X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=summaryqualcommand.cpp;h=5d7971349656d4400e5d41a24c15e576ccdf57f7;hb=957d67f7d8bbadfd2930de061e89fd9b149270fd;hp=a0d786f47518290bd71b88d15f386326d61acd64;hpb=b302d221847b504388ec044c6929e9dde42f9bb1;p=mothur.git

diff --git a/summaryqualcommand.cpp b/summaryqualcommand.cpp
index a0d786f..5d79713 100644
--- a/summaryqualcommand.cpp
+++ b/summaryqualcommand.cpp
@@ -45,7 +45,26 @@ string SummaryQualCommand::getHelpString(){
 		exit(1);
 	}
 }
-
+//**********************************************************************************************************************
+string SummaryQualCommand::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 == "summary")            {   outputFileName =  "qual.summary";   }
+            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, "SummaryQualCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
 //**********************************************************************************************************************
 SummaryQualCommand::SummaryQualCommand(){	
 	try {
@@ -162,7 +181,7 @@ int SummaryQualCommand::execute(){
 		if (namefile != "") { nameMap = m->readNames(namefile); }
 		
 		vector<unsigned long long> positions; 
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 		positions = m->divideFile(qualfile, processors);
 		for (int i = 0; i < (positions.size()-1); i++) {	lines.push_back(linePair(positions[i], positions[(i+1)]));	}
 #else	
@@ -170,6 +189,7 @@ int SummaryQualCommand::execute(){
 			lines.push_back(linePair(0, 1000)); 
 		}else {
 			positions = m->setFilePosFasta(qualfile, numSeqs); 
+            if (positions.size() < processors) { processors = positions.size(); }
 			
 			//figure out how many sequences you have to process
 			int numSeqsPerProcessor = numSeqs / processors;
@@ -188,7 +208,7 @@ int SummaryQualCommand::execute(){
 		if (m->control_pressed) {  return 0; }
 		
 		//print summary file
-		string summaryFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + "qual.summary";
+		string summaryFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + getOutputFileNameTag("summary");
 		printQual(summaryFile, position, averageQ, scores);
 		
 		if (m->control_pressed) {  m->mothurRemove(summaryFile); return 0; }
@@ -267,7 +287,7 @@ int SummaryQualCommand::driverCreateSummary(vector<int>& position, vector<int>&
 				count += num;
 			}
 			
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			unsigned long long pos = in.tellg();
 			if ((pos == -1) || (pos >= filePos.end)) { break; }
 #else
@@ -291,7 +311,7 @@ int SummaryQualCommand::createProcessesCreateSummary(vector<int>& position, vect
 		int numSeqs = 0;
 		processIDS.clear();
 		
-#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) {