gentoo-overlay/sci-biology/mothur/files/mothur-1.13.0-overflows2.patch

 clearcutcommand.cpp |   32 ++++++++++++++++----------------
 1 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/clearcutcommand.cpp b/clearcutcommand.cpp
index 1a7ab1f..256aa4d 100644
--- a/clearcutcommand.cpp
+++ b/clearcutcommand.cpp
@@ -180,33 +180,33 @@ int ClearcutCommand::execute() {
 		
 		vector<char*> cPara;
 		
-		char* tempClearcut = new char[8];  strcpy(tempClearcut, "clearcut");  cPara.push_back(tempClearcut);
+		char* tempClearcut = new char[16];  strcpy(tempClearcut, "clearcut");  cPara.push_back(tempClearcut);
 				
 		//you gave us a distance matrix
-		if (phylipfile != "") {  char* temp = new char[10];  strcpy(temp, "--distance");  cPara.push_back(temp);	}
+		if (phylipfile != "") {  char* temp = new char[16];  strcpy(temp, "--distance");  cPara.push_back(temp);	}
 		
 		//you gave us a fastafile
-		if (fastafile != "") { char* temp = new char[11];  strcpy(temp, "--alignment");  cPara.push_back(temp); 	}
+		if (fastafile != "") { char* temp = new char[16];  strcpy(temp, "--alignment");  cPara.push_back(temp); 	}
 		
-		if (version)			{  char* temp = new char[9];  strcpy(temp, "--version");  cPara.push_back(temp);	}
-		if (verbose)			{  char* temp = new char[9];  strcpy(temp, "--verbose");  cPara.push_back(temp);	}
-		if (quiet)				{  char* temp = new char[7];  strcpy(temp, "--quiet");  cPara.push_back(temp);	}
+		if (version)			{  char* temp = new char[16];  strcpy(temp, "--version");  cPara.push_back(temp);	}
+		if (verbose)			{  char* temp = new char[16];  strcpy(temp, "--verbose");  cPara.push_back(temp);	}
+		if (quiet)				{  char* temp = new char[16];  strcpy(temp, "--quiet");  cPara.push_back(temp);	}
 		if (seed != "*")		{  
 			string tempSeed = "--seed=" + seed;
 			char* temp = new char[tempSeed.length()];
 			strcpy(temp, tempSeed.c_str());
 			cPara.push_back(temp);
 		}
-		if (norandom)			{  char* temp = new char[10];  strcpy(temp, "--norandom");  cPara.push_back(temp);	}
-		if (shuffle)			{  char* temp = new char[9];  strcpy(temp, "--shuffle");  cPara.push_back(temp);	}
-		if (neighbor)			{  char* temp = new char[10];  strcpy(temp, "--neighbor");  cPara.push_back(temp);	}
+		if (norandom)			{  char* temp = new char[16];  strcpy(temp, "--norandom");  cPara.push_back(temp);	}
+		if (shuffle)			{  char* temp = new char[16];  strcpy(temp, "--shuffle");  cPara.push_back(temp);	}
+		if (neighbor)			{  char* temp = new char[16];  strcpy(temp, "--neighbor");  cPara.push_back(temp);	}
 		
 		string tempIn = "--in=" + inputFile;  
 		char* tempI = new char[tempIn.length()];
 		strcpy(tempI, tempIn.c_str());
 		cPara.push_back(tempI);
 		
-		if (stdoutWanted)		{  char* temp = new char[8];  strcpy(temp, "--stdout");  cPara.push_back(temp);	}
+		if (stdoutWanted)		{  char* temp = new char[16];  strcpy(temp, "--stdout");  cPara.push_back(temp);	}
 		else{  
 			string tempOut = "--out=" + outputName;  
 			
@@ -215,10 +215,10 @@ int ClearcutCommand::execute() {
 			cPara.push_back(temp);
 		}
 			
-		if (DNA)				{  char* temp = new char[5];  strcpy(temp, "--DNA");  cPara.push_back(temp);		}
-		if (protein)			{  char* temp = new char[9];  strcpy(temp, "--protein");  cPara.push_back(temp);	}
-		if (jukes)				{  char* temp = new char[7];  strcpy(temp, "--jukes");  cPara.push_back(temp);		}
-		if (kimura)				{ char* temp = new char[8];  strcpy(temp, "--kimura");  cPara.push_back(temp);		}
+		if (DNA)				{  char* temp = new char[16];  strcpy(temp, "--DNA");  cPara.push_back(temp);		}
+		if (protein)			{  char* temp = new char[16];  strcpy(temp, "--protein");  cPara.push_back(temp);	}
+		if (jukes)				{  char* temp = new char[16];  strcpy(temp, "--jukes");  cPara.push_back(temp);		}
+		if (kimura)				{ char* temp = new char[16];  strcpy(temp, "--kimura");  cPara.push_back(temp);		}
 		if (matrixout != "")	{  
 			string tempMatrix =  "--matrixout=" + outputDir + matrixout; 
 			char* temp = new char[tempMatrix.length()];
@@ -233,8 +233,8 @@ int ClearcutCommand::execute() {
 			cPara.push_back(temp);
 		}
 
-		if (expblen)			{ char* temp = new char[9];  strcpy(temp, "--expblen");  cPara.push_back(temp); 	}
-		if (expdist)			{ char* temp = new char[9];  strcpy(temp, "--expdist");  cPara.push_back(temp);	}
+		if (expblen)			{ char* temp = new char[16];  strcpy(temp, "--expblen");  cPara.push_back(temp); 	}
+		if (expdist)			{ char* temp = new char[16];  strcpy(temp, "--expdist");  cPara.push_back(temp);	}
 		
 		char** clearcutParameters;
 		clearcutParameters = new char*[cPara.size()];