X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=summaryqualcommand.cpp;h=e1e626ea273a650840dd849442e43762e9a100cf;hp=48852a7d7d5d46491340062c4b989cc425bc6512;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=79a7d3273749b08d4f9f8dfe350c964ff0c4351e

diff --git a/summaryqualcommand.cpp b/summaryqualcommand.cpp
index 48852a7..e1e626e 100644
--- a/summaryqualcommand.cpp
+++ b/summaryqualcommand.cpp
@@ -13,12 +13,12 @@
 //**********************************************************************************************************************
 vector<string> SummaryQualCommand::setParameters(){	
 	try {
-		CommandParameter pqual("qfile", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pqual);
-		CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pname);
-        CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none",false,false); parameters.push_back(pcount);
-		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors);
-		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+		CommandParameter pqual("qfile", "InputTypes", "", "", "none", "none", "none","summary",false,true,true); parameters.push_back(pqual);
+		CommandParameter pname("name", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pname);
+        CommandParameter pcount("count", "InputTypes", "", "", "namecount", "none", "none","",false,false,true); parameters.push_back(pcount);
+		CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
+		CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+		CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
 		
 		vector<string> myArray;
 		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
@@ -48,24 +48,19 @@ string SummaryQualCommand::getHelpString(){
 	}
 }
 //**********************************************************************************************************************
-string SummaryQualCommand::getOutputFileNameTag(string type, string inputName=""){	
-	try {
-        string outputFileName = "";
-		map<string, vector<string> >::iterator it;
+string SummaryQualCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
         
-        //is this a type this command creates
-        it = outputTypes.find(type);
-        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
-        else {
-            if (type == "summary")            {   outputFileName =  "qual.summary";   }
-            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
-        }
-        return outputFileName;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "SummaryQualCommand", "getOutputFileNameTag");
-		exit(1);
-	}
+        if (type == "summary") {  pattern = "[filename],qual.summary"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "SummaryQualCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 SummaryQualCommand::SummaryQualCommand(){	
@@ -201,7 +196,7 @@ int SummaryQualCommand::execute(){
 		if (namefile != "") { nameMap = m->readNames(namefile); }
 		else if (countfile != "") {
             CountTable ct;
-            ct.readTable(countfile);
+            ct.readTable(countfile, false);
             nameMap = ct.getNameMap();
         }
         
@@ -233,7 +228,9 @@ int SummaryQualCommand::execute(){
 		if (m->control_pressed) {  return 0; }
 		
 		//print summary file
-		string summaryFile = outputDir + m->getRootName(m->getSimpleName(qualfile)) + getOutputFileNameTag("summary");
+        map<string, string> variables; 
+		variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(qualfile));
+		string summaryFile = getOutputFileName("summary",variables);
 		printQual(summaryFile, position, averageQ, scores);
 		
 		if (m->control_pressed) {  m->mothurRemove(summaryFile); return 0; }
@@ -444,7 +441,10 @@ int SummaryQualCommand::createProcessesCreateSummary(vector<int>& position, vect
 		
 		//Close all thread handles and free memory allocations.
 		for(int i=0; i < pDataArray.size(); i++){
-			numSeqs += pDataArray[i]->count;
+			numSeqs += pDataArray[i]->numSeqs;
+            if (pDataArray[i]->count != pDataArray[i]->end) {
+                m->mothurOut("[ERROR]: process " + toString(i) + " only processed " + toString(pDataArray[i]->count) + " of " + toString(pDataArray[i]->end) + " sequences assigned to it, quitting. \n"); m->control_pressed = true; 
+            }
             int tempNum = pDataArray[i]->position.size();
             if (position.size() < tempNum) { position.resize(tempNum, 0); }
 			if (averageQ.size() < tempNum) { averageQ.resize(tempNum, 0); }