re-used what I had implemented for the -g option to warn the user that there...

re-used what I had implemented for the -g option to warn the user that there is not enough memory on the machine to process all reads with the given or default low filter.

src/ROCKparams.cpp

@@ -61,15 +61,6 @@ void ROCKparams::optArgConsistency(const string& input_file,const string& output
         cout<<"-l and -n options are mutually exclusive."<<endl;
         usage(EXIT_FAILURE);
     }
-    float avail_mem=getNodePhysMemory()-defaultGRPMAXSize;
-    // cout<<avail_mem;
-    /*if (g>avail_mem) {
-        std::cout<<"This machine only has "<<getNodePhysMemory()<<" Gigabytes of RAM. This is not enough to run ROCK with a CMS of size: "<<g<<endl;
-        exit(EXIT_FAILURE);
-    } else if (g!=0) {
-        parms.filter_size=g;
-        computeLambda();
-    }*/
     if (nb_k_mers) { // user indicated number of k-mers; use it to minimize parms.lambda
         //parms.lambda=getBestLambdaForN(nb_k_mers,parms.lambda);
     	int smallest_kappa;
@@ -92,25 +83,18 @@ void ROCKparams::optArgConsistency(const string& input_file,const string& output
     }
     if (parms.lambda==0) {
         // This happens when the user doesn't specify lambda nor nb_k_mers.
-        //computeLambda();
         parms.lambda=k_proposed_lamda;
- /*       if (parms.lambda==0) {
-            cout<<"Not enough RAM on the machine. Total RAM in GB must be bigger than UINT_MAX to allow at least 1 array in the CMS."<<endl;
-            exit(EXIT_FAILURE);
-        }*/
     }
 #ifdef DEBUG
     cout<<"parms.lambda="<<parms.lambda<<" UINT_MAX="<<UINT_MAX<<endl;
 #endif
     unsigned long cms_size=k_arr_cms_size;
     cms_size*=parms.lambda;
-    //cout<<"minimum cms size:"<<cms_size<<endl;
     if (parms.kappa>get_mask<unsigned char>::value) cms_size=cms_size*sizeof(unsigned short);
-    //cout<<"cms_size in B="<<cms_size<<endl;
     cms_size=ceil(cms_size/1024.0/1024/1024); // convert to gigabytes.
-    //cout<<"cms_size in GB="<<cms_size<<endl;
     if (cms_size>getNodePhysMemory()-defaultGRPMAXSize) {
         cout<<"Not enough RAM on the machine to run rock with a CMS of size:"<<cms_size<<" GB."<<endl;
+        cout<<" Maybe you should think of increasing the value for the low filter (-c option)"<<endl;
         exit(EXIT_FAILURE);
     }
 }

test/rock.sh

@@ -61,7 +61,7 @@ echo "doing more checks on options and error messages"
 ../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 -n 50000000000 -c 1 -i ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100.txt -o ${srcdir}/data/iofiles.args/extract_klebsiella_long_reads_100_filtered.txt|grep "think of increasing the value for the low filter" >/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  -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