X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=seqsummarycommand.cpp;h=830643d12f2fc03d9f2985f2c722a891f0b95371;hb=f509429e06e545bde69c97cacc0eb436775bd329;hp=647334af7f8d66711c8db37b8d6fd00f9a9e38bb;hpb=b302d221847b504388ec044c6929e9dde42f9bb1;p=mothur.git

diff --git a/seqsummarycommand.cpp b/seqsummarycommand.cpp
index 647334a..830643d 100644
--- a/seqsummarycommand.cpp
+++ b/seqsummarycommand.cpp
@@ -45,6 +45,26 @@ string SeqSummaryCommand::getHelpString(){
 		exit(1);
 	}
 }
+//**********************************************************************************************************************
+string SeqSummaryCommand::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 =  "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, "SeqSummaryCommand", "getOutputFileNameTag");
+		exit(1);
+	}
+}
 
 //**********************************************************************************************************************
 SeqSummaryCommand::SeqSummaryCommand(){	
@@ -155,7 +175,7 @@ int SeqSummaryCommand::execute(){
 		//set current fasta to fastafile
 		m->setFastaFile(fastafile);
 		
-		string summaryFile = outputDir + m->getSimpleName(fastafile) + ".summary";
+		string summaryFile = outputDir + m->getRootName(m->getSimpleName(fastafile)) + getOutputFileNameTag("summary");
 				
 		int numSeqs = 0;
 		
@@ -286,11 +306,12 @@ int SeqSummaryCommand::execute(){
 				MPI_Barrier(MPI_COMM_WORLD); //make everyone wait - just in case
 #else
 			vector<unsigned long long> positions; 
-			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 				positions = m->divideFile(fastafile, processors);
 				for (int i = 0; i < (positions.size()-1); i++) {	lines.push_back(new linePair(positions[i], positions[(i+1)]));	}
 			#else
 				positions = m->setFilePosFasta(fastafile, numSeqs); 
+                if (positions.size() < processors) { processors = positions.size(); }
 		
 				//figure out how many sequences you have to process
 				int numSeqsPerProcessor = numSeqs / processors;
@@ -399,7 +420,7 @@ int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<in
 
 		bool done = false;
 		int count = 0;
-	
+       
 		while (!done) {
 				
 			if (m->control_pressed) { in.close(); outSummary.close(); return 1; }
@@ -413,7 +434,7 @@ int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<in
 					//make sure this sequence is in the namefile, else error 
 					map<string, int>::iterator it = nameMap.find(current.getName());
 					
-					if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+					if (it == nameMap.end()) { m->mothurOut("[ERROR]: '" + current.getName() + "' is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
 					else { num = it->second; }
 				}
 				
@@ -433,7 +454,7 @@ int SeqSummaryCommand::driverCreateSummary(vector<int>& startPosition, vector<in
 				outSummary << current.getLongHomoPolymer() << '\t' << num << endl;
 			}
 			
-			#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
@@ -529,7 +550,7 @@ int SeqSummaryCommand::createProcessesCreateSummary(vector<int>& startPosition,
 		int num = 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) {