Use standard process and exponential functions on OS X

BoevaLab · Dec 7, 2016 · bb60f86 · bb60f86
1 parent b9db18a
commit bb60f86
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Showing 4 changed files with 20 additions and 20 deletions.
diff --git a/src/BAFpileup.cpp b/src/BAFpileup.cpp
@@ -77,7 +77,7 @@ 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");
@@ -124,7 +124,7 @@ 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);
@@ -233,13 +233,13 @@ 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);
@@ -283,13 +283,13 @@ 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);

diff --git a/src/GenomeCopyNumber.cpp b/src/GenomeCopyNumber.cpp
@@ -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");
@@ -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);

diff --git a/src/SNPinGenome.cpp b/src/SNPinGenome.cpp
@@ -119,7 +119,7 @@ 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");
@@ -129,7 +129,7 @@ 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);
@@ -390,14 +390,14 @@ 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);

diff --git a/src/myFunc.cpp b/src/myFunc.cpp
@@ -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);
@@ -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");
@@ -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);
@@ -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");
@@ -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);
@@ -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];
@@ -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;