did some optimization for rock 1.6; still need to debug some thing

src/CountMinSketch.hpp

@@ -380,9 +380,19 @@ template<typename T> int CountMinSketch<T>::addRead(const T_read_numericValues&
     int keep_r=isRCovBelowThres(read_val,kappa);
     if (keep_r) {
         readNumericValues::const_iterator it;
-        for (it=read_val.single_or_PE_val.begin();it!=read_val.single_or_PE_val.end();it++) {
+        // according to the intel profiler, we spend a lot of time in this loop. Try to use something slightly faster.
+        long const * p=(long const *) &read_val.single_or_PE_val[0];
+        int cnt;
+        int stop=read_val.single_or_PE_val.size();
+        for (cnt=0;cnt<stop;cnt++) {
+            this->addKMer(*p);
+            p=p+1;
+        }
+/*
+        for (it=read_val.single_or_PE_val.begin();it!=read_val.single_or_PE_val.end();it++) { 
             this->addKMer(*it);
         }
+*/
     }
     return keep_r;
 }

src/FqBaseBackend.cpp

@@ -236,6 +236,7 @@ void FqBaseBackend::keepCurFastqRecord(char * buf,const int& start_rec_in_buf,co
 
 void FqBaseBackend::onIncScore(T_fq_rec_info& rec_info,T_buf_info& buf_info,int& n) {
     unsigned int s=(int)*buf_info.pchar;
+    // printf("s=%u; qual_thres.nucl_score_threshold=%d \n",s,qual_thres.nucl_score_threshold);
     unsigned int remaining_nucl=rec_info.nb_nucleotides_in_read-rec_info.idx_nucl_in_read;
     if (s<=qual_thres.nucl_score_threshold) { // maybe TODO rewrite this with chained ternary operators once it is clear to see if it improves performances.Not useful: performance bottleneck is not here but in median calculation (42% of time approximatively for both filters).
         if (rec_info.idx_nucl_in_read<=qual_thres.k-1) { // error is found in the first k nucleotides

src/ROCKparams.h

@@ -14,6 +14,7 @@
 #include <vector>
 #include <getopt.h>
 #include <iostream>
+#include "FqConstants.h"
 #include "CountMinSketch.hpp"
 #include "main_utils.h"
 
@@ -89,7 +90,8 @@ public:
         parms.lambda=0;
         parms.filter_PE_as_single=0;
         qual_thres.min_correct_k_mers_in_read=1;
-        qual_thres.nucl_score_threshold=10;
+        qual_thres.nucl_score_threshold=10+k_phred_32;
+        qual_thres.k=k;
         verbose_mode=0;
         cms_size=0;
         expected_collision_proba=0.0;

src/ReadProcessor.cpp

@@ -46,7 +46,7 @@ unsigned long ReadProcessor::kMerToNumber(char * k_m,unsigned long * p_prev) {
     return nbr;
 }
 
-
+// Tried to inline this but it is sligntly slower. Put it back not inline.
 unsigned long ReadProcessor::kMerToNumberReverse(char * k_m,unsigned long * p_prev) {
     unsigned long nbr=0;
     unsigned long c;

src/ReadProcessor.h

@@ -83,6 +83,8 @@ public:
         this->k=k;
         init_mask(k);
     }
+
+    // Do not inline this; it is slightly slower.    
     unsigned long kMerToNumberReverse(char * k_m,unsigned long * p_prev);