fixed calculation of the size of the CMS

src/Filter.hpp

@@ -31,9 +31,10 @@ class Filter {
     ShortCountMinSketch * pShortCMS;
 
     FasqQualThreshold qual_thres;
-    long nb_bytes_before_fill_CMS,nb_bytes_after_fill_CMS;
+    // long nb_bytes_before_fill_CMS,nb_bytes_after_fill_CMS;
+    long nb_bytes_CMS; //! Number of bytes taken by the underlying CMS.
 
-    void getRSS(int before_fill=0);
+    void getRSS();
 
 
     template <typename T> void underlyingfillCMS(FqBaseBackend* map_id_backend[],int nb_be, int k, srp* io_sr, CountMinSketch<T>* cms);
@@ -44,12 +45,12 @@ public:
     Filter(const CMSparams& parms,const FasqQualThreshold& the_qual_thres) {
         pByteCMS=NULL;
         pShortCMS=NULL;
-        getRSS();
         if (parms.kappa<ubytemask) pByteCMS=new ByteCountMinSketch(parms);
         else pShortCMS=new ShortCountMinSketch(parms);
         qual_thres=the_qual_thres;
-
-        nb_bytes_after_fill_CMS=0;
+        getRSS();
+        //nb_bytes_CMS=0;
+        //nb_bytes_after_fill_CMS=0;
     }
 
     void fillCMS(FqBaseBackend* map_id_backend[],int nb_be,int k,srp* io_sr);
@@ -142,7 +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(1);
+    getRSS();
 }
 
 void Filter::lowFilterCMS(FqBaseBackend* map_id_backend[],int nb_be,int k, srp* io_sr) {
@@ -160,16 +161,15 @@ std::vector<unsigned long> Filter::getUnsetBuckets() const {
 	else return pShortCMS->getUnsetBuckets();
 }
 
-void Filter::getRSS(int before_fill) {
+void Filter::getRSS() {
     struct rusage usage;
     int res2=getrusage(RUSAGE_SELF,&usage);
     if (res2==-1) err(errno,"cannot get resource usage.");
-    if (before_fill==0) nb_bytes_before_fill_CMS=usage.ru_maxrss;
-    else nb_bytes_after_fill_CMS=usage.ru_maxrss;
+    nb_bytes_CMS=usage.ru_maxrss;
 }
 
 unsigned long Filter::getSize() {
-    unsigned long cms_size=nb_bytes_after_fill_CMS-nb_bytes_before_fill_CMS;
+    unsigned long cms_size=nb_bytes_CMS;
     // cms_size/=8; ru_maxrss seems to be already in Bytes.
     return cms_size;
 }