X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerapintailcommand.cpp;h=7311173265d55bbac59af028922de1f7f7e5d447;hb=ee8403d4eb5760187d62b42a9cf4272de8fc0ec4;hp=062779335148afcc61fb1fd51236467776b9d19b;hpb=7f0cae4f4853cc3f12bc751ee06ea31c7c97496e;p=mothur.git

diff --git a/chimerapintailcommand.cpp b/chimerapintailcommand.cpp
index 0627793..7311173 100644
--- a/chimerapintailcommand.cpp
+++ b/chimerapintailcommand.cpp
@@ -225,13 +225,13 @@ ChimeraPintailCommand::ChimeraPintailCommand(string option)  {
 			
 			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, "window", false);			if (temp == "not found") { temp = "0"; }
-			convert(temp, window);
+			m->mothurConvert(temp, window);
 			
 			temp = validParameter.validFile(parameters, "increment", false);		if (temp == "not found") { temp = "25"; }
-			convert(temp, increment);
+			m->mothurConvert(temp, increment);
 			
 			temp = validParameter.validFile(parameters, "save", false);			if (temp == "not found"){	temp = "f";				}
 			save = m->isTrue(temp); 
@@ -488,7 +488,7 @@ int ChimeraPintailCommand::execute(){
 		#else
 						
 			//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[s], processors);
 			
 				for (int i = 0; i < (positions.size()-1); i++) {
@@ -611,7 +611,7 @@ int ChimeraPintailCommand::driver(linePair* filePos, string outputFName, string
 			}
 			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
@@ -697,7 +697,7 @@ int ChimeraPintailCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_Fi
 
 int ChimeraPintailCommand::createProcesses(string outputFileName, string filename, string accnos) {
 	try {
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		int process = 0;
 		int num = 0;