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-std=c++11 to force g++ using c+=11
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jessieren committed Aug 16, 2017
1 parent b25f072 commit a4d4ddb
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Showing 8 changed files with 13 additions and 12 deletions.
Binary file modified bin/macDarwin/computeMeasure.out
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Binary file modified bin/macDarwin/computeMeasure_onlyd2star.out
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Binary file modified bin/macDarwin/countKmer.out
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4 changes: 2 additions & 2 deletions computeMeasure.cpp
Expand Up @@ -25,8 +25,8 @@ using namespace std;
#include <sys/stat.h>

#include<algorithm>
#include <tr1/unordered_map>
using namespace std::tr1;
#include <unordered_map>
//using namespace std::tr1;

//#include<ext/hash_map>
//using __gnu_cxx::hash_map;
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4 changes: 2 additions & 2 deletions computeMeasure_onlyd2star.cpp
Expand Up @@ -22,8 +22,8 @@ using namespace std;
#include <sys/stat.h>

#include<algorithm>
#include <tr1/unordered_map>
using namespace std::tr1;
#include <unordered_map>
//using namespace std::tr1;

//#include<ext/hash_map>
//using __gnu_cxx::hash_map;
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4 changes: 2 additions & 2 deletions countKmer.cpp
Expand Up @@ -17,8 +17,8 @@
#include <vector>
//
#include <algorithm>
#include <tr1/unordered_map>
using namespace std::tr1;
#include <unordered_map>
//using namespace std::tr1;
//#include<ext/hash_map>
//using __gnu_cxx::hash_map;

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7 changes: 4 additions & 3 deletions vhm.py
Expand Up @@ -98,7 +98,7 @@
filelog.write("WARNING: can't recognize the operating system" + optSys + " \n")
filelog.write( "Trying to compile..." + "\n")
if os.path.exists(countKmerCpp) :
os.system("g++ " + countKmerCpp + " -o " + countKmerOut)
os.system("g++ " + countKmerCpp + " -o " + countKmerOut + " -std=c++11" )
else :
sys.stderr.write( "ERROR: can't find file " + countKmerCpp + ". \n Please run make under the main directory! \n" )
filelog.write( "ERROR: can't find file " + countKmerCpp + ". \n Please run make under the main directory! \n" )
Expand Down Expand Up @@ -129,7 +129,7 @@
filelog.write("WARNING: can't recognize the operating system" + optSys + " \n")
filelog.write( "Trying to compile..." + "\n")
if os.path.exists(computeMeasureCpp) :
os.system("g++ " + computeMeasureCpp + " -o " + computeMeasureOut)
os.system("g++ " + computeMeasureCpp + " -o " + computeMeasureOut + " -std=c++11" )
else :
sys.stderr.write( "ERROR: can't find file " + computeMeasureCpp + ". \n Please run make under the main directory! \n" )
filelog.write( "ERROR: can't find file " + computeMeasureCpp + ". \n Please run make under the main directory! \n" )
Expand Down Expand Up @@ -159,7 +159,7 @@
filelog.write("WARNING: can't recognize the operating system" + optSys + " \n")
filelog.write( "Trying to compile..." + "\n")
if os.path.exists(computed2starCpp) :
os.system("g++ " + computed2starCpp + " -o " + computed2starOut)
os.system("g++ " + computed2starCpp + " -o " + computed2starOut + " -std=c++11" )
else :
sys.stderr.write( "ERROR: can't find file " + computed2starCpp + ". \n Please run make under the main directory! \n" )
filelog.write( "ERROR: can't find file " + computed2starCpp + ". \n Please run make under the main directory! \n" )
Expand Down Expand Up @@ -259,6 +259,7 @@
filelog.write("Step 1: counting kmers for virus " + currentFileNameS + "\n")
for w in range(1, (kmax+1)) :
currentFilePath = os.path.join(options.virusFaDir, currentFileName)

currentKmerCountPath = os.path.join(kmerCountPath, currentFileNameS)
cmdKmer = countKmerOut + " -l -k " + str(w) + \
" -i " + currentFilePath +\
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6 changes: 3 additions & 3 deletions vhm_NGS.py
Expand Up @@ -98,7 +98,7 @@
filelog.write("WARNING: can't recognize the operating system" + optSys + " \n")
filelog.write( "Trying to compile..." + "\n")
if os.path.exists(countKmerCpp) :
os.system("g++ " + countKmerCpp + " -o " + countKmerOut)
os.system("g++ " + countKmerCpp + " -o " + countKmerOut + " -std=c++11" )
else :
sys.stderr.write( "ERROR: can't find file " + countKmerCpp + ". \n Please run make under the main directory! \n" )
filelog.write( "ERROR: can't find file " + countKmerCpp + ". \n Please run make under the main directory! \n" )
Expand Down Expand Up @@ -129,7 +129,7 @@
filelog.write("WARNING: can't recognize the operating system" + optSys + " \n")
filelog.write( "Trying to compile..." + "\n")
if os.path.exists(computeMeasureCpp) :
os.system("g++ " + computeMeasureCpp + " -o " + computeMeasureOut)
os.system("g++ " + computeMeasureCpp + " -o " + computeMeasureOut + " -std=c++11" )
else :
sys.stderr.write( "ERROR: can't find file " + computeMeasureCpp + ". \n Please run make under the main directory! \n" )
filelog.write( "ERROR: can't find file " + computeMeasureCpp + ". \n Please run make under the main directory! \n" )
Expand Down Expand Up @@ -159,7 +159,7 @@
filelog.write("WARNING: can't recognize the operating system" + optSys + " \n")
filelog.write( "Trying to compile..." + "\n")
if os.path.exists(computed2starCpp) :
os.system("g++ " + computed2starCpp + " -o " + computed2starOut)
os.system("g++ " + computed2starCpp + " -o " + computed2starOut + " -std=c++11" )
else :
sys.stderr.write( "ERROR: can't find file " + computed2starCpp + ". \n Please run make under the main directory! \n" )
filelog.write( "ERROR: can't find file " + computed2starCpp + ". \n Please run make under the main directory! \n" )
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