Further code cleanup

* convert some CR/LF line endings to LF
* be explicit about assignment operations within conditionals
* remove some unused variables
* add const to string literal argument types

Helps fix BoevaLab#11.

src/BAFpileup.h

@@ -1,14 +1,14 @@
 #pragma once
-#ifndef BAFPILEUP_H
-#define BAFPILEUP_H
-
-#include <string>
+#ifndef BAFPILEUP_H
+#define BAFPILEUP_H
+
+#include <string>
 #include <vector>
 #include "GenomeCopyNumber.h"
-
-class BAFpileup
-{
-    public:
+
+class BAFpileup
+{
+    public:
         BAFpileup();
         void makepileup(GenomeCopyNumber & sampleCopyNumber, GenomeCopyNumber & controlCopyNumber,
             std::string sample_MateFile,std::string control_MateFile,
@@ -35,7 +35,7 @@ class BAFpileup
         std::vector < std::vector<int> > A_nb;
         std::vector < std::vector<int> > B_nb;
         std::vector < std::vector<std::string> > AB_nb;
-
+
     private:
 
         int length_;
@@ -50,7 +50,7 @@ class BAFpileup
         std::vector <std::string> length_with_flanksTmp;
         std::vector <std::string> strand;
         std::vector <std::string> ref_name;
-        std::string pathToBedtools_;
-};
-
-#endif // BAFPILEUP_H
+        std::string pathToBedtools_;
+};
+
+#endif // BAFPILEUP_H

src/GenomeCopyNumber.cpp

@@ -1062,7 +1062,7 @@ int GenomeCopyNumber::getNumberOfChromosomes() {
     return chrCopyNumber_.size();
 }
 
-long double GenomeCopyNumber::calculateRSS(int ploidy)
+long double GenomeCopyNumber::calculateRSS(int ploidy)
 {
     string::size_type pos = 0;
     vector<float> observedvalues;
@@ -1104,7 +1104,7 @@ long double GenomeCopyNumber::calculateRSS(int ploidy)
             RSS = RSS + (long double)pow(diff,2);
             }
         }
-    return RSS;
+    return RSS;
 }
 
 

src/GenomeCopyNumber.h

@@ -123,7 +123,7 @@ class GenomeCopyNumber
     void setWESanalysis(bool WESgiven);
      void setmakingPileup(bool makingPileup_given);
     double Percentage_GenomeExplained(int &);
-    long double calculateRSS(int ploidy);
+    long double calculateRSS(int ploidy);
 
 
 private:

src/RSSerror.cpp

@@ -1,12 +1,12 @@
-#include "RSSerror.h"
+#include "RSSerror.h"
 
 using namespace std;
-
-RSSerror::RSSerror()
+
+RSSerror::RSSerror()
 {
-}
+}
 
-long double calculateRSS(GenomeCopyNumber & samplecopynumber, int ploidy)
+long double calculateRSS(GenomeCopyNumber & samplecopynumber, int ploidy)
 {
     string::size_type pos = 0;
     vector<float> observedvalues;
@@ -48,5 +48,5 @@ long double calculateRSS(GenomeCopyNumber & samplecopynumber, int ploidy)
             RSS = RSS + (long double)pow(diff,2);
             }
         }
-    return RSS;
+    return RSS;
 }

src/RSSerror.h

@@ -1,7 +1,7 @@
 #pragma once
-#ifndef RSSERROR_H
-#define RSSERROR_H
-
+#ifndef RSSERROR_H
+#define RSSERROR_H
+
 #include <iostream>
 #include <stdlib.h>
 #include <fstream>
@@ -13,13 +13,13 @@
 #include "GenomeCopyNumber.h"
 #include "ChrCopyNumber.h"
 
-
-class RSSerror
-{
-    public:
-        RSSerror();
+
+class RSSerror
+{
+    public:
+        RSSerror();
 };
 
-long double calculateRSS(GenomeCopyNumber & samplecopynumber, int ploidy);
-
-#endif // RSSERROR_H
+long double calculateRSS(GenomeCopyNumber & samplecopynumber, int ploidy);
+
+#endif // RSSERROR_H

src/SNPatChr.h

@@ -1,15 +1,15 @@
-#ifndef SNPATCHR_H
-#define SNPATCHR_H
+#ifndef SNPATCHR_H
+#define SNPATCHR_H
 
 #include <string>
-#include <vector>
+#include <vector>
 
 #include "SNPposition.h"
 
-
-class SNPatChr
-{
-    public:
+
+class SNPatChr
+{
+    public:
         SNPatChr(const std::string&);
         SNPatChr();
         void setChromosome(const std::string& chromosome);
@@ -25,11 +25,11 @@ class SNPatChr
 
         void setStatusAt(int index,float value) ;
         int getSize();
-        virtual ~SNPatChr();
-    protected:
+        virtual ~SNPatChr();
+    protected:
     private:
     std::vector <SNPposition> SNPpositionArray_;
-    std::string chromosome_;
-};
-
-#endif // SNPATCHR_H
+    std::string chromosome_;
+};
+
+#endif // SNPATCHR_H

src/SNPinGenome.cpp

@@ -269,7 +269,7 @@ long SNPinGenome::processPileUPLine(int & positionCount, char* line, string & ol
                 processChrName(chr);
                 int lindex = p_genomeCopyNumber->findIndex(chr);
                 if (lindex != NA) {
-                    if (valueToReturn = strccnt(strs[4], '^')) {
+                    if ((valueToReturn = strccnt(strs[4], '^'))) {
                         ChrCopyNumber& chrCopyNumber = p_genomeCopyNumber->getChrCopyNumberAt(lindex);
                         int step = p_genomeCopyNumber->getStep();
                         for (int i=0; i<valueToReturn; i++)
@@ -283,7 +283,7 @@ long SNPinGenome::processPileUPLine(int & positionCount, char* line, string & ol
                  processChrName(chr);
                 int lindex = p_genomeCopyNumber->findIndex(chr);
                 if (lindex != NA) {
-                    if (valueToReturn = strccnt(strs[4], '^')) {
+                    if ((valueToReturn = strccnt(strs[4], '^'))) {
                         ChrCopyNumber& chrCopyNumber = p_genomeCopyNumber->getChrCopyNumberAt(lindex);
                         int l = 0;
                         bool leftIsInTheWindow = false;
@@ -312,7 +312,7 @@ long SNPinGenome::processPileUPLine(int & positionCount, char* line, string & ol
 
     if (currentPosition==sNPpositionToProceed) {
         try {
-            float localBAF=addInfoFromAPileUp(atoi(strs[3]),minimalTotalLetterCountPerPosition,(*SNP_atChr_)[index].getNucleotideAt(positionCount),
+            addInfoFromAPileUp(atoi(strs[3]),minimalTotalLetterCountPerPosition,(*SNP_atChr_)[index].getNucleotideAt(positionCount),
                                            index,positionCount,sNPpositionToProceed,strs[4], minimalQualityPerPosition,strs[5]);
 //                    if (localBAF>=0) {
 //                        heterozygousBAFs.push_back(localBAF);
@@ -333,8 +333,8 @@ long SNPinGenome::processPileUPLine(int & positionCount, char* line, string & ol
                     sNPpositionToProceed=NA;
         }
         if (currentPosition==sNPpositionToProceed) {
-                 try {
-                    float localBAF=addInfoFromAPileUp(atoi(strs[3]),minimalTotalLetterCountPerPosition,(*SNP_atChr_)[index].getNucleotideAt(positionCount),
+                try {
+                    addInfoFromAPileUp(atoi(strs[3]),minimalTotalLetterCountPerPosition,(*SNP_atChr_)[index].getNucleotideAt(positionCount),
                                            index,positionCount,sNPpositionToProceed,strs[4], minimalQualityPerPosition,strs[5]);
 //                        if (localBAF>=0) {
 //                            heterozygousBAFs.push_back(localBAF);

src/SNPposition.cpp

@@ -28,7 +28,7 @@ SNPposition::SNPposition(int position, char* alt) //for a VCF line
         nucleotide_ = alt[0];
     }  else  {
         char* strs[4];
-        unsigned strs_cnt = split(alt, ',', strs);
+        split(alt, ',', strs);
         nucleotide_ = strs[0][0];
     }
     freq_ = 0; // EV: must be initialized
@@ -45,7 +45,7 @@ SNPposition::SNPposition(int position, char* letters, const char* strand, const
     if (strlen(letters) == 1)    { //should not get here
         nucleotide_ = letters[0];
     }   else    {
-        unsigned strs_cnt = split(letters, '/', strs);
+        split(letters, '/', strs);
         char c_ref;
         if (reverse) {
             c_ref = complement(ref[0]);
@@ -66,19 +66,19 @@ SNPposition::SNPposition(int position, char* letters, const char* strand, const
     bin_=NA; //before initialization
 }
 
-
-SNPposition::~SNPposition()
-{
-    //dtor
-}
+
+SNPposition::~SNPposition()
+{
+    //dtor
+}
 
 int SNPposition::getPosition() {
     return position_;
 }
 
 char SNPposition::getNucleotide() {
     return nucleotide_;
-}
+}
 
 void SNPposition::setFrequency(float freq) {
         freq_ = freq;
@@ -87,7 +87,7 @@ void SNPposition::setFrequency(float freq) {
 void SNPposition::setStatus(float status) {
         status_ = status;
 }
-
+
 float SNPposition::getValue() {
     return freq_ ;
 }

src/SNPposition.h

@@ -1,14 +1,14 @@
-#ifndef SNPPOSITION_H
-#define SNPPOSITION_H
-
+#ifndef SNPPOSITION_H
+#define SNPPOSITION_H
+
 #include <string>
 #include <vector>
 
 #include "myFunc.h"
-
-class SNPposition
-{
-    public:
+
+class SNPposition
+{
+    public:
 	    SNPposition(int position, char* letters, const char* strand, const char* ref); //from TXT
         SNPposition(int position, char* alt); //for VCF
         virtual ~SNPposition();
@@ -19,14 +19,14 @@ class SNPposition
         void setFrequency(float freq);
         void setStatus(float status);
         void setBin(int i);
-        int getBin();
-    protected:
+        int getBin();
+    protected:
     private:
         unsigned int position_;
         char nucleotide_;
         float freq_;
         float status_; //0 - AA/BB, 0.5 - AB
         int bin_; //bin in the copy number array
-};
-
-#endif // SNPPOSITION_H
+};
+
+#endif // SNPPOSITION_H

src/SeekSubclones.cpp

@@ -19,24 +19,24 @@ A copy of the GNU General Public License is available at
 *************************************************************************/
 
 
-#include "SeekSubclones.h"
+#include "SeekSubclones.h"
 
 using namespace std;
 
-SeekSubclones::SeekSubclones(void)
+SeekSubclones::SeekSubclones(void)
 {
 }
 
 SeekSubclones::~SeekSubclones(void)
 {
 }
 
-
+
 SeekSubclones::SeekSubclones(GenomeCopyNumber & samplecopynumber, int ploidy, std::string myName, float minimal_pop) {
     ploidy_ = ploidy;
-    minimal_pop_  = minimal_pop/100;
-    getSegmentsInfo(samplecopynumber, myName);
-}
+    minimal_pop_  = minimal_pop/100;
+    getSegmentsInfo(samplecopynumber, myName);
+}
 
 
 void SeekSubclones::getSegmentsInfo(GenomeCopyNumber & samplecopynumber, std::string myName)
@@ -191,7 +191,7 @@ bool SeekSubclones::PercentageTest(std::vector <float>& data, float& threshold)
         subclone = true;
         }
     return subclone;
-}
+}
 
 
 void SeekSubclones::EstimateSubclonalPopulation(vector <float> data, float threshold, int ploidy_)

src/SeekSubclones.h

@@ -1,6 +1,6 @@
 #pragma once
-#ifndef SEEKSUBCLONES_H
-#define SEEKSUBCLONES_H
+#ifndef SEEKSUBCLONES_H
+#define SEEKSUBCLONES_H
 
 #include<cstdlib>
 #include<ctime>
@@ -13,23 +13,23 @@
 #include <algorithm>
 #include <map>
 #include <fstream>
-
-class SeekSubclones
-{
-    public:
+
+class SeekSubclones
+{
+    public:
         SeekSubclones(GenomeCopyNumber & samplecopynumber, int ploidy, std::string myName, float minimal_pop);
         SeekSubclones();
         ~SeekSubclones(void);
         void getSegmentsInfo(GenomeCopyNumber & samplecopynumber, std::string myName);
         bool SignTest(std::vector <float>& data, float& threshold, int bonfer_correction);
-        void EstimateSubclonalPopulation(std::vector <float> data, float threshold, int ploidy_);
-        bool PercentageTest(std::vector <float>& data, float& threshold);
+        void EstimateSubclonalPopulation(std::vector <float> data, float threshold, int ploidy_);
+        bool PercentageTest(std::vector <float>& data, float& threshold);
     protected:
         int ploidy_;
         float minimal_pop_;
         std::vector <int> copynumber_;
-        std::vector <float> population_;
-    private:
+        std::vector <float> population_;
+    private:
 };
-
-#endif // SEEKSUBCLONES_H
+
+#endif // SEEKSUBCLONES_H