diff --git a/src/Filter.hpp b/src/Filter.hpp index 5da669ca5326f43737aac273e164eaca8cb4b842..a1797a2e4db2a2140bb20a17c5b1f4e087761f8d 100644 --- a/src/Filter.hpp +++ b/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; diff --git a/src/ROCKparams.cpp b/src/ROCKparams.cpp index 06c9c9f36c1c14c123c7db05246326c1cf1dc92a..86547ee31422641eb54e1eb46816e8b2ea31e991 100755 --- a/src/ROCKparams.cpp +++ b/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. diff --git a/src/ROCKparams.h b/src/ROCKparams.h index 5a5e1b43f7358ee65b538fb922608ce67096e577..a8213843f1ce938b217cd87bd2c1cc5cd0ef39ad 100755 --- a/src/ROCKparams.h +++ b/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; } diff --git a/src/rock.cpp b/src/rock.cpp index 2254664616acc54ffb77fe1050ffd7f67ebdef2a..5f889c7652240954b1299805352db5553d0dbd55 100755 --- a/src/rock.cpp +++ b/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);