X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimeraperseuscommand.cpp;h=353b124f8d556760b57a8086573caefe65e575f8;hb=60928795782d8f8648ec373d6a96b53032a77429;hp=fd94fcab7e289590da462eef7f03fc7069ab551f;hpb=c48d91112209b841444923670dca5454da0e2a4d;p=mothur.git

diff --git a/chimeraperseuscommand.cpp b/chimeraperseuscommand.cpp
index fd94fca..353b124 100644
--- a/chimeraperseuscommand.cpp
+++ b/chimeraperseuscommand.cpp
@@ -516,7 +516,7 @@ int ChimeraPerseusCommand::execute(){
             
             if (hasCount) {
                 CountTable* ct = new CountTable();
-                ct->readTable(nameFile);
+                ct->readTable(nameFile, true, false);
                 
                 if (ct->hasGroupInfo()) {
                     cparser = new SequenceCountParser(fastaFileNames[s], *ct);
@@ -534,7 +534,7 @@ int ChimeraPerseusCommand::execute(){
                     
                     if(processors == 1)	{	numSeqs = driverGroups(outputFileName, accnosFileName, newCountFile, 0, groups.size(), groups);
                         if (dups) {
-                            CountTable c; c.readTable(nameFile);
+                            CountTable c; c.readTable(nameFile, true, false);
                             if (!m->isBlank(newCountFile)) {
                                 ifstream in2;
                                 m->openInputFile(newCountFile, in2);
@@ -559,7 +559,7 @@ int ChimeraPerseusCommand::execute(){
                         numChimeras = deconvoluteResults(uniqueNames, outputFileName, accnosFileName);
                     }else {
                         set<string> doNotRemove;
-                        CountTable c; c.readTable(newCountFile);
+                        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]);
@@ -1070,20 +1070,23 @@ int ChimeraPerseusCommand::createProcessesGroups(string outputFName, string accn
 		int num = 0;
 		
         CountTable newCount;
-        if (hasCount && dups) { newCount.readTable(name); }
+        if (hasCount && dups) { newCount.readTable(name, 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)		
 		
@@ -1095,11 +1098,11 @@ int ChimeraPerseusCommand::createProcessesGroups(string outputFName, string accn
 				processIDS.push_back(pid);  //create map from line number to pid so you can append files in correct order later
 				process++;
 			}else if (pid == 0){
-				num = driverGroups(outputFName + toString(getpid()) + ".temp", accnos + toString(getpid()) + ".temp", accnos + ".byCount." + toString(getpid()) + ".temp", lines[process].start, lines[process].end, groups);
+				num = driverGroups(outputFName + toString(m->mothurGetpid(process)) + ".temp", accnos + toString(m->mothurGetpid(process)) + ".temp", accnos + ".byCount." + toString(m->mothurGetpid(process)) + ".temp", lines[process].start, lines[process].end, groups);
 				
 				//pass numSeqs to parent
 				ofstream out;
-				string tempFile = outputFName + toString(getpid()) + ".num.temp";
+				string tempFile = outputFName + toString(m->mothurGetpid(process)) + ".num.temp";
 				m->openOutputFile(tempFile, out);
 				out << num << endl;
 				out.close();