disabled the -p option. Default is now to process PE as single

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);

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);

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;

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;

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