Merge in v.1.39.0

source/commandfactory.cpp

@@ -152,6 +152,7 @@
 #include "biominfocommand.h"
 #include "renamefilecommand.h"
 #include "chimeravsearchcommand.h"
+#include "mergecountcommand.hpp"
 
 //needed for testing project
 //CommandFactory* CommandFactory::_uniqueInstance;
@@ -327,6 +328,7 @@ CommandFactory::CommandFactory(){
     commands["biom.info"]           = "biom.info";
     commands["set.seed"]            = "set.seed";
     commands["rename.file"]         = "rename.file";
+    commands["merge.count"]         = "merge.count";
 
 
 }
@@ -526,6 +528,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
 		else if(commandName == "corr.axes")				{	command = new CorrAxesCommand(optionString);				}
 		else if(commandName == "remove.rare")			{	command = new RemoveRareCommand(optionString);				}
 		else if(commandName == "merge.groups")			{	command = new MergeGroupsCommand(optionString);				}
+        else if(commandName == "merge.count")			{	command = new MergeCountCommand(optionString);				}
 		else if(commandName == "amova")					{	command = new AmovaCommand(optionString);					}
 		else if(commandName == "homova")				{	command = new HomovaCommand(optionString);					}
 		else if(commandName == "mantel")				{	command = new MantelCommand(optionString);					}
@@ -699,6 +702,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
 		else if(commandName == "corr.axes")				{	pipecommand = new CorrAxesCommand(optionString);				}
 		else if(commandName == "remove.rare")			{	pipecommand = new RemoveRareCommand(optionString);				}
 		else if(commandName == "merge.groups")			{	pipecommand = new MergeGroupsCommand(optionString);				}
+        else if(commandName == "merge.count")			{	pipecommand = new MergeCountCommand(optionString);				}
 		else if(commandName == "amova")					{	pipecommand = new AmovaCommand(optionString);					}
 		else if(commandName == "homova")				{	pipecommand = new HomovaCommand(optionString);					}
 		else if(commandName == "mantel")				{	pipecommand = new MantelCommand(optionString);					}
@@ -858,6 +862,7 @@ Command* CommandFactory::getCommand(string commandName){
 		else if(commandName == "corr.axes")				{	shellcommand = new CorrAxesCommand();				}
 		else if(commandName == "remove.rare")			{	shellcommand = new RemoveRareCommand();				}
 		else if(commandName == "merge.groups")			{	shellcommand = new MergeGroupsCommand();			}
+        else if(commandName == "merge.count")			{	shellcommand = new MergeCountCommand();				}
 		else if(commandName == "amova")					{	shellcommand = new AmovaCommand();					}
 		else if(commandName == "homova")				{	shellcommand = new HomovaCommand();					}
 		else if(commandName == "mantel")				{	shellcommand = new MantelCommand();					}
@@ -973,11 +978,15 @@ bool CommandFactory::isValidCommand(string command, string noError) {
 /***********************************************************************/
 void CommandFactory::printCommands(ostream& out) {
 	try {
-		out << "Valid commands are: ";
-		for (it = commands.begin(); it != commands.end(); it++) {
-			out << it->first << ",";
+        it = commands.begin();
+		out << "Valid commands are: " << it->first << ", ";
+        it++;
+        out << it->first;
+        it++;
+		for (; it != commands.end(); it++) {
+			out << ", " << it->first;
 		}
-		out << endl;
+		out <<  "." << endl;
 	}
 	catch(exception& e) {
 		m->errorOut(e, "CommandFactory", "printCommands");

source/commands/clustercommand.cpp

@@ -32,8 +32,7 @@ vector<string> ClusterCommand::setParameters(){
 		CommandParameter pshowabund("showabund", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pshowabund);
 		CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ptiming);
 		CommandParameter psim("sim", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psim);
-		CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard);
-		CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
+        CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
         CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
         //CommandParameter padjust("adjust", "String", "", "F", "", "", "","",false,false); parameters.push_back(padjust);
         CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
@@ -259,10 +258,7 @@ ClusterCommand::ClusterCommand(string option)  {
 			if (temp == "not found") { temp = "100"; }
 			//saves precision legnth for formatting below
 			length = temp.length();
-			m->mothurConvert(temp, precision); 
-			
-			temp = validParameter.validFile(parameters, "hard", false);			if (temp == "not found") { temp = "T"; }
-			hard = m->isTrue(temp);
+			m->mothurConvert(temp, precision);
 			
 			temp = validParameter.validFile(parameters, "sim", false);				if (temp == "not found") { temp = "F"; }
 			sim = m->isTrue(temp); 
@@ -323,7 +319,6 @@ ClusterCommand::ClusterCommand(string option)  {
             if (temp == "not found") { temp = "10"; }
             //else { cutoffSet = true; }
             m->mothurConvert(temp, cutoff);
-            if ((method != "agc") && (method != "dgc")) { cutoff += (5 / (precision * 10.0)); }
             
 			showabund = validParameter.validFile(parameters, "showabund", false);
 			if (showabund == "not found") { showabund = "T"; }
@@ -356,9 +351,7 @@ int ClusterCommand::execute(){
             else if (countfile != "") { inputString += ", count=" + countfile; }
 			inputString += ", precision=" + toString(precision);
 			inputString += ", method=" + method;
-			if (hard)	{ inputString += ", hard=T";	}
-			else		{ inputString += ", hard=F";	}
-			if (sim)	{ inputString += ", sim=T";		}
+            if (sim)	{ inputString += ", sim=T";		}
 			else		{ inputString += ", sim=F";		}
 
 			
@@ -736,12 +729,7 @@ int ClusterCommand::runMothurCluster(){
             cluster->update(cutoff);
             
             float dist = matrix->getSmallDist();
-            float rndDist;
-            if (hard) {
-                rndDist = m->ceilDist(dist, precision);
-            }else{
-                rndDist = m->roundDist(dist, precision);
-            }
+            float rndDist = m->ceilDist(dist, precision);
             
             if(previousDist <= 0.0000 && dist != previousDist){
                 printData("unique", counts);
@@ -780,10 +768,8 @@ int ClusterCommand::runMothurCluster(){
         }
         listFile.close();
         
-        if (saveCutoff != cutoff) { 
-            if (hard)	{  saveCutoff = m->ceilDist(saveCutoff, precision);	}
-            else		{	saveCutoff = m->roundDist(saveCutoff, precision);  }
-            
+        if (saveCutoff != cutoff) {
+            saveCutoff = m->ceilDist(saveCutoff, precision);
             m->mothurOut("changed cutoff to " + toString(cutoff)); m->mothurOutEndLine(); 
         }
 

source/commands/clusterdoturcommand.cpp

@@ -19,7 +19,6 @@ vector<string> ClusterDoturCommand::setParameters(){
 		CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false,true); parameters.push_back(pcutoff);
 		CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
 		CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted", "average", "", "", "","",false,false); parameters.push_back(pmethod);
-		CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard);
 		CommandParameter psim("sim", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psim);
 		CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
         CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
@@ -39,7 +38,7 @@ string ClusterDoturCommand::getHelpString(){
 	try {
 		string helpString = "";
 		helpString += "The cluster.classic command clusters using the algorithm from dotur. \n";
-		helpString += "The cluster.classic command parameter options are phylip, name, count, method, cuttoff, hard, sim, precision. Phylip is required, unless you have a valid current file.\n";
+		helpString += "The cluster.classic command parameter options are phylip, name, count, method, cuttoff, sim, precision. Phylip is required, unless you have a valid current file.\n";
 		helpString += "The cluster.classic command should be in the following format: \n";
 		helpString += "cluster.classic(phylip=yourDistanceMatrix, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n";
 		helpString += "The acceptable cluster methods are furthest, nearest, weighted and average.  If no method is provided then average is assumed.\n";	
@@ -183,11 +182,7 @@ ClusterDoturCommand::ClusterDoturCommand(string option)  {
 			
 			temp = validParameter.validFile(parameters, "cutoff", false);
 			if (temp == "not found") { temp = "10"; }
-			m->mothurConvert(temp, cutoff); 
-			cutoff += (5 / (precision * 10.0));  
-			
-			temp = validParameter.validFile(parameters, "hard", false);			if (temp == "not found") { temp = "T"; }
-			hard = m->isTrue(temp);
+			m->mothurConvert(temp, cutoff);
 			
 			temp = validParameter.validFile(parameters, "sim", false);				if (temp == "not found") { temp = "F"; }
 			sim = m->isTrue(temp); 
@@ -280,12 +275,7 @@ int ClusterDoturCommand::execute(){
 			cluster->update(cutoff);
 	
 			float dist = cluster->getSmallDist();
-			float rndDist;
-			if (hard) {
-				rndDist = m->ceilDist(dist, precision); 
-			}else{
-				rndDist = m->roundDist(dist, precision); 
-			}
+			float rndDist = m->ceilDist(dist, precision);
 
 			if(previousDist <= 0.0000 && dist != previousDist){
 				printData("unique", counts);

source/commands/clusterdoturcommand.h

@@ -37,7 +37,7 @@ class ClusterDoturCommand : public Command {
 	void help() { m->mothurOut(getHelpString()); }	
 	
 private:
-	bool abort, hard, sim;
+	bool abort, sim;
 	string method, fileroot, tag, outputDir, phylipfile, namefile, countfile;
 	double cutoff;
 	int precision, length;

source/commands/clustersplitcommand.cpp

@@ -341,9 +341,6 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
 			length = temp.length();
 			m->mothurConvert(temp, precision); 
 			
-			temp = validParameter.validFile(parameters, "hard", false);			if (temp == "not found") { temp = "T"; }
-			hard = m->isTrue(temp);
-			
 			temp = validParameter.validFile(parameters, "large", false);			if (temp == "not found") { temp = "F"; }
 			large = m->isTrue(temp);
             
@@ -395,6 +392,7 @@ ClusterSplitCommand::ClusterSplitCommand(string option)  {
 
             temp = validParameter.validFile(parameters, "cutoff", false);		if (temp == "not found")  { cutoffNotSet = true; temp = "1.0"; }
             m->mothurConvert(temp, cutoff);
+
             if (method != "opti") { cutoff += (5 / (precision * 10.0)); }
 
 			if ((splitmethod == "distance") || (splitmethod == "classify") || (splitmethod == "fasta")) { }
@@ -1188,13 +1186,8 @@ string ClusterSplitCommand::clusterClassicFile(string thisDistFile, string thisN
 			cluster->update(cutoff);
             
 			float dist = cluster->getSmallDist();
-			float rndDist;
-			if (hard) {
-				rndDist = m->ceilDist(dist, precision); 
-			}else{
-				rndDist = m->roundDist(dist, precision); 
-			}
-            
+			float rndDist = m->ceilDist(dist, precision);
+			
             if(previousDist <= 0.0000 && dist != previousDist){
                 oldList.setLabel("unique");
                 oldList.print(listFile);
@@ -1328,12 +1321,7 @@ string ClusterSplitCommand::clusterFile(string thisDistFile, string thisNamefile
                 cluster->update(saveCutoff);
                 
                 float dist = matrix->getSmallDist();
-                float rndDist;
-                if (hard) {
-                    rndDist = m->ceilDist(dist, precision);
-                }else{
-                    rndDist = m->roundDist(dist, precision);
-                }
+                float rndDist = m->ceilDist(dist, precision);
                 
                 if(previousDist <= 0.0000 && dist != previousDist){
                     oldList.setLabel("unique");
@@ -1378,9 +1366,7 @@ string ClusterSplitCommand::clusterFile(string thisDistFile, string thisNamefile
             }
             
             if (saveCutoff != cutoff) { 
-                if (hard)	{  saveCutoff = m->ceilDist(saveCutoff, precision);	}
-                else		{	saveCutoff = m->roundDist(saveCutoff, precision);  }
-                
+                saveCutoff = m->ceilDist(saveCutoff, precision);
                 m->mothurOut("Cutoff was " + toString(cutoff) + " changed cutoff to " + toString(saveCutoff)); m->mothurOutEndLine();  
             }
             

source/commands/clustersplitcommand.h

@@ -54,6 +54,7 @@ class ClusterSplitCommand : public Command {
 	double cutoff, splitcutoff, stableMetric, numSingletons;
 	int precision, length, processors, taxLevelCutoff, maxIters;
 	bool print_start, abort, hard, large, classic, runCluster, deleteFiles, isList, cutoffNotSet, makeDist;
+
 	time_t start;
 	ofstream outList, outRabund, outSabund;
 	

source/commands/getmimarkspackagecommand.cpp

@@ -589,7 +589,7 @@ set<string> GetMIMarksPackageCommand::createGroupNames(Oligos& oligos) {
             //overwrite global oligos - assume fastq data like make.contigs
             Oligos oligos;
             if ((fileOption == 3) || (fileOption == 5)) { oligos.read(oligosfile, false);  } //like make.contigs
-            else {  oligos.read(oligosfile);  }
+            else {  oligos.read(oligosfile, false);  }
             
             map<int, oligosPair> barcodes = oligos.getPairedBarcodes();
             map<int, oligosPair> primers = oligos.getPairedPrimers();