X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=preclustercommand.cpp;h=05c8b7d42a1ba7de160449f02707097800357bea;hp=24d22845c5a4fc33d109888e5f2007d25134672e;hb=b206f634aae1b4ce13978d203247fb64757d5482;hpb=af0a94ea8f02421b2b73e77e68753a2b4c37768e

diff --git a/preclustercommand.cpp b/preclustercommand.cpp
index 24d2284..05c8b7d 100644
--- a/preclustercommand.cpp
+++ b/preclustercommand.cpp
@@ -192,7 +192,7 @@ PreClusterCommand::PreClusterCommand(string option) {
 			else if (countfile == "not open") { abort = true; countfile =  ""; }	
 			else {   
                 m->setCountTableFile(countfile); 
-                ct.readTable(countfile, true);
+                ct.readTable(countfile, true, false);
                 if (ct.hasGroupInfo()) { bygroup = true; }
                 else { bygroup = false;  }
             }
@@ -300,6 +300,7 @@ int PreClusterCommand::execute(){
 			m->mothurOut("It took " + toString(time(NULL) - start) + " secs to run pre.cluster."); m->mothurOutEndLine(); 
 				
 		}else {
+            if (processors != 1) { m->mothurOut("When using running without group information mothur can only use 1 processor, continuing."); m->mothurOutEndLine(); processors = 1; }
 			if (namefile != "") { readNameFile(); }
 		
 			//reads fasta file and return number of seqs
@@ -368,13 +369,15 @@ int PreClusterCommand::createProcessesGroups(string newFName, string newNName, s
 		
 		//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)		
 		
@@ -903,15 +906,9 @@ void PreClusterCommand::readNameFile(){
 		while (!in.eof()) {
 			in >> firstCol >> secondCol; m->gobble(in);
             
-            for (int i = 0; i < firstCol.length(); i++) {
-                if (firstCol[i] == ':') { firstCol[i] = '_'; m->changedSeqNames = true; }
-            }
-            
-            int size = 1;
-            for (int i = 0; i < secondCol.length(); i++) {
-                if (secondCol[i] == ':') { secondCol[i] = '_'; m->changedSeqNames = true; }
-                else if(secondCol[i] == ','){	size++;	}
-            }
+            m->checkName(firstCol);
+            m->checkName(secondCol);
+            int size = m->getNumNames(secondCol);
             
 			names[firstCol] = secondCol;
             sizes[firstCol] = size;