FIX warnings and problems

Author: h-2

Makefile

@@ -19,11 +19,11 @@ CXXFLAGS+=-O3
 LDFLAGS=-O3
 
 #Debug build
-#CXXFLAGS+=-g -O0
-#LDFLAGS=-g -O0
+# CXXFLAGS+=-g -O0
+# LDFLAGS=-g -O0
 
 # set std to c++0x to allow using 'auto' etc.
-CXXFLAGS+=-std=c++0x -DSEQAN_ENABLE_TESTING=0 -DSEQAN_ENABLE_DEBUG=0 -DSEQAN_HAS_ZLIB=1
+CXXFLAGS+=-std=c++0x -DSEQAN_ENABLE_TESTING=0 -DSEQAN_ENABLE_DEBUG=0 -DSEQAN_HAS_ZLIB=1 -Wmaybe-uninitialized
 LDFLAGS+=-pthread -L$(HTSLIB) -Wl,-rpath,$(HTSLIB) -lz -lhts -L$(BOOST_LIB) -Wl,-rpath,$(BOOST_LIB) -lboost_iostreams
 
 all: popSTR

computePnSlippage.cpp

@@ -259,7 +259,7 @@ void parseNextLine(float winner, float second, ifstream& attributeFile, Marker&
 
 long int readOffSets(ifstream & attsFile, unsigned firstPnIdx, unsigned nPns)
 {
-    long int offset;
+    long int offset = 0;
     for (unsigned i = 1; i<=firstPnIdx; ++i)
     {
         attsFile >> offset;
@@ -282,8 +282,8 @@ long int readOffSets(ifstream & attsFile, unsigned firstPnIdx, unsigned nPns)
 void readMarkerData_level2(CharString attributesDirectory, Marker& marker, map <string, Pair<float> >& pnToLabels, map<string, Pair<double, unsigned> >& pnToPrevSlipp, unsigned minNpns, unsigned firstPnIdx)
 {
     //variables
-    int numberOfReads, pnsFound = 0;
-    float winner, second, numOfRepeats;
+    int numberOfReads = 0, pnsFound = 0;
+    float winner = 0, second = 0, numOfRepeats = 0;
     string nextLine, temp;
     Pair<int, String<string> > numberOfWordsAndWords;
     //make input stream
@@ -456,7 +456,7 @@ map<string, Pair<double, unsigned> > readPrevSlipp(CharString & previousSlippage
 {
     CharString filePath = previousSlippageRate;
     string prevIterIdx;
-    int itNum;
+    int itNum = 0;
     lexicalCast(itNum, iterationNumber);
     --itNum;
     prevIterIdx = to_string(itNum);

computePnSlippageDefault.cpp

@@ -486,7 +486,7 @@ map<string, LabelProps> readPnList(CharString & pnInfoFile)
 
 long int readOffSets(ifstream & attsFile, unsigned firstPnIdx, unsigned nPns)
 {
-    long int offset;
+    long int offset = 0;
     for (unsigned i = 1; i<=firstPnIdx; ++i)
     {
         attsFile >> offset;
@@ -544,18 +544,20 @@ Pair<float> findMostFrequent(std::vector<String<string> > & currentReadList)
     }
     if (secondFreq < 0.10*winnerFreq)
         second = winner;
+
+    return {winner, second};
 }
 
 void readMarkerData(CharString attributesDirectory, Marker marker, map<string, LabelProps>& pnToLabelProps, unsigned firstPnIdx)
 {
     //variables
-    int numberOfReads, nReadsThisBatch, pnsFound = 0;
-    float winner, second, numOfRepeats;
+    int numberOfReads = 0, nReadsThisBatch = 0, pnsFound = 0;
+    float winner = 0, second = 0, numOfRepeats = 0;
     string nextLine, temp, prevPn= "PeterGriffin";
     Pair<int, String<string> > numberOfWordsAndWords;
     AttributeLine currentLine;
     std::vector<String<string> > currentReadList;
-    bool moreThanOneBam;
+    bool moreThanOneBam = false;
     //make input stream
     append(attributesDirectory, "/");
     append(attributesDirectory, to_string(marker.start));

computeReadAttributes.cpp

@@ -466,8 +466,8 @@ Pair<Triple<CharString, CharString, int>,ReadInfo> computeReadInfo(BamAlignmentR
     mapValue.motif = markerInfo.motif;
     mapValue.refRepeatNum = markerInfo.refRepeatNum;
 
-    int scoreBf, scoreAf, startCoord, endCoord, leftFlank, rightFlank;
-    float rBf, rAf;
+    int scoreBf = 0, scoreAf = 0, startCoord = 0, endCoord = 0, leftFlank = 0, rightFlank = 0;
+    float rBf = 0.0, rAf = 0.0;
     //check if 8-mer in front of and behind repeat in read match reference with edit-distance max 1
     //This is the best case scenario, then I skip flanking alignment
     before_8 = infix(record.seq, max(0,coordinates.i1.i1-8), coordinates.i1.i1);
@@ -1560,8 +1560,8 @@ int main(int argc, char const ** argv)
         //Set for storing allele-types and vector for storing reported alleles, count occurences in vector for all elements in set to get frequency of each allele
         std::set<float> presentAlleles;
         vector<float> allAlleles;
-        int winnerFreq, secondFreq, currentFreq;
-        float winner, second;
+        int winnerFreq = 0, secondFreq = 0, currentFreq = 0;
+        float winner = 0, second = 0;
         //Loop over map of markers and look at all reads for each of them
         unordered_map<STRinfoSmall, Triple<std::set<float>,vector<float>, String<ReadPairInfo> > >::const_iterator ite2 = finalMap.end();
         unordered_map<STRinfoSmall, Triple<std::set<float>,vector<float>, String<ReadPairInfo> > >::iterator it = finalMap.begin();
@@ -1615,7 +1615,7 @@ int main(int argc, char const ** argv)
             if (secondFreq < 0.10*winnerFreq)
                 second = winner;
             //Write attributes and initial labelling to output file
-            fprintf(startAndEndToStreamAndOffsets[mapKey].i2,"%s\t%u\t%u\t%s\t%.1f\t%u\t%.1f\t%.1f\n",toCString(it->first.chrom),it->first.STRstart,it->first.STRend,toCString(it->first.motif),it->first.refRepeatNum,length(readPairs),winner,second);
+            fprintf(startAndEndToStreamAndOffsets[mapKey].i2,"%s\t%u\t%u\t%s\t%.1f\t%lu\t%.1f\t%.1f\n",toCString(it->first.chrom),it->first.STRstart,it->first.STRend,toCString(it->first.motif),it->first.refRepeatNum,length(readPairs),winner,second);
             for (unsigned i=0; i < length(readPairs); ++i)
             {
                 ReadPairInfo printMe = readPairs[i];
@@ -1656,7 +1656,7 @@ int main(int argc, char const ** argv)
         rewind(marker.second.i2);
         for (unsigned i=0; i<length(marker.second.i1); ++i)
         {
-            fprintf(marker.second.i2, "%u ", marker.second.i1[i]);
+            fprintf(marker.second.i2, "%li ", marker.second.i1[i]);
             fflush(marker.second.i2);
             //Check if I am writing passed the reserved space at front
             if (ftell(marker.second.i2) > marker.second.i1[idx])

msGenotyper.cpp

@@ -805,7 +805,7 @@ String<Pair<int, string> > readMarkers(CharString & markerFile)
 void readMarkerSlippage(CharString markerSlippageFile, CharString iterationNumber, CharString regressionModelDirectory, CharString intervalIndex)
 {
     string prevItNum;
-    int itNum;
+    int itNum = 0;
     lexicalCast(itNum, iterationNumber);
     --itNum;
     prevItNum = to_string(itNum);
@@ -853,7 +853,7 @@ map<string, Pair<double, int> > readPnSlippage(CharString pnSlippagePath, CharSt
     int nMarkers;
     double currPnSlipp;
     string prevItNum;
-    int itNum;
+    int itNum = 0;
     lexicalCast(itNum, iterationNumber);
     --itNum;
     prevItNum = to_string(itNum);
@@ -1032,7 +1032,7 @@ map<string, Pair<float> > readLabels(CharString modelAndLabelDir, Pair<int, stri
     append(modelAndLabelDir, "_");
     append(modelAndLabelDir, marker.i2);
     string prevItNum;
-    int itNum;
+    int itNum = 0;
     lexicalCast(itNum, iterationNumber);
     --itNum;
     prevItNum = to_string(itNum);
@@ -1055,7 +1055,7 @@ map<string, Pair<float> > readLabels(CharString modelAndLabelDir, Pair<int, stri
 
 long int readOffSets(ifstream & attsFile, unsigned firstPnIdx)
 {
-    long int offset;
+    long int offset = 0;
     for (unsigned i = 1; i<=firstPnIdx; ++i)
     {
         attsFile >> offset;

msGenotyperDefault.cpp

@@ -1028,7 +1028,7 @@ Triple<bool> genotypeIsConfident(GenotypeInfo& genotypeInfo)
 
 long int readOffSets(ifstream & attsFile, unsigned firstPnIdx)
 {
-    long int offset;
+    long int offset = 0;
     for (unsigned i = 1; i<=firstPnIdx; ++i)
     {
         attsFile >> offset;
@@ -1045,7 +1045,7 @@ Pair<float> findMostFrequent(std::vector<String<string> > & currentReadList)
     std::set<string> presentAlleles;
     std::vector<string> allAlleles;
     int winnerFreq = 0, secondFreq = 0, currentFreq;
-    float winner, second, fallele;
+    float winner = 0, second = 0, fallele = 0;
     for (auto read : currentReadList)
     {
         presentAlleles.insert(read[0]);
@@ -1078,6 +1078,8 @@ Pair<float> findMostFrequent(std::vector<String<string> > & currentReadList)
     }
     if (secondFreq < 0.10*winnerFreq)
         second = winner;
+
+    return {winner, second};
 }
 
 int main(int argc, char const ** argv)
@@ -1097,8 +1099,8 @@ int main(int argc, char const ** argv)
     string PnId, chrom, motif, nextWord;
     String<string> PnIds;
     std::set<Marker> markers;
-    int start, end, numberOfReads;
-    float refRepeatNum, winner, second;
+    int start = 0, end = 0, numberOfReads = 0;
+    float refRepeatNum = 0, winner = 0, second{};
     //Read the slippage rate for all PNs into the pnToSize map and list of markers to genotype.
     readPnSlippage(options.pnSlippageFile, PnIds);
     if (length(PnIds) == 0)
@@ -1140,7 +1142,7 @@ int main(int argc, char const ** argv)
     Pair<int, String<string> > numberOfWordsAndWords;
     bool moreThanOneBam = false, enoughReads = true;
     //Iterate over all markers in the markerList and read from their attribute files
-    unsigned nProcessedMarkers = 0, processedPns, nReadsThisBatch;
+    unsigned nProcessedMarkers = 0, processedPns = 0, nReadsThisBatch = 0;
     for (auto const & listMarker : markerToSlippStuttAndRefSeq)
     {
         //Make path to attributefile for current marker

runSmall.sh

@@ -14,8 +14,8 @@ echo "${CODE_DIR}/popSTR computeReadAttributes ${BAMLIST} . <(cut -d ' ' -f 1-11
 ${CODE_DIR}/popSTR computeReadAttributes ${BAMLIST} . <(cut -d ' ' -f 1-11,14- ${CODE_DIR}/kernel/kernelMarkersInfo) 8 135 chr21 ${REFERENCE} ${CODE_DIR}/markerInfo/longRepeats N
 
 #Compute pnSlippage for samples in BAMLIST
-echo "${CODE_DIR}/popSTR computePnSlippageDefault -PL <(cat $BAMLIST | tr '\t' ' ' | sed 's/ .*//') -AD ./attributes/chr21 -OF pnSlippage -FP 1 -MS ${CODE_DIR}/kernel/kernelSlippageRates -MD ${CODE_DIR}/kernel/kernelModels"
-${CODE_DIR}/popSTR computePnSlippageDefault -PL <(cat $BAMLIST | tr '\t' ' ' | sed 's/ .*//') -AD ./attributes/chr21 -OF pnSlippage -FP 1 -MS ${CODE_DIR}/kernel/kernelSlippageRates -MD ${CODE_DIR}/kernel/kernelModels
+echo "${CODE_DIR}/popSTR computePnSlippageDefault -PL <(cat $BAMLIST | '{ print $1 }') -AD ./attributes/chr21 -OF pnSlippage -FP 1 -MS ${CODE_DIR}/kernel/kernelSlippageRates -MD ${CODE_DIR}/kernel/kernelModels"
+${CODE_DIR}/popSTR computePnSlippageDefault -PL <(cat $BAMLIST | awk '{ print $1 }') -AD ./attributes/chr21 -OF pnSlippage -FP 1 -MS ${CODE_DIR}/kernel/kernelSlippageRates -MD ${CODE_DIR}/kernel/kernelModels
 
 #make directory for vcf files
 echo "mkdir -p vcfs"