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Use standard process and exponential functions on OS X #10

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Use standard process and exponential functions on OS X #10

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12 changes: 6 additions & 6 deletions src/BAFpileup.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -98,7 +98,7 @@ float BAFpileup::calculateFlankLength(std::string const& mateFileName, std::stri
command = "gzip -c -d "+mateFileName;
}
stream =
#if defined(_WIN32) || (defined(__APPLE__) && defined(__MACH__))
#if defined(_WIN32)
_popen(command.c_str(), "r");
#else
popen(command.c_str(), "r");
Expand Down Expand Up @@ -143,7 +143,7 @@ float BAFpileup::calculateFlankLength(std::string const& mateFileName, std::stri
fragmentLength = fragmentLength/j;
float flanks = fragmentLength/2;
if (zgOrbam) {
#if defined(_WIN32) || (defined(__APPLE__) && defined(__MACH__))
#if defined(_WIN32)
_pclose(stream);
#else
pclose(stream);
Expand Down Expand Up @@ -251,13 +251,13 @@ std::string BAFpileup::intersectWithBedtools(std::string makeminipileup, std::st
string command = pathToBedtools_ +" intersect -a " + makeminipileup + " -b " + bedFileWithRegionsOfInterest + " > " + intersected;

stream =
#if defined(_WIN32) || (defined(__APPLE__) && defined(__MACH__))
#if defined(_WIN32)
_popen(command.c_str(), "w");
#else
popen(command.c_str(), "w");
#endif

#if defined(_WIN32) || (defined(__APPLE__) && defined(__MACH__))
#if defined(_WIN32)
_pclose(stream);
#else
pclose(stream);
Expand Down Expand Up @@ -301,13 +301,13 @@ std::string BAFpileup::createPileUpFile(std::string outputDir, std::string samto
}

stream =
#if defined(_WIN32) || (defined(__APPLE__) && defined(__MACH__))
#if defined(_WIN32)
_popen(command.c_str(), "w");
#else
popen(command.c_str(), "w");
#endif

#if defined(_WIN32) || (defined(__APPLE__) && defined(__MACH__))
#if defined(_WIN32)
_pclose(stream);
#else
pclose(stream);
Expand Down
4 changes: 2 additions & 2 deletions src/GenomeCopyNumber.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -320,7 +320,7 @@ void GenomeCopyNumber::fillMyHash(std::string const& mateFileName ,std::string c

inputFormat = getInputFormat(myInputFormat);
stream =
#if defined(_WIN32) || (defined(__APPLE__) && defined(__MACH__))
#if defined(_WIN32)
_popen(command.c_str(), "r");
#else
popen(command.c_str(), "r");
Expand All @@ -330,7 +330,7 @@ void GenomeCopyNumber::fillMyHash(std::string const& mateFileName ,std::string c
count++;
normalCount+=processRead(inputFormat,matesOrientation,line_buffer, bin,targetBed, mateFileName);
}
#if defined(_WIN32) || (defined(__APPLE__) && defined(__MACH__))
#if defined(_WIN32)
_pclose(stream);
#else
pclose(stream);
Expand Down
8 changes: 4 additions & 4 deletions src/SNPinGenome.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -118,7 +118,7 @@ void SNPinGenome::readSNPs(std::string const& inFile)
char buffer[MAX_BUFFER];
string command = "gzip -cd "+inFile;
stream =
#if defined(_WIN32) || (defined(__APPLE__) && defined(__MACH__))
#if defined(_WIN32)
_popen(command.c_str(), "r");
#else
popen(command.c_str(), "r");
Expand All @@ -128,7 +128,7 @@ void SNPinGenome::readSNPs(std::string const& inFile)
if (line_buffer[0] == '#') continue;
count+=processSNPLine(ifVCF,line_buffer,myChr,index,previousPos);
}
#if defined(_WIN32) || (defined(__APPLE__) && defined(__MACH__))
#if defined(_WIN32)
_pclose(stream);
#else
pclose(stream);
Expand Down Expand Up @@ -389,14 +389,14 @@ void SNPinGenome::assignValues(std::string const& inFile, string inputFormat, in
if (inFile.substr(inFile.size()-3,3).compare(".gz")==0) {
string command = "gzip -cd "+inFile;
FILE* stream =
#if defined(_WIN32) || (defined(__APPLE__) && defined(__MACH__))
#if defined(_WIN32)
_popen(command.c_str(), "r");
#else
popen(command.c_str(), "r");
#endif
readPileUP(stream, minimalTotalLetterCountPerPosition, minimalQualityPerPosition, p_genomeCopyNumber);

#if defined(_WIN32) || (defined(__APPLE__) && defined(__MACH__))
#if defined(_WIN32)
_pclose(stream);
#else
pclose(stream);
Expand Down
16 changes: 8 additions & 8 deletions src/myFunc.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -277,15 +277,15 @@ long getLineNumber(std::string const& fileName, const std::string& pathToSamtool
if (fileName.substr(fileName.size()-3,3).compare(".gz")==0) {
string command = "gzip -cd "+fileName;
stream =
#if defined(_WIN32) || (defined(__APPLE__) && defined(__MACH__))
#if defined(_WIN32)
_popen(command.c_str(), "r");
#else
popen(command.c_str(), "r");
#endif
while ( fgets(buffer, MAX_BUFFER, stream) != NULL ) {
count++;
}
#if defined(_WIN32) || (defined(__APPLE__) && defined(__MACH__))
#if defined(_WIN32)
_pclose(stream);
#else
pclose(stream);
Expand All @@ -305,7 +305,7 @@ long getLineNumber(std::string const& fileName, const std::string& pathToSamtool
cout << "..samtools should be installed to be able to read BAM files\n";
}
stream =
#if defined(_WIN32) || (defined(__APPLE__) && defined(__MACH__))
#if defined(_WIN32)
_popen(command.c_str(), "r");
#else
popen(command.c_str(), "r");
Expand All @@ -314,7 +314,7 @@ long getLineNumber(std::string const& fileName, const std::string& pathToSamtool
while ( fgets(buffer, MAX_BUFFER, stream) != NULL ) {
count++;
}
#if defined(_WIN32) || (defined(__APPLE__) && defined(__MACH__))
#if defined(_WIN32)
_pclose(stream);
#else
pclose(stream);
Expand Down Expand Up @@ -353,7 +353,7 @@ long getReadNumberFromPileup(std::string const& fileName) {
char buffer[MAX_BUFFER];
string command = "gzip -cd "+fileName;
stream =
#if defined(_WIN32) || (defined(__APPLE__) && defined(__MACH__))
#if defined(_WIN32)
_popen(command.c_str(), "r");
#else
popen(command.c_str(), "r");
Expand All @@ -373,7 +373,7 @@ long getReadNumberFromPileup(std::string const& fileName) {
}
strs.clear();
}
#if defined(_WIN32) || (defined(__APPLE__) && defined(__MACH__))
#if defined(_WIN32)
_pclose(stream);
#else
pclose(stream);
Expand Down Expand Up @@ -1224,7 +1224,7 @@ string pathAppend(const string& p1, const string& p2) {
char sep = '/';
string tmp = p1;
char sep2=sep;
#if defined(_WIN32) || (defined(__APPLE__) && defined(__MACH__))
#if defined(_WIN32)
sep2 = '\\';
#endif
char lastSymb= p1[p1.length( )-1];
Expand Down Expand Up @@ -2496,7 +2496,7 @@ void myReplace(std::string& str, const std::string& oldStr, const std::string& n
}


#if defined(_WIN32) || (defined(__APPLE__) && defined(__MACH__))
#if defined(_WIN32)
double expm1(double x) {
if (fabs(x) < 1e-5)
return x + 0.5*x*x;
Expand Down