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[rsem.git] / SingleQModel.h

diff --git a/SingleQModel.h b/SingleQModel.h
index ffc0639909b2f49a5d501c7ecb85be20f2f19f4f..5da47545370bdaf94991d36c50b474270d876bd4 100644 (file)
--- a/SingleQModel.h
+++ b/SingleQModel.h
@@ -8,6 +8,7 @@
 #include<string>
 #include<algorithm>
 #include<sstream>
+#include<iostream>
 
 #include "utils.h"
 #include "my_assert.h"
@@ -238,7 +239,7 @@ public:
        const LenDist& getGLD() { return *gld; }
 
        void startSimulation(simul*, double*);
-       bool simulate(int, SingleReadQ&, int&);
+       bool simulate(READ_INT_TYPE, SingleReadQ&, int&);
        void finishSimulation();
 
        //Use it after function 'read' or 'estimateFromReads'
@@ -254,7 +255,7 @@ private:
        static const int read_type = 1;
 
        int M;
-       int N[3];
+        READ_INT_TYPE N[3];
        Refs *refs;
        double mean, sd;
        int seedLen;
@@ -289,7 +290,7 @@ void SingleQModel::estimateFromReads(const char* readFN) {
                        genReadFileNames(readFN, i, read_type, s, readFs);
                        ReadReader<SingleReadQ> reader(s, readFs, refs->hasPolyA(), seedLen); // allow calculation of calc_lq() function
 
-                       int cnt = 0;
+                       READ_INT_TYPE cnt = 0;
                        while (reader.next(read)) {
                                if (!read.isLowQuality()) {
                                        mld != NULL ? mld->update(read.getReadLength(), 1.0) : gld->update(read.getReadLength(), 1.0);
@@ -297,14 +298,14 @@ void SingleQModel::estimateFromReads(const char* readFN) {
                                        if (i == 0) { nqpro->updateC(read.getReadSeq(), read.getQScore()); }
                                }
                                else if (verbose && read.getReadLength() < seedLen) {
-                                       printf("Warning: Read %s is ignored due to read length %d < seed length %d!\n", read.getName().c_str(), read.getReadLength(), seedLen);
+                                       std::cout<< "Warning: Read "<< read.getName()<< " is ignored due to read length "<< read.getReadLength()<< " < 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 != NULL ? mld->finish() : gld->finish();
@@ -419,7 +420,7 @@ void SingleQModel::startSimulation(simul* sampler, double* theta) {
        nqpro->startSimulation();
 }
 
-bool SingleQModel::simulate(int rid, SingleReadQ& read, int& sid) {
+bool SingleQModel::simulate(READ_INT_TYPE rid, SingleReadQ& read, int& sid) {
        int dir, pos, readLen, fragLen;
        std::string name;
        std::string qual, readseq;