X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerauchimecommand.cpp;h=026e91b01f188ce180c3b645de8451138efe0e02;hb=d2390ede25cc211f95f99e377d5654bad7e6950e;hp=01289a0d0edf66969827d65a11a703c24da86845;hpb=0ca63a8165baa0afa459e644ebe140ba496d5ba0;p=mothur.git

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index 01289a0..026e91b 100644
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -461,7 +461,7 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
 			path = path.substr(0, (tempPath.find_last_of('m')));
 			
 			string uchimeCommand;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			uchimeCommand = path + "uchime";	//	format the database, -o option gives us the ability
 #else
 			uchimeCommand = path + "uchime.exe";
@@ -544,7 +544,7 @@ int ChimeraUchimeCommand::execute(){
 				int totalSeqs = 0;
 				
 				if(processors == 1)	{	totalSeqs = driverGroups(parser, outputFileName, newFasta, accnosFileName, alnsFileName, 0, groups.size(), groups);	}
-				else				{	totalSeqs = createProcessesGroups(parser, outputFileName, newFasta, accnosFileName, alnsFileName, groups);			}
+				else				{	totalSeqs = createProcessesGroups(parser, outputFileName, newFasta, accnosFileName, alnsFileName, groups, nameFile, groupFile, fastaFileNames[s]);			}
 
 				if (m->control_pressed) {  for (int j = 0; j < outputNames.size(); j++) {	m->mothurRemove(outputNames[j]);	}  return 0;	}				
 
@@ -927,14 +927,15 @@ string ChimeraUchimeCommand::getNamesFile(string& inputFile){
 		string inputString = "fasta=" + inputFile;
 		m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
 		m->mothurOut("Running command: unique.seqs(" + inputString + ")"); m->mothurOutEndLine(); 
-		
+		m->mothurCalling = true;
+        
 		Command* uniqueCommand = new DeconvoluteCommand(inputString);
 		uniqueCommand->execute();
 		
 		map<string, vector<string> > filenames = uniqueCommand->getOutputFiles();
 		
 		delete uniqueCommand;
-		
+		m->mothurCalling = false;
 		m->mothurOut("/******************************************/"); m->mothurOutEndLine(); 
 		
 		nameFile = filenames["name"][0];
@@ -1005,7 +1006,7 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
 		path = path.substr(0, (tempPath.find_last_of('m')));
 		
 		string uchimeCommand = path;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		uchimeCommand += "uchime ";
 #else
 		uchimeCommand += "uchime";
@@ -1243,7 +1244,7 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc
 		
 		//uchime_main(numArgs, uchimeParameters); 
 		//cout << "commandString = " << commandString << endl;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 #else
 		commandString = "\"" + commandString + "\"";
 #endif
@@ -1309,7 +1310,7 @@ int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename
 		int num = 0;
 		vector<string> files;
 		
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)		
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)		
 		//break up file into multiple files
 		m->divideFile(filename, processors, files);
 		
@@ -1472,7 +1473,7 @@ int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename
 }
 /**************************************************************************************************/
 
-int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string outputFName, string filename, string accnos, string alns, vector<string> groups) {
+int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string outputFName, string filename, string accnos, string alns, vector<string> groups, string nameFile, string groupFile, string fastaFile) {
 	try {
 		
 		processIDS.clear();
@@ -1492,7 +1493,7 @@ int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string o
 			lines.push_back(linePair(startIndex, endIndex));
 		}
 		
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)		
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)		
 				
 		//loop through and create all the processes you want
 		while (process != processors) {
@@ -1551,7 +1552,7 @@ int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string o
 			// Allocate memory for thread data.
 			string extension = toString(i) + ".temp";
 			
-			uchimeData* tempUchime = new uchimeData(outputFName+extension, templatefile, filename+extension, fastafile, namefile, groupfile, accnos+extension, alns+extension, groups, m, lines[i].start, lines[i].end,  i);
+			uchimeData* tempUchime = new uchimeData(outputFName+extension, templatefile, filename+extension, fastaFile, nameFile, groupFile, accnos+extension, alns+extension, groups, m, lines[i].start, lines[i].end,  i);
 			tempUchime->setBooleans(useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract);
 			tempUchime->setVariables(abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract);