fixed getting CMS size

src/Filter.hpp

@@ -32,7 +32,7 @@ class Filter {
 
     FasqQualThreshold qual_thres;
     // long nb_bytes_before_fill_CMS,nb_bytes_after_fill_CMS;
-    long nb_bytes_CMS; //! Number of bytes taken by the underlying CMS.
+    //long nb_bytes_CMS; //! Number of bytes taken by the underlying CMS.
 
     void getRSS();
 
@@ -48,7 +48,7 @@ public:
         if (parms.kappa<ubytemask) pByteCMS=new ByteCountMinSketch(parms);
         else pShortCMS=new ShortCountMinSketch(parms);
         qual_thres=the_qual_thres;
-        getRSS();
+        //getRSS();
         //nb_bytes_CMS=0;
         //nb_bytes_after_fill_CMS=0;
     }
@@ -143,7 +143,7 @@ template <typename T> void Filter::underlyinglowFilterCMS(FqBaseBackend* map_id_
 void Filter::fillCMS(FqBaseBackend* map_id_backend[],int nb_be,int k,srp* io_sr) {
     if (pByteCMS!=NULL) underlyingfillCMS<unsigned char>(map_id_backend,nb_be, k, io_sr,pByteCMS);
     else underlyingfillCMS<unsigned short>(map_id_backend,nb_be, k, io_sr,pShortCMS);
-    getRSS();
+    //getRSS();
 }
 
 void Filter::lowFilterCMS(FqBaseBackend* map_id_backend[],int nb_be,int k, srp* io_sr) {
@@ -161,6 +161,7 @@ std::vector<unsigned long> Filter::getUnsetBuckets() const {
 	else return pShortCMS->getUnsetBuckets();
 }
 
+/*
 void Filter::getRSS() {
     struct rusage usage;
     int res2=getrusage(RUSAGE_SELF,&usage);
@@ -172,7 +173,7 @@ unsigned long Filter::getSize() {
     unsigned long cms_size=nb_bytes_CMS;
     // cms_size/=8; ru_maxrss seems to be already in Bytes.
     return cms_size;
-}
+}*/
 
 unsigned int Filter::getNbBitsForCounters() const {
 	if (pByteCMS!=NULL) return sizeof(unsigned char)*8;

src/ROCKparams.cpp

@@ -144,7 +144,7 @@ void ROCKparams::optArgConsistency(const string& input_file,const string& output
 #ifdef DEBUG
     cout<<"parms.lambda="<<parms.lambda<<" UINT_MAX="<<UINT_MAX<<endl;
 #endif
-    unsigned long cms_size=k_arr_cms_size;
+    cms_size=k_arr_cms_size;
     cms_size*=parms.lambda;
     if (parms.kappa>get_mask<unsigned char>::value) cms_size=cms_size*sizeof(unsigned short);
     cms_size=ceil(cms_size/1024.0/1024/1024); // convert to gigabytes.

src/ROCKparams.h

@@ -146,15 +146,17 @@ public:
         return k;
     }
 
-    void setFilterSize(unsigned long fsize) {
+    // cms_size is computed when ROCK starts.
+    /*void setFilterSize(unsigned long fsize) {
         cms_size=fsize;
-    }
+    }*/
 
     unsigned long getFilterSize() const {
-    	unsigned long cms_size_in_GB=cms_size/1024;
+    	/*unsigned long cms_size_in_GB=cms_size/1024;
     	cms_size_in_GB/=1024;
     	cms_size_in_GB/=1024;
-    	return cms_size_in_GB;
+    	return cms_size_in_GB;*/
+    	return cms_size;
     }
 
 

src/rock.cpp

@@ -167,7 +167,7 @@ int main(int argc,char * argv[]) {
     cout<<"Now going to remove read with cov<kappa_prime"<<endl;
 #endif
 
-    main_parms.setFilterSize(the_filter.getSize());
+    // main_parms.setFilterSize(the_filter.getSize()); // no more used max_rss is not precise enough
     // Now, remove reads that are beneath kappa_prime
     if (parms.kappa_prime) the_filter.lowFilterCMS(map_id_backend,f_id,k,&sr);