sffinfo bug with flow grams right index when clipQualRight=0

[mothur.git] / getoturepcommand.cpp

diff --git a/getoturepcommand.cpp b/getoturepcommand.cpp
index 1d26b47b39c3ee998fb018bad12fb4e904b1e333..b8de5a62f6a8678c8b6f3e7f5de39b4da13aa817 100644 (file)
--- a/getoturepcommand.cpp
+++ b/getoturepcommand.cpp
@@ -39,22 +39,22 @@ inline bool compareGroup(repStruct left, repStruct right){
 //**********************************************************************************************************************
 vector<string> GetOTURepCommand::setParameters(){      
        try {
-               CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(plist);
-               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pfasta);
-               CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none",false,false); parameters.push_back(pphylip);
-        CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName",false,false); parameters.push_back(pname);
-        CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "ColumnName",false,false); parameters.push_back(pcount);
-               CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup);
-               CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName",false,false); parameters.push_back(pcolumn);
-               CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-               CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-               CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "",false,false); parameters.push_back(pcutoff);
-               CommandParameter pprecision("precision", "Number", "", "100", "", "", "",false,false); parameters.push_back(pprecision);
-               CommandParameter pweighted("weighted", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pweighted);
-               CommandParameter psorted("sorted", "Multiple", "none-name-bin-size-group", "none", "", "", "",false,false); parameters.push_back(psorted);
-               CommandParameter plarge("large", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(plarge);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","name",false,true, true); parameters.push_back(plist);
+               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta",false,false, true); parameters.push_back(pfasta);
+               CommandParameter pphylip("phylip", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "none","",false,false, true); parameters.push_back(pphylip);
+        CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName","",false,false, true); parameters.push_back(pname);
+        CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "ColumnName","count",false,false, true); parameters.push_back(pcount);
+               CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false, true); parameters.push_back(pgroup);
+               CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumn", "PhylipColumn", "ColumnName","",false,false, true); parameters.push_back(pcolumn);
+               CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+               CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+               CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false); parameters.push_back(pcutoff);
+               CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
+               CommandParameter pweighted("weighted", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pweighted);
+               CommandParameter psorted("sorted", "Multiple", "none-name-bin-size-group", "none", "", "", "","",false,false); parameters.push_back(psorted);
+               CommandParameter plarge("large", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(plarge);
+               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);          }
@@ -96,26 +96,21 @@ string GetOTURepCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string GetOTURepCommand::getOutputFileNameTag(string type, string inputName=""){       
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string GetOTURepCommand::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 == "fasta")            {   outputFileName =  "rep.fasta";   }
-            else if (type == "name")        {   outputFileName =  "rep.names";   }
-            else if (type == "count")        {   outputFileName =  "rep.count_table";   }
-            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, "GetOTURepCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        if (type == "fasta") {  pattern = "[filename],[tag],rep.fasta-[filename],[tag],[group],rep.fasta"; } 
+        else if (type == "name") {  pattern = "[filename],[tag],rep.names-[filename],[tag],[group],rep.names"; } 
+        else if (type == "count") {  pattern = "[filename],[tag],rep.count_table-[filename],[tag],[group],rep.count_table"; }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "GetOTURepCommand", "getOutputPattern");
+        exit(1);
+    }
 }
 //**********************************************************************************************************************
 GetOTURepCommand::GetOTURepCommand(){  
@@ -861,13 +856,16 @@ int GetOTURepCommand::process(ListVector* processList) {
                string outputNamesFile;
                map<string, ofstream*> filehandles;
                
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+        
                if (Groups.size() == 0) { //you don't want to use groups
-                       outputNamesFile  = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + ".";
+            variables["[tag]"] = processList->getLabel();
             if (countfile == "") { 
-                outputNamesFile += getOutputFileNameTag("name");
+                outputNamesFile = getOutputFileName("name", variables);
                 outputNames.push_back(outputNamesFile); outputTypes["name"].push_back(outputNamesFile); 
             }else {
-                outputNamesFile += getOutputFileNameTag("count");
+                outputNamesFile = getOutputFileName("count", variables);
                 outputNames.push_back(outputNamesFile); outputTypes["count"].push_back(outputNamesFile); 
             }
                        outputNameFiles[outputNamesFile] = processList->getLabel();
@@ -877,13 +875,15 @@ int GetOTURepCommand::process(ListVector* processList) {
                        ofstream* temp;
                        for (int i=0; i<Groups.size(); i++) {
                                temp = new ofstream;
+                variables["[tag]"] = processList->getLabel();
+                variables["[group]"] = Groups[i];
                                filehandles[Groups[i]] = temp;
                                outputNamesFile = outputDir + m->getRootName(m->getSimpleName(listfile)) + processList->getLabel() + "." + Groups[i] + ".";
                 if (countfile == "") { 
-                    outputNamesFile += getOutputFileNameTag("name");
+                    outputNamesFile = getOutputFileName("name", variables);
                     outputNames.push_back(outputNamesFile); outputTypes["name"].push_back(outputNamesFile); 
                 }else {
-                    outputNamesFile += getOutputFileNameTag("count");
+                    outputNamesFile = getOutputFileName("count", variables);
                     outputNames.push_back(outputNamesFile); outputTypes["count"].push_back(outputNamesFile); 
                 }
                                
@@ -978,7 +978,10 @@ int GetOTURepCommand::processFastaNames(string filename, string label) {
 
                //create output file
                if (outputDir == "") { outputDir += m->hasPath(listfile); }
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(listfile)) + label + "." + getOutputFileNameTag("fasta");
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(listfile));
+        variables["[tag]"] = label;
+               string outputFileName = getOutputFileName("fasta",variables);
                m->openOutputFile(outputFileName, out);
                vector<repStruct> reps;
                outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);