added dereplicate parameter to chimera.slayer and chimera.persues. added minnumsample...

[mothur.git] / filterseqscommand.cpp

diff --git a/filterseqscommand.cpp b/filterseqscommand.cpp
index a7d42b331bc3044de372c030175da4663f9e3a9c..f6ca47988809f623b940f2ae04703d276ad90fa8 100644 (file)
--- a/filterseqscommand.cpp
+++ b/filterseqscommand.cpp
@@ -14,14 +14,14 @@
 //**********************************************************************************************************************
 vector<string> FilterSeqsCommand::setParameters(){     
        try {
-               CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta);
-               CommandParameter phard("hard", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(phard);
-               CommandParameter ptrump("trump", "String", "", "*", "", "", "",false,false); parameters.push_back(ptrump);
-               CommandParameter psoft("soft", "Number", "", "0", "", "", "",false,false); parameters.push_back(psoft);
-               CommandParameter pvertical("vertical", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pvertical);
-               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 pfasta("fasta", "InputTypes", "", "", "none", "none", "none","fasta-filter",false,true, true); parameters.push_back(pfasta);
+               CommandParameter phard("hard", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(phard);
+               CommandParameter ptrump("trump", "String", "", "*", "", "", "","",false,false, true); parameters.push_back(ptrump);
+               CommandParameter psoft("soft", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psoft);
+               CommandParameter pvertical("vertical", "Boolean", "", "T", "", "", "","",false,false, true); parameters.push_back(pvertical);
+               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);          }
@@ -57,6 +57,22 @@ string FilterSeqsCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
+string FilterSeqsCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "fasta") {  pattern = "[filename],filter.fasta"; } 
+        else if (type == "filter") {  pattern =  "[filename],filter"; }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "FilterSeqsCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+//**********************************************************************************************************************
 FilterSeqsCommand::FilterSeqsCommand(){        
        try {
                abort = true; calledHelp = true; 
@@ -277,9 +293,10 @@ int FilterSeqsCommand::execute() {
                ofstream outFilter;
                
                //prevent giantic file name
-               string filterFile;
-               if (fastafileNames.size() > 3) { filterFile = outputDir + "merge.filter"; }
-               else {  filterFile = outputDir + filterFileName + ".filter";  }
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + filterFileName + ".";
+               if (fastafileNames.size() > 3) { variables["[filename]"] = outputDir + "merge."; }
+               string filterFile = getOutputFileName("filter", variables);  
                
                m->openOutputFile(filterFile, outFilter);
                outFilter << filter << endl;
@@ -342,7 +359,9 @@ int FilterSeqsCommand::filterSequences() {
                        
                                for (int i = 0; i < lines.size(); i++) {  delete lines[i];  }  lines.clear();
                                
-                               string filteredFasta = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s])) + "filter.fasta";
+                map<string, string> variables; 
+                variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(fastafileNames[s]));
+                               string filteredFasta = getOutputFileName("fasta", variables);
 #ifdef USE_MPI 
                                int pid, numSeqsPerProcessor, num; 
                                int tag = 2001;