Updated WHAT_IS_NEW

[rsem.git] / PairedEndModel.h

diff --git a/PairedEndModel.h b/PairedEndModel.h
index 575344c348c6aa1783b66e98a3d760484ec27e22..0d2c9b3f216db8df91fa47a85c57065123fe2331 100644 (file)
--- a/PairedEndModel.h
+++ b/PairedEndModel.h
@@ -8,6 +8,8 @@
 #include<string>
 #include<algorithm>
 #include<sstream>
+#include<iostream>
+#include<vector>
 
 #include "utils.h"
 #include "my_assert.h"
@@ -192,12 +194,12 @@ public:
 
        const LenDist& getGLD() { return *gld; }
 
-       void startSimulation(simul*, double*);
-       bool simulate(int, PairedEndRead&, int&);
+       void startSimulation(simul*, const std::vector<double>&);
+       bool simulate(READ_INT_TYPE, PairedEndRead&, int&);
        void finishSimulation();
 
        //Use it after function 'read' or 'estimateFromReads'
-       double* getMW() { 
+       const double* getMW() { 
          assert(mw != NULL);
          return mw;
        }
@@ -209,7 +211,7 @@ private:
        static const int read_type = 2;
 
        int M;
-       int N[3];
+       READ_INT_TYPE N[3];
        Refs *refs;
        int seedLen;
 
@@ -241,7 +243,7 @@ void PairedEndModel::estimateFromReads(const char* readFN) {
                genReadFileNames(readFN, i, read_type, s, readFs);
                ReadReader<PairedEndRead> reader(s, readFs, refs->hasPolyA(), seedLen); // allow calculation of calc_lq() function
 
-               int cnt = 0;
+               READ_INT_TYPE cnt = 0;
                while (reader.next(read)) {
                        SingleRead mate1 = read.getMate1();
                        SingleRead mate2 = read.getMate2();
@@ -256,14 +258,14 @@ void PairedEndModel::estimateFromReads(const char* readFN) {
                                }
                        }
                        else if (verbose && (mate1.getReadLength() < seedLen || mate2.getReadLength() < seedLen)) {
-                               printf("Warning: Read %s is ignored due to at least one of the mates' length < seed length %d!\n", read.getName().c_str(), seedLen);
+                               std::cout<< "Warning: Read "<< read.getName()<< " is ignored due to at least one of the mates' length < seed length "<< seedLen<< "!"<< std::endl;
                        }
 
                        ++cnt;
-                       if (verbose && cnt % 1000000 == 0) { printf("%d READS PROCESSED\n", cnt); }
+                       if (verbose && cnt % 1000000 == 0) { std::cout<< cnt<< " READS PROCESSED"<< std::endl; }
                }
 
-               if (verbose) { printf("estimateFromReads, N%d finished.\n", i); }
+               if (verbose) { std::cout<< "estimateFromReads, N"<< i<< " finished."<< std::endl; }
        }
 
     mld->finish();
@@ -348,7 +350,7 @@ void PairedEndModel::write(const char* outF) {
        fclose(fo);
 }
 
-void PairedEndModel::startSimulation(simul* sampler, double* theta) {
+void PairedEndModel::startSimulation(simul* sampler, const std::vector<double>& theta) {
        this->sampler = sampler;
 
        theta_cdf = new double[M + 1];
@@ -362,7 +364,7 @@ void PairedEndModel::startSimulation(simul* sampler, double* theta) {
        npro->startSimulation();
 }
 
-bool PairedEndModel::simulate(int rid, PairedEndRead& read, int& sid) {
+bool PairedEndModel::simulate(READ_INT_TYPE rid, PairedEndRead& read, int& sid) {
        int dir, pos;
        int insertL, mateL1, mateL2;
        std::string name;