X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraccodecommand.cpp;h=fc98e0fc45c3b576a3e2420ac415c016266b4c1c;hb=36a6b02cf7f09d2bc34376b588944a9ca73429c5;hp=321ae77cf743420284e4dfac274d9c88b9b4557f;hpb=ae57e166b2ed7b475ec3f466106bd76fabadd063;p=mothur.git

diff --git a/chimeraccodecommand.cpp b/chimeraccodecommand.cpp
index 321ae77..fc98e0f 100644
--- a/chimeraccodecommand.cpp
+++ b/chimeraccodecommand.cpp
@@ -223,13 +223,13 @@ ChimeraCcodeCommand::ChimeraCcodeCommand(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, "numwanted", false);		if (temp == "not found") { temp = "20"; }
-			convert(temp, numwanted);
+			m->mothurConvert(temp, numwanted);
 			
 			temp = validParameter.validFile(parameters, "save", false);			if (temp == "not found"){	temp = "f";				}
 			save = m->isTrue(temp); 
@@ -390,14 +390,16 @@ int ChimeraCcodeCommand::execute(){
 
 			outHeader.close();
 			
-			vector<unsigned long long> positions = m->divideFile(fastaFileNames[s], processors);
-				
-			for (int i = 0; i < (positions.size()-1); i++) {
-				lines.push_back(new linePair(positions[i], positions[(i+1)]));
-			}	
+			
 			
 			//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++) {
+					lines.push_back(new linePair(positions[i], positions[(i+1)]));
+				}	
+			
 				if(processors == 1){
 										
 					numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
@@ -436,6 +438,7 @@ int ChimeraCcodeCommand::execute(){
 				}
 
 			#else
+				lines.push_back(new linePair(0, 1000));
 				numSeqs = driver(lines[0], outputFileName, fastaFileNames[s], accnosFileName);
 				
 				if (m->control_pressed) { m->mothurRemove(outputFileName); m->mothurRemove(tempHeader); m->mothurRemove(accnosFileName); for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	} for (int i = 0; i < lines.size(); i++) {  delete lines[i];  } outputTypes.clear();  lines.clear(); delete chimera; return 0; }
@@ -521,7 +524,7 @@ int ChimeraCcodeCommand::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
@@ -608,7 +611,7 @@ int ChimeraCcodeCommand::driverMPI(int start, int num, MPI_File& inMPI, MPI_File
 
 int ChimeraCcodeCommand::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;