X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeracheckcommand.cpp;h=cc486d3ab690fd655c1de8a22ae406eafc2c242f;hb=d205e70ae86dbee2efc2df02f2717975854de6ba;hp=400a715aeedf604efb80e580f6c345677f74a430;hpb=7f0cae4f4853cc3f12bc751ee06ea31c7c97496e;p=mothur.git

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index 400a715..cc486d3 100644
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -281,7 +281,7 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
 
 			string temp = validParameter.validFile(parameters, "processors", false);	if (temp == "not found"){	temp = m->getProcessors();	}
 			m->setProcessors(temp);
-			convert(temp, processors);
+			m->mothurConvert(temp, processors);
 			
 			temp = validParameter.validFile(parameters, "save", false);			if (temp == "not found"){	temp = "f";				}
 			save = m->isTrue(temp); 
@@ -306,14 +306,14 @@ ChimeraCheckCommand::ChimeraCheckCommand(string option)  {
 			
 			
 			temp = validParameter.validFile(parameters, "ksize", false);			if (temp == "not found") { temp = "7"; }
-			convert(temp, ksize);
+			m->mothurConvert(temp, ksize);
 			
 			temp = validParameter.validFile(parameters, "svg", false);				if (temp == "not found") { temp = "F"; }
 			svg = m->isTrue(temp);
 			if (nameFileNames.size() != 0) { svg = true; }
 			
 			temp = validParameter.validFile(parameters, "increment", false);		if (temp == "not found") { temp = "10"; }
-			convert(temp, increment);			
+			m->mothurConvert(temp, increment);			
 		}
 	}
 	catch(exception& e) {
@@ -427,7 +427,7 @@ int ChimeraCheckCommand::execute(){
 			
 			
 			//break up file
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 				vector<unsigned long long> positions = m->divideFile(fastaFileNames[i], processors);
 			
 				for (int s = 0; s < (positions.size()-1); s++) {
@@ -522,7 +522,7 @@ int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string fi
 			}
 			delete candidateSeq;
 			
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 				unsigned long long pos = inFASTA.tellg();
 				if ((pos == -1) || (pos >= filePos->end)) { break; }
 			#else
@@ -599,7 +599,7 @@ int ChimeraCheckCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File
 
 int ChimeraCheckCommand::createProcesses(string outputFileName, string filename) {
 	try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		int process = 0;
 		int num = 0;