X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimerauchimecommand.cpp;h=7a48cf70d092f7d05c8b3bc3656bd66bf17c02d8;hp=422792a68525b495008694360c393e26ba358c09;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=af0a94ea8f02421b2b73e77e68753a2b4c37768e

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index 422792a..7a48cf7 100644
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -569,6 +569,7 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
 
 			
 			if (hasName && (templatefile != "self")) { m->mothurOut("You have provided a namefile and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
+            if (hasCount && (templatefile != "self")) { m->mothurOut("You have provided a countfile and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
 			if (hasGroup && (templatefile != "self")) { m->mothurOut("You have provided a group file and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
 			
 			//look for uchime exe
@@ -674,7 +675,7 @@ int ChimeraUchimeCommand::execute(){
                 int error;
                 if (hasCount) {
                     CountTable ct;
-                    ct.readTable(nameFile, true);
+                    ct.readTable(nameFile, true, false);
                     for(map<string, string>::iterator it = seqs.begin(); it != seqs.end(); it++) {
                         int num = ct.getNumSeqs(it->first);
                         if (num == 0) { error = 1; }
@@ -725,7 +726,7 @@ int ChimeraUchimeCommand::execute(){
 				if(processors == 1)	{	totalSeqs = driverGroups(outputFileName, newFasta, accnosFileName, alnsFileName, newCountFile, 0, groups.size(), groups);
                     
                     if (hasCount && dups) {
-                        CountTable c; c.readTable(nameFile, true);
+                        CountTable c; c.readTable(nameFile, true, false);
                         if (!m->isBlank(newCountFile)) {
                             ifstream in2;
                             m->openInputFile(newCountFile, in2);
@@ -755,7 +756,7 @@ int ChimeraUchimeCommand::execute(){
                     
                     if (hasCount) {
                         set<string> doNotRemove;
-                        CountTable c; c.readTable(newCountFile, true);
+                        CountTable c; c.readTable(newCountFile, true, true);
                         vector<string> namesInTable = c.getNamesOfSeqs();
                         for (int i = 0; i < namesInTable.size(); i++) {
                             int temp = c.getNumSeqs(namesInTable[i]);
@@ -1795,21 +1796,23 @@ int ChimeraUchimeCommand::createProcessesGroups(string outputFName, string filen
 		int num = 0;
         
         CountTable newCount;
-        if (hasCount && dups) { newCount.readTable(nameFile, true); }
+        if (hasCount && dups) { newCount.readTable(nameFile, true, false); }
 		
 		//sanity check
 		if (groups.size() < processors) { processors = groups.size(); }
 		
 		//divide the groups between the processors
 		vector<linePair> lines;
-		int numGroupsPerProcessor = groups.size() / processors;
-		for (int i = 0; i < processors; i++) {
-			int startIndex =  i * numGroupsPerProcessor;
-			int endIndex = (i+1) * numGroupsPerProcessor;
-			if(i == (processors - 1)){	endIndex = groups.size(); 	}
-			lines.push_back(linePair(startIndex, endIndex));
-		}
-		
+        int remainingPairs = groups.size();
+        int startIndex = 0;
+        for (int remainingProcessors = processors; remainingProcessors > 0; remainingProcessors--) {
+            int numPairs = remainingPairs; //case for last processor
+            if (remainingProcessors != 1) { numPairs = ceil(remainingPairs / remainingProcessors); }
+            lines.push_back(linePair(startIndex, (startIndex+numPairs))); //startIndex, endIndex
+            startIndex = startIndex + numPairs;
+            remainingPairs = remainingPairs - numPairs;
+        }
+
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)		
 				
 		//loop through and create all the processes you want