X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeracheckcommand.cpp;h=6a4732cf72cd4222e539beb93c6b0b45226d2a08;hb=dc383fb61b6d165a8d36e6108df8bc7129243ae6;hp=9f53b1753903a44b469f0766a261894cb3177476;hpb=0ca63a8165baa0afa459e644ebe140ba496d5ba0;p=mothur.git

diff --git a/chimeracheckcommand.cpp b/chimeracheckcommand.cpp
index 9f53b17..6a4732c 100644
--- a/chimeracheckcommand.cpp
+++ b/chimeracheckcommand.cpp
@@ -65,6 +65,26 @@ string ChimeraCheckCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
+string ChimeraCheckCommand::getOutputFileNameTag(string type, string inputName=""){	
+	try {
+        string outputFileName = "";
+		map<string, vector<string> >::iterator it;
+        
+        //is this a type this command creates
+        it = outputTypes.find(type);
+        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
+        else {
+            if (type == "chimera") {  outputFileName =  "chimeracheck.chimeras"; }
+            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
+        }
+        return outputFileName;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "ChimeraCcodeCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
 ChimeraCheckCommand::ChimeraCheckCommand(){	
 	try {
 		abort = true; calledHelp = true;
@@ -342,7 +362,7 @@ int ChimeraCheckCommand::execute(){
 			if (m->control_pressed) { delete chimera;	return 0;	}
 			
 			if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[i]);  }//if user entered a file with a path then preserve it
-			string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i]))  + "chimeracheck.chimeras";
+			string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[i])) + getOutputFileNameTag("chimera");
 			outputNames.push_back(outputFileName); outputTypes["chimera"].push_back(outputFileName);
 			
 		#ifdef USE_MPI
@@ -427,7 +447,7 @@ 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 +542,7 @@ 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
@@ -531,6 +551,7 @@ int ChimeraCheckCommand::driver(linePair* filePos, string outputFName, string fi
 			
 			//report progress
 			if((count) % 100 == 0){	m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();		}
+            count++;
 		}
 		//report progress
 		if((count) % 100 != 0){	m->mothurOut("Processing sequence: " + toString(count)); m->mothurOutEndLine();		}
@@ -599,7 +620,7 @@ 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;