X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=chimerauchimecommand.cpp;h=3a9f42b22e0715ccf1f68313439342269da81bf8;hp=cb155eb2e53c3b8ba47c4ed36aa495efaef4460a;hb=ac03f1f6c27b5bfdf2cfb6d45c3667c3e0281f51;hpb=e9845ee4c8db2e044e87d721cc2d94f8d609e03d

diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp
index cb155eb..3a9f42b 100644
--- a/chimerauchimecommand.cpp
+++ b/chimerauchimecommand.cpp
@@ -564,14 +564,12 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option)  {
             
             
 			temp = validParameter.validFile(parameters, "dereplicate", false);	
-			if (temp == "not found") { 
-				if (groupfile != "")    {  temp = "false";					}
-				else                    {  temp = "true"; 	}
-			}
+			if (temp == "not found") { temp = "false";			}
 			dups = m->isTrue(temp);
 
 			
 			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
@@ -677,7 +675,7 @@ int ChimeraUchimeCommand::execute(){
                 int error;
                 if (hasCount) {
                     CountTable ct;
-                    ct.readTable(nameFile);
+                    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; }
@@ -728,7 +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);
+                        CountTable c; c.readTable(nameFile, true, false);
                         if (!m->isBlank(newCountFile)) {
                             ifstream in2;
                             m->openInputFile(newCountFile, in2);
@@ -758,7 +756,7 @@ int ChimeraUchimeCommand::execute(){
                     
                     if (hasCount) {
                         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]);
@@ -774,6 +772,7 @@ int ChimeraUchimeCommand::execute(){
                         }
                         out2.close();
                         c.printTable(newCountFile);
+                        outputNames.push_back(newCountFile); outputTypes["count"].push_back(newCountFile);
                     }
                 }
                 
@@ -819,6 +818,11 @@ int ChimeraUchimeCommand::execute(){
 		if (itTypes != outputTypes.end()) {
 			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setAccnosFile(current); }
 		}
+        
+        itTypes = outputTypes.find("count");
+		if (itTypes != outputTypes.end()) {
+			if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
+		}
 		
 		m->mothurOutEndLine();
 		m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -839,10 +843,6 @@ int ChimeraUchimeCommand::deconvoluteResults(map<string, string>& uniqueNames, s
 		map<string, string>::iterator itUnique;
 		int total = 0;
 		
-		//edit accnos file
-		ifstream in2; 
-		m->openInputFile(accnosFileName, in2);
-		
 		ofstream out2;
 		m->openOutputFile(accnosFileName+".temp", out2);
 		
@@ -852,27 +852,32 @@ int ChimeraUchimeCommand::deconvoluteResults(map<string, string>& uniqueNames, s
 		set<string> chimerasInFile;
 		set<string>::iterator itChimeras;
 
-		
-		while (!in2.eof()) {
-			if (m->control_pressed) { in2.close(); out2.close(); m->mothurRemove(outputFileName); m->mothurRemove((accnosFileName+".temp")); return 0; }
-			
-			in2 >> name; m->gobble(in2);
-			
-			//find unique name
-			itUnique = uniqueNames.find(name);
-			
-			if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing accnos results. Cannot find " + name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
-			else {
-				itChimeras = chimerasInFile.find((itUnique->second));
-				
-				if (itChimeras == chimerasInFile.end()) {
-					out2 << itUnique->second << endl;
-					chimerasInFile.insert((itUnique->second));
-					total++;
-				}
-			}
-		}
-		in2.close();
+        if (!m->isBlank(accnosFileName)) {
+            //edit accnos file
+            ifstream in2;
+            m->openInputFile(accnosFileName, in2);
+            
+            while (!in2.eof()) {
+                if (m->control_pressed) { in2.close(); out2.close(); m->mothurRemove(outputFileName); m->mothurRemove((accnosFileName+".temp")); return 0; }
+                
+                in2 >> name; m->gobble(in2);
+                
+                //find unique name
+                itUnique = uniqueNames.find(name);
+                
+                if (itUnique == uniqueNames.end()) { m->mothurOut("[ERROR]: trouble parsing accnos results. Cannot find " + name + "."); m->mothurOutEndLine(); m->control_pressed = true; }
+                else {
+                    itChimeras = chimerasInFile.find((itUnique->second));
+                    
+                    if (itChimeras == chimerasInFile.end()) {
+                        out2 << itUnique->second << endl;
+                        chimerasInFile.insert((itUnique->second));
+                        total++;
+                    }
+                }
+            }
+            in2.close();
+        }
 		out2.close();
 		
 		m->mothurRemove(accnosFileName);
@@ -1181,6 +1186,7 @@ int ChimeraUchimeCommand::driverGroups(string outputFName, string filename, stri
 		int totalSeqs = 0;
 		int numChimeras = 0;
         
+        
         ofstream outCountList;
         if (hasCount && dups) { m->openOutputFile(countlist, outCountList); }
         
@@ -1790,7 +1796,7 @@ int ChimeraUchimeCommand::createProcessesGroups(string outputFName, string filen
 		int num = 0;
         
         CountTable newCount;
-        if (hasCount && dups) { newCount.readTable(nameFile); }
+        if (hasCount && dups) { newCount.readTable(nameFile, true, false); }
 		
 		//sanity check
 		if (groups.size() < processors) { processors = groups.size(); }