ret1 -eq 2 || exit 172
-test $ret2 -eq 2 || exit 172
-
-ret1=`grep -c SRR1222430.4 tmp/klebsiella_5_1_bad_scores.undefined.fq`
-ret2=`grep -c SRR1222430.4 tmp/klebsiella_5_2_bad_scores.undefined.fq`
-
-test $ret1 -eq 2 || exit 173
-test $ret2 -eq 2 || exit 173
-
-ret1=`grep -c SRR1222430.2 tmp/klebsiella_5_1_bad_scores.undefined.fq`
-ret2=`grep -c SRR1222430.2 tmp/klebsiella_5_2_bad_scores.undefined.fq`
-
-test $ret1 -eq 0 || exit 174
-test $ret2 -eq 0 || exit 174
-
-ret1=`grep -c SRR1222430.3 tmp/klebsiella_5_1_bad_scores.undefined.fq`
-ret2=`grep -c SRR1222430.3 tmp/klebsiella_5_2_bad_scores.undefined.fq`
-
-test $ret1 -eq 0 || exit 175
-test $ret2 -eq 0 || exit 175
-
-ret1=`grep -c SRR1222430.5 tmp/klebsiella_5_1_bad_scores.undefined.fq`
-ret2=`grep -c SRR1222430.5 tmp/klebsiella_5_2_bad_scores.undefined.fq`
-
-test $ret1 -eq 0 || exit 176
-test $ret2 -eq 0 || exit 176
-
-ret1=`cat tmp/klebsiella_5_1_2_qual_thres.fq|wc -l`
-ret2=`cat tmp/klebsiella_5_1_2_qual_thres.fq|wc -l`
-
-test $ret1 -eq 8 || exit 177
-test $ret2 -eq 8 || exit 177
-
-ret1=`grep -c SRR1222430.2 tmp/klebsiella_5_1_2_qual_thres.fq`
-ret2=`grep -c SRR1222430.2 tmp/klebsiella_5_2_2_qual_thres.fq`
-
-test $ret1 -eq 2 || exit 178
-test $ret2 -eq 2 || exit 178
-
-ret1=`grep -c SRR1222430.3 tmp/klebsiella_5_1_2_qual_thres.fq`
-ret2=`grep -c SRR1222430.3 tmp/klebsiella_5_2_2_qual_thres.fq`
-
-test $ret1 -eq 0 || exit 179
-test $ret2 -eq 0 || exit 179
-
-ret1=`grep -c SRR1222430.5 tmp/klebsiella_5_1_2_qual_thres.fq`
-ret2=`grep -c SRR1222430.5 tmp/klebsiella_5_2_2_qual_thres.fq`
-
-test $ret1 -eq 2 || exit 180
-test $ret2 -eq 2 || exit 180
-
-rm -f tmp/klebsiella_5_1_bad_scores.undefined.fq
-rm -f tmp/klebsiella_5_2_bad_scores.undefined.fq
-rm -f tmp/klebsiella_5_1_2_qual_thres.fq
-rm -f tmp/klebsiella_5_2_2_qual_thres.fq
-
-
-echo " "
-echo "##################################################################################"
-echo "testing ROCK with a quality score threshold for nucleotides, PE processed separately (strict filter)  and -m option"
-../src/rock -C 100 -c 1 -l 2 -q 2 -m 2 -p 1 -o ${srcdir}/data/iofiles.args/output_files_2_PE_separated.txt ${srcdir}/data/fastq.raw/klebsiella_5_1_bad_scores.fq,${srcdir}/data/fastq.raw/klebsiella_5_2_bad_scores.fq >/dev/null || exit 281
-
-[ -f "tmp/klebsiella_5_1_bad_scores.undefined.fq" ] || exit 182
-[ -f "tmp/klebsiella_5_2_bad_scores.undefined.fq" ] || exit 182
-
-ret1=`cat tmp/klebsiella_5_1_bad_scores.undefined.fq|wc -l`
-ret2=`cat tmp/klebsiella_5_2_bad_scores.undefined.fq|wc -l`
-
-test $ret1 -eq 8 || exit 183
-test $ret2 -eq 8 || exit 183
-
-ret1=`grep -c SRR1222430.1 tmp/klebsiella_5_1_bad_scores.undefined.fq`
-ret2=`grep -c SRR1222430.1 tmp/klebsiella_5_2_bad_scores.undefined.fq`
-
-test $ret1 -eq 2 || exit 184
-test $ret2 -eq 2 || exit 184
-
-ret1=`grep -c SRR1222430.4 tmp/klebsiella_5_1_bad_scores.undefined.fq`
-ret2=`grep -c SRR1222430.4 tmp/klebsiella_5_2_bad_scores.undefined.fq`
-
-test $ret1 -eq 2 || exit 185
-test $ret2 -eq 2 || exit 185
-
-ret1=`grep -c SRR1222430.2 tmp/klebsiella_5_1_bad_scores.undefined.fq`
-ret2=`grep -c SRR1222430.2 tmp/klebsiella_5_2_bad_scores.undefined.fq`
-
-test $ret1 -eq 0 || exit 186
-test $ret2 -eq 0 || exit 186
-
-ret1=`grep -c SRR1222430.3 tmp/klebsiella_5_1_bad_scores.undefined.fq`
-ret2=`grep -c SRR1222430.3 tmp/klebsiella_5_2_bad_scores.undefined.fq`
-
-test $ret1 -eq 0 || exit 187
-test $ret2 -eq 0 || exit 187
-
-ret1=`grep -c SRR1222430.5 tmp/klebsiella_5_1_bad_scores.undefined.fq`
-ret2=`grep -c SRR1222430.5 tmp/klebsiella_5_2_bad_scores.undefined.fq`
-
-test $ret1 -eq 0 || exit 188
-test $ret2 -eq 0 || exit 188
-
-ret1=`cat tmp/klebsiella_5_1_2_qual_thres.fq|wc -l`
-ret2=`cat tmp/klebsiella_5_1_2_qual_thres.fq|wc -l`
-
-test $ret1 -eq 8 || exit 189
-test $ret2 -eq 8 || exit 189
-
-ret1=`grep -c SRR1222430.2 tmp/klebsiella_5_1_2_qual_thres.fq`
-ret2=`grep -c SRR1222430.2 tmp/klebsiella_5_2_2_qual_thres.fq`
-
-test $ret1 -eq 2 || exit 190
-test $ret2 -eq 2 || exit 190
-
-ret1=`grep -c SRR1222430.3 tmp/klebsiella_5_1_2_qual_thres.fq`
-ret2=`grep -c SRR1222430.3 tmp/klebsiella_5_2_2_qual_thres.fq`
-
-test $ret1 -eq 0 || exit 191
-test $ret2 -eq 0 || exit 191
-
-ret1=`grep -c SRR1222430.5 tmp/klebsiella_5_1_2_qual_thres.fq`
-ret2=`grep -c SRR1222430.5 tmp/klebsiella_5_2_2_qual_thres.fq`
-
-test $ret1 -eq 2 || exit 192
-test $ret2 -eq 2 || exit 192
-
-rm -f tmp/klebsiella_5_1_bad_scores.undefined.fq
-rm -f tmp/klebsiella_5_2_bad_scores.undefined.fq
-rm -f tmp/klebsiella_5_1_2_qual_thres.fq
-rm -f tmp/klebsiella_5_2_2_qual_thres.fq
-
-
-
-echo " "
-echo "##################################################################################"
-echo "testing ROCK with no quality score threshold for nucleotides, no low filter and PE processed separately (strict filter)"
-
-../src/rock -C 100 -c 0 -l 2 -q 0 -p 1 -o ${srcdir}/data/iofiles.args/output_files_2_PE_separated.txt ${srcdir}/data/fastq.raw/klebsiella_5_1_bad_scores.fq,${srcdir}/data/fastq.raw/klebsiella_5_2_bad_scores.fq >/dev/null || exit 193
-
-[ -f "tmp/klebsiella_5_1_bad_scores.undefined.fq" ] || exit 194
-[ -f "tmp/klebsiella_5_2_bad_scores.undefined.fq" ] || exit 194
-
-ret1=`cat tmp/klebsiella_5_1_bad_scores.undefined.fq|wc -l`
-ret2=`cat tmp/klebsiella_5_2_bad_scores.undefined.fq|wc -l`
-
-test $ret1 -eq 0 || exit 195
-test $ret2 -eq 0 || exit 195
-
-ret1=`cat tmp/klebsiella_5_1_2_qual_thres.fq|wc -l`
-ret2=`cat tmp/klebsiella_5_1_2_qual_thres.fq|wc -l`
-
-test $ret1 -eq 20 || exit 196
-test $ret2 -eq 20 || exit 196
-
-ret1=`grep -c SRR1222430.2 tmp/klebsiella_5_1_2_qual_thres.fq`
-ret2=`grep -c SRR1222430.2 tmp/klebsiella_5_2_2_qual_thres.fq`
-
-test $ret1 -eq 2 || exit 197
-test $ret2 -eq 2 || exit 197
-
-ret1=`grep -c SRR1222430.3 tmp/klebsiella_5_1_2_qual_thres.fq`
-ret2=`grep -c SRR1222430.3 tmp/klebsiella_5_2_2_qual_thres.fq`
-
-test $ret1 -eq 2 || exit 198
-test $ret2 -eq 2 || exit 198
-
-ret1=`grep -c SRR1222430.4 tmp/klebsiella_5_1_2_qual_thres.fq`
-ret2=`grep -c SRR1222430.4 tmp/klebsiella_5_2_2_qual_thres.fq`
-
-test $ret1 -eq 2 || exit 199
-test $ret2 -eq 2 || exit 199
-
-ret1=`grep -c SRR1222430.1 tmp/klebsiella_5_1_2_qual_thres.fq`
-ret2=`grep -c SRR1222430.1 tmp/klebsiella_5_2_2_qual_thres.fq`
-
-test $ret1 -eq 2 || exit 200
-test $ret2 -eq 2 || exit 200
-
-ret1=`grep -c SRR1222430.5 tmp/klebsiella_5_1_2_qual_thres.fq`
-ret2=`grep -c SRR1222430.5 tmp/klebsiella_5_2_2_qual_thres.fq`
-
-test $ret1 -eq 2 || exit 201
-test $ret2 -eq 2 || exit 201
-
-rm -f tmp/klebsiella_5_1_bad_scores.undefined.fq
-rm -f tmp/klebsiella_5_2_bad_scores.undefined.fq
-rm -f tmp/klebsiella_5_1_2_qual_thres.fq
-rm -f tmp/klebsiella_5_2_2_qual_thres.fq
-
-
-echo " "
-echo "##################################################################################"
-echo "testing ROCK with no quality score threshold for nucleotides, no low filter and PE processed separately (lenient filter). Results should be the same as with strict filter"
-
-../src/rock -C 100 -c 0 -l 2 -q 0 -p 2 -o ${srcdir}/data/iofiles.args/output_files_2_PE_separated.txt ${srcdir}/data/fastq.raw/klebsiella_5_1_bad_scores.fq,${srcdir}/data/fastq.raw/klebsiella_5_2_bad_scores.fq >/dev/null || exit 202
-
-[ -f "tmp/klebsiella_5_1_bad_scores.undefined.fq" ] || exit 202
-[ -f "tmp/klebsiella_5_2_bad_scores.undefined.fq" ] || exit 202
-
-ret1=`cat tmp/klebsiella_5_1_bad_scores.undefined.fq|wc -l`
-ret2=`cat tmp/klebsiella_5_2_bad_scores.undefined.fq|wc -l`
-
-test $ret1 -eq 0 || exit 203
-test $ret2 -eq 0 || exit 203
-
-ret1=`cat tmp/klebsiella_5_1_2_qual_thres.fq|wc -l`
-ret2=`cat tmp/klebsiella_5_1_2_qual_thres.fq|wc -l`
-
-test $ret1 -eq 20 || exit 204
-test $ret2 -eq 20 || exit 204
-
-ret1=`grep -c SRR1222430.2 tmp/klebsiella_5_1_2_qual_thres.fq`
-ret2=`grep -c SRR1222430.2 tmp/klebsiella_5_2_2_qual_thres.fq`
-
-test $ret1 -eq 2 || exit 205
-test $ret2 -eq 2 || exit 205
-
-ret1=`grep -c SRR1222430.3 tmp/klebsiella_5_1_2_qual_thres.fq`
-ret2=`grep -c SRR1222430.3 tmp/klebsiella_5_2_2_qual_thres.fq`
-
-test $ret1 -eq 2 || exit 206
-test $ret2 -eq 2 || exit 206
-
-ret1=`grep -c SRR1222430.4 tmp/klebsiella_5_1_2_qual_thres.fq`
-ret2=`grep -c SRR1222430.4 tmp/klebsiella_5_2_2_qual_thres.fq`
-
-test $ret1 -eq 2 || exit 207
-test $ret2 -eq 2 || exit 207
-
-ret1=`grep -c SRR1222430.1 tmp/klebsiella_5_1_2_qual_thres.fq`
-ret2=`grep -c SRR1222430.1 tmp/klebsiella_5_2_2_qual_thres.fq`
-
-test $ret1 -eq 2 || exit 208
-test $ret2 -eq 2 || exit 208
-
-ret1=`grep -c SRR1222430.5 tmp/klebsiella_5_1_2_qual_thres.fq`
-ret2=`grep -c SRR1222430.5 tmp/klebsiella_5_2_2_qual_thres.fq`
-
-test $ret1 -eq 2 || exit 209
-test $ret2 -eq 2 || exit 209
-
-
-rm -f tmp/klebsiella_5_1_bad_scores.undefined.fq
-rm -f tmp/klebsiella_5_2_bad_scores.undefined.fq
-rm -f tmp/klebsiella_5_1_2_qual_thres.fq
-rm -f tmp/klebsiella_5_2_2_qual_thres.fq
-
-
-echo " "
-echo "##################################################################################"
-echo "testing ROCK with a quality score threshold for nucleotides, PE processed separately (lenient filter)  and -m option"
-../src/rock -C 100 -c 1 -l 2 -q 2 -m 2 -p 2 -o ${srcdir}/data/iofiles.args/output_files_2_PE_separated_lenient.txt ${srcdir}/data/fastq.raw/klebsiella_6_1_bad_scores.fq,${srcdir}/data/fastq.raw/klebsiella_6_2_bad_scores.fq >/dev/null || exit 210
-
-[ -f "tmp/klebsiella_6_1_bad_scores.undefined.fq" ] || exit 211
-[ -f "tmp/klebsiella_6_2_bad_scores.undefined.fq" ] || exit 211
-
-ret1=`cat tmp/klebsiella_6_1_bad_scores.undefined.fq|wc -l`
-ret2=`cat tmp/klebsiella_6_2_bad_scores.undefined.fq|wc -l`
-
-test $ret1 -eq 8 || exit 212
-test $ret2 -eq 8 || exit 212
-
-ret1=`grep -c SRR1222430.1 tmp/klebsiella_6_1_bad_scores.undefined.fq`
-ret2=`grep -c SRR1222430.1 tmp/klebsiella_6_2_bad_scores.undefined.fq`
-
-test $ret1 -eq 2 || exit 213
-test $ret2 -eq 2 || exit 213
-
-ret1=`grep -c SRR1222430.4 tmp/klebsiella_6_1_bad_scores.undefined.fq`
-ret2=`grep -c SRR1222430.4 tmp/klebsiella_6_2_bad_scores.undefined.fq`
-
-test $ret1 -eq 2 || exit 214
-test $ret2 -eq 2 || exit 214
-
-ret1=`grep -c SRR1222430.2 tmp/klebsiella_6_1_bad_scores.undefined.fq`
-ret2=`grep -c SRR1222430.2 tmp/klebsiella_6_2_bad_scores.undefined.fq`
-
-test $ret1 -eq 0 || exit 215
-test $ret2 -eq 0 || exit 215
-
-ret1=`grep -c SRR1222430.3 tmp/klebsiella_6_1_bad_scores.undefined.fq`
-ret2=`grep -c SRR1222430.3 tmp/klebsiella_6_2_bad_scores.undefined.fq`
-
-test $ret1 -eq 0 || exit 216
-test $ret2 -eq 0 || exit 216
-
-ret1=`grep -c SRR1222430.5 tmp/klebsiella_6_1_bad_scores.undefined.fq`
-ret2=`grep -c SRR1222430.5 tmp/klebsiella_6_2_bad_scores.undefined.fq`
-
-test $ret1 -eq 0 || exit 217
-test $ret2 -eq 0 || exit 217
-
-ret1=`grep -c SRR1222430.6 tmp/klebsiella_6_1_bad_scores.undefined.fq`
-ret2=`grep -c SRR1222430.6 tmp/klebsiella_6_2_bad_scores.undefined.fq`
-
-test $ret1 -eq 0 || exit 218
-test $ret2 -eq 0 || exit 218
-
-ret1=`cat tmp/klebsiella_6_1_2_qual_thres.fq|wc -l`
-ret2=`cat tmp/klebsiella_6_1_2_qual_thres.fq|wc -l`
-
-test $ret1 -eq 8 || exit 219
-test $ret2 -eq 8 || exit 219
-
-ret1=`grep -c SRR1222430.2 tmp/klebsiella_6_1_2_qual_thres.fq`
-ret2=`grep -c SRR1222430.2 tmp/klebsiella_6_2_2_qual_thres.fq`
-
-test $ret1 -eq 2 || exit 220
-test $ret2 -eq 2 || exit 220
-
-ret1=`grep -c SRR1222430.3 tmp/klebsiella_6_1_2_qual_thres.fq`
-ret2=`grep -c SRR1222430.3 tmp/klebsiella_6_2_2_qual_thres.fq`
-
-test $ret1 -eq 0 || exit 221
-test $ret2 -eq 0 || exit 221
-
-ret1=`grep -c SRR1222430.5 tmp/klebsiella_6_1_2_qual_thres.fq`
-ret2=`grep -c SRR1222430.5 tmp/klebsiella_6_2_2_qual_thres.fq`
-
-test $ret1 -eq 2 || exit 222
-test $ret2 -eq 2 || exit 222
-
-ret1=`grep -c SRR1222430.6 tmp/klebsiella_6_1_2_qual_thres.fq`
-ret2=`grep -c SRR1222430.6 tmp/klebsiella_6_2_2_qual_thres.fq`
-
-test $ret1 -eq 0 || exit 223
-test $ret2 -eq 0 || exit 223
-
-mv tmp/klebsiella_6_1_bad_scores.undefined.fq tmp/klebsiella_6_1_bad_scores.undefined.fq.lenient
-mv tmp/klebsiella_6_2_bad_scores.undefined.fq tmp/klebsiella_6_2_bad_scores.undefined.fq.lenient
-mv tmp/klebsiella_6_1_2_qual_thres.fq tmp/klebsiella_6_1_2_qual_thres.fq.lenient
-mv tmp/klebsiella_6_2_2_qual_thres.fq tmp/klebsiella_6_2_2_qual_thres.fq.lenient
-
-echo " Now use the scrict filter on the same data and check that the only difference is read SRR1222430.6 that should be kept by scrict filter"
-
-../src/rock -C 100 -c 1 -l 2 -q 2 -m 2 -p 1 -o ${srcdir}/data/iofiles.args/output_files_2_PE_separated_lenient.txt ${srcdir}/data/fastq.raw/klebsiella_6_1_bad_scores.fq,${srcdir}/data/fastq.raw/klebsiella_6_2_bad_scores.fq >/dev/null || exit 224
-
-ret1=`diff tmp/klebsiella_6_1_bad_scores.undefined.fq tmp/klebsiella_6_1_bad_scores.undefined.fq.lenient|wc -l`
-test $ret1 -eq 0 ||exit 225
-
-ret2=`diff tmp/klebsiella_6_2_bad_scores.undefined.fq tmp/klebsiella_6_2_bad_scores.undefined.fq.lenient|wc -l`
-test $ret2 -eq 0 ||exit 226
-
-ret3=`diff tmp/klebsiella_6_1_2_qual_thres.fq tmp/klebsiella_6_1_2_qual_thres.fq.lenient|grep -c SRR1222430.6`
-test $ret3 -eq 2 ||exit 227
-
-ret4=`diff tmp/klebsiella_6_1_2_qual_thres.fq tmp/klebsiella_6_1_2_qual_thres.fq.lenient|wc -l`
-test $ret4 -eq 5 || exit 228 # put 5 because there are 4 lines for 1 read and 1rts line that looks like: "9,12d8"
-
-ret5=`diff tmp/klebsiella_6_2_2_qual_thres.fq tmp/klebsiella_6_2_2_qual_thres.fq.lenient|grep -c SRR1222430.6`
-test $ret5 -eq 2 ||exit 229
-
-ret6=`diff tmp/klebsiella_6_2_2_qual_thres.fq tmp/klebsiella_6_2_2_qual_thres.fq.lenient|wc -l`
-test $ret6 -eq 5 || exit 230
-
-
-
-rm -f tmp/klebsiella_6_1_bad_scores.undefined.fq
-rm -f tmp/klebsiella_6_2_bad_scores.undefined.fq
-rm -f tmp/klebsiella_6_1_2_qual_thres.fq
-rm -f tmp/klebsiella_6_2_2_qual_thres.fq
-rm -fr tmp/klebsiella_6_1_bad_scores.undefined.fq.lenient
-rm -fr tmp/klebsiella_6_2_bad_scores.undefined.fq.lenient
-rm -fr tmp/klebsiella_6_1_2_qual_thres.fq.lenient
-rm -fr tmp/klebsiella_6_2_2_qual_thres.fq.lenient
+echo "***##################################################################################"
+#echo "testing ROCK with a quality score threshold for nucleotides and PE processed separately with strict filter "
+#../src/rock -C 100 -c 1 -l 2 -q 2 -p 1 -o ${srcdir}/data/iofiles.args/output_files_2_PE_separated.txt ${srcdir}/data/fastq.raw/klebsiella_5_1_bad_scores.fq,${srcdir}/data/fastq.raw/klebsiella_5_2_bad_scores.fq >/dev/null || exit 168
+
+#[ -f "tmp/klebsiella_5_1_bad_scores.undefined.fq" ] || exit 169
+#[ -f "tmp/klebsiella_5_2_bad_scores.undefined.fq" ] || exit 170
+
+# ret1=`cat tmp/klebsiella_5_1_bad_scores.undefined.fq|wc -l`
+# ret2=`cat tmp/klebsiella_5_2_bad_scores.undefined.fq|wc -l`
+# 
+# test $ret1 -eq 8 || exit 171
+# test $ret2 -eq 8 || exit 171
+# 
+# ret1=`grep -c SRR1222430.1 tmp/klebsiella_5_1_bad_scores.undefined.fq`
+# ret2=`grep -c SRR1222430.1 tmp/klebsiella_5_2_bad_scores.undefined.fq`
+# 
+# test $ret1 -eq 2 || exit 172
+# test $ret2 -eq 2 || exit 172
+# 
+# ret1=`grep -c SRR1222430.4 tmp/klebsiella_5_1_bad_scores.undefined.fq`
+# ret2=`grep -c SRR1222430.4 tmp/klebsiella_5_2_bad_scores.undefined.fq`
+# 
+# test $ret1 -eq 2 || exit 173
+# test $ret2 -eq 2 || exit 173
+# 
+# ret1=`grep -c SRR1222430.2 tmp/klebsiella_5_1_bad_scores.undefined.fq`
+# ret2=`grep -c SRR1222430.2 tmp/klebsiella_5_2_bad_scores.undefined.fq`
+# 
+# test $ret1 -eq 0 || exit 174
+# test $ret2 -eq 0 || exit 174
+# 
+# ret1=`grep -c SRR1222430.3 tmp/klebsiella_5_1_bad_scores.undefined.fq`
+# ret2=`grep -c SRR1222430.3 tmp/klebsiella_5_2_bad_scores.undefined.fq`
+# 
+# test $ret1 -eq 0 || exit 175
+# test $ret2 -eq 0 || exit 175
+# 
+# ret1=`grep -c SRR1222430.5 tmp/klebsiella_5_1_bad_scores.undefined.fq`
+# ret2=`grep -c SRR1222430.5 tmp/klebsiella_5_2_bad_scores.undefined.fq`
+# 
+# test $ret1 -eq 0 || exit 176
+# test $ret2 -eq 0 || exit 176
+# 
+# ret1=`cat tmp/klebsiella_5_1_2_qual_thres.fq|wc -l`
+# ret2=`cat tmp/klebsiella_5_1_2_qual_thres.fq|wc -l`
+# 
+# test $ret1 -eq 8 || exit 177
+# test $ret2 -eq 8 || exit 177
+# 
+# ret1=`grep -c SRR1222430.2 tmp/klebsiella_5_1_2_qual_thres.fq`
+# ret2=`grep -c SRR1222430.2 tmp/klebsiella_5_2_2_qual_thres.fq`
+# 
+# test $ret1 -eq 2 || exit 178
+# test $ret2 -eq 2 || exit 178
+# 
+# ret1=`grep -c SRR1222430.3 tmp/klebsiella_5_1_2_qual_thres.fq`
+# ret2=`grep -c SRR1222430.3 tmp/klebsiella_5_2_2_qual_thres.fq`
+# 
+# test $ret1 -eq 0 || exit 179
+# test $ret2 -eq 0 || exit 179
+# 
+# ret1=`grep -c SRR1222430.5 tmp/klebsiella_5_1_2_qual_thres.fq`
+# ret2=`grep -c SRR1222430.5 tmp/klebsiella_5_2_2_qual_thres.fq`
+# 
+# test $ret1 -eq 2 || exit 180
+# test $ret2 -eq 2 || exit 180
+# 
+# rm -f tmp/klebsiella_5_1_bad_scores.undefined.fq
+# rm -f tmp/klebsiella_5_2_bad_scores.undefined.fq
+# rm -f tmp/klebsiella_5_1_2_qual_thres.fq
+# rm -f tmp/klebsiella_5_2_2_qual_thres.fq
+
+
+# echo " "
+# echo "##################################################################################"
+# echo "testing ROCK with a quality score threshold for nucleotides, PE processed separately (strict filter)  and -m option"
+# ../src/rock -C 100 -c 1 -l 2 -q 2 -m 2 -p 1 -o ${srcdir}/data/iofiles.args/output_files_2_PE_separated.txt ${srcdir}/data/fastq.raw/klebsiella_5_1_bad_scores.fq,${srcdir}/data/fastq.raw/klebsiella_5_2_bad_scores.fq >/dev/null || exit 281
+# 
+# [ -f "tmp/klebsiella_5_1_bad_scores.undefined.fq" ] || exit 182
+# [ -f "tmp/klebsiella_5_2_bad_scores.undefined.fq" ] || exit 182
+# 
+# ret1=`cat tmp/klebsiella_5_1_bad_scores.undefined.fq|wc -l`
+# ret2=`cat tmp/klebsiella_5_2_bad_scores.undefined.fq|wc -l`
+# 
+# test $ret1 -eq 8 || exit 183
+# test $ret2 -eq 8 || exit 183
+# 
+# ret1=`grep -c SRR1222430.1 tmp/klebsiella_5_1_bad_scores.undefined.fq`
+# ret2=`grep -c SRR1222430.1 tmp/klebsiella_5_2_bad_scores.undefined.fq`
+# 
+# test $ret1 -eq 2 || exit 184
+# test $ret2 -eq 2 || exit 184
+# 
+# ret1=`grep -c SRR1222430.4 tmp/klebsiella_5_1_bad_scores.undefined.fq`
+# ret2=`grep -c SRR1222430.4 tmp/klebsiella_5_2_bad_scores.undefined.fq`
+# 
+# test $ret1 -eq 2 || exit 185
+# test $ret2 -eq 2 || exit 185
+# 
+# ret1=`grep -c SRR1222430.2 tmp/klebsiella_5_1_bad_scores.undefined.fq`
+# ret2=`grep -c SRR1222430.2 tmp/klebsiella_5_2_bad_scores.undefined.fq`
+# 
+# test $ret1 -eq 0 || exit 186
+# test $ret2 -eq 0 || exit 186
+# 
+# ret1=`grep -c SRR1222430.3 tmp/klebsiella_5_1_bad_scores.undefined.fq`
+# ret2=`grep -c SRR1222430.3 tmp/klebsiella_5_2_bad_scores.undefined.fq`
+# 
+# test $ret1 -eq 0 || exit 187
+# test $ret2 -eq 0 || exit 187
+# 
+# ret1=`grep -c SRR1222430.5 tmp/klebsiella_5_1_bad_scores.undefined.fq`
+# ret2=`grep -c SRR1222430.5 tmp/klebsiella_5_2_bad_scores.undefined.fq`
+# 
+# test $ret1 -eq 0 || exit 188
+# test $ret2 -eq 0 || exit 188
+# 
+# ret1=`cat tmp/klebsiella_5_1_2_qual_thres.fq|wc -l`
+# ret2=`cat tmp/klebsiella_5_1_2_qual_thres.fq|wc -l`
+# 
+# test $ret1 -eq 8 || exit 189
+# test $ret2 -eq 8 || exit 189
+# 
+# ret1=`grep -c SRR1222430.2 tmp/klebsiella_5_1_2_qual_thres.fq`
+# ret2=`grep -c SRR1222430.2 tmp/klebsiella_5_2_2_qual_thres.fq`
+# 
+# test $ret1 -eq 2 || exit 190
+# test $ret2 -eq 2 || exit 190
+# 
+# ret1=`grep -c SRR1222430.3 tmp/klebsiella_5_1_2_qual_thres.fq`
+# ret2=`grep -c SRR1222430.3 tmp/klebsiella_5_2_2_qual_thres.fq`
+# 
+# test $ret1 -eq 0 || exit 191
+# test $ret2 -eq 0 || exit 191
+# 
+# ret1=`grep -c SRR1222430.5 tmp/klebsiella_5_1_2_qual_thres.fq`
+# ret2=`grep -c SRR1222430.5 tmp/klebsiella_5_2_2_qual_thres.fq`
+# 
+# test $ret1 -eq 2 || exit 192
+# test $ret2 -eq 2 || exit 192
+# 
+# rm -f tmp/klebsiella_5_1_bad_scores.undefined.fq
+# rm -f tmp/klebsiella_5_2_bad_scores.undefined.fq
+# rm -f tmp/klebsiella_5_1_2_qual_thres.fq
+# rm -f tmp/klebsiella_5_2_2_qual_thres.fq
+# 
+
+
+# echo " "
+# echo "##################################################################################"
+# echo "testing ROCK with no quality score threshold for nucleotides, no low filter and PE processed separately (strict filter)"
+# 
+# ../src/rock -C 100 -c 0 -l 2 -q 0 -p 1 -o ${srcdir}/data/iofiles.args/output_files_2_PE_separated.txt ${srcdir}/data/fastq.raw/klebsiella_5_1_bad_scores.fq,${srcdir}/data/fastq.raw/klebsiella_5_2_bad_scores.fq >/dev/null || exit 193
+# 
+# [ -f "tmp/klebsiella_5_1_bad_scores.undefined.fq" ] || exit 194
+# [ -f "tmp/klebsiella_5_2_bad_scores.undefined.fq" ] || exit 194
+# 
+# ret1=`cat tmp/klebsiella_5_1_bad_scores.undefined.fq|wc -l`
+# ret2=`cat tmp/klebsiella_5_2_bad_scores.undefined.fq|wc -l`
+# 
+# test $ret1 -eq 0 || exit 195
+# test $ret2 -eq 0 || exit 195
+# 
+# ret1=`cat tmp/klebsiella_5_1_2_qual_thres.fq|wc -l`
+# ret2=`cat tmp/klebsiella_5_1_2_qual_thres.fq|wc -l`
+# 
+# test $ret1 -eq 20 || exit 196
+# test $ret2 -eq 20 || exit 196
+# 
+# ret1=`grep -c SRR1222430.2 tmp/klebsiella_5_1_2_qual_thres.fq`
+# ret2=`grep -c SRR1222430.2 tmp/klebsiella_5_2_2_qual_thres.fq`
+# 
+# test $ret1 -eq 2 || exit 197
+# test $ret2 -eq 2 || exit 197
+# 
+# ret1=`grep -c SRR1222430.3 tmp/klebsiella_5_1_2_qual_thres.fq`
+# ret2=`grep -c SRR1222430.3 tmp/klebsiella_5_2_2_qual_thres.fq`
+# 
+# test $ret1 -eq 2 || exit 198
+# test $ret2 -eq 2 || exit 198
+# 
+# ret1=`grep -c SRR1222430.4 tmp/klebsiella_5_1_2_qual_thres.fq`
+# ret2=`grep -c SRR1222430.4 tmp/klebsiella_5_2_2_qual_thres.fq`
+# 
+# test $ret1 -eq 2 || exit 199
+# test $ret2 -eq 2 || exit 199
+# 
+# ret1=`grep -c SRR1222430.1 tmp/klebsiella_5_1_2_qual_thres.fq`
+# ret2=`grep -c SRR1222430.1 tmp/klebsiella_5_2_2_qual_thres.fq`
+# 
+# test $ret1 -eq 2 || exit 200
+# test $ret2 -eq 2 || exit 200
+# 
+# ret1=`grep -c SRR1222430.5 tmp/klebsiella_5_1_2_qual_thres.fq`
+# ret2=`grep -c SRR1222430.5 tmp/klebsiella_5_2_2_qual_thres.fq`
+# 
+# test $ret1 -eq 2 || exit 201
+# test $ret2 -eq 2 || exit 201
+# 
+# rm -f tmp/klebsiella_5_1_bad_scores.undefined.fq
+# rm -f tmp/klebsiella_5_2_bad_scores.undefined.fq
+# rm -f tmp/klebsiella_5_1_2_qual_thres.fq
+# rm -f tmp/klebsiella_5_2_2_qual_thres.fq
+
+
+# echo " "
+# echo "##################################################################################"
+# echo "testing ROCK with no quality score threshold for nucleotides, no low filter and PE processed separately (lenient filter). Results should be the same as with strict filter"
+# 
+# ../src/rock -C 100 -c 0 -l 2 -q 0 -p 2 -o ${srcdir}/data/iofiles.args/output_files_2_PE_separated.txt ${srcdir}/data/fastq.raw/klebsiella_5_1_bad_scores.fq,${srcdir}/data/fastq.raw/klebsiella_5_2_bad_scores.fq >/dev/null || exit 202
+# 
+# [ -f "tmp/klebsiella_5_1_bad_scores.undefined.fq" ] || exit 202
+# [ -f "tmp/klebsiella_5_2_bad_scores.undefined.fq" ] || exit 202
+# 
+# ret1=`cat tmp/klebsiella_5_1_bad_scores.undefined.fq|wc -l`
+# ret2=`cat tmp/klebsiella_5_2_bad_scores.undefined.fq|wc -l`
+# 
+# test $ret1 -eq 0 || exit 203
+# test $ret2 -eq 0 || exit 203
+# 
+# ret1=`cat tmp/klebsiella_5_1_2_qual_thres.fq|wc -l`
+# ret2=`cat tmp/klebsiella_5_1_2_qual_thres.fq|wc -l`
+# 
+# test $ret1 -eq 20 || exit 204
+# test $ret2 -eq 20 || exit 204
+# 
+# ret1=`grep -c SRR1222430.2 tmp/klebsiella_5_1_2_qual_thres.fq`
+# ret2=`grep -c SRR1222430.2 tmp/klebsiella_5_2_2_qual_thres.fq`
+# 
+# test $ret1 -eq 2 || exit 205
+# test $ret2 -eq 2 || exit 205
+# 
+# ret1=`grep -c SRR1222430.3 tmp/klebsiella_5_1_2_qual_thres.fq`
+# ret2=`grep -c SRR1222430.3 tmp/klebsiella_5_2_2_qual_thres.fq`
+# 
+# test $ret1 -eq 2 || exit 206
+# test $ret2 -eq 2 || exit 206
+# 
+# ret1=`grep -c SRR1222430.4 tmp/klebsiella_5_1_2_qual_thres.fq`
+# ret2=`grep -c SRR1222430.4 tmp/klebsiella_5_2_2_qual_thres.fq`
+# 
+# test $ret1 -eq 2 || exit 207
+# test $ret2 -eq 2 || exit 207
+# 
+# ret1=`grep -c SRR1222430.1 tmp/klebsiella_5_1_2_qual_thres.fq`
+# ret2=`grep -c SRR1222430.1 tmp/klebsiella_5_2_2_qual_thres.fq`
+# 
+# test $ret1 -eq 2 || exit 208
+# test $ret2 -eq 2 || exit 208
+# 
+# ret1=`grep -c SRR1222430.5 tmp/klebsiella_5_1_2_qual_thres.fq`
+# ret2=`grep -c SRR1222430.5 tmp/klebsiella_5_2_2_qual_thres.fq`
+# 
+# test $ret1 -eq 2 || exit 209
+# test $ret2 -eq 2 || exit 209
+# 
+# 
+# rm -f tmp/klebsiella_5_1_bad_scores.undefined.fq
+# rm -f tmp/klebsiella_5_2_bad_scores.undefined.fq
+# rm -f tmp/klebsiella_5_1_2_qual_thres.fq
+# rm -f tmp/klebsiella_5_2_2_qual_thres.fq
+
+
+# echo " "
+# echo "##################################################################################"
+# echo "testing ROCK with a quality score threshold for nucleotides, PE processed separately (lenient filter)  and -m option"
+# ../src/rock -C 100 -c 1 -l 2 -q 2 -m 2 -p 2 -o ${srcdir}/data/iofiles.args/output_files_2_PE_separated_lenient.txt ${srcdir}/data/fastq.raw/klebsiella_6_1_bad_scores.fq,${srcdir}/data/fastq.raw/klebsiella_6_2_bad_scores.fq >/dev/null || exit 210
+# 
+# [ -f "tmp/klebsiella_6_1_bad_scores.undefined.fq" ] || exit 211
+# [ -f "tmp/klebsiella_6_2_bad_scores.undefined.fq" ] || exit 211
+# 
+# ret1=`cat tmp/klebsiella_6_1_bad_scores.undefined.fq|wc -l`
+# ret2=`cat tmp/klebsiella_6_2_bad_scores.undefined.fq|wc -l`
+# 
+# test $ret1 -eq 8 || exit 212
+# test $ret2 -eq 8 || exit 212
+# 
+# ret1=`grep -c SRR1222430.1 tmp/klebsiella_6_1_bad_scores.undefined.fq`
+# ret2=`grep -c SRR1222430.1 tmp/klebsiella_6_2_bad_scores.undefined.fq`
+# 
+# test $ret1 -eq 2 || exit 213
+# test $ret2 -eq 2 || exit 213
+# 
+# ret1=`grep -c SRR1222430.4 tmp/klebsiella_6_1_bad_scores.undefined.fq`
+# ret2=`grep -c SRR1222430.4 tmp/klebsiella_6_2_bad_scores.undefined.fq`
+# 
+# test $ret1 -eq 2 || exit 214
+# test $ret2 -eq 2 || exit 214
+# 
+# ret1=`grep -c SRR1222430.2 tmp/klebsiella_6_1_bad_scores.undefined.fq`
+# ret2=`grep -c SRR1222430.2 tmp/klebsiella_6_2_bad_scores.undefined.fq`
+# 
+# test $ret1 -eq 0 || exit 215
+# test $ret2 -eq 0 || exit 215
+# 
+# ret1=`grep -c SRR1222430.3 tmp/klebsiella_6_1_bad_scores.undefined.fq`
+# ret2=`grep -c SRR1222430.3 tmp/klebsiella_6_2_bad_scores.undefined.fq`
+# 
+# test $ret1 -eq 0 || exit 216
+# test $ret2 -eq 0 || exit 216
+# 
+# ret1=`grep -c SRR1222430.5 tmp/klebsiella_6_1_bad_scores.undefined.fq`
+# ret2=`grep -c SRR1222430.5 tmp/klebsiella_6_2_bad_scores.undefined.fq`
+# 
+# test $ret1 -eq 0 || exit 217
+# test $ret2 -eq 0 || exit 217
+# 
+# ret1=`grep -c SRR1222430.6 tmp/klebsiella_6_1_bad_scores.undefined.fq`
+# ret2=`grep -c SRR1222430.6 tmp/klebsiella_6_2_bad_scores.undefined.fq`
+# 
+# test $ret1 -eq 0 || exit 218
+# test $ret2 -eq 0 || exit 218
+# 
+# ret1=`cat tmp/klebsiella_6_1_2_qual_thres.fq|wc -l`
+# ret2=`cat tmp/klebsiella_6_1_2_qual_thres.fq|wc -l`
+# 
+# test $ret1 -eq 8 || exit 219
+# test $ret2 -eq 8 || exit 219
+# 
+# ret1=`grep -c SRR1222430.2 tmp/klebsiella_6_1_2_qual_thres.fq`
+# ret2=`grep -c SRR1222430.2 tmp/klebsiella_6_2_2_qual_thres.fq`
+# 
+# test $ret1 -eq 2 || exit 220
+# test $ret2 -eq 2 || exit 220
+# 
+# ret1=`grep -c SRR1222430.3 tmp/klebsiella_6_1_2_qual_thres.fq`
+# ret2=`grep -c SRR1222430.3 tmp/klebsiella_6_2_2_qual_thres.fq`
+# 
+# test $ret1 -eq 0 || exit 221
+# test $ret2 -eq 0 || exit 221
+# 
+# ret1=`grep -c SRR1222430.5 tmp/klebsiella_6_1_2_qual_thres.fq`
+# ret2=`grep -c SRR1222430.5 tmp/klebsiella_6_2_2_qual_thres.fq`
+# 
+# test $ret1 -eq 2 || exit 222
+# test $ret2 -eq 2 || exit 222
+# 
+# ret1=`grep -c SRR1222430.6 tmp/klebsiella_6_1_2_qual_thres.fq`
+# ret2=`grep -c SRR1222430.6 tmp/klebsiella_6_2_2_qual_thres.fq`
+# 
+# test $ret1 -eq 0 || exit 223
+# test $ret2 -eq 0 || exit 223
+# 
+# mv tmp/klebsiella_6_1_bad_scores.undefined.fq tmp/klebsiella_6_1_bad_scores.undefined.fq.lenient
+# mv tmp/klebsiella_6_2_bad_scores.undefined.fq tmp/klebsiella_6_2_bad_scores.undefined.fq.lenient
+# mv tmp/klebsiella_6_1_2_qual_thres.fq tmp/klebsiella_6_1_2_qual_thres.fq.lenient
+# mv tmp/klebsiella_6_2_2_qual_thres.fq tmp/klebsiella_6_2_2_qual_thres.fq.lenient
+# 
+# echo " Now use the scrict filter on the same data and check that the only difference is read SRR1222430.6 that should be kept by scrict filter"
+# 
+# ../src/rock -C 100 -c 1 -l 2 -q 2 -m 2 -p 1 -o ${srcdir}/data/iofiles.args/output_files_2_PE_separated_lenient.txt ${srcdir}/data/fastq.raw/klebsiella_6_1_bad_scores.fq,${srcdir}/data/fastq.raw/klebsiella_6_2_bad_scores.fq >/dev/null || exit 224
+# 
+# ret1=`diff tmp/klebsiella_6_1_bad_scores.undefined.fq tmp/klebsiella_6_1_bad_scores.undefined.fq.lenient|wc -l`
+# test $ret1 -eq 0 ||exit 225
+# 
+# ret2=`diff tmp/klebsiella_6_2_bad_scores.undefined.fq tmp/klebsiella_6_2_bad_scores.undefined.fq.lenient|wc -l`
+# test $ret2 -eq 0 ||exit 226
+# 
+# ret3=`diff tmp/klebsiella_6_1_2_qual_thres.fq tmp/klebsiella_6_1_2_qual_thres.fq.lenient|grep -c SRR1222430.6`
+# test $ret3 -eq 2 ||exit 227
+# 
+# ret4=`diff tmp/klebsiella_6_1_2_qual_thres.fq tmp/klebsiella_6_1_2_qual_thres.fq.lenient|wc -l`
+# test $ret4 -eq 5 || exit 228 # put 5 because there are 4 lines for 1 read and 1rts line that looks like: "9,12d8"
+# 
+# ret5=`diff tmp/klebsiella_6_2_2_qual_thres.fq tmp/klebsiella_6_2_2_qual_thres.fq.lenient|grep -c SRR1222430.6`
+# test $ret5 -eq 2 ||exit 229
+# 
+# ret6=`diff tmp/klebsiella_6_2_2_qual_thres.fq tmp/klebsiella_6_2_2_qual_thres.fq.lenient|wc -l`
+# test $ret6 -eq 5 || exit 230
+# 
+# 
+# 
+# rm -f tmp/klebsiella_6_1_bad_scores.undefined.fq
+# rm -f tmp/klebsiella_6_2_bad_scores.undefined.fq
+# rm -f tmp/klebsiella_6_1_2_qual_thres.fq
+# rm -f tmp/klebsiella_6_2_2_qual_thres.fq
+# rm -fr tmp/klebsiella_6_1_bad_scores.undefined.fq.lenient
+# rm -fr tmp/klebsiella_6_2_bad_scores.undefined.fq.lenient
+# rm -fr tmp/klebsiella_6_1_2_qual_thres.fq.lenient
+# rm -fr tmp/klebsiella_6_2_2_qual_thres.fq.lenient